Starting phenix.real_space_refine
on Fri Nov 15 16:19:35 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jis_36326/11_2024/8jis_36326.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jis_36326/11_2024/8jis_36326.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.46
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jis_36326/11_2024/8jis_36326.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jis_36326/11_2024/8jis_36326.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jis_36326/11_2024/8jis_36326.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jis_36326/11_2024/8jis_36326.cif"
  }
  resolution = 2.46
  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=   0.020
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      57      5.16       5
     C    5828      2.51       5
     N    1574      2.21       5
     O    1699      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 9158
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1856
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 238, 1856
          Classifications: {'peptide': 238}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'PTRANS': 6, 'TRANS': 231}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 119
          Unresolved non-hydrogen angles: 144
          Unresolved non-hydrogen dihedrals: 101
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 73
    Chain: "B"
      Number of atoms: 2572
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2572
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 25
    Chain: "P"
      Number of atoms: 238
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 238
          Classifications: {'peptide': 29}
          Link IDs: {'TRANS': 28}
    Chain: "G"
      Number of atoms: 427
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 427
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "N"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 961
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
    Chain: "R"
      Number of atoms: 3104
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 386, 3104
          Classifications: {'peptide': 386}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 14, 'TRANS': 371}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 96
          Unresolved non-hydrogen angles: 121
          Unresolved non-hydrogen dihedrals: 85
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 70
  Time building chain proxies: 5.73, per 1000 atoms: 0.63
  Number of scatterers: 9158
  At special positions: 0
  Unit cell: (86.751, 95.319, 173.502, 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      57     16.00
     O    1699      8.00
     N    1574      7.00
     C    5828      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  46 " - pdb=" SG  CYS R  71 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  62 " - pdb=" SG  CYS R 104 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  85 " - pdb=" SG  CYS R 126 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 226 " - pdb=" SG  CYS R 296 " distance=2.02

  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: 2.52
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2218

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 11 sheets defined
      40.5% alpha, 17.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 32
      removed outlier: 3.643A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ALA A  32 " --> pdb=" O   GLN A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
      removed outlier: 3.723A  pdb=" N   VAL A  50 " --> pdb=" O   LYS A  46 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   LYS A  51 " --> pdb=" O   SER A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 216
      removed outlier: 3.648A  pdb=" N   GLN A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   CYS A 214 " --> pdb=" O   TRP A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 231
      No H-bonds generated for 'chain 'A' and resid 229 through 231'
    Processing helix  chain 'A' and resid 232 through 246
    Processing helix  chain 'A' and resid 263 through 268
      removed outlier: 3.796A  pdb=" N   LYS A 267 " --> pdb=" O   LEU A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 320
      removed outlier: 4.051A  pdb=" N   ILE A 315 " --> pdb=" O   GLU A 311 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   SER A 319 " --> pdb=" O   ILE A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 358
      removed outlier: 4.074A  pdb=" N   VAL A 342 " --> pdb=" O   ASN A 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 24
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'P' and resid 2 through 27
    Processing helix  chain 'G' and resid 7 through 23
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.655A  pdb=" N   ASP G  36 " --> pdb=" O   LYS G  32 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   LEU G  37 " --> pdb=" O   ALA G  33 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'R' and resid 31 through 49
    Processing helix  chain 'R' and resid 89 through 93
    Processing helix  chain 'R' and resid 139 through 169
    Processing helix  chain 'R' and resid 174 through 205
      removed outlier: 3.683A  pdb=" N   TYR R 205 " --> pdb=" O   LEU R 201 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 205 through 211
    Processing helix  chain 'R' and resid 216 through 221
    Processing helix  chain 'R' and resid 223 through 256
      removed outlier: 3.584A  pdb=" N   ARG R 227 " --> pdb=" O   SER R 223 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   VAL R 229 " --> pdb=" O   SER R 225 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   PHE R 230 " --> pdb=" O   CYS R 226 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   LEU R 251 " --> pdb=" O   GLU R 247 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 261 through 292
      Proline residue:  R 277  - end of helix
      removed outlier: 3.963A  pdb=" N   PHE R 280 " --> pdb=" O   VAL R 276 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   VAL R 282 " --> pdb=" O   LEU R 278 " (cutoff:3.500A)
      Proline residue:  R 283  - end of helix
    Processing helix  chain 'R' and resid 302 through 337
      removed outlier: 3.830A  pdb=" N   ILE R 308 " --> pdb=" O   ASN R 304 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   ILE R 309 " --> pdb=" O   TYR R 305 " (cutoff:3.500A)
      Proline residue:  R 312  - end of helix
      removed outlier: 3.587A  pdb=" N   ALA R 337 " --> pdb=" O   SER R 333 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 343 through 354
      removed outlier: 4.145A  pdb=" N   CYS R 347 " --> pdb=" O   THR R 343 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 356 through 361
    Processing helix  chain 'R' and resid 364 through 368
    Processing helix  chain 'R' and resid 377 through 404
      removed outlier: 3.762A  pdb=" N   PHE R 381 " --> pdb=" O   GLY R 377 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   GLY R 395 " --> pdb=" O   THR R 391 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   LEU R 396 " --> pdb=" O   SER R 392 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 406 through 423
      removed outlier: 3.814A  pdb=" N   GLU R 423 " --> pdb=" O   ARG R 419 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191
      removed outlier: 4.630A  pdb=" N   VAL A 201 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 8.740A  pdb=" N   GLY A  40 " --> pdb=" O   VAL A 201 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   ALA A 220 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 6.352A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 255 " (cutoff:3.500A)
      removed outlier: 7.281A  pdb=" N   PHE A 257 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 257 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   ASN A 259 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 259 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.528A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.502A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.797A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.763A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.062A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.159A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.742A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.428A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 5.885A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.993A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.978A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.211A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.369A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.541A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.900A  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 232
      removed outlier: 6.734A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.980A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ASN B 295 " --> pdb=" O   ALA B 287 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   ASP B 303 " --> 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 58 through 60
      removed outlier: 3.516A  pdb=" N   SER N  59 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.759A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 112 through 114
      removed outlier: 4.646A  pdb=" N   ASP R 114 " --> pdb=" O   LEU R 118 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   LEU R 118 " --> pdb=" O   ASP R 114 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2

