Starting phenix.real_space_refine
on Fri Aug 22 23:19:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jsp_36626/08_2025/8jsp_36626.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jsp_36626/08_2025/8jsp_36626.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jsp_36626/08_2025/8jsp_36626.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jsp_36626/08_2025/8jsp_36626.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jsp_36626/08_2025/8jsp_36626.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jsp_36626/08_2025/8jsp_36626.cif"
  }
  resolution = 3.65
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.032
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      63      5.16       5
     C    5480      2.51       5
     N    1470      2.21       5
     O    1586      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8599
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1743
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1743
          Classifications: {'peptide': 216}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 213}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2516
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 328, 2516
          Classifications: {'peptide': 328}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 322}
    Chain: "E"
      Number of atoms: 1717
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1717
          Classifications: {'peptide': 227}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 10, 'TRANS': 216}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 26
    Chain: "G"
      Number of atoms: 347
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 347
          Classifications: {'peptide': 45}
          Link IDs: {'PTRANS': 4, 'TRANS': 40}
    Chain: "R"
      Number of atoms: 2264
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2264
          Classifications: {'peptide': 286}
          Link IDs: {'PTRANS': 12, 'TRANS': 273}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 12
          Unusual residues: {'UJL': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.77, per 1000 atoms: 0.21
  Number of scatterers: 8599
  At special positions: 0
  Unit cell: (103.96, 115.92, 129.72, 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      63     16.00
     O    1586      8.00
     N    1470      7.00
     C    5480      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 121 " - pdb=" SG  CYS B 149 " distance=2.07
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 159 " - pdb=" SG  CYS E 229 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 109 " - pdb=" SG  CYS R 187 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.76
  Conformation dependent library (CDL) restraints added in 440.0 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2058

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 13 sheets defined
      39.2% alpha, 18.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 30
    Processing helix  chain 'A' and resid 45 through 55
    Processing helix  chain 'A' and resid 207 through 211
      removed outlier: 3.509A  pdb=" N   TRP A 211 " --> pdb=" O   ARG A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 216
      removed outlier: 3.503A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 232
      removed outlier: 4.055A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   LEU A 232 " --> pdb=" O   ASP A 229 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 228 through 232'
    Processing helix  chain 'A' and resid 243 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 3.960A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 281
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 3.517A  pdb=" N   VAL A 335 " --> pdb=" O   ASN A 331 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   LYS A 349 " --> pdb=" O   LYS A 345 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   ASP A 350 " --> pdb=" O   ASN A 346 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   CYS A 351 " --> pdb=" O   ASN A 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 14 through 26
      removed outlier: 3.523A  pdb=" N   ALA B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.847A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 53 through 56
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.774A  pdb=" N   THR E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 19 through 24
    Processing helix  chain 'G' and resid 29 through 45
      removed outlier: 3.961A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 46 through 48
      No H-bonds generated for 'chain 'G' and resid 46 through 48'
    Processing helix  chain 'G' and resid 55 through 59
      removed outlier: 3.806A  pdb=" N   ASN G  59 " --> pdb=" O   ALA G  56 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 36 through 63
      removed outlier: 3.686A  pdb=" N   VAL R  58 " --> pdb=" O   ASN R  54 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 69 through 99
      Proline residue:  R  91  - end of helix
    Processing helix  chain 'R' and resid 105 through 123
    Processing helix  chain 'R' and resid 124 through 140
      removed outlier: 4.227A  pdb=" N   CYS R 128 " --> pdb=" O   ILE R 124 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   ASP R 140 " --> pdb=" O   TRP R 136 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 147
      removed outlier: 3.551A  pdb=" N   TYR R 144 " --> pdb=" O   ASP R 140 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 150 through 174
      removed outlier: 3.937A  pdb=" N   ALA R 154 " --> pdb=" O   PRO R 150 " (cutoff:3.500A)
      Proline residue:  R 170  - end of helix
    Processing helix  chain 'R' and resid 192 through 228
      removed outlier: 4.060A  pdb=" N   THR R 200 " --> pdb=" O   THR R 196 " (cutoff:3.500A)
      removed outlier: 5.924A  pdb=" N   ILE R 206 " --> pdb=" O   GLY R 202 " (cutoff:3.500A)
      Proline residue:  R 207  - end of helix
      removed outlier: 3.661A  pdb=" N   ILE R 226 " --> pdb=" O   ALA R 222 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 325 through 357
      removed outlier: 3.741A  pdb=" N   THR R 343 " --> pdb=" O   ARG R 339 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   VAL R 344 " --> pdb=" O   GLU R 340 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 358 through 368
    Processing helix  chain 'R' and resid 369 through 373
      removed outlier: 4.324A  pdb=" N   GLU R 372 " --> pdb=" O   PRO R 369 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 378 through 401
