Starting phenix.real_space_refine
on Thu Feb 13 16:00:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6lmk_0917/02_2025/6lmk_0917.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6lmk_0917/02_2025/6lmk_0917.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6lmk_0917/02_2025/6lmk_0917.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6lmk_0917/02_2025/6lmk_0917.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6lmk_0917/02_2025/6lmk_0917.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6lmk_0917/02_2025/6lmk_0917.cif"
  }
  resolution = 3.7
  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=   0.002
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      58      5.16       5
     C    5863      2.51       5
     N    1631      2.21       5
     O    1688      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 45 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9240
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1889
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1889
          Classifications: {'peptide': 231}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 6, 'TRANS': 224}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 35
          Unresolved non-hydrogen dihedrals: 25
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 18
    Chain: "B"
      Number of atoms: 2584
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2584
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 17
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "C"
      Number of atoms: 420
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 420
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "N"
      Number of atoms: 964
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 964
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "R"
      Number of atoms: 3138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 395, 3138
          Classifications: {'peptide': 395}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 15, 'TRANS': 379}
          Unresolved non-hydrogen bonds: 70
          Unresolved non-hydrogen angles: 89
          Unresolved non-hydrogen dihedrals: 62
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 51
    Chain: "E"
      Number of atoms: 245
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 245
          Classifications: {'peptide': 29}
          Link IDs: {'TRANS': 28}
  Time building chain proxies: 5.64, per 1000 atoms: 0.61
  Number of scatterers: 9240
  At special positions: 0
  Unit cell: (97.58, 163.18, 86.92, 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      58     16.00
     O    1688      8.00
     N    1631      7.00
     C    5863      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  43 " - pdb=" SG  CYS R  67 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  58 " - pdb=" SG  CYS R 100 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  81 " - pdb=" SG  CYS R 121 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 224 " - pdb=" SG  CYS R 294 " distance=2.03

  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: 2.14
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2208

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 11 sheets defined
      39.9% alpha, 16.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.96
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 38
      removed outlier: 4.404A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 56
      removed outlier: 3.986A  pdb=" N   THR A  55 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ILE A  56 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 52 through 56'
    Processing helix  chain 'A' and resid 264 through 278
      removed outlier: 3.789A  pdb=" N   ALA A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 298
      removed outlier: 3.907A  pdb=" N   ALA A 298 " --> pdb=" O   GLN A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 303
      removed outlier: 3.634A  pdb=" N   LEU A 302 " --> pdb=" O   ALA A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
    Processing helix  chain 'A' and resid 313 through 316
      removed outlier: 3.729A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 313 through 316'
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.659A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 5 through 25
      removed outlier: 4.253A  pdb=" N   GLN B   9 " --> pdb=" O   ASP B   5 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.547A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'C' and resid 8 through 24
      removed outlier: 4.455A  pdb=" N   LYS C  14 " --> pdb=" O   ALA C  10 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   LEU C  15 " --> pdb=" O   GLN C  11 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLN C  18 " --> pdb=" O   LYS C  14 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   ASN C  24 " --> pdb=" O   LYS C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'N' and resid 61 through 65
      removed outlier: 3.608A  pdb=" N   LYS N  65 " --> pdb=" O   GLY N  62 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 4.050A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 28 through 48
    Processing helix  chain 'R' and resid 87 through 91
    Processing helix  chain 'R' and resid 117 through 122
      removed outlier: 4.487A  pdb=" N   GLN R 120 " --> pdb=" O   ASP R 117 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   CYS R 121 " --> pdb=" O   ALA R 118 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 126 through 164
      removed outlier: 3.882A  pdb=" N   LEU R 151 " --> pdb=" O   VAL R 147 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   LEU R 158 " --> pdb=" O   GLY R 154 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 173 through 202
      removed outlier: 3.588A  pdb=" N   HIS R 177 " --> pdb=" O   ARG R 173 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   SER R 183 " --> pdb=" O   ASN R 179 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   SER R 190 " --> pdb=" O   LEU R 186 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   VAL R 193 " --> pdb=" O   SER R 189 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   GLY R 196 " --> pdb=" O   LEU R 192 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   TYR R 202 " --> pdb=" O   LEU R 198 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 208 through 217
    Processing helix  chain 'R' and resid 220 through 251
      removed outlier: 3.759A  pdb=" N   CYS R 224 " --> pdb=" O   ALA R 220 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   VAL R 236 " --> pdb=" O   GLN R 232 " (cutoff:3.500A)
      removed outlier: 4.639A  pdb=" N   TYR R 239 " --> pdb=" O   ILE R 235 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   LEU R 249 " --> pdb=" O   GLU R 245 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 263 through 273
    Processing helix  chain 'R' and resid 273 through 289
      Proline residue:  R 281  - end of helix
    Processing helix  chain 'R' and resid 304 through 333
      Proline residue:  R 310  - end of helix
      removed outlier: 4.879A  pdb=" N   ASN R 318 " --> pdb=" O   ALA R 314 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   ILE R 321 " --> pdb=" O   ILE R 317 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   VAL R 326 " --> pdb=" O   PHE R 322 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   LEU R 328 " --> pdb=" O   ARG R 324 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   ALA R 331 " --> pdb=" O   GLN R 327 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 342 through 347
    Processing helix  chain 'R' and resid 374 through 402
      removed outlier: 3.535A  pdb=" N   ARG R 378 " --> pdb=" O   GLN R 374 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   SER R 379 " --> pdb=" O   GLY R 375 " (cutoff:3.500A)
      removed outlier: 4.873A  pdb=" N   GLY R 393 " --> pdb=" O   SER R 389 " (cutoff:3.500A)
      removed outlier: 5.277A  pdb=" N   LEU R 394 " --> pdb=" O   SER R 390 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 404 through 419
      removed outlier: 3.565A  pdb=" N   ARG R 414 " --> pdb=" O   GLU R 410 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 2 through 13
      removed outlier: 3.853A  pdb=" N   THR E   7 " --> pdb=" O   GLN E   3 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   SER E   8 " --> pdb=" O   GLY E   4 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 13 through 29
    Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214
      removed outlier: 4.031A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   LEU A  44 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 50
      removed outlier: 6.577A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   ALA B 328 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.943A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.598A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ILE B  93 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.503A  pdb=" N   SER B 122 " --> pdb=" O   CYS B 114 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   LEU B 139 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 5.987A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.978A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151
      removed outlier: 6.854A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 5.047A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   GLN B 175 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.571A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.057A  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: 4.070A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   CYS B 250 " --> pdb=" O   TYR B 264 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 5.899A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278
      removed outlier: 3.585A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12
      removed outlier: 6.667A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 75 through 80
      removed outlier: 3.539A  pdb=" N   THR R  75 " --> pdb=" O   CYS R 100 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   LYS R  98 " --> pdb=" O   ALA R  77 " (cutoff:3.500A)