    443 hydrogen bonds defined for protein.
    1275 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: 2.51

  Time building geometry restraints manager: 2.83 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1496
        1.31 -     1.44: 2689
        1.44 -     1.56: 5100
        1.56 -     1.69: 1
        1.69 -     1.82: 78
  Bond restraints: 9364
  Sorted by residual:
  bond pdb=" C   ASP R  53 "
       pdb=" N   PRO R  54 "
    ideal  model  delta    sigma   weight residual
    1.331  1.385 -0.054 8.70e-03 1.32e+04 3.87e+01
  bond pdb=" C   GLU A 311 "
       pdb=" O   GLU A 311 "
    ideal  model  delta    sigma   weight residual
    1.236  1.180  0.057 1.26e-02 6.30e+03 2.01e+01
  bond pdb=" CA  ALA R 368 "
       pdb=" C   ALA R 368 "
    ideal  model  delta    sigma   weight residual
    1.523  1.487  0.036 8.20e-03 1.49e+04 1.97e+01
  bond pdb=" CA  ALA B 328 "
       pdb=" C   ALA B 328 "
    ideal  model  delta    sigma   weight residual
    1.523  1.472  0.051 1.18e-02 7.18e+03 1.90e+01
  bond pdb=" CA  SER B 191 "
       pdb=" C   SER B 191 "
    ideal  model  delta    sigma   weight residual
    1.520  1.472  0.048 1.12e-02 7.97e+03 1.83e+01
  ... (remaining 9359 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.97: 12304
        2.97 -     5.93: 343
        5.93 -     8.90: 65
        8.90 -    11.86: 10
       11.86 -    14.83: 2
  Bond angle restraints: 12724
  Sorted by residual:
  angle pdb=" N   HIS R 374 "
        pdb=" CA  HIS R 374 "
        pdb=" C   HIS R 374 "
      ideal   model   delta    sigma   weight residual
     114.12   99.29   14.83 1.39e+00 5.18e-01 1.14e+02
  angle pdb=" N   ASP R 344 "
        pdb=" CA  ASP R 344 "
        pdb=" C   ASP R 344 "
      ideal   model   delta    sigma   weight residual
     113.19  101.25   11.94 1.19e+00 7.06e-01 1.01e+02
  angle pdb=" N   GLU A 281 "
        pdb=" CA  GLU A 281 "
        pdb=" C   GLU A 281 "
      ideal   model   delta    sigma   weight residual
     112.34  101.39   10.95 1.30e+00 5.92e-01 7.09e+01
  angle pdb=" N   ILE R 345 "
        pdb=" CA  ILE R 345 "
        pdb=" C   ILE R 345 "
      ideal   model   delta    sigma   weight residual
     110.42  102.95    7.47 9.60e-01 1.09e+00 6.06e+01
  angle pdb=" N   SER R  93 "
        pdb=" CA  SER R  93 "
        pdb=" C   SER R  93 "
      ideal   model   delta    sigma   weight residual
     112.23  103.05    9.18 1.26e+00 6.30e-01 5.31e+01
  ... (remaining 12719 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.50: 4676
       17.50 -    35.01: 523
       35.01 -    52.51: 231
       52.51 -    70.02: 75
       70.02 -    87.52: 20
  Dihedral angle restraints: 5525
    sinusoidal: 2097
      harmonic: 3428
  Sorted by residual:
  dihedral pdb=" CB  CYS R  85 "
           pdb=" SG  CYS R  85 "
           pdb=" SG  CYS R 126 "
           pdb=" CB  CYS R 126 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -179.90  -87.10     1      1.00e+01 1.00e-02 9.11e+01
  dihedral pdb=" CB  CYS R  46 "
           pdb=" SG  CYS R  46 "
           pdb=" SG  CYS R  71 "
           pdb=" CB  CYS R  71 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -127.73   41.73     1      1.00e+01 1.00e-02 2.44e+01
  dihedral pdb=" CA  CYS R  46 "
           pdb=" CB  CYS R  46 "
           pdb=" SG  CYS R  46 "
           pdb=" SG  CYS R  71 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00   -6.57  -66.43     1      2.00e+01 2.50e-03 1.44e+01
  ... (remaining 5522 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.081: 1140
       0.081 -    0.161: 214
       0.161 -    0.242: 52
       0.242 -    0.322: 18
       0.322 -    0.402: 7
  Chirality restraints: 1431
  Sorted by residual:
  chirality pdb=" CA  THR N 111 "
            pdb=" N   THR N 111 "
            pdb=" C   THR N 111 "
            pdb=" CB  THR N 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.12    0.40 2.00e-01 2.50e+01 4.05e+00
  chirality pdb=" CA  PHE B 292 "
            pdb=" N   PHE B 292 "
            pdb=" C   PHE B 292 "
            pdb=" CB  PHE B 292 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.39 2.00e-01 2.50e+01 3.82e+00
  chirality pdb=" CA  SER B 136 "
            pdb=" N   SER B 136 "
            pdb=" C   SER B 136 "
            pdb=" CB  SER B 136 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.27e+00
  ... (remaining 1428 not shown)