      removed outlier: 3.785A  pdb=" N   ILE R 384 " --> pdb=" O   LEU R 380 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   GLY R 389 " --> pdb=" O   ILE R 385 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   TYR R 390 " --> pdb=" O   ASN R 386 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   SER R 393 " --> pdb=" O   GLY R 389 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   LEU R 394 " --> pdb=" O   TYR R 390 " (cutoff:3.500A)
      Proline residue:  R 397  - end of helix
      removed outlier: 3.692A  pdb=" N   TYR R 400 " --> pdb=" O   ASN R 396 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 404 through 415
    Processing sheet with id=AA1, first strand: chain 'A' and resid 196 through 200
      removed outlier: 4.142A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 5.691A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.290A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.724A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.556A  pdb=" N   VAL B 327 " --> pdb=" O   TRP B 339 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   ALA B 328 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 4.332A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.811A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.130A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.115A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.785A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 111 through 112
      removed outlier: 4.076A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.546A  pdb=" N   CYS B 166 " --> pdb=" O   PHE B 180 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.831A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   SER B 201 " --> pdb=" O   LYS B 209 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 5.836A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.830A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 7.741A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 7.302A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278
      removed outlier: 3.896A  pdb=" N   SER B 277 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 5.026A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
      removed outlier: 3.679A  pdb=" N   GLN E   3 " --> pdb=" O   SER E  25 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   SER E  25 " --> pdb=" O   GLN E   3 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   MET E  83 " --> pdb=" O   ARG E  18 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   PHE E  80 " --> pdb=" O   SER E  71 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   SER E  71 " --> pdb=" O   PHE E  80 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 11
      removed outlier: 6.481A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   LEU E 117 " --> pdb=" O   ALA E  92 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   ALA E  92 " --> pdb=" O   LEU E 117 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   VAL E  37 " --> pdb=" O   TYR E  95 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   TYR E  50 " --> pdb=" O   TYR E  59 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   TYR E  59 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 142
      removed outlier: 4.008A  pdb=" N   THR E 141 " --> pdb=" O   ARG E 160 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   ARG E 160 " --> pdb=" O   THR E 141 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   SER E 206 " --> pdb=" O   THR E 213 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148
      removed outlier: 3.736A  pdb=" N   GLU E 246 " --> pdb=" O   VAL E 147 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 194 through 195
      removed outlier: 3.702A  pdb=" N   LEU E 178 " --> pdb=" O   GLN E 186 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   LEU E 188 " --> pdb=" O   TRP E 176 " (cutoff:3.500A)
      removed outlier: 7.283A  pdb=" N   TRP E 176 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)
      removed outlier: 5.130A  pdb=" N   TYR E 190 " --> pdb=" O   LEU E 174 " (cutoff:3.500A)
      removed outlier: 7.006A  pdb=" N   LEU E 174 " --> pdb=" O   TYR E 190 " (cutoff:3.500A)

    373 hydrogen bonds defined for protein.
    1065 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: 1.37

  Time building geometry restraints manager: 0.95 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1561
        1.32 -     1.45: 2279
        1.45 -     1.57: 4849
        1.57 -     1.69: 0
        1.69 -     1.82: 90
  Bond restraints: 8779
  Sorted by residual:
  bond pdb=" C   VAL R  89 "
       pdb=" O   VAL R  89 "
    ideal  model  delta    sigma   weight residual
    1.236  1.279 -0.043 1.19e-02 7.06e+03 1.31e+01
  bond pdb=" N   LEU R 118 "
       pdb=" CA  LEU R 118 "
    ideal  model  delta    sigma   weight residual
    1.459  1.500 -0.041 1.19e-02 7.06e+03 1.16e+01
  bond pdb=" N   CYS B 149 "
       pdb=" CA  CYS B 149 "
    ideal  model  delta    sigma   weight residual
    1.462  1.500 -0.038 1.20e-02 6.94e+03 1.00e+01
  bond pdb=" C   VAL R  85 "
       pdb=" O   VAL R  85 "
    ideal  model  delta    sigma   weight residual
    1.237  1.202  0.035 1.12e-02 7.97e+03 9.49e+00
  bond pdb=" N   CYS R 120 "
       pdb=" CA  CYS R 120 "
    ideal  model  delta    sigma   weight residual
    1.458  1.498 -0.040 1.33e-02 5.65e+03 9.11e+00
  ... (remaining 8774 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.93: 11470
        1.93 -     3.87: 356
        3.87 -     5.80: 56
        5.80 -     7.73: 8
        7.73 -     9.67: 3
  Bond angle restraints: 11893
  Sorted by residual:
  angle pdb=" C   GLU E 234 "
        pdb=" N   TYR E 235 "
        pdb=" CA  TYR E 235 "
      ideal   model   delta    sigma   weight residual
     122.89  113.22    9.67 1.12e+00 7.97e-01 7.45e+01
  angle pdb=" N   VAL R  85 "
        pdb=" CA  VAL R  85 "
        pdb=" CB  VAL R  85 "
      ideal   model   delta    sigma   weight residual
     110.62  116.10   -5.48 1.05e+00 9.07e-01 2.72e+01
  angle pdb=" C   CYS B 121 "
        pdb=" CA  CYS B 121 "
        pdb=" CB  CYS B 121 "
      ideal   model   delta    sigma   weight residual
     111.23  118.17   -6.94 1.42e+00 4.96e-01 2.39e+01
  angle pdb=" CA  VAL R  85 "
        pdb=" C   VAL R  85 "
        pdb=" O   VAL R  85 "
      ideal   model   delta    sigma   weight residual
     121.41  116.94    4.47 1.04e+00 9.25e-01 1.85e+01