    413 hydrogen bonds defined for protein.
    1197 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: 2.42

  Time building geometry restraints manager: 2.49 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: 2936
        1.34 -     1.46: 2091
        1.46 -     1.58: 4340
        1.58 -     1.70: 0
        1.70 -     1.82: 80
  Bond restraints: 9447
  Sorted by residual:
  bond pdb=" CG1 ILE R 321 "
       pdb=" CD1 ILE R 321 "
    ideal  model  delta    sigma   weight residual
    1.513  1.399  0.114 3.90e-02 6.57e+02 8.58e+00
  bond pdb=" CB  TRP R 241 "
       pdb=" CG  TRP R 241 "
    ideal  model  delta    sigma   weight residual
    1.498  1.429  0.069 3.10e-02 1.04e+03 4.94e+00
  bond pdb=" CB  ILE R 355 "
       pdb=" CG2 ILE R 355 "
    ideal  model  delta    sigma   weight residual
    1.521  1.452  0.069 3.30e-02 9.18e+02 4.43e+00
  bond pdb=" CB  ASN A 239 "
       pdb=" CG  ASN A 239 "
    ideal  model  delta    sigma   weight residual
    1.516  1.464  0.052 2.50e-02 1.60e+03 4.34e+00
  bond pdb=" CB  VAL B 315 "
       pdb=" CG2 VAL B 315 "
    ideal  model  delta    sigma   weight residual
    1.521  1.457  0.064 3.30e-02 9.18e+02 3.73e+00
  ... (remaining 9442 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 12135
        1.92 -     3.85: 581
        3.85 -     5.77: 59
        5.77 -     7.69: 25
        7.69 -     9.62: 10
  Bond angle restraints: 12810
  Sorted by residual:
  angle pdb=" CA  TYR R 145 "
        pdb=" CB  TYR R 145 "
        pdb=" CG  TYR R 145 "
      ideal   model   delta    sigma   weight residual
     113.90  120.39   -6.49 1.80e+00 3.09e-01 1.30e+01
  angle pdb=" C   GLN R  42 "
        pdb=" N   CYS R  43 "
        pdb=" CA  CYS R  43 "
      ideal   model   delta    sigma   weight residual
     122.06  115.58    6.48 1.86e+00 2.89e-01 1.21e+01
  angle pdb=" N   VAL R 280 "
        pdb=" CA  VAL R 280 "
        pdb=" C   VAL R 280 "
      ideal   model   delta    sigma   weight residual
     108.88  116.30   -7.42 2.16e+00 2.14e-01 1.18e+01
  angle pdb=" N   GLY R 302 "
        pdb=" CA  GLY R 302 "
        pdb=" C   GLY R 302 "
      ideal   model   delta    sigma   weight residual
     111.15  105.43    5.72 1.76e+00 3.23e-01 1.06e+01
  angle pdb=" CA  ILE R 355 "
        pdb=" C   ILE R 355 "
        pdb=" N   PRO R 356 "
      ideal   model   delta    sigma   weight residual
     118.88  123.73   -4.85 1.54e+00 4.22e-01 9.93e+00
  ... (remaining 12805 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 4945
       17.94 -    35.88: 523
       35.88 -    53.82: 105
       53.82 -    71.76: 12
       71.76 -    89.70: 7
  Dihedral angle restraints: 5592
    sinusoidal: 2176
      harmonic: 3416
  Sorted by residual:
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00    5.98   87.02     1      1.00e+01 1.00e-02 9.10e+01
  dihedral pdb=" CA  CYS R  58 "
           pdb=" C   CYS R  58 "
           pdb=" N   ASN R  59 "
           pdb=" CA  ASN R  59 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -141.89  -38.11     0      5.00e+00 4.00e-02 5.81e+01
  dihedral pdb=" CA  PHE R 303 "
           pdb=" C   PHE R 303 "
           pdb=" N   TRP R 304 "
           pdb=" CA  TRP R 304 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  142.15   37.85     0      5.00e+00 4.00e-02 5.73e+01
  ... (remaining 5589 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 977
       0.055 -    0.109: 350
       0.109 -    0.164: 75
       0.164 -    0.218: 15
       0.218 -    0.273: 2
  Chirality restraints: 1419
  Sorted by residual:
  chirality pdb=" CB  VAL A 241 "
            pdb=" CA  VAL A 241 "
            pdb=" CG1 VAL A 241 "
            pdb=" CG2 VAL A 241 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.27 2.00e-01 2.50e+01 1.86e+00
  chirality pdb=" CB  ILE N  70 "
            pdb=" CA  ILE N  70 "
            pdb=" CG1 ILE N  70 "
            pdb=" CG2 ILE N  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.24 2.00e-01 2.50e+01 1.38e+00
  chirality pdb=" CB  VAL R 280 "
            pdb=" CA  VAL R 280 "
            pdb=" CG1 VAL R 280 "
            pdb=" CG2 VAL R 280 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.19e+00
  ... (remaining 1416 not shown)

  Planarity restraints: 1641
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE R 355 "   -0.049 5.00e-02 4.00e+02   7.38e-02 8.72e+00
        pdb=" N   PRO R 356 "    0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO R 356 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO R 356 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.047 5.00e-02 4.00e+02   7.08e-02 8.02e+00
        pdb=" N   PRO B 236 "    0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP R  63 "   -0.013 2.00e-02 2.50e+03   2.57e-02 6.59e+00
        pdb=" C   ASP R  63 "    0.044 2.00e-02 2.50e+03
        pdb=" O   ASP R  63 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   LYS R  64 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1638 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 2835
        2.81 -     3.33: 8440
        3.33 -     3.85: 15588
        3.85 -     4.38: 17632
        4.38 -     4.90: 30462
  Nonbonded interactions: 74957
  Sorted by model distance:
  nonbonded pdb=" OH  TYR R 145 "
            pdb=" OD2 ASP R 195 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" OG  SER A 251 "
            pdb=" O   LYS A 293 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" O   SER R 189 "
            pdb=" OG  SER R 189 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" OD1 ASP B 290 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" NE1 TRP N  47 "
            pdb=" O   SER N  49 "
     model   vdw
     2.320 3.120
  ... (remaining 74952 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
========== 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 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:                  0.010
  Normalize map: mean=0, sd=1:             2.190
  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:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     22.550
  Find NCS groups from input model:        0.100
  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:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
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      :  0.009   0.114   9447  Z= 0.565
  Angle     :  0.960   9.616  12810  Z= 0.522
  Chirality :  0.058   0.273   1419
  Planarity :  0.007   0.074   1641
  Dihedral  : 15.097  89.701   3366
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 10.36 %
    Favored  : 89.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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: -4.19 (0.20), residues: 1162
  helix: -2.62 (0.18), residues: 420
  sheet: -2.88 (0.31), residues: 189
  loop : -2.80 (0.22), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP R 241 
 HIS   0.013   0.002   HIS R 361 
 PHE   0.032   0.003   PHE N 108 
 TYR   0.036   0.003   TYR B  59 
 ARG   0.005   0.001   ARG A 228 