  Planarity restraints: 1619
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO R  90 "   -0.020 2.00e-02 2.50e+03   3.86e-02 1.49e+01
        pdb=" C   PRO R  90 "    0.067 2.00e-02 2.50e+03
        pdb=" O   PRO R  90 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   TRP R  91 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 280 "    0.015 2.00e-02 2.50e+03   3.00e-02 8.99e+00
        pdb=" C   PRO A 280 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   PRO A 280 "    0.019 2.00e-02 2.50e+03
        pdb=" N   GLU A 281 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU G  42 "    0.014 2.00e-02 2.50e+03   2.98e-02 8.90e+00
        pdb=" C   GLU G  42 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   GLU G  42 "    0.020 2.00e-02 2.50e+03
        pdb=" N   ALA G  43 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1616 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 2581
        2.79 -     3.32: 8268
        3.32 -     3.85: 15774
        3.85 -     4.37: 18580
        4.37 -     4.90: 30732
  Nonbonded interactions: 75935
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A  26 "
            pdb=" NZ  LYS B  78 "
     model   vdw
     2.266 3.120
  nonbonded pdb=" O   SER A  44 "
            pdb=" OG  SER A  44 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" O   LEU R 349 "
            pdb=" OG1 THR R 353 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" N   HIS R 374 "
            pdb=" N   ALA R 375 "
     model   vdw
     2.320 2.560
  nonbonded pdb=" OE2 GLU A  20 "
            pdb=" NZ  LYS B  89 "
     model   vdw
     2.346 3.120
  ... (remaining 75930 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.820
  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:         0.060
  Set scattering table:                    0.100
  Process input model:                     23.310
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
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   0.057   9364  Z= 0.611
  Angle     :  1.200  14.827  12724  Z= 0.787
  Chirality :  0.077   0.402   1431
  Planarity :  0.005   0.067   1619
  Dihedral  : 19.441  87.521   3292
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.86 %
    Allowed  :  6.91 %
    Favored  : 92.23 %
  Rotamer:
    Outliers : 14.75 %
    Allowed  : 17.86 %
    Favored  : 67.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.24), residues: 1158
  helix:  0.00 (0.25), residues: 418
  sheet: -0.37 (0.33), residues: 215
  loop : -1.64 (0.27), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 211 
 HIS   0.006   0.001   HIS A 324 
 PHE   0.024   0.002   PHE B 199 
 TYR   0.027   0.002   TYR R 148 
 ARG   0.008   0.001   ARG G  62 

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

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

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  313 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 142
    poor density    : 171
  time to evaluate  : 1.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8569 (m)
REVERT: A  324 HIS cc_start: 0.8824 (OUTLIER) cc_final: 0.8622 (p-80)
REVERT: A  359 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8143 (mt-10)
REVERT: B  175 GLN cc_start: 0.8090 (mm-40) cc_final: 0.7625 (mp10)
REVERT: B  186 ASP cc_start: 0.7561 (OUTLIER) cc_final: 0.7015 (m-30)
REVERT: B  228 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.8042 (m-30)
REVERT: B  292 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.8551 (m-10)
REVERT: P   21 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8520 (tm-30)
REVERT: G   21 MET cc_start: 0.6642 (ppp) cc_final: 0.6419 (ppp)
REVERT: G   46 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8699 (tppt)
REVERT: G   50 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7350 (mm)
REVERT: N   34 MET cc_start: 0.8307 (mmm) cc_final: 0.8043 (mmm)
REVERT: N   46 GLU cc_start: 0.8158 (pt0) cc_final: 0.7764 (mm-30)
REVERT: N   53 GLN cc_start: 0.8153 (mp10) cc_final: 0.7910 (mp10)
REVERT: R   31 SER cc_start: 0.8894 (OUTLIER) cc_final: 0.8264 (p)
REVERT: R   42 TYR cc_start: 0.7920 (OUTLIER) cc_final: 0.7429 (m-80)
REVERT: R  107 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.4978 (pm20)
REVERT: R  261 SER cc_start: 0.7272 (OUTLIER) cc_final: 0.6972 (t)
REVERT: R  346 LYS cc_start: 0.6139 (OUTLIER) cc_final: 0.5609 (mmtt)
REVERT: R  351 LYS cc_start: 0.8762 (tmtp) cc_final: 0.8389 (tptp)
REVERT: R  369 PHE cc_start: 0.8034 (m-80) cc_final: 0.7719 (m-80)
  outliers start: 142
  outliers final: 20
  residues processed: 272
  average time/residue: 1.2730
  time to fit residues: 369.0864
Evaluate side-chains
  173 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 140
  time to evaluate  : 1.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  209 ARG
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  324 HIS
Chi-restraints excluded: chain A residue  336 THR
Chi-restraints excluded: chain A residue  359 GLU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue   31 SER
Chi-restraints excluded: chain R residue   42 TYR
Chi-restraints excluded: chain R residue  107 GLU
Chi-restraints excluded: chain R residue  110 TRP
Chi-restraints excluded: chain R residue  261 SER
Chi-restraints excluded: chain R residue  343 THR
Chi-restraints excluded: chain R residue  346 LYS
Chi-restraints excluded: chain R residue  353 THR
Chi-restraints excluded: chain R residue  370 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 95 optimal weight:    0.6980
   chunk 85 optimal weight:    0.8980
   chunk 47 optimal weight:    8.9990
   chunk 29 optimal weight:    0.8980
   chunk 57 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9990
   chunk 88 optimal weight:    0.5980
   chunk 34 optimal weight:    0.4980
   chunk 53 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 102 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
A 190 GLN
B 230 ASN
G  44 HIS
R  63 ASN
R 180 HIS
R 406 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9364  Z= 0.220
  Angle     :  0.648  12.226  12724  Z= 0.344
  Chirality :  0.042   0.159   1431
  Planarity :  0.005   0.064   1619
  Dihedral  :  8.547  85.235   1332
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.15 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  6.02 %
    Allowed  : 23.68 %
    Favored  : 70.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.06 (0.25), residues: 1158
  helix:  1.36 (0.25), residues: 442
  sheet:  0.19 (0.34), residues: 211
  loop : -1.44 (0.28), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 110 
 HIS   0.004   0.001   HIS A 197 
 PHE   0.018   0.002   PHE A 307 
 TYR   0.024   0.001   TYR R 148 
 ARG   0.013   0.001   ARG B 214 