  angle pdb=" N   MET R  84 "
        pdb=" CA  MET R  84 "
        pdb=" C   MET R  84 "
      ideal   model   delta    sigma   weight residual
     111.02  105.89    5.13 1.22e+00 6.72e-01 1.77e+01
  ... (remaining 11888 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.31: 4688
       17.31 -    34.62: 435
       34.62 -    51.93: 78
       51.93 -    69.24: 13
       69.24 -    86.55: 9
  Dihedral angle restraints: 5223
    sinusoidal: 2031
      harmonic: 3192
  Sorted by residual:
  dihedral pdb=" CA  LEU B  79 "
           pdb=" C   LEU B  79 "
           pdb=" N   ILE B  80 "
           pdb=" CA  ILE B  80 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.54  -21.46     0      5.00e+00 4.00e-02 1.84e+01
  dihedral pdb=" CA  TYR E 235 "
           pdb=" C   TYR E 235 "
           pdb=" N   PRO E 236 "
           pdb=" CA  PRO E 236 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.20   20.80     0      5.00e+00 4.00e-02 1.73e+01
  dihedral pdb=" CA  ASP B 118 "
           pdb=" C   ASP B 118 "
           pdb=" N   ASN B 119 "
           pdb=" CA  ASN B 119 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.37  -20.63     0      5.00e+00 4.00e-02 1.70e+01
  ... (remaining 5220 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 923
       0.045 -    0.089: 318
       0.089 -    0.134: 94
       0.134 -    0.179: 16
       0.179 -    0.223: 2
  Chirality restraints: 1353
  Sorted by residual:
  chirality pdb=" CB  THR A 327 "
            pdb=" CA  THR A 327 "
            pdb=" OG1 THR A 327 "
            pdb=" CG2 THR A 327 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.33    0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CB  VAL R  85 "
            pdb=" CA  VAL R  85 "
            pdb=" CG1 VAL R  85 "
            pdb=" CG2 VAL R  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 9.99e-01
  chirality pdb=" CB  ILE B 157 "
            pdb=" CA  ILE B 157 "
            pdb=" CG1 ILE B 157 "
            pdb=" CG2 ILE B 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.17 2.00e-01 2.50e+01 7.49e-01
  ... (remaining 1350 not shown)

  Planarity restraints: 1497
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 120 "    0.013 2.00e-02 2.50e+03   2.65e-02 7.01e+00
        pdb=" C   ILE B 120 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   ILE B 120 "    0.018 2.00e-02 2.50e+03
        pdb=" N   CYS B 121 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE R 407 "    0.022 2.00e-02 2.50e+03   1.86e-02 6.03e+00
        pdb=" CG  PHE R 407 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD1 PHE R 407 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE R 407 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE R 407 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE R 407 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE R 407 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP R 140 "    0.038 5.00e-02 4.00e+02   5.78e-02 5.34e+00
        pdb=" N   PRO R 141 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO R 141 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO R 141 "    0.032 5.00e-02 4.00e+02
  ... (remaining 1494 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 985
        2.74 -     3.28: 8673
        3.28 -     3.82: 13698
        3.82 -     4.36: 15583
        4.36 -     4.90: 27107
  Nonbonded interactions: 66046
  Sorted by model distance:
  nonbonded pdb=" NE1 TRP E  47 "
            pdb=" O   ALA E  49 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" OG  SER A 293 "
            pdb=" OE1 GLU A 298 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" O   ARG E  98 "
            pdb=" OG  SER E  99 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" O   ILE B  37 "
            pdb=" NZ  LYS B 301 "
     model   vdw
     2.237 3.120
  nonbonded pdb=" O   ASP E  90 "
            pdb=" OH  TYR E  94 "
     model   vdw
     2.239 3.040
  ... (remaining 66041 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.660
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  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:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6955
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      :  0.006   0.052   8783  Z= 0.291
  Angle     :  0.794   9.666  11901  Z= 0.461
  Chirality :  0.049   0.223   1353
  Planarity :  0.005   0.058   1497
  Dihedral  : 14.057  86.552   3153
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 13.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  0.86 %
    Favored  : 98.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.89 (0.25), residues: 1084
  helix:  0.72 (0.26), residues: 383
  sheet: -0.93 (0.34), residues: 239
  loop : -1.47 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E 191 
 TYR   0.026   0.003   TYR R  96 
 PHE   0.042   0.003   PHE R 407 
 TRP   0.034   0.003   TRP B  82 
 HIS   0.008   0.002   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00605 ( 8779)
  covalent geometry    : angle       0.79441 (11893)
  SS BOND              : bond        0.01735 (    4)
  SS BOND              : angle       0.48708 (    8)
  hydrogen bonds       : bond        0.20229 (  373)
  hydrogen bonds       : angle       7.46001 ( 1065)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 164
  time to evaluate  : 0.339 
Fit side-chains
REVERT: A  346 ASN cc_start: 0.7768 (m110) cc_final: 0.7446 (m-40)
REVERT: E   93 MET cc_start: 0.7738 (mpp) cc_final: 0.6880 (mpp)
REVERT: R  330 GLU cc_start: 0.8616 (tp30) cc_final: 0.8403 (tp30)
REVERT: R  337 LEU cc_start: 0.8831 (mm) cc_final: 0.8514 (mm)
  outliers start: 8
  outliers final: 3
  residues processed: 172
  average time/residue: 0.0916
  time to fit residues: 22.1284
Evaluate side-chains
  124 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 121
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   86 SER
Chi-restraints excluded: chain R residue  113 ILE
Chi-restraints excluded: chain R residue  115 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    0.5980
   chunk 53 optimal weight:   20.0000
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   chunk 106 optimal weight:    0.5980
   chunk 38 optimal weight:    0.8980
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
A 322 HIS
B 230 ASN