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 201
  time to evaluate  : 1.059 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LYS cc_start: 0.8535 (mtmt) cc_final: 0.8283 (mtmm)
REVERT: A  265 ARG cc_start: 0.7718 (ttm-80) cc_final: 0.7002 (ttm110)
REVERT: A  344 GLU cc_start: 0.8015 (tp30) cc_final: 0.7789 (tp30)
REVERT: B  169 TRP cc_start: 0.8671 (m100) cc_final: 0.8397 (m100)
REVERT: B  270 ILE cc_start: 0.8485 (tp) cc_final: 0.8216 (tp)
REVERT: B  291 ASP cc_start: 0.8426 (p0) cc_final: 0.8205 (p0)
REVERT: C   17 GLU cc_start: 0.7923 (tp30) cc_final: 0.7601 (tp30)
REVERT: C   50 LEU cc_start: 0.8880 (mm) cc_final: 0.8503 (mm)
REVERT: N   38 ARG cc_start: 0.8542 (ptt180) cc_final: 0.7916 (ptt90)
REVERT: N   91 THR cc_start: 0.8621 (p) cc_final: 0.8364 (p)
REVERT: R  123 MET cc_start: 0.7719 (mmm) cc_final: 0.7372 (mmm)
REVERT: R  127 GLU cc_start: 0.8645 (mp0) cc_final: 0.8195 (mp0)
REVERT: R  133 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8073 (tp30)
REVERT: R  270 ILE cc_start: 0.9062 (tt) cc_final: 0.8838 (tt)
REVERT: R  410 GLU cc_start: 0.7758 (tp30) cc_final: 0.7448 (tp30)
REVERT: E   15 ASP cc_start: 0.8414 (p0) cc_final: 0.7991 (p0)
REVERT: E   17 ARG cc_start: 0.8664 (tpt90) cc_final: 0.7984 (tpp80)
REVERT: E   21 ASP cc_start: 0.8596 (m-30) cc_final: 0.8222 (m-30)
REVERT: E   24 GLN cc_start: 0.9100 (tm-30) cc_final: 0.8678 (tm-30)
  outliers start: 6
  outliers final: 1
  residues processed: 207
  average time/residue: 0.2741
  time to fit residues: 74.2754
Evaluate side-chains
  152 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 151
  time to evaluate  : 1.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   45 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 29 optimal weight:    0.3980
   chunk 58 optimal weight:   30.0000
   chunk 46 optimal weight:    0.9990
   chunk 89 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 54 optimal weight:    8.9990
   chunk 66 optimal weight:   10.0000
   chunk 103 optimal weight:    1.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
A  31 GLN
** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  88 ASN
B 230 ASN
B 293 ASN
B 295 ASN
C  11 GLN
R 142 GLN
R 238 ASN
R 404 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.129874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.098160 restraints weight = 17520.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.100034 restraints weight = 11262.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.101486 restraints weight = 8057.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.1913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9447  Z= 0.184
  Angle     :  0.619   9.905  12810  Z= 0.324
  Chirality :  0.042   0.156   1419
  Planarity :  0.005   0.064   1641
  Dihedral  :  5.721  35.296   1285
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 15.28 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -2.70 (0.23), residues: 1162
  helix: -0.61 (0.24), residues: 422
  sheet: -2.66 (0.30), residues: 230
  loop : -2.31 (0.26), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 241 
 HIS   0.009   0.001   HIS R 361 
 PHE   0.020   0.001   PHE B 235 
 TYR   0.021   0.001   TYR R 145 
 ARG   0.003   0.000   ARG R 116 

