Starting phenix.real_space_refine
on Wed Feb 12 15:26:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8smv_40603/02_2025/8smv_40603.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8smv_40603/02_2025/8smv_40603.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.74
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8smv_40603/02_2025/8smv_40603.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8smv_40603/02_2025/8smv_40603.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8smv_40603/02_2025/8smv_40603.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8smv_40603/02_2025/8smv_40603.cif"
  }
  resolution = 2.74
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.008 sd=   0.817
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      55      5.16       5
     C    5217      2.51       5
     N    1404      2.21       5
     O    1493      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8169
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2152
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 268, 2152
          Classifications: {'peptide': 268}
          Link IDs: {'PTRANS': 10, 'TRANS': 257}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 438
          Classifications: {'peptide': 58}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "N"
      Number of atoms: 970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 970
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 1989
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 240, 1989
          Classifications: {'peptide': 240}
          Link IDs: {'PTRANS': 6, 'TRANS': 233}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2592
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2592
          Classifications: {'peptide': 340}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 22
    Chain: "R"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.78, per 1000 atoms: 0.59
  Number of scatterers: 8169
  At special positions: 0
  Unit cell: (76.54, 104.06, 131.58, 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      55     16.00
     O    1493      8.00
     N    1404      7.00
     C    5217      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 100 " - pdb=" SG  CYS R 178 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.10
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1940

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 11 sheets defined
      42.7% alpha, 21.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.01
  Creating SS restraints...
    Processing helix  chain 'R' and resid 30 through 55
      removed outlier: 3.788A  pdb=" N   ILE R  34 " --> pdb=" O   GLN R  30 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   ILE R  35 " --> pdb=" O   PHE R  31 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ASN R  45 " --> pdb=" O   VAL R  41 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 56 through 59
    Processing helix  chain 'R' and resid 62 through 80
      removed outlier: 4.081A  pdb=" N   VAL R  66 " --> pdb=" O   SER R  62 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   VAL R  78 " --> pdb=" O   PHE R  74 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   VAL R  80 " --> pdb=" O   LEU R  76 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 80 through 91
    Processing helix  chain 'R' and resid 96 through 131
      removed outlier: 3.654A  pdb=" N   CYS R 100 " --> pdb=" O   GLY R  96 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ASN R 101 " --> pdb=" O   VAL R  97 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   PHE R 102 " --> pdb=" O   VAL R  98 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   LEU R 118 " --> pdb=" O   SER R 114 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   GLY R 119 " --> pdb=" O   MET R 115 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 134 through 139
    Processing helix  chain 'R' and resid 140 through 164
      removed outlier: 3.654A  pdb=" N   TRP R 152 " --> pdb=" O   LEU R 148 " (cutoff:3.500A)
      Proline residue:  R 161  - end of helix
    Processing helix  chain 'R' and resid 182 through 185
    Processing helix  chain 'R' and resid 187 through 197
      removed outlier: 3.666A  pdb=" N   GLN R 193 " --> pdb=" O   THR R 189 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ALA R 197 " --> pdb=" O   GLN R 193 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 197 through 220
      removed outlier: 3.669A  pdb=" N   ARG R 213 " --> pdb=" O   GLY R 209 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   VAL R 214 " --> pdb=" O   PHE R 210 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   ARG R 220 " --> pdb=" O   ARG R 216 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 267 through 297
      removed outlier: 3.940A  pdb=" N   PHE R 279 " --> pdb=" O   VAL R 275 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   MET R 280 " --> pdb=" O   LEU R 276 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   THR R 282 " --> pdb=" O   ALA R 278 " (cutoff:3.500A)
      Proline residue:  R 285  - end of helix
    Processing helix  chain 'R' and resid 298 through 301
      removed outlier: 3.843A  pdb=" N   VAL R 301 " --> pdb=" O   LYS R 298 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 298 through 301'
    Processing helix  chain 'R' and resid 302 through 315
      removed outlier: 3.635A  pdb=" N   SER R 313 " --> pdb=" O   ALA R 309 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   PHE R 314 " --> pdb=" O   THR R 310 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ALA R 315 " --> pdb=" O   TRP R 311 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 315 through 325
      removed outlier: 3.652A  pdb=" N   CYS R 319 " --> pdb=" O   ALA R 315 " (cutoff:3.500A)