E 231 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4571 r_free = 0.4571 target = 0.214747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.171358 restraints weight = 11194.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.172281 restraints weight = 8012.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.175447 restraints weight = 6563.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.177993 restraints weight = 5046.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.177839 restraints weight = 4759.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.4218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7036
moved from start:          0.1567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8783  Z= 0.149
  Angle     :  0.640   7.599  11901  Z= 0.338
  Chirality :  0.044   0.194   1353
  Planarity :  0.004   0.043   1497
  Dihedral  :  5.701  84.541   1212
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  :  9.39 %
    Favored  : 87.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.60 (0.26), residues: 1084
  helix:  1.09 (0.27), residues: 386
  sheet: -0.88 (0.33), residues: 242
  loop : -1.38 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 129 
 TYR   0.028   0.002   TYR E 235 
 PHE   0.015   0.002   PHE B 292 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 8779)
  covalent geometry    : angle       0.63962 (11893)
  SS BOND              : bond        0.00510 (    4)
  SS BOND              : angle       0.68704 (    8)
  hydrogen bonds       : bond        0.05152 (  373)
  hydrogen bonds       : angle       5.21194 ( 1065)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 141
  time to evaluate  : 0.327 
Fit side-chains
REVERT: A  346 ASN cc_start: 0.7621 (m110) cc_final: 0.7250 (m110)
REVERT: B  221 THR cc_start: 0.8395 (p) cc_final: 0.8173 (p)
REVERT: B  262 MET cc_start: 0.6727 (tpt) cc_final: 0.6207 (tpp)
REVERT: E  231 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.6853 (pp30)
REVERT: R  113 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7728 (mm)
REVERT: R  333 ARG cc_start: 0.8513 (ptp-170) cc_final: 0.8253 (ptp-170)
  outliers start: 26
  outliers final: 19
  residues processed: 158
  average time/residue: 0.0933
  time to fit residues: 20.6714
Evaluate side-chains
  147 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 126
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  325 CYS
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain E residue   85 SER
Chi-restraints excluded: chain E residue   99 SER
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  172 THR
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain E residue  231 GLN
Chi-restraints excluded: chain R residue  113 ILE
Chi-restraints excluded: chain R residue  115 LEU
Chi-restraints excluded: chain R residue  133 ASP
Chi-restraints excluded: chain R residue  162 LEU
Chi-restraints excluded: chain R residue  344 VAL
Chi-restraints excluded: chain R residue  353 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 66 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   chunk 102 optimal weight:    0.0870
   chunk 16 optimal weight:    0.8980
   chunk 33 optimal weight:   10.0000
   chunk 42 optimal weight:    0.4980
   chunk 54 optimal weight:   10.0000
   chunk 15 optimal weight:    9.9990
   chunk 94 optimal weight:    0.0980
   chunk 50 optimal weight:    0.0970
   chunk 88 optimal weight:    2.9990
   overall best weight:    0.3356

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

Flipped N/Q/H residues before XYZ refinement:
B 183 HIS
E 231 GLN
R  54 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4637 r_free = 0.4637 target = 0.221786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.180175 restraints weight = 11026.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.181674 restraints weight = 7534.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.185693 restraints weight = 5934.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.185617 restraints weight = 4881.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.187118 restraints weight = 4661.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.4308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6916
moved from start:          0.2185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8783  Z= 0.108
  Angle     :  0.566   6.449  11901  Z= 0.300
  Chirality :  0.042   0.157   1353
  Planarity :  0.003   0.040   1497
  Dihedral  :  5.098  87.319   1211
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 14.46 %
    Favored  : 83.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.30 (0.26), residues: 1084
  helix:  1.39 (0.27), residues: 387
  sheet: -0.79 (0.31), residues: 256
  loop : -1.22 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 197 
 TYR   0.029   0.001   TYR A 230 
 PHE   0.012   0.001   PHE E  68 
 TRP   0.011   0.001   TRP B 297 
 HIS   0.003   0.000   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 8779)
  covalent geometry    : angle       0.56575 (11893)
  SS BOND              : bond        0.00628 (    4)
  SS BOND              : angle       0.47852 (    8)
  hydrogen bonds       : bond        0.03843 (  373)
  hydrogen bonds       : angle       4.68080 ( 1065)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 148
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ASN cc_start: 0.8210 (p0) cc_final: 0.7958 (p0)
REVERT: A  247 MET cc_start: 0.6788 (mmm) cc_final: 0.6581 (mmm)
REVERT: A  346 ASN cc_start: 0.7596 (m110) cc_final: 0.7209 (m110)
REVERT: B  266 HIS cc_start: 0.7342 (t-90) cc_final: 0.7011 (t-90)
REVERT: R  113 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7630 (mm)
REVERT: R  335 MET cc_start: 0.7414 (ttp) cc_final: 0.7137 (ttm)
  outliers start: 17
  outliers final: 12
  residues processed: 157
  average time/residue: 0.1035
  time to fit residues: 22.3156
Evaluate side-chains
  149 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 136
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  325 CYS
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain R residue  113 ILE
Chi-restraints excluded: chain R residue  133 ASP
Chi-restraints excluded: chain R residue  162 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   chunk 68 optimal weight:    5.9990
   chunk 20 optimal weight:    0.8980
   chunk 14 optimal weight:   10.0000
   chunk 45 optimal weight:    0.0000
   chunk 31 optimal weight:    0.5980
   chunk 72 optimal weight:    6.9990
   chunk 80 optimal weight:    0.6980
   chunk 39 optimal weight:    0.4980
   chunk 24 optimal weight:    5.9990
   overall best weight:    0.5384

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