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 200
  time to evaluate  : 1.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  265 ARG cc_start: 0.7718 (ttm-80) cc_final: 0.6882 (ttm-80)
REVERT: B  169 TRP cc_start: 0.8404 (m100) cc_final: 0.8200 (m100)
REVERT: B  264 TYR cc_start: 0.8266 (m-80) cc_final: 0.7136 (m-80)
REVERT: B  270 ILE cc_start: 0.8247 (tp) cc_final: 0.7991 (tp)
REVERT: B  297 TRP cc_start: 0.8620 (m100) cc_final: 0.8400 (m-10)
REVERT: C   51 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8544 (mp)
REVERT: N    5 GLN cc_start: 0.8220 (mp10) cc_final: 0.7830 (mp10)
REVERT: N   38 ARG cc_start: 0.8674 (ptt180) cc_final: 0.8047 (ptt90)
REVERT: N   46 GLU cc_start: 0.6476 (pt0) cc_final: 0.5562 (pt0)
REVERT: N   51 ILE cc_start: 0.8950 (tt) cc_final: 0.8664 (tt)
REVERT: N   73 ASP cc_start: 0.8104 (t0) cc_final: 0.7245 (t0)
REVERT: N   91 THR cc_start: 0.8688 (p) cc_final: 0.8486 (p)
REVERT: R  123 MET cc_start: 0.7707 (mmm) cc_final: 0.7411 (mmm)
REVERT: R  127 GLU cc_start: 0.8563 (mp0) cc_final: 0.7969 (mp0)
REVERT: R  133 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8049 (tp30)
REVERT: R  231 MET cc_start: 0.7722 (tmm) cc_final: 0.7461 (ttp)
REVERT: R  358 LEU cc_start: 0.5672 (OUTLIER) cc_final: 0.5377 (pt)
REVERT: E   12 LYS cc_start: 0.9171 (mtmt) cc_final: 0.8773 (mtmm)
REVERT: E   17 ARG cc_start: 0.8704 (tpt90) cc_final: 0.8230 (tpp80)
REVERT: E   21 ASP cc_start: 0.8593 (m-30) cc_final: 0.8207 (m-30)
REVERT: E   24 GLN cc_start: 0.8992 (tm-30) cc_final: 0.8670 (tm-30)
REVERT: E   27 MET cc_start: 0.8091 (mmp) cc_final: 0.7676 (mmm)
  outliers start: 24
  outliers final: 13
  residues processed: 216
  average time/residue: 0.2619
  time to fit residues: 75.2574
Evaluate side-chains
  182 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 167
  time to evaluate  : 1.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain N residue   43 LYS
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain R residue   45 HIS
Chi-restraints excluded: chain R residue  206 ILE
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  351 THR
Chi-restraints excluded: chain R residue  358 LEU
Chi-restraints excluded: chain R residue  363 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 82 optimal weight:   30.0000
   chunk 59 optimal weight:    8.9990
   chunk 48 optimal weight:    7.9990
   chunk 42 optimal weight:    0.2980
   chunk 6 optimal weight:    9.9990
   chunk 50 optimal weight:    0.5980
   chunk 86 optimal weight:    7.9990
   chunk 53 optimal weight:    9.9990
   chunk 58 optimal weight:    6.9990
   chunk 34 optimal weight:    7.9990
   chunk 99 optimal weight:    5.9990
   overall best weight:    4.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
A 267 GLN
B  88 ASN
B 183 HIS
R 142 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.124421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.093836 restraints weight = 18047.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.093534 restraints weight = 12393.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.095060 restraints weight = 10174.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.2210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.073   9447  Z= 0.431
  Angle     :  0.718   7.766  12810  Z= 0.378
  Chirality :  0.046   0.163   1419
  Planarity :  0.005   0.063   1641
  Dihedral  :  5.834  36.940   1285
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 19.08 %
    Favored  : 76.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -2.20 (0.24), residues: 1162
  helix: -0.00 (0.26), residues: 423
  sheet: -2.58 (0.31), residues: 214
  loop : -2.15 (0.26), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP R 241 
 HIS   0.010   0.001   HIS R 361 
 PHE   0.026   0.002   PHE N 108 
 TYR   0.023   0.002   TYR R 145 
 ARG   0.003   0.000   ARG B  22 

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 170
  time to evaluate  : 1.063 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 LYS cc_start: 0.8456 (tttt) cc_final: 0.8175 (mmtm)
REVERT: A  265 ARG cc_start: 0.7767 (ttm-80) cc_final: 0.7189 (ttm-80)
REVERT: B   59 TYR cc_start: 0.8975 (OUTLIER) cc_final: 0.8095 (m-80)
REVERT: B   82 TRP cc_start: 0.8758 (m100) cc_final: 0.8461 (m100)
REVERT: B  169 TRP cc_start: 0.8546 (m100) cc_final: 0.8332 (m100)
REVERT: B  188 MET cc_start: 0.8123 (mmm) cc_final: 0.7881 (mmm)
REVERT: B  229 ILE cc_start: 0.8787 (mt) cc_final: 0.8559 (tt)
REVERT: B  262 MET cc_start: 0.6702 (ttm) cc_final: 0.6481 (ttm)
REVERT: B  264 TYR cc_start: 0.8274 (m-80) cc_final: 0.7574 (m-80)
REVERT: B  270 ILE cc_start: 0.8453 (tp) cc_final: 0.8139 (tp)
REVERT: B  297 TRP cc_start: 0.8752 (m100) cc_final: 0.8530 (m-10)
REVERT: C   51 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8714 (mp)
REVERT: N    5 GLN cc_start: 0.8371 (mp10) cc_final: 0.8128 (mp10)
REVERT: N   38 ARG cc_start: 0.8728 (ptt180) cc_final: 0.8064 (ptt90)
REVERT: N   46 GLU cc_start: 0.6547 (pt0) cc_final: 0.5553 (pt0)
REVERT: N   51 ILE cc_start: 0.9191 (tt) cc_final: 0.8674 (tt)
REVERT: N   72 ARG cc_start: 0.8283 (ptm160) cc_final: 0.7313 (ptm160)
REVERT: N   76 LYS cc_start: 0.8950 (mtmt) cc_final: 0.8516 (tptt)
REVERT: R  123 MET cc_start: 0.7873 (mmm) cc_final: 0.7529 (mmm)
REVERT: R  133 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8110 (tp30)
REVERT: R  317 ILE cc_start: 0.8801 (tp) cc_final: 0.8474 (tt)
REVERT: R  325 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7990 (mt)
REVERT: E   12 LYS cc_start: 0.9252 (mtmt) cc_final: 0.8858 (mtmm)
REVERT: E   17 ARG cc_start: 0.8744 (tpt90) cc_final: 0.8215 (tpp80)
REVERT: E   21 ASP cc_start: 0.8730 (m-30) cc_final: 0.8297 (m-30)
REVERT: E   24 GLN cc_start: 0.8932 (tm-30) cc_final: 0.8666 (tm-30)
REVERT: E   27 MET cc_start: 0.8150 (mmp) cc_final: 0.7605 (mmm)
  outliers start: 48
  outliers final: 35
  residues processed: 208
  average time/residue: 0.2386
  time to fit residues: 66.6405
Evaluate side-chains
  191 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 153
  time to evaluate  : 1.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 GLN
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue   43 LYS
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain R residue   45 HIS
Chi-restraints excluded: chain R residue   64 LYS
Chi-restraints excluded: chain R residue   65 TYR
Chi-restraints excluded: chain R residue  140 SER
Chi-restraints excluded: chain R residue  147 VAL
Chi-restraints excluded: chain R residue  193 VAL
Chi-restraints excluded: chain R residue  206 ILE
Chi-restraints excluded: chain R residue  210 LEU
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  316 LEU
Chi-restraints excluded: chain R residue  321 ILE
Chi-restraints excluded: chain R residue  325 ILE
Chi-restraints excluded: chain R residue  330 VAL
Chi-restraints excluded: chain R residue  351 THR
Chi-restraints excluded: chain R residue  358 LEU
Chi-restraints excluded: chain R residue  363 VAL
Chi-restraints excluded: chain R residue  411 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 107 optimal weight:   20.0000
   chunk 91 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   chunk 110 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 7 optimal weight:    0.4980
   chunk 5 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
A 278 ASN
A 294 GLN
** R 318 ASN ** 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 = 0.3884 r_free = 0.3884 target = 0.130516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.099553 restraints weight = 17437.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.101244 restraints weight = 10422.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.102538 restraints weight = 7784.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.2641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9447  Z= 0.171
  Angle     :  0.589   9.065  12810  Z= 0.304
  Chirality :  0.041   0.155   1419
  Planarity :  0.004   0.057   1641
  Dihedral  :  5.207  34.282   1285
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 21.23 %
    Favored  : 74.97 %
  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: -1.68 (0.25), residues: 1162
  helix:  0.59 (0.26), residues: 421
  sheet: -2.43 (0.31), residues: 229
  loop : -1.89 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 241 
 HIS   0.009   0.001   HIS R 361 
 PHE   0.013   0.001   PHE B 235 
 TYR   0.019   0.001   TYR N  60 
 ARG   0.003   0.000   ARG A 333 