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

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

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 162
  time to evaluate  : 1.075 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  190 GLN cc_start: 0.8594 (mt0) cc_final: 0.8334 (mt0)
REVERT: A  209 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8511 (ptp-170)
REVERT: B   59 TYR cc_start: 0.9051 (OUTLIER) cc_final: 0.8059 (m-80)
REVERT: B  175 GLN cc_start: 0.8025 (mm-40) cc_final: 0.7796 (mp10)
REVERT: B  186 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.7033 (m-30)
REVERT: B  217 MET cc_start: 0.8612 (pmt) cc_final: 0.8294 (pmm)
REVERT: P   21 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8493 (tm-30)
REVERT: G   21 MET cc_start: 0.7004 (OUTLIER) cc_final: 0.6714 (ppp)
REVERT: G   46 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8558 (tppt)
REVERT: G   50 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7387 (mm)
REVERT: N   53 GLN cc_start: 0.8282 (mp10) cc_final: 0.7926 (mp10)
REVERT: N  122 THR cc_start: 0.7382 (m) cc_final: 0.6958 (p)
REVERT: R   31 SER cc_start: 0.9118 (m) cc_final: 0.8875 (p)
REVERT: R   42 TYR cc_start: 0.8132 (OUTLIER) cc_final: 0.7615 (m-80)
REVERT: R  107 GLU cc_start: 0.6517 (OUTLIER) cc_final: 0.5986 (pm20)
REVERT: R  112 GLN cc_start: 0.7160 (mm110) cc_final: 0.6588 (mm110)
REVERT: R  261 SER cc_start: 0.6878 (OUTLIER) cc_final: 0.6619 (t)
REVERT: R  346 LYS cc_start: 0.5925 (OUTLIER) cc_final: 0.5284 (mmtt)
REVERT: R  351 LYS cc_start: 0.8813 (tmtp) cc_final: 0.8411 (tptp)
REVERT: R  370 VAL cc_start: 0.5158 (OUTLIER) cc_final: 0.4789 (t)
REVERT: R  371 MET cc_start: 0.8340 (mpp) cc_final: 0.7844 (mpp)
  outliers start: 58
  outliers final: 16
  residues processed: 205
  average time/residue: 1.2355
  time to fit residues: 270.2699
Evaluate side-chains
  168 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 141
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  209 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain P residue   23 ILE
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain R residue   42 TYR
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue  100 VAL
Chi-restraints excluded: chain R residue  107 GLU
Chi-restraints excluded: chain R residue  111 LEU
Chi-restraints excluded: chain R residue  222 ASP
Chi-restraints excluded: chain R residue  261 SER
Chi-restraints excluded: chain R residue  343 THR
Chi-restraints excluded: chain R residue  346 LYS
Chi-restraints excluded: chain R residue  370 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 57 optimal weight:    0.7980
   chunk 31 optimal weight:    0.4980
   chunk 85 optimal weight:    4.9990
   chunk 69 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 102 optimal weight:    2.9990
   chunk 111 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 101 optimal weight:    0.4980
   chunk 35 optimal weight:    3.9990
   chunk 82 optimal weight:    9.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 357 GLN
B 230 ASN
R 180 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.2461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9364  Z= 0.252
  Angle     :  0.593   8.244  12724  Z= 0.317
  Chirality :  0.042   0.156   1431
  Planarity :  0.004   0.050   1619
  Dihedral  :  7.067  81.700   1307
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  5.40 %
    Allowed  : 25.44 %
    Favored  : 69.16 %
  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:  0.37 (0.25), residues: 1158
  helix:  1.81 (0.25), residues: 440
  sheet:  0.31 (0.34), residues: 219
  loop : -1.26 (0.28), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 243 
 HIS   0.002   0.001   HIS B 225 
 PHE   0.016   0.001   PHE A 307 
 TYR   0.025   0.001   TYR R 148 
 ARG   0.006   0.000   ARG B 214 

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

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

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 150
  time to evaluate  : 1.169 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8072 (mm-30)
REVERT: B   37 ILE cc_start: 0.7629 (OUTLIER) cc_final: 0.6728 (pp)
REVERT: B   59 TYR cc_start: 0.9043 (OUTLIER) cc_final: 0.7979 (m-80)
REVERT: B  217 MET cc_start: 0.8696 (pmt) cc_final: 0.8382 (pmm)
REVERT: B  336 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8823 (mp)
REVERT: P   16 GLU cc_start: 0.8631 (tp30) cc_final: 0.8171 (mm-30)
REVERT: P   17 GLN cc_start: 0.8515 (tt0) cc_final: 0.8168 (tt0)
REVERT: P   21 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8487 (tm-30)
REVERT: G   38 MET cc_start: 0.7656 (mtp) cc_final: 0.7387 (mtm)
REVERT: N   53 GLN cc_start: 0.8436 (mp10) cc_final: 0.7906 (mp10)
REVERT: N  122 THR cc_start: 0.7397 (m) cc_final: 0.7044 (p)
REVERT: R   31 SER cc_start: 0.9125 (m) cc_final: 0.8908 (p)
REVERT: R   42 TYR cc_start: 0.8202 (OUTLIER) cc_final: 0.7488 (m-80)
REVERT: R  112 GLN cc_start: 0.7540 (mm110) cc_final: 0.7015 (mm110)
REVERT: R  221 GLN cc_start: 0.8108 (mm110) cc_final: 0.7835 (mm110)
REVERT: R  371 MET cc_start: 0.8305 (mpp) cc_final: 0.7853 (mpp)
  outliers start: 52
  outliers final: 20
  residues processed: 191
  average time/residue: 1.2621
  time to fit residues: 256.8887
Evaluate side-chains
  161 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 137
  time to evaluate  : 1.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain P residue   23 ILE
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue   42 TYR
Chi-restraints excluded: chain R residue   60 LEU
Chi-restraints excluded: chain R residue   74 ASP
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue  100 VAL
Chi-restraints excluded: chain R residue  110 TRP
Chi-restraints excluded: chain R residue  213 GLN
Chi-restraints excluded: chain R residue  343 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 101 optimal weight:    6.9990
   chunk 77 optimal weight:   10.0000
   chunk 53 optimal weight:    4.9990
   chunk 11 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 103 optimal weight:    0.6980
   chunk 109 optimal weight:    2.9990
   chunk 97 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 90 optimal weight:    0.5980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
** R  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 410 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.2754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9364  Z= 0.220
  Angle     :  0.579   8.074  12724  Z= 0.308
  Chirality :  0.041   0.150   1431
  Planarity :  0.004   0.051   1619
  Dihedral  :  5.775  82.110   1284
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 24.92 %
    Favored  : 70.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.25), residues: 1158
  helix:  2.11 (0.25), residues: 434
  sheet:  0.40 (0.35), residues: 227
  loop : -1.17 (0.28), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP R  39 
 HIS   0.001   0.000   HIS B 183 
 PHE   0.014   0.001   PHE A 189 
 TYR   0.023   0.001   TYR R 148 
 ARG   0.005   0.000   ARG B  96 