Flipped N/Q/H residues before XYZ refinement:
B 183 HIS
** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4634 r_free = 0.4634 target = 0.221419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.180504 restraints weight = 11184.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.181721 restraints weight = 7555.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.184711 restraints weight = 6119.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.186681 restraints weight = 4813.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.187006 restraints weight = 4437.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.4310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6922
moved from start:          0.2452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8783  Z= 0.107
  Angle     :  0.559   6.677  11901  Z= 0.292
  Chirality :  0.041   0.140   1353
  Planarity :  0.003   0.044   1497
  Dihedral  :  4.958  88.022   1209
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 16.40 %
    Favored  : 81.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.23 (0.26), residues: 1084
  helix:  1.43 (0.27), residues: 388
  sheet: -0.67 (0.31), residues: 257
  loop : -1.23 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  67 
 TYR   0.031   0.001   TYR E 235 
 PHE   0.016   0.001   PHE E  68 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.005   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 8779)
  covalent geometry    : angle       0.55898 (11893)
  SS BOND              : bond        0.00583 (    4)
  SS BOND              : angle       0.33973 (    8)
  hydrogen bonds       : bond        0.03730 (  373)
  hydrogen bonds       : angle       4.50758 ( 1065)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 143
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ASN cc_start: 0.8370 (p0) cc_final: 0.7993 (p0)
REVERT: A  346 ASN cc_start: 0.7635 (m110) cc_final: 0.7185 (m110)
REVERT: B  266 HIS cc_start: 0.7203 (t-90) cc_final: 0.6981 (t70)
REVERT: B  268 ASN cc_start: 0.7666 (m110) cc_final: 0.7346 (m110)
REVERT: E  230 MET cc_start: 0.5142 (ppp) cc_final: 0.4617 (ttp)
  outliers start: 19
  outliers final: 16
  residues processed: 152
  average time/residue: 0.1015
  time to fit residues: 21.2093
Evaluate side-chains
  150 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 134
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  287 TYR
Chi-restraints excluded: chain A residue  325 CYS
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain E residue    6 GLU
Chi-restraints excluded: chain E residue   99 SER
Chi-restraints excluded: chain R residue  133 ASP
Chi-restraints excluded: chain R residue  162 LEU
Chi-restraints excluded: chain R residue  330 GLU
Chi-restraints excluded: chain R residue  355 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 102 optimal weight:    0.8980
   chunk 18 optimal weight:    0.8980
   chunk 97 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 64 optimal weight:    9.9990
   chunk 12 optimal weight:    0.8980
   chunk 104 optimal weight:    0.7980
   chunk 3 optimal weight:    4.9990
   chunk 93 optimal weight:    0.0470
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.6678

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

Flipped N/Q/H residues before XYZ refinement:
E 231 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4617 r_free = 0.4617 target = 0.219723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.175294 restraints weight = 11111.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.179682 restraints weight = 7432.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.182627 restraints weight = 5733.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.184021 restraints weight = 4866.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.185456 restraints weight = 4428.529|
|-----------------------------------------------------------------------------|
r_work (final): 0.4306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6921
moved from start:          0.2568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8783  Z= 0.108
  Angle     :  0.554   6.856  11901  Z= 0.290
  Chirality :  0.041   0.142   1353
  Planarity :  0.003   0.045   1497
  Dihedral  :  4.876  88.966   1207
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 16.29 %
    Favored  : 80.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.14 (0.26), residues: 1084
  helix:  1.48 (0.27), residues: 388
  sheet: -0.62 (0.31), residues: 266
  loop : -1.17 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 333 
 TYR   0.035   0.001   TYR E 235 
 PHE   0.016   0.001   PHE E  68 
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 8779)
  covalent geometry    : angle       0.55432 (11893)
  SS BOND              : bond        0.00621 (    4)
  SS BOND              : angle       0.27679 (    8)
  hydrogen bonds       : bond        0.03749 (  373)
  hydrogen bonds       : angle       4.42199 ( 1065)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 142
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  346 ASN cc_start: 0.7506 (m110) cc_final: 0.7073 (m110)
REVERT: B  268 ASN cc_start: 0.7529 (m110) cc_final: 0.7229 (m110)
REVERT: E   58 ILE cc_start: 0.7584 (mp) cc_final: 0.7283 (mt)
REVERT: E  186 GLN cc_start: 0.7223 (mt0) cc_final: 0.6981 (tt0)
REVERT: E  228 TYR cc_start: 0.5917 (m-80) cc_final: 0.5643 (m-80)
REVERT: R   65 ARG cc_start: 0.7187 (ttp-110) cc_final: 0.6754 (tpt90)
  outliers start: 28
  outliers final: 21
  residues processed: 159
  average time/residue: 0.1005
  time to fit residues: 22.0742
Evaluate side-chains
  156 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 135
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  287 TYR
Chi-restraints excluded: chain A residue  325 CYS
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain E residue    6 GLU
Chi-restraints excluded: chain E residue  110 PHE
Chi-restraints excluded: chain E residue  189 ILE
Chi-restraints excluded: chain E residue  224 VAL
Chi-restraints excluded: chain R residue  133 ASP
Chi-restraints excluded: chain R residue  162 LEU
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  414 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 78 optimal weight:    9.9990
   chunk 84 optimal weight:    0.6980
   chunk 55 optimal weight:    8.9990
   chunk 101 optimal weight:    3.9990
   chunk 81 optimal weight:    5.9990