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 179
  time to evaluate  : 1.047 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  265 ARG cc_start: 0.7564 (ttm-80) cc_final: 0.6904 (ttm-80)
REVERT: A  390 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7448 (mp10)
REVERT: B   82 TRP cc_start: 0.8607 (m100) cc_final: 0.8284 (m100)
REVERT: B  264 TYR cc_start: 0.8155 (m-80) cc_final: 0.7663 (m-80)
REVERT: C   51 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8628 (mp)
REVERT: N    5 GLN cc_start: 0.8272 (mp10) cc_final: 0.7980 (mp10)
REVERT: N   38 ARG cc_start: 0.8706 (ptt180) cc_final: 0.7858 (ptt90)
REVERT: N   46 GLU cc_start: 0.6533 (pt0) cc_final: 0.5524 (pt0)
REVERT: N   51 ILE cc_start: 0.9090 (tt) cc_final: 0.8747 (tt)
REVERT: N   72 ARG cc_start: 0.7916 (ptm160) cc_final: 0.7557 (ttp-170)
REVERT: N   76 LYS cc_start: 0.8954 (mtmt) cc_final: 0.8464 (tptt)
REVERT: R  123 MET cc_start: 0.7919 (mmm) cc_final: 0.7623 (mmm)
REVERT: R  133 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8091 (tp30)
REVERT: E   12 LYS cc_start: 0.9186 (mtmt) cc_final: 0.8816 (mtmm)
REVERT: E   24 GLN cc_start: 0.8919 (tm-30) cc_final: 0.8699 (tm-30)
  outliers start: 37
  outliers final: 25
  residues processed: 204
  average time/residue: 0.2573
  time to fit residues: 69.4060
Evaluate side-chains
  186 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 159
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain A residue  390 GLN
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain N residue   43 LYS
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain R residue   45 HIS
Chi-restraints excluded: chain R residue   64 LYS
Chi-restraints excluded: chain R residue   65 TYR
Chi-restraints excluded: chain R residue  140 SER
Chi-restraints excluded: chain R residue  193 VAL
Chi-restraints excluded: chain R residue  206 ILE
Chi-restraints excluded: chain R residue  210 LEU
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  279 VAL
Chi-restraints excluded: chain R residue  351 THR
Chi-restraints excluded: chain R residue  363 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 78 optimal weight:    6.9990
   chunk 71 optimal weight:    0.0270
   chunk 4 optimal weight:    9.9990
   chunk 98 optimal weight:    0.8980
   chunk 97 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   chunk 56 optimal weight:   20.0000
   chunk 70 optimal weight:    7.9990
   chunk 75 optimal weight:    0.0470
   chunk 48 optimal weight:   10.0000
   chunk 76 optimal weight:   20.0000
   overall best weight:    0.5536

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.132157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.101025 restraints weight = 17526.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.103184 restraints weight = 10597.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.104378 restraints weight = 7793.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.3053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9447  Z= 0.166
  Angle     :  0.593   9.154  12810  Z= 0.303
  Chirality :  0.041   0.160   1419
  Planarity :  0.004   0.058   1641
  Dihedral  :  4.850  33.004   1285
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 22.26 %
    Favored  : 74.15 %
  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: -1.27 (0.25), residues: 1162
  helix:  1.00 (0.26), residues: 419
  sheet: -2.20 (0.32), residues: 227
  loop : -1.73 (0.27), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 169 
 HIS   0.009   0.001   HIS R 361 
 PHE   0.021   0.001   PHE N 103 
 TYR   0.017   0.001   TYR R 145 
 ARG   0.005   0.000   ARG N 105 

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 180
  time to evaluate  : 1.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 LYS cc_start: 0.8392 (tttt) cc_final: 0.8149 (mmtm)
REVERT: A  265 ARG cc_start: 0.7645 (ttm-80) cc_final: 0.6993 (ttm-80)
REVERT: B  118 ASP cc_start: 0.6323 (t0) cc_final: 0.6047 (t0)
REVERT: B  264 TYR cc_start: 0.8142 (m-80) cc_final: 0.7239 (m-80)
REVERT: C   51 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8584 (mp)
REVERT: N    5 GLN cc_start: 0.8221 (mp10) cc_final: 0.7925 (mp10)
REVERT: N   38 ARG cc_start: 0.8718 (ptt180) cc_final: 0.8307 (ptt90)
REVERT: N   43 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8005 (mtmm)
REVERT: N   51 ILE cc_start: 0.9024 (tt) cc_final: 0.8717 (tt)
REVERT: N   72 ARG cc_start: 0.7821 (ptm160) cc_final: 0.7375 (ttp-170)
REVERT: N   76 LYS cc_start: 0.8963 (mtmt) cc_final: 0.8405 (tptt)
REVERT: R  123 MET cc_start: 0.7974 (mmm) cc_final: 0.7712 (mmm)
REVERT: R  127 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8118 (mp0)
REVERT: R  133 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8198 (tp30)
REVERT: R  297 SER cc_start: 0.8815 (m) cc_final: 0.8556 (t)
REVERT: E   12 LYS cc_start: 0.9216 (mtmt) cc_final: 0.8830 (mtmm)
REVERT: E   24 GLN cc_start: 0.8863 (tm-30) cc_final: 0.8630 (tm-30)
  outliers start: 35
  outliers final: 19
  residues processed: 203
  average time/residue: 0.2551
  time to fit residues: 69.1474
Evaluate side-chains
  183 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 162
  time to evaluate  : 1.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain N residue   43 LYS
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain R residue   64 LYS
Chi-restraints excluded: chain R residue   65 TYR
Chi-restraints excluded: chain R residue  147 VAL
Chi-restraints excluded: chain R residue  193 VAL
Chi-restraints excluded: chain R residue  206 ILE
Chi-restraints excluded: chain R residue  210 LEU
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  279 VAL
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  363 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 86 optimal weight:    4.9990
   chunk 76 optimal weight:    7.9990
   chunk 55 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 102 optimal weight:    0.9990
   chunk 51 optimal weight:    5.9990
   chunk 7 optimal weight:    0.0470
   chunk 29 optimal weight:    0.7980
   chunk 20 optimal weight:    9.9990
   chunk 68 optimal weight:    6.9990
   overall best weight:    1.1684