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

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

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 149
  time to evaluate  : 1.098 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.8343 (mm-30) cc_final: 0.8099 (mm-30)
REVERT: A  281 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7867 (tm-30)
REVERT: B   37 ILE cc_start: 0.7597 (OUTLIER) cc_final: 0.6795 (pt)
REVERT: B   59 TYR cc_start: 0.9048 (OUTLIER) cc_final: 0.7982 (m-80)
REVERT: B  217 MET cc_start: 0.8753 (pmt) cc_final: 0.8415 (pmm)
REVERT: B  220 GLN cc_start: 0.8347 (mp10) cc_final: 0.8102 (mp10)
REVERT: B  336 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8792 (mp)
REVERT: P   16 GLU cc_start: 0.8631 (tp30) cc_final: 0.8151 (mm-30)
REVERT: P   17 GLN cc_start: 0.8530 (tt0) cc_final: 0.8286 (tp40)
REVERT: P   21 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8460 (tm-30)
REVERT: G   38 MET cc_start: 0.7719 (mtp) cc_final: 0.7457 (mtm)
REVERT: N   53 GLN cc_start: 0.8432 (mp10) cc_final: 0.7709 (mp10)
REVERT: N  122 THR cc_start: 0.7340 (m) cc_final: 0.6990 (p)
REVERT: R   37 GLN cc_start: 0.9142 (pp30) cc_final: 0.8903 (pp30)
REVERT: R  112 GLN cc_start: 0.7608 (mm110) cc_final: 0.7243 (mm110)
REVERT: R  371 MET cc_start: 0.8306 (mpp) cc_final: 0.7794 (mpp)
  outliers start: 47
  outliers final: 24
  residues processed: 186
  average time/residue: 1.3050
  time to fit residues: 259.0154
Evaluate side-chains
  165 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 137
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  353 MET
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   76 LYS
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue   60 LEU
Chi-restraints excluded: chain R residue   64 ARG
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue   95 VAL
Chi-restraints excluded: chain R residue  100 VAL
Chi-restraints excluded: chain R residue  343 THR
Chi-restraints excluded: chain R residue  370 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 81 optimal weight:   10.0000
   chunk 45 optimal weight:    5.9990
   chunk 93 optimal weight:    5.9990
   chunk 75 optimal weight:    5.9990
   chunk 0 optimal weight:    0.8980
   chunk 55 optimal weight:    3.9990
   chunk 98 optimal weight:    0.0000
   chunk 27 optimal weight:    2.9990
   chunk 36 optimal weight:    5.9990
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
N   3 GLN
R  37 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.2859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   9364  Z= 0.337
  Angle     :  0.613   7.721  12724  Z= 0.327
  Chirality :  0.043   0.162   1431
  Planarity :  0.004   0.053   1619
  Dihedral  :  5.684  81.587   1282
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 25.23 %
    Favored  : 69.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.66 (0.25), residues: 1158
  helix:  2.10 (0.25), residues: 435
  sheet:  0.38 (0.35), residues: 225
  loop : -1.07 (0.29), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP R  39 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.018   0.002   PHE N 108 
 TYR   0.025   0.002   TYR R 148 
 ARG   0.007   0.001   ARG G  62 

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

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

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 146
  time to evaluate  : 1.100 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8109 (mm-30)
REVERT: A  235 GLU cc_start: 0.8030 (tp30) cc_final: 0.7824 (tp30)
REVERT: A  281 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8043 (tm-30)
REVERT: B   37 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.6999 (pt)
REVERT: B   59 TYR cc_start: 0.9104 (OUTLIER) cc_final: 0.8064 (m-80)
REVERT: B  186 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7102 (m-30)
REVERT: B  217 MET cc_start: 0.8743 (pmt) cc_final: 0.8391 (pmm)
REVERT: B  336 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8839 (mp)
REVERT: P   16 GLU cc_start: 0.8637 (tp30) cc_final: 0.8401 (tp30)
REVERT: P   17 GLN cc_start: 0.8560 (tt0) cc_final: 0.8293 (tp40)
REVERT: P   21 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8517 (tm-30)
REVERT: G   38 MET cc_start: 0.7677 (mtp) cc_final: 0.7461 (mtm)
REVERT: N   53 GLN cc_start: 0.8459 (mp10) cc_final: 0.7721 (mp10)
REVERT: N   65 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.8937 (ttpp)
REVERT: N  120 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8460 (mm-40)
REVERT: N  122 THR cc_start: 0.7414 (m) cc_final: 0.6972 (p)
REVERT: R  112 GLN cc_start: 0.7783 (mm110) cc_final: 0.7396 (mm110)
REVERT: R  371 MET cc_start: 0.8365 (mpp) cc_final: 0.7978 (mpp)
  outliers start: 47
  outliers final: 24
  residues processed: 181
  average time/residue: 1.3260
  time to fit residues: 256.3033
Evaluate side-chains
  162 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 132
  time to evaluate  : 1.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   65 LYS
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue   60 LEU
Chi-restraints excluded: chain R residue   74 ASP
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue   95 VAL
Chi-restraints excluded: chain R residue  100 VAL
Chi-restraints excluded: chain R residue  343 THR
Chi-restraints excluded: chain R residue  370 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   chunk 64 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 109 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   chunk 36 optimal weight:    5.9990
   chunk 57 optimal weight:    0.7980
   chunk 105 optimal weight:   10.0000
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
N   3 GLN
** R  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.2989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9364  Z= 0.215
  Angle     :  0.580   8.862  12724  Z= 0.310
  Chirality :  0.041   0.146   1431
  Planarity :  0.004   0.053   1619
  Dihedral  :  5.546  82.394   1282
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 25.75 %
    Favored  : 69.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.25), residues: 1158
  helix:  2.25 (0.25), residues: 434
  sheet:  0.54 (0.35), residues: 223
  loop : -1.07 (0.28), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R  39 
 HIS   0.001   0.000   HIS B 183 
 PHE   0.014   0.001   PHE A 189 
 TYR   0.021   0.001   TYR R 148 
 ARG   0.006   0.000   ARG A 250 