   chunk 18 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 41 optimal weight:    5.9990
   chunk 5 optimal weight:    0.1980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4617 r_free = 0.4617 target = 0.219615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.176954 restraints weight = 11045.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.180919 restraints weight = 7349.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.181154 restraints weight = 5279.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.181316 restraints weight = 5235.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.181495 restraints weight = 5154.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.4259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6982
moved from start:          0.2755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8783  Z= 0.109
  Angle     :  0.564   7.508  11901  Z= 0.293
  Chirality :  0.041   0.155   1353
  Planarity :  0.003   0.048   1497
  Dihedral  :  4.887  89.367   1207
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 17.37 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.09 (0.27), residues: 1084
  helix:  1.52 (0.28), residues: 388
  sheet: -0.61 (0.31), residues: 270
  loop : -1.11 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 197 
 TYR   0.039   0.001   TYR E 235 
 PHE   0.013   0.001   PHE E  68 
 TRP   0.007   0.001   TRP B 297 
 HIS   0.003   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 8779)
  covalent geometry    : angle       0.56343 (11893)
  SS BOND              : bond        0.00602 (    4)
  SS BOND              : angle       0.91634 (    8)
  hydrogen bonds       : bond        0.03732 (  373)
  hydrogen bonds       : angle       4.36695 ( 1065)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 142
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  346 ASN cc_start: 0.7543 (m110) cc_final: 0.7072 (m110)
REVERT: E   58 ILE cc_start: 0.7594 (mp) cc_final: 0.7277 (mt)
REVERT: E  186 GLN cc_start: 0.7233 (mt0) cc_final: 0.7002 (tt0)
REVERT: E  228 TYR cc_start: 0.5986 (m-80) cc_final: 0.5601 (m-80)
REVERT: E  230 MET cc_start: 0.5198 (ppp) cc_final: 0.4658 (ttp)
REVERT: R   65 ARG cc_start: 0.7128 (ttp-110) cc_final: 0.6705 (tpt90)
REVERT: R  333 ARG cc_start: 0.8299 (ptp-170) cc_final: 0.7633 (ptp-170)
REVERT: R  334 LYS cc_start: 0.8358 (mtmm) cc_final: 0.8150 (mtmm)
REVERT: R  335 MET cc_start: 0.7298 (ttp) cc_final: 0.6921 (ttm)
  outliers start: 26
  outliers final: 21
  residues processed: 156
  average time/residue: 0.0874
  time to fit residues: 19.2008
Evaluate side-chains
  155 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 134
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  287 TYR
Chi-restraints excluded: chain A residue  325 CYS
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain E residue    6 GLU
Chi-restraints excluded: chain E residue  189 ILE
Chi-restraints excluded: chain E residue  224 VAL
Chi-restraints excluded: chain R residue  133 ASP
Chi-restraints excluded: chain R residue  162 LEU
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  414 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 61 optimal weight:    8.9990
   chunk 67 optimal weight:    5.9990
   chunk 10 optimal weight:    9.9990
   chunk 64 optimal weight:    0.0470
   chunk 5 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   chunk 96 optimal weight:    0.8980
   chunk 100 optimal weight:    3.9990
   overall best weight:    1.1080

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

Flipped N/Q/H residues before XYZ refinement:
** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4591 r_free = 0.4591 target = 0.216549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.173394 restraints weight = 11183.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.174420 restraints weight = 7810.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.177332 restraints weight = 6612.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.178556 restraints weight = 5283.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.178860 restraints weight = 4893.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.4229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7024
moved from start:          0.2730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8783  Z= 0.132
  Angle     :  0.589   8.436  11901  Z= 0.306
  Chirality :  0.042   0.159   1353
  Planarity :  0.003   0.049   1497
  Dihedral  :  4.916  86.002   1207
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 18.12 %
    Favored  : 78.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.26), residues: 1084
  helix:  1.51 (0.27), residues: 387
  sheet: -0.61 (0.31), residues: 267
  loop : -1.21 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 327 
 TYR   0.036   0.002   TYR E 235 
 PHE   0.013   0.001   PHE E  68 
 TRP   0.008   0.001   TRP B 297 
 HIS   0.004   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 8779)
  covalent geometry    : angle       0.58892 (11893)
  SS BOND              : bond        0.00845 (    4)
  SS BOND              : angle       0.86906 (    8)
  hydrogen bonds       : bond        0.04210 (  373)
  hydrogen bonds       : angle       4.41829 ( 1065)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 134
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 ASN cc_start: 0.8197 (m-40) cc_final: 0.7975 (m-40)
REVERT: A  346 ASN cc_start: 0.7640 (m110) cc_final: 0.7124 (m110)
REVERT: E   58 ILE cc_start: 0.7683 (mp) cc_final: 0.7410 (mt)
REVERT: E   98 ARG cc_start: 0.7475 (ttp-170) cc_final: 0.7116 (ttp-170)
REVERT: E  186 GLN cc_start: 0.7311 (mt0) cc_final: 0.7067 (tt0)
REVERT: E  228 TYR cc_start: 0.5988 (m-80) cc_final: 0.5553 (m-80)
REVERT: R   65 ARG cc_start: 0.7079 (ttp-110) cc_final: 0.6769 (tpt90)
REVERT: R  334 LYS cc_start: 0.8377 (mtmm) cc_final: 0.8082 (mtmm)
  outliers start: 27
  outliers final: 25
  residues processed: 154
  average time/residue: 0.1001
  time to fit residues: 21.1986
Evaluate side-chains
  154 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 129
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  287 TYR
Chi-restraints excluded: chain A residue  325 CYS
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue    6 GLU
Chi-restraints excluded: chain E residue   47 TRP
Chi-restraints excluded: chain E residue   99 SER
Chi-restraints excluded: chain E residue  189 ILE
Chi-restraints excluded: chain E residue  224 VAL
Chi-restraints excluded: chain E residue  233 LEU