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
R  88 HIS
** R 318 ASN ** 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 = 0.3906 r_free = 0.3906 target = 0.131814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.100710 restraints weight = 17484.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.102380 restraints weight = 11095.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.103903 restraints weight = 8079.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.3191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9447  Z= 0.193
  Angle     :  0.623   9.921  12810  Z= 0.317
  Chirality :  0.042   0.152   1419
  Planarity :  0.004   0.056   1641
  Dihedral  :  4.690  25.544   1283
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 22.56 %
    Favored  : 73.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.25), residues: 1162
  helix:  1.09 (0.26), residues: 420
  sheet: -2.12 (0.32), residues: 227
  loop : -1.57 (0.28), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 297 
 HIS   0.009   0.001   HIS R 361 
 PHE   0.011   0.001   PHE N 108 
 TYR   0.017   0.001   TYR R 145 
 ARG   0.006   0.000   ARG A 333 

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 172
  time to evaluate  : 1.035 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 PHE cc_start: 0.6775 (t80) cc_final: 0.6529 (t80)
REVERT: B  118 ASP cc_start: 0.6450 (t0) cc_final: 0.6153 (t0)
REVERT: B  262 MET cc_start: 0.7737 (tmm) cc_final: 0.7367 (tmm)
REVERT: B  264 TYR cc_start: 0.7962 (m-80) cc_final: 0.7577 (m-80)
REVERT: C   51 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8607 (mp)
REVERT: N   32 TYR cc_start: 0.8391 (m-80) cc_final: 0.8111 (m-80)
REVERT: N   38 ARG cc_start: 0.8676 (ptt180) cc_final: 0.8032 (ptt90)
REVERT: N   43 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.7994 (mtmm)
REVERT: N   46 GLU cc_start: 0.6404 (pt0) cc_final: 0.5832 (pt0)
REVERT: N   68 PHE cc_start: 0.7409 (m-80) cc_final: 0.7131 (m-80)
REVERT: N   76 LYS cc_start: 0.8975 (mtmt) cc_final: 0.8359 (tptt)
REVERT: R  123 MET cc_start: 0.7968 (mmm) cc_final: 0.7723 (mmm)
REVERT: R  133 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8135 (tp30)
REVERT: R  355 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7817 (tt)
REVERT: E   12 LYS cc_start: 0.9210 (mtmt) cc_final: 0.8841 (mtmm)
REVERT: E   24 GLN cc_start: 0.8909 (tm-30) cc_final: 0.8686 (tm-30)
  outliers start: 39
  outliers final: 24
  residues processed: 199
  average time/residue: 0.2499
  time to fit residues: 66.3771
Evaluate side-chains
  182 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 155
  time to evaluate  : 1.004 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain N residue   43 LYS
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain R residue   45 HIS
Chi-restraints excluded: chain R residue   64 LYS
Chi-restraints excluded: chain R residue   65 TYR
Chi-restraints excluded: chain R residue   67 CYS
Chi-restraints excluded: chain R residue  140 SER
Chi-restraints excluded: chain R residue  147 VAL
Chi-restraints excluded: chain R residue  193 VAL
Chi-restraints excluded: chain R residue  206 ILE
Chi-restraints excluded: chain R residue  210 LEU
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  351 THR
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  363 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 72 optimal weight:   10.0000
   chunk 1 optimal weight:    9.9990
   chunk 103 optimal weight:    2.9990
   chunk 85 optimal weight:    5.9990
   chunk 41 optimal weight:    2.9990
   chunk 78 optimal weight:    0.0980
   chunk 49 optimal weight:    8.9990
   chunk 30 optimal weight:    0.7980
   chunk 50 optimal weight:    0.3980
   chunk 31 optimal weight:    0.8980
   chunk 3 optimal weight:    5.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B 340 ASN
R 318 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.132296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.102390 restraints weight = 17615.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.102733 restraints weight = 11354.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.104329 restraints weight = 9028.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.3396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9447  Z= 0.186
  Angle     :  0.628  14.574  12810  Z= 0.315
  Chirality :  0.042   0.147   1419
  Planarity :  0.004   0.054   1641
  Dihedral  :  4.571  24.429   1283
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 23.49 %
    Favored  : 72.31 %
  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: -0.97 (0.25), residues: 1162
  helix:  1.20 (0.26), residues: 419
  sheet: -2.01 (0.33), residues: 228
  loop : -1.50 (0.28), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 297 
 HIS   0.010   0.001   HIS R 361 
 PHE   0.011   0.001   PHE R 391 
 TYR   0.016   0.001   TYR R 145 
 ARG   0.005   0.000   ARG N  72 