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

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

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 147
  time to evaluate  : 1.044 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8003 (mm-30)
REVERT: A  235 GLU cc_start: 0.8025 (tp30) cc_final: 0.7799 (tp30)
REVERT: A  239 ASP cc_start: 0.8351 (m-30) cc_final: 0.8104 (t0)
REVERT: A  281 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7941 (tm-30)
REVERT: A  359 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8187 (mt-10)
REVERT: B   37 ILE cc_start: 0.7727 (OUTLIER) cc_final: 0.6974 (pt)
REVERT: B   59 TYR cc_start: 0.9061 (OUTLIER) cc_final: 0.7987 (m-80)
REVERT: B  186 ASP cc_start: 0.7654 (OUTLIER) cc_final: 0.7061 (m-30)
REVERT: B  217 MET cc_start: 0.8784 (pmt) cc_final: 0.8450 (pmm)
REVERT: B  336 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8810 (mp)
REVERT: P   16 GLU cc_start: 0.8669 (tp30) cc_final: 0.8421 (tp30)
REVERT: P   17 GLN cc_start: 0.8546 (tt0) cc_final: 0.8292 (tp40)
REVERT: P   21 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8472 (tm-30)
REVERT: G   38 MET cc_start: 0.7566 (mtp) cc_final: 0.7323 (mtm)
REVERT: N   53 GLN cc_start: 0.8499 (mp10) cc_final: 0.7912 (mp10)
REVERT: N   87 LYS cc_start: 0.8425 (ptpp) cc_final: 0.8032 (ptpp)
REVERT: N  120 GLN cc_start: 0.8791 (mm-40) cc_final: 0.8477 (mm-40)
REVERT: N  122 THR cc_start: 0.7372 (m) cc_final: 0.7036 (p)
REVERT: R   37 GLN cc_start: 0.9105 (pp30) cc_final: 0.8894 (pp30)
REVERT: R   42 TYR cc_start: 0.7980 (OUTLIER) cc_final: 0.7766 (m-80)
REVERT: R  112 GLN cc_start: 0.7643 (mm110) cc_final: 0.7263 (mm110)
REVERT: R  351 LYS cc_start: 0.8474 (tptm) cc_final: 0.8263 (tmtp)
  outliers start: 47
  outliers final: 23
  residues processed: 185
  average time/residue: 1.2714
  time to fit residues: 250.8017
Evaluate side-chains
  163 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 134
  time to evaluate  : 1.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  353 MET
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue   42 TYR
Chi-restraints excluded: chain R residue   60 LEU
Chi-restraints excluded: chain R residue   74 ASP
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue   95 VAL
Chi-restraints excluded: chain R residue  100 VAL
Chi-restraints excluded: chain R residue  224 LEU
Chi-restraints excluded: chain R residue  343 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 12 optimal weight:    0.6980
   chunk 62 optimal weight:    0.3980
   chunk 79 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 92 optimal weight:    8.9990
   chunk 108 optimal weight:    0.1980
   chunk 68 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9990
   chunk 50 optimal weight:    3.9990
   chunk 67 optimal weight:    0.7980
   chunk 43 optimal weight:    3.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
A 216 ASN
N   3 GLN
** R  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 410 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.3112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9364  Z= 0.186
  Angle     :  0.584  14.036  12724  Z= 0.314
  Chirality :  0.041   0.207   1431
  Planarity :  0.004   0.052   1619
  Dihedral  :  5.411  80.898   1282
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 27.52 %
    Favored  : 68.95 %
  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: 1158
  helix:  2.52 (0.25), residues: 428
  sheet:  0.51 (0.34), residues: 225
  loop : -1.11 (0.28), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP R  39 
 HIS   0.001   0.000   HIS B 183 
 PHE   0.014   0.001   PHE A 189 
 TYR   0.020   0.001   TYR R 148 
 ARG   0.006   0.000   ARG A 250 

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

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

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 143
  time to evaluate  : 1.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.8297 (mm-30) cc_final: 0.8060 (mm-30)
REVERT: A  239 ASP cc_start: 0.8393 (m-30) cc_final: 0.8130 (t0)
REVERT: A  281 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7885 (tm-30)
REVERT: A  297 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8043 (pp20)
REVERT: B   37 ILE cc_start: 0.7654 (OUTLIER) cc_final: 0.6915 (pt)
REVERT: B   59 TYR cc_start: 0.9051 (OUTLIER) cc_final: 0.7779 (m-80)
REVERT: B  217 MET cc_start: 0.8794 (pmt) cc_final: 0.8479 (pmm)
REVERT: B  228 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8381 (m-30)
REVERT: B  280 LYS cc_start: 0.8749 (tppp) cc_final: 0.7752 (tptp)
REVERT: B  336 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8784 (mp)
REVERT: P   16 GLU cc_start: 0.8693 (tp30) cc_final: 0.8447 (tp30)
REVERT: P   17 GLN cc_start: 0.8532 (tt0) cc_final: 0.8298 (tp40)
REVERT: P   21 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8465 (tm-30)
REVERT: G   38 MET cc_start: 0.7686 (mtp) cc_final: 0.7433 (mtm)
REVERT: N   53 GLN cc_start: 0.8493 (mp10) cc_final: 0.7894 (mp10)
REVERT: N   87 LYS cc_start: 0.8367 (ptpp) cc_final: 0.7866 (ptpp)
REVERT: N  120 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8458 (mm-40)
REVERT: N  122 THR cc_start: 0.7316 (m) cc_final: 0.7029 (p)
REVERT: R  112 GLN cc_start: 0.7633 (mm110) cc_final: 0.7255 (mm110)
REVERT: R  351 LYS cc_start: 0.8429 (tptm) cc_final: 0.8210 (tmtp)
  outliers start: 34
  outliers final: 22
  residues processed: 173
  average time/residue: 1.2919
  time to fit residues: 238.3602
Evaluate side-chains
  165 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 137
  time to evaluate  : 1.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain P residue   23 ILE
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue   60 LEU
Chi-restraints excluded: chain R residue   74 ASP
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue   95 VAL
Chi-restraints excluded: chain R residue  100 VAL
Chi-restraints excluded: chain R residue  224 LEU
Chi-restraints excluded: chain R residue  343 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 74 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0980
   chunk 85 optimal weight:    0.0470
   chunk 99 optimal weight:    1.9990
   chunk 104 optimal weight:    1.9990
   chunk 95 optimal weight:    1.9990
   overall best weight:    0.5880