Chi-restraints excluded: chain R residue  133 ASP
Chi-restraints excluded: chain R residue  162 LEU
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  414 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 96 optimal weight:    0.7980
   chunk 98 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 54 optimal weight:    8.9990
   chunk 30 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9980
   chunk 92 optimal weight:    0.8980
   chunk 44 optimal weight:   10.0000
   chunk 78 optimal weight:    0.0570
   chunk 68 optimal weight:    0.8980
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
E 231 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4615 r_free = 0.4615 target = 0.219361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.174717 restraints weight = 11087.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.179019 restraints weight = 7510.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.181326 restraints weight = 5828.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.183719 restraints weight = 5009.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.184716 restraints weight = 4503.703|
|-----------------------------------------------------------------------------|
r_work (final): 0.4298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6925
moved from start:          0.2976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   8783  Z= 0.109
  Angle     :  0.567   7.718  11901  Z= 0.292
  Chirality :  0.041   0.153   1353
  Planarity :  0.003   0.047   1497
  Dihedral  :  4.895  89.513   1207
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 18.12 %
    Favored  : 78.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.05 (0.26), residues: 1084
  helix:  1.57 (0.28), residues: 388
  sheet: -0.55 (0.31), residues: 271
  loop : -1.14 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 327 
 TYR   0.034   0.001   TYR E 235 
 PHE   0.015   0.001   PHE E  68 
 TRP   0.006   0.001   TRP R 161 
 HIS   0.011   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 8779)
  covalent geometry    : angle       0.56649 (11893)
  SS BOND              : bond        0.00655 (    4)
  SS BOND              : angle       0.68586 (    8)
  hydrogen bonds       : bond        0.03613 (  373)
  hydrogen bonds       : angle       4.27821 ( 1065)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 138
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  346 ASN cc_start: 0.7476 (m110) cc_final: 0.6959 (m110)
REVERT: E   58 ILE cc_start: 0.7603 (mp) cc_final: 0.7348 (mt)
REVERT: E  186 GLN cc_start: 0.7272 (mt0) cc_final: 0.7019 (tt0)
REVERT: E  228 TYR cc_start: 0.5873 (m-80) cc_final: 0.5485 (m-80)
REVERT: E  230 MET cc_start: 0.5114 (ppp) cc_final: 0.4558 (ttp)
REVERT: R   65 ARG cc_start: 0.7077 (ttp-110) cc_final: 0.6724 (tpt90)
  outliers start: 27
  outliers final: 23
  residues processed: 156
  average time/residue: 0.0866
  time to fit residues: 19.1313
Evaluate side-chains
  152 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 129
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  287 TYR
Chi-restraints excluded: chain A residue  325 CYS
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue    6 GLU
Chi-restraints excluded: chain E residue   47 TRP
Chi-restraints excluded: chain E residue   99 SER
Chi-restraints excluded: chain E residue  189 ILE
Chi-restraints excluded: chain E residue  224 VAL
Chi-restraints excluded: chain E residue  233 LEU
Chi-restraints excluded: chain R residue  133 ASP
Chi-restraints excluded: chain R residue  162 LEU
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  414 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 101 optimal weight:    3.9990
   chunk 82 optimal weight:    4.9990
   chunk 83 optimal weight:    1.9990
   chunk 79 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 22 optimal weight:   10.0000
   chunk 8 optimal weight:    0.6980
   chunk 64 optimal weight:    9.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
B 183 HIS
** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4575 r_free = 0.4575 target = 0.214800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.171232 restraints weight = 11162.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.173066 restraints weight = 7761.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.175843 restraints weight = 6532.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.176889 restraints weight = 5226.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.177462 restraints weight = 4971.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.4218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7046
moved from start:          0.2883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8783  Z= 0.146
  Angle     :  0.617   8.765  11901  Z= 0.323
  Chirality :  0.043   0.156   1353
  Planarity :  0.004   0.054   1497
  Dihedral  :  4.938  83.335   1207
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 18.88 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.19 (0.26), residues: 1084
  helix:  1.41 (0.28), residues: 388
  sheet: -0.58 (0.31), residues: 254
  loop : -1.19 (0.30), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 333 
 TYR   0.030   0.002   TYR E 235 
 PHE   0.021   0.002   PHE E  68 
 TRP   0.007   0.001   TRP R 387 
 HIS   0.011   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 8779)
  covalent geometry    : angle       0.61693 (11893)
  SS BOND              : bond        0.00903 (    4)
  SS BOND              : angle       0.85843 (    8)
  hydrogen bonds       : bond        0.04422 (  373)
  hydrogen bonds       : angle       4.48428 ( 1065)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 135
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  346 ASN cc_start: 0.7595 (m110) cc_final: 0.7066 (m110)
REVERT: B   48 ARG cc_start: 0.7824 (mmt180) cc_final: 0.7404 (mmm-85)
REVERT: E   29 PHE cc_start: 0.6325 (t80) cc_final: 0.5922 (t80)
REVERT: E   58 ILE cc_start: 0.7575 (mp) cc_final: 0.7332 (mt)
REVERT: E   98 ARG cc_start: 0.7545 (ttp-170) cc_final: 0.7014 (ttp-170)
REVERT: E  186 GLN cc_start: 0.7335 (mt0) cc_final: 0.7072 (tt0)
REVERT: E  228 TYR cc_start: 0.5978 (m-80) cc_final: 0.5536 (m-80)
REVERT: R   65 ARG cc_start: 0.7159 (ttp-110) cc_final: 0.6808 (tpt90)
REVERT: R  335 MET cc_start: 0.7211 (ttp) cc_final: 0.6862 (ttp)
  outliers start: 28
  outliers final: 25
  residues processed: 152
  average time/residue: 0.1014
  time to fit residues: 20.8743