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 165
  time to evaluate  : 1.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  265 ARG cc_start: 0.7610 (ttm-80) cc_final: 0.6970 (ttm-80)
REVERT: B  118 ASP cc_start: 0.6462 (t0) cc_final: 0.6167 (t0)
REVERT: B  262 MET cc_start: 0.7684 (tmm) cc_final: 0.7096 (tmm)
REVERT: B  264 TYR cc_start: 0.7805 (m-80) cc_final: 0.7591 (m-80)
REVERT: C   51 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8614 (mp)
REVERT: N   38 ARG cc_start: 0.8654 (ptt180) cc_final: 0.7993 (ptt90)
REVERT: N   43 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8107 (mtmm)
REVERT: N   46 GLU cc_start: 0.6413 (pt0) cc_final: 0.5646 (pt0)
REVERT: N   51 ILE cc_start: 0.8987 (tt) cc_final: 0.8685 (tt)
REVERT: N   68 PHE cc_start: 0.7419 (m-80) cc_final: 0.7001 (m-80)
REVERT: N   73 ASP cc_start: 0.7694 (t0) cc_final: 0.7427 (p0)
REVERT: R  123 MET cc_start: 0.8007 (mmm) cc_final: 0.7747 (mmm)
REVERT: R  133 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8157 (tp30)
REVERT: E   12 LYS cc_start: 0.9213 (mtmt) cc_final: 0.8835 (mtmm)
  outliers start: 41
  outliers final: 28
  residues processed: 194
  average time/residue: 0.2503
  time to fit residues: 64.8491
Evaluate side-chains
  185 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 155
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain N residue   43 LYS
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain R residue   64 LYS
Chi-restraints excluded: chain R residue   65 TYR
Chi-restraints excluded: chain R residue  140 SER
Chi-restraints excluded: chain R residue  147 VAL
Chi-restraints excluded: chain R residue  193 VAL
Chi-restraints excluded: chain R residue  206 ILE
Chi-restraints excluded: chain R residue  210 LEU
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  279 VAL
Chi-restraints excluded: chain R residue  318 ASN
Chi-restraints excluded: chain R residue  351 THR
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  363 VAL
Chi-restraints excluded: chain R residue  394 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 69 optimal weight:    7.9990
   chunk 43 optimal weight:    0.7980
   chunk 52 optimal weight:    0.6980
   chunk 12 optimal weight:    0.8980
   chunk 50 optimal weight:    0.6980
   chunk 90 optimal weight:    3.9990
   chunk 23 optimal weight:    9.9990
   chunk 38 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.133523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.102673 restraints weight = 17808.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.104345 restraints weight = 10873.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.105975 restraints weight = 7911.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.3562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   9447  Z= 0.183
  Angle     :  0.643  13.333  12810  Z= 0.319
  Chirality :  0.042   0.150   1419
  Planarity :  0.004   0.055   1641
  Dihedral  :  4.503  23.474   1283
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 24.82 %
    Favored  : 71.79 %
  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: -0.91 (0.25), residues: 1162
  helix:  1.16 (0.26), residues: 425
  sheet: -1.91 (0.33), residues: 228
  loop : -1.45 (0.28), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 297 
 HIS   0.009   0.001   HIS R 361 
 PHE   0.017   0.001   PHE R 230 
 TYR   0.016   0.001   TYR R 145 
 ARG   0.009   0.000   ARG B 214 

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 165
  time to evaluate  : 1.117 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  265 ARG cc_start: 0.7569 (ttm-80) cc_final: 0.6972 (ttm-80)
REVERT: B  118 ASP cc_start: 0.6399 (t0) cc_final: 0.6103 (t0)
REVERT: B  262 MET cc_start: 0.7654 (tmm) cc_final: 0.7118 (tmm)
REVERT: C   51 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8586 (mp)
REVERT: N   43 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8019 (mtmm)
REVERT: N   51 ILE cc_start: 0.8974 (tt) cc_final: 0.8645 (tt)
REVERT: N   68 PHE cc_start: 0.7400 (m-80) cc_final: 0.6942 (m-80)
REVERT: N   73 ASP cc_start: 0.7449 (t0) cc_final: 0.5699 (t0)
REVERT: R  123 MET cc_start: 0.8031 (mmm) cc_final: 0.7770 (mmm)
REVERT: R  133 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8139 (tp30)
REVERT: R  230 PHE cc_start: 0.8450 (t80) cc_final: 0.8223 (t80)
REVERT: R  301 MET cc_start: 0.8131 (ppp) cc_final: 0.7896 (ppp)
REVERT: R  317 ILE cc_start: 0.8272 (tp) cc_final: 0.8063 (tt)
REVERT: E   12 LYS cc_start: 0.9200 (mtmt) cc_final: 0.8834 (mtmm)
  outliers start: 33
  outliers final: 27
  residues processed: 188
  average time/residue: 0.2886
  time to fit residues: 72.6237
Evaluate side-chains
  188 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 159
  time to evaluate  : 1.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain A residue  390 GLN
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  176 GLN
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain N residue   43 LYS
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain R residue   65 TYR
Chi-restraints excluded: chain R residue  140 SER
Chi-restraints excluded: chain R residue  147 VAL
Chi-restraints excluded: chain R residue  193 VAL
Chi-restraints excluded: chain R residue  206 ILE
Chi-restraints excluded: chain R residue  210 LEU
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  279 VAL
Chi-restraints excluded: chain R residue  351 THR
Chi-restraints excluded: chain R residue  363 VAL
Chi-restraints excluded: chain R residue  394 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9990
   chunk 30 optimal weight:    5.9990
   chunk 61 optimal weight:    6.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    7.9990
   chunk 110 optimal weight:    3.9990
   chunk 102 optimal weight:    0.9990
   chunk 1 optimal weight:    4.9990
   chunk 72 optimal weight:    3.9990
   chunk 101 optimal weight:    1.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
R 318 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.130460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.099310 restraints weight = 17651.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.100614 restraints weight = 11144.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.102140 restraints weight = 8328.716|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.3479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   9447  Z= 0.267
  Angle     :  0.679  12.774  12810  Z= 0.340
  Chirality :  0.044   0.151   1419
  Planarity :  0.004   0.050   1641
  Dihedral  :  4.776  24.534   1283
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 24.10 %
    Favored  : 71.69 %
  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: -0.91 (0.25), residues: 1162
  helix:  1.10 (0.26), residues: 427
  sheet: -1.85 (0.33), residues: 227
  loop : -1.44 (0.28), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 297 
 HIS   0.010   0.001   HIS R 361 
 PHE   0.031   0.002   PHE A 238 
 TYR   0.018   0.002   TYR R 145 
 ARG   0.010   0.000   ARG B 214 