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
R  47 GLN
R 410 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.3216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   9364  Z= 0.191
  Angle     :  0.578  10.472  12724  Z= 0.309
  Chirality :  0.040   0.154   1431
  Planarity :  0.004   0.053   1619
  Dihedral  :  5.268  78.802   1281
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 28.25 %
    Favored  : 68.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.26), residues: 1158
  helix:  2.56 (0.25), residues: 430
  sheet:  0.55 (0.35), residues: 225
  loop : -1.05 (0.28), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP R  39 
 HIS   0.002   0.000   HIS G  44 
 PHE   0.013   0.001   PHE A 189 
 TYR   0.020   0.001   TYR R 148 
 ARG   0.008   0.000   ARG G  62 

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

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

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 149
  time to evaluate  : 0.931 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8064 (mm-30)
REVERT: A  239 ASP cc_start: 0.8386 (m-30) cc_final: 0.8124 (t0)
REVERT: A  281 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7832 (tm-30)
REVERT: A  297 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8146 (pp20)
REVERT: B   37 ILE cc_start: 0.7602 (OUTLIER) cc_final: 0.6888 (pt)
REVERT: B   59 TYR cc_start: 0.9048 (OUTLIER) cc_final: 0.7784 (m-80)
REVERT: B  186 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.7000 (m-30)
REVERT: B  217 MET cc_start: 0.8785 (pmt) cc_final: 0.8482 (pmm)
REVERT: B  226 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7581 (mt-10)
REVERT: B  228 ASP cc_start: 0.8689 (OUTLIER) cc_final: 0.8361 (m-30)
REVERT: B  280 LYS cc_start: 0.8757 (tppp) cc_final: 0.7758 (tptp)
REVERT: B  336 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8782 (mp)
REVERT: P   16 GLU cc_start: 0.8694 (tp30) cc_final: 0.8173 (mm-30)
REVERT: P   17 GLN cc_start: 0.8469 (tt0) cc_final: 0.8249 (tp40)
REVERT: P   21 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8465 (tm-30)
REVERT: G   38 MET cc_start: 0.7683 (mtp) cc_final: 0.7435 (mtm)
REVERT: N   53 GLN cc_start: 0.8472 (mp10) cc_final: 0.7809 (mp10)
REVERT: N   87 LYS cc_start: 0.8276 (ptpp) cc_final: 0.7849 (ptpp)
REVERT: N  120 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8399 (mm-40)
REVERT: N  122 THR cc_start: 0.7299 (m) cc_final: 0.7008 (p)
REVERT: R  112 GLN cc_start: 0.7622 (mm110) cc_final: 0.7320 (mm110)
REVERT: R  351 LYS cc_start: 0.8435 (tptm) cc_final: 0.8198 (tmtp)
  outliers start: 34
  outliers final: 20
  residues processed: 178
  average time/residue: 1.3190
  time to fit residues: 249.9078
Evaluate side-chains
  171 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 144
  time to evaluate  : 1.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain P residue   23 ILE
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue   60 LEU
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue   95 VAL
Chi-restraints excluded: chain R residue  100 VAL
Chi-restraints excluded: chain R residue  343 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 101 optimal weight:    0.9990
   chunk 104 optimal weight:    0.9990
   chunk 61 optimal weight:    7.9990
   chunk 44 optimal weight:    1.9990
   chunk 79 optimal weight:   40.0000
   chunk 31 optimal weight:    0.9990
   chunk 91 optimal weight:    5.9990
   chunk 95 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   chunk 107 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.9988

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
A 246 ASN
R 410 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.3233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9364  Z= 0.238
  Angle     :  0.611  10.937  12724  Z= 0.326
  Chirality :  0.041   0.150   1431
  Planarity :  0.004   0.054   1619
  Dihedral  :  4.698  56.253   1278
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 28.76 %
    Favored  : 67.81 %
  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: 1158
  helix:  2.55 (0.24), residues: 427
  sheet:  0.54 (0.34), residues: 225
  loop : -1.03 (0.28), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP R  39 
 HIS   0.001   0.000   HIS B 183 
 PHE   0.017   0.001   PHE A 189 
 TYR   0.021   0.001   TYR R 148 
 ARG   0.010   0.000   ARG R  43 