Evaluate side-chains
  155 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 130
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  287 TYR
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  325 CYS
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue    6 GLU
Chi-restraints excluded: chain E residue   47 TRP
Chi-restraints excluded: chain E residue   99 SER
Chi-restraints excluded: chain E residue  189 ILE
Chi-restraints excluded: chain E residue  233 LEU
Chi-restraints excluded: chain R residue  133 ASP
Chi-restraints excluded: chain R residue  162 LEU
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  414 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 84 optimal weight:    0.9980
   chunk 94 optimal weight:    0.9990
   chunk 74 optimal weight:    0.1980
   chunk 44 optimal weight:    8.9990
   chunk 2 optimal weight:    0.7980
   chunk 11 optimal weight:    0.4980
   chunk 91 optimal weight:    5.9990
   chunk 45 optimal weight:    0.4980
   chunk 25 optimal weight:    0.9980
   chunk 18 optimal weight:    5.9990
   chunk 66 optimal weight:   10.0000
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B 110 ASN
** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4607 r_free = 0.4607 target = 0.218637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.174319 restraints weight = 11134.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.178639 restraints weight = 7526.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.181598 restraints weight = 5837.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.182988 restraints weight = 4976.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.184474 restraints weight = 4537.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.4297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6927
moved from start:          0.3070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8783  Z= 0.112
  Angle     :  0.590   8.118  11901  Z= 0.307
  Chirality :  0.042   0.157   1353
  Planarity :  0.003   0.049   1497
  Dihedral  :  4.912  88.370   1207
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 19.20 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.10 (0.26), residues: 1084
  helix:  1.53 (0.28), residues: 388
  sheet: -0.55 (0.30), residues: 257
  loop : -1.18 (0.31), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 197 
 TYR   0.041   0.001   TYR E 235 
 PHE   0.015   0.001   PHE E  68 
 TRP   0.007   0.001   TRP E 176 
 HIS   0.010   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 8779)
  covalent geometry    : angle       0.59006 (11893)
  SS BOND              : bond        0.00650 (    4)
  SS BOND              : angle       0.68420 (    8)
  hydrogen bonds       : bond        0.03685 (  373)
  hydrogen bonds       : angle       4.31799 ( 1065)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 125
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   48 ARG cc_start: 0.7785 (mmt180) cc_final: 0.7391 (mmm-85)
REVERT: E   29 PHE cc_start: 0.6321 (t80) cc_final: 0.5969 (t80)
REVERT: E   58 ILE cc_start: 0.7550 (mp) cc_final: 0.7305 (mt)
REVERT: E  186 GLN cc_start: 0.7072 (mt0) cc_final: 0.6860 (tt0)
REVERT: E  228 TYR cc_start: 0.5828 (m-80) cc_final: 0.5463 (m-80)
REVERT: R   65 ARG cc_start: 0.7086 (ttp-110) cc_final: 0.6800 (tpt90)
REVERT: R  335 MET cc_start: 0.7129 (ttp) cc_final: 0.6912 (ttp)
  outliers start: 25
  outliers final: 24
  residues processed: 141
  average time/residue: 0.0895
  time to fit residues: 17.7349
Evaluate side-chains
  146 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 122
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  287 TYR
Chi-restraints excluded: chain A residue  325 CYS
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue    6 GLU
Chi-restraints excluded: chain E residue   47 TRP
Chi-restraints excluded: chain E residue   99 SER
Chi-restraints excluded: chain E residue  189 ILE
Chi-restraints excluded: chain R residue  133 ASP
Chi-restraints excluded: chain R residue  162 LEU
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  414 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 77 optimal weight:    0.9980
   chunk 65 optimal weight:   10.0000
   chunk 40 optimal weight:    7.9990
   chunk 24 optimal weight:    0.0050
   chunk 106 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9980
   chunk 95 optimal weight:    0.8980
   chunk 71 optimal weight:    8.9990
   chunk 46 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9980
   chunk 75 optimal weight:    6.9990
   overall best weight:    0.7794

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

Flipped N/Q/H residues before XYZ refinement:
** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4604 r_free = 0.4604 target = 0.218150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.173941 restraints weight = 11143.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.177968 restraints weight = 7548.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.180363 restraints weight = 5897.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.182571 restraints weight = 5078.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.183537 restraints weight = 4588.126|
|-----------------------------------------------------------------------------|
r_work (final): 0.4286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6945
moved from start:          0.3145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8783  Z= 0.118
  Angle     :  0.598   8.167  11901  Z= 0.311
  Chirality :  0.042   0.164   1353
  Planarity :  0.004   0.051   1497
  Dihedral  :  4.864  87.086   1207
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 19.53 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.13 (0.26), residues: 1084
  helix:  1.46 (0.28), residues: 389
  sheet: -0.56 (0.30), residues: 257
  loop : -1.16 (0.31), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 327 
 TYR   0.040   0.002   TYR E 235 
 PHE   0.012   0.001   PHE E  68 
 TRP   0.007   0.001   TRP R 161 
 HIS   0.010   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 8779)
  covalent geometry    : angle       0.59841 (11893)
  SS BOND              : bond        0.00711 (    4)
  SS BOND              : angle       0.68159 (    8)
  hydrogen bonds       : bond        0.03793 (  373)
  hydrogen bonds       : angle       4.32748 ( 1065)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1704.15 seconds
wall clock time: 30 minutes 9.73 seconds (1809.73 seconds total)