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 161
  time to evaluate  : 0.959 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  265 ARG cc_start: 0.7678 (ttm-80) cc_final: 0.7043 (ttm-80)
REVERT: A  344 GLU cc_start: 0.8119 (tp30) cc_final: 0.7771 (tp30)
REVERT: B   82 TRP cc_start: 0.8652 (m100) cc_final: 0.8362 (m100)
REVERT: B  264 TYR cc_start: 0.7407 (m-80) cc_final: 0.6851 (m-80)
REVERT: C   51 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8642 (mp)
REVERT: N   43 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8093 (mtmm)
REVERT: N   51 ILE cc_start: 0.8963 (tt) cc_final: 0.8621 (tt)
REVERT: N   68 PHE cc_start: 0.7604 (m-80) cc_final: 0.7279 (m-80)
REVERT: R  123 MET cc_start: 0.8060 (mmm) cc_final: 0.7799 (mmm)
REVERT: R  133 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8141 (tp30)
REVERT: E   12 LYS cc_start: 0.9229 (mtmt) cc_final: 0.8918 (mtmm)
  outliers start: 41
  outliers final: 32
  residues processed: 191
  average time/residue: 0.2375
  time to fit residues: 60.4244
Evaluate side-chains
  184 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 150
  time to evaluate  : 1.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain A residue  390 GLN
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  176 GLN
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain N residue   43 LYS
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain R residue   64 LYS
Chi-restraints excluded: chain R residue   65 TYR
Chi-restraints excluded: chain R residue   67 CYS
Chi-restraints excluded: chain R residue  140 SER
Chi-restraints excluded: chain R residue  147 VAL
Chi-restraints excluded: chain R residue  193 VAL
Chi-restraints excluded: chain R residue  206 ILE
Chi-restraints excluded: chain R residue  210 LEU
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  279 VAL
Chi-restraints excluded: chain R residue  318 ASN
Chi-restraints excluded: chain R residue  321 ILE
Chi-restraints excluded: chain R residue  351 THR
Chi-restraints excluded: chain R residue  363 VAL
Chi-restraints excluded: chain R residue  394 LEU
Chi-restraints excluded: chain R residue  399 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 71 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9980
   chunk 16 optimal weight:    6.9990
   chunk 47 optimal weight:    0.9980
   chunk 67 optimal weight:    6.9990
   chunk 27 optimal weight:    6.9990
   chunk 98 optimal weight:    0.8980
   chunk 38 optimal weight:    4.9990
   chunk 69 optimal weight:   10.0000
   chunk 4 optimal weight:    5.9990
   chunk 78 optimal weight:    7.9990
   overall best weight:    1.7182

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

Flipped N/Q/H residues before XYZ refinement:
R 318 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.131209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.101109 restraints weight = 17700.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.100766 restraints weight = 11395.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.102489 restraints weight = 9031.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.3551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   9447  Z= 0.243
  Angle     :  0.705  12.744  12810  Z= 0.351
  Chirality :  0.043   0.162   1419
  Planarity :  0.004   0.051   1641
  Dihedral  :  4.772  24.485   1283
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 11.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 24.92 %
    Favored  : 71.49 %
  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 (0.25), residues: 1162
  helix:  1.08 (0.26), residues: 425
  sheet: -1.71 (0.34), residues: 215
  loop : -1.50 (0.27), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP B 297 
 HIS   0.010   0.001   HIS R 361 
 PHE   0.023   0.001   PHE A 238 
 TYR   0.017   0.002   TYR R 145 
 ARG   0.008   0.000   ARG B 214 

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 151
  time to evaluate  : 1.066 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  265 ARG cc_start: 0.7652 (ttm-80) cc_final: 0.7034 (ttm-80)
REVERT: A  344 GLU cc_start: 0.8123 (tp30) cc_final: 0.7769 (tp30)
REVERT: B   82 TRP cc_start: 0.8607 (m100) cc_final: 0.8285 (m100)
REVERT: B  264 TYR cc_start: 0.7405 (m-80) cc_final: 0.6770 (m-80)
REVERT: C   51 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8644 (mp)
REVERT: N   43 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8094 (mtmm)
REVERT: N   51 ILE cc_start: 0.8965 (tt) cc_final: 0.8625 (tt)
REVERT: N   68 PHE cc_start: 0.7616 (m-80) cc_final: 0.7305 (m-80)
REVERT: R  123 MET cc_start: 0.8095 (mmm) cc_final: 0.7820 (mmm)
REVERT: R  133 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8153 (tp30)
REVERT: R  230 PHE cc_start: 0.8533 (t80) cc_final: 0.8297 (t80)
REVERT: R  301 MET cc_start: 0.8178 (ppp) cc_final: 0.7793 (ppp)
REVERT: E   12 LYS cc_start: 0.9232 (mtmt) cc_final: 0.8914 (mtmm)
  outliers start: 35
  outliers final: 30
  residues processed: 175
  average time/residue: 0.2433
  time to fit residues: 57.8029
Evaluate side-chains
  180 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 148
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain A residue  390 GLN
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  176 GLN
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain N residue   43 LYS
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain R residue   64 LYS
Chi-restraints excluded: chain R residue   65 TYR
Chi-restraints excluded: chain R residue   67 CYS
Chi-restraints excluded: chain R residue  140 SER
Chi-restraints excluded: chain R residue  147 VAL
Chi-restraints excluded: chain R residue  193 VAL
Chi-restraints excluded: chain R residue  206 ILE
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  279 VAL
Chi-restraints excluded: chain R residue  318 ASN
Chi-restraints excluded: chain R residue  351 THR
Chi-restraints excluded: chain R residue  363 VAL
Chi-restraints excluded: chain R residue  394 LEU
Chi-restraints excluded: chain R residue  399 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 36 optimal weight:    4.9990
   chunk 87 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 23 optimal weight:    0.3980
   chunk 1 optimal weight:    8.9990
   chunk 6 optimal weight:    7.9990
   chunk 10 optimal weight:    4.9990
   chunk 24 optimal weight:    5.9990
   chunk 96 optimal weight:    0.3980
   chunk 9 optimal weight:    0.9980
   chunk 71 optimal weight:    4.9990
   overall best weight:    1.7584

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

Flipped N/Q/H residues before XYZ refinement:
B  91 HIS
** N  77 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 = 0.3899 r_free = 0.3899 target = 0.131110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.100350 restraints weight = 17620.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.101234 restraints weight = 11403.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.102823 restraints weight = 8554.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.3612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   9447  Z= 0.245
  Angle     :  0.698  12.511  12810  Z= 0.350
  Chirality :  0.043   0.156   1419
  Planarity :  0.004   0.049   1641
  Dihedral  :  4.790  24.528   1283
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 11.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 24.92 %
    Favored  : 71.49 %
  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: -0.88 (0.25), residues: 1162
  helix:  1.05 (0.26), residues: 431
  sheet: -1.67 (0.34), residues: 215
  loop : -1.49 (0.28), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP B 297 
 HIS   0.010   0.001   HIS R 361 
 PHE   0.028   0.002   PHE A 238 
 TYR   0.017   0.002   TYR R 145 
 ARG   0.008   0.000   ARG B 214 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2989.02 seconds
wall clock time: 54 minutes 32.66 seconds (3272.66 seconds total)