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

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

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 144
  time to evaluate  : 1.143 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.8292 (mm-30) cc_final: 0.8022 (mm-30)
REVERT: A  239 ASP cc_start: 0.8391 (m-30) cc_final: 0.8139 (t0)
REVERT: A  281 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7898 (tm-30)
REVERT: A  297 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8164 (pp20)
REVERT: B   37 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.6920 (pt)
REVERT: B   59 TYR cc_start: 0.9073 (OUTLIER) cc_final: 0.7997 (m-80)
REVERT: B  186 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7023 (m-30)
REVERT: B  217 MET cc_start: 0.8801 (pmt) cc_final: 0.8470 (pmm)
REVERT: B  226 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7559 (mt-10)
REVERT: B  228 ASP cc_start: 0.8750 (OUTLIER) cc_final: 0.8349 (m-30)
REVERT: B  280 LYS cc_start: 0.8756 (tppp) cc_final: 0.8333 (tptp)
REVERT: B  336 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8812 (mp)
REVERT: P   16 GLU cc_start: 0.8690 (tp30) cc_final: 0.8424 (tp30)
REVERT: P   21 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8504 (tm-30)
REVERT: G   38 MET cc_start: 0.7556 (mtp) cc_final: 0.7309 (mtm)
REVERT: N   53 GLN cc_start: 0.8538 (mp10) cc_final: 0.7998 (mp10)
REVERT: N   87 LYS cc_start: 0.8274 (ptpp) cc_final: 0.7903 (ptpp)
REVERT: N  120 GLN cc_start: 0.8754 (mm-40) cc_final: 0.8450 (mm-40)
REVERT: N  122 THR cc_start: 0.7365 (m) cc_final: 0.7033 (p)
REVERT: R  112 GLN cc_start: 0.7439 (mm110) cc_final: 0.7114 (mm110)
REVERT: R  351 LYS cc_start: 0.8411 (tptm) cc_final: 0.8174 (tmtp)
  outliers start: 33
  outliers final: 19
  residues processed: 172
  average time/residue: 1.4060
  time to fit residues: 257.2568
Evaluate side-chains
  165 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 139
  time to evaluate  : 1.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain P residue   23 ILE
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue   95 VAL
Chi-restraints excluded: chain R residue  100 VAL
Chi-restraints excluded: chain R residue  265 ILE
Chi-restraints excluded: chain R residue  343 THR
Chi-restraints excluded: chain R residue  370 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 74 optimal weight:    0.6980
   chunk 112 optimal weight:    0.9990
   chunk 103 optimal weight:    0.6980
   chunk 89 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 71 optimal weight:    0.7980
   chunk 95 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
B 175 GLN
** R 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 410 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.3343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9364  Z= 0.210
  Angle     :  0.607  11.002  12724  Z= 0.323
  Chirality :  0.041   0.145   1431
  Planarity :  0.004   0.053   1619
  Dihedral  :  4.635  54.910   1278
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.40 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 29.49 %
    Favored  : 67.81 %
  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:  1.02 (0.25), residues: 1158
  helix:  2.61 (0.24), residues: 428
  sheet:  0.58 (0.35), residues: 225
  loop : -1.04 (0.28), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R  39 
 HIS   0.001   0.000   HIS B 183 
 PHE   0.013   0.001   PHE A 189 
 TYR   0.020   0.001   TYR R 148 
 ARG   0.009   0.000   ARG R  64 

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

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

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 145
  time to evaluate  : 1.102 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.8301 (mm-30) cc_final: 0.8050 (mm-30)
REVERT: A   53 MET cc_start: 0.6524 (tmt) cc_final: 0.6215 (tmm)
REVERT: A  239 ASP cc_start: 0.8385 (m-30) cc_final: 0.8140 (t0)
REVERT: A  297 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8134 (pp20)
REVERT: B   37 ILE cc_start: 0.7615 (OUTLIER) cc_final: 0.6903 (pt)
REVERT: B   59 TYR cc_start: 0.9074 (OUTLIER) cc_final: 0.7894 (m-80)
REVERT: B  186 ASP cc_start: 0.7533 (OUTLIER) cc_final: 0.6998 (m-30)
REVERT: B  217 MET cc_start: 0.8818 (pmt) cc_final: 0.8489 (pmm)
REVERT: B  226 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7556 (mt-10)
REVERT: B  228 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8361 (m-30)
REVERT: B  280 LYS cc_start: 0.8751 (tppp) cc_final: 0.7746 (tptp)
REVERT: B  336 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8797 (mp)
REVERT: P   16 GLU cc_start: 0.8740 (tp30) cc_final: 0.8477 (tp30)
REVERT: P   17 GLN cc_start: 0.8463 (tp40) cc_final: 0.8029 (mt0)
REVERT: P   21 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8412 (tm-30)
REVERT: G   38 MET cc_start: 0.7608 (mtp) cc_final: 0.7354 (mtm)
REVERT: N   53 GLN cc_start: 0.8514 (mp10) cc_final: 0.7956 (mp10)
REVERT: N   87 LYS cc_start: 0.8336 (ptpp) cc_final: 0.7951 (ptpp)
REVERT: N  120 GLN cc_start: 0.8791 (mm-40) cc_final: 0.8466 (mm-40)
REVERT: N  122 THR cc_start: 0.7333 (m) cc_final: 0.7026 (p)
REVERT: R  112 GLN cc_start: 0.7455 (mm110) cc_final: 0.7143 (mm110)
REVERT: R  351 LYS cc_start: 0.8405 (tptm) cc_final: 0.8169 (tmtp)
REVERT: R  415 LYS cc_start: 0.7967 (mtmt) cc_final: 0.7713 (ptpt)
  outliers start: 26
  outliers final: 20
  residues processed: 170
  average time/residue: 1.3520
  time to fit residues: 244.6076
Evaluate side-chains
  168 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 142
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain P residue   23 ILE
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue   95 VAL
Chi-restraints excluded: chain R residue  100 VAL
Chi-restraints excluded: chain R residue  265 ILE
Chi-restraints excluded: chain R residue  343 THR
Chi-restraints excluded: chain R residue  370 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 82 optimal weight:    7.9990
   chunk 13 optimal weight:    1.9990
   chunk 24 optimal weight:    7.9990
   chunk 89 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 92 optimal weight:    4.9990
   chunk 11 optimal weight:    0.6980
   chunk 16 optimal weight:    3.9990
   chunk 78 optimal weight:   50.0000
   chunk 5 optimal weight:    0.7980
   chunk 64 optimal weight:    0.6980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
A 246 ASN
** R 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 410 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.125964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.081508 restraints weight = 15384.279|
|-----------------------------------------------------------------------------|
r_work (start): 0.3094 rms_B_bonded: 3.08
r_work: 0.2946 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.3347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9364  Z= 0.271
  Angle     :  0.623  10.860  12724  Z= 0.332
  Chirality :  0.042   0.151   1431
  Planarity :  0.004   0.054   1619
  Dihedral  :  4.736  55.051   1278
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.49 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 28.56 %
    Favored  : 67.91 %
  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:  1.01 (0.25), residues: 1158
  helix:  2.53 (0.24), residues: 430
  sheet:  0.55 (0.34), residues: 223
  loop : -0.96 (0.29), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R  39 
 HIS   0.001   0.000   HIS B 183 
 PHE   0.013   0.001   PHE R 230 
 TYR   0.022   0.002   TYR R 148 
 ARG   0.009   0.000   ARG R  64 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4519.76 seconds
wall clock time: 86 minutes 6.04 seconds (5166.04 seconds total)