      Proline residue:  R 321  - end of helix
    Processing helix  chain 'R' and resid 328 through 340
    Processing helix  chain 'G' and resid 6 through 24
      removed outlier: 3.764A  pdb=" N   MET G  21 " --> pdb=" O   GLU G  17 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.682A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.804A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'A' and resid 10 through 39
      removed outlier: 3.970A  pdb=" N   ASN A  23 " --> pdb=" O   GLN A  19 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   LYS A  24 " --> pdb=" O   ARG A  20 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LYS A  25 " --> pdb=" O   GLU A  21 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 64
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.698A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
      removed outlier: 3.540A  pdb=" N   ALA A 269 " --> pdb=" O   ARG A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 3.716A  pdb=" N   GLU A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   GLY A 304 " --> pdb=" O   LYS A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 318
      removed outlier: 3.596A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 3.711A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.606A  pdb=" N   TYR A 391 " --> pdb=" O   HIS A 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 25
      removed outlier: 3.986A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing sheet with id=AA1, first strand: chain 'R' and resid 169 through 172
      removed outlier: 3.983A  pdb=" N   MET R 177 " --> pdb=" O   ASP R 172 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'N' and resid 3 through 8
      removed outlier: 3.548A  pdb=" N   THR N  78 " --> pdb=" O   ASP N  73 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   SER N  71 " --> pdb=" O   TYR N  80 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'N' and resid 10 through 12
      removed outlier: 6.344A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 7.137A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.677A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   SER N  59 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 214
      removed outlier: 3.526A  pdb=" N   PHE A 212 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 7.195A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.434A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 8.019A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 7.084A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 6.299A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.584A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.737A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  49 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.991A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.145A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.573A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.178A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.799A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.450A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.875A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.558A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   GLN B 175 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.954A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.678A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.168A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.778A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.023A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    392 hydrogen bonds defined for protein.
    1113 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.18

  Time building geometry restraints manager: 2.41 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2634
        1.34 -     1.46: 2053
        1.46 -     1.58: 3586
        1.58 -     1.70: 0
        1.70 -     1.82: 78
  Bond restraints: 8351
  Sorted by residual:
  bond pdb=" C6  CLR R 601 "
       pdb=" C7  CLR R 601 "
    ideal  model  delta    sigma   weight residual
    1.492  1.399  0.093 2.00e-02 2.50e+03 2.14e+01
  bond pdb=" C10 CLR R 601 "
       pdb=" C5  CLR R 601 "
    ideal  model  delta    sigma   weight residual
    1.519  1.428  0.091 2.00e-02 2.50e+03 2.09e+01
  bond pdb=" C4  CLR R 601 "
       pdb=" C5  CLR R 601 "
    ideal  model  delta    sigma   weight residual
    1.506  1.416  0.090 2.00e-02 2.50e+03 2.04e+01
  bond pdb=" C5  CLR R 601 "
       pdb=" C6  CLR R 601 "
    ideal  model  delta    sigma   weight residual
    1.332  1.412 -0.080 2.00e-02 2.50e+03 1.60e+01
  bond pdb=" N   THR A   9 "
       pdb=" CA  THR A   9 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.90e-02 2.77e+03 3.22e+00
  ... (remaining 8346 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.19: 10637
        1.19 -     2.37: 555
        2.37 -     3.56: 96
        3.56 -     4.75: 35
        4.75 -     5.93: 8
  Bond angle restraints: 11331
  Sorted by residual:
  angle pdb=" N   THR B 181 "
        pdb=" CA  THR B 181 "
        pdb=" C   THR B 181 "
      ideal   model   delta    sigma   weight residual
     110.44  113.70   -3.26 1.20e+00 6.94e-01 7.39e+00
  angle pdb=" CA  LYS A 338 "
        pdb=" CB  LYS A 338 "
        pdb=" CG  LYS A 338 "
      ideal   model   delta    sigma   weight residual
     114.10  118.98   -4.88 2.00e+00 2.50e-01 5.95e+00
  angle pdb=" C   ASN B 313 "
        pdb=" N   ARG B 314 "
        pdb=" CA  ARG B 314 "
      ideal   model   delta    sigma   weight residual
     121.56  125.17   -3.61 1.56e+00 4.11e-01 5.36e+00
  angle pdb=" N   MET R 137 "
        pdb=" CA  MET R 137 "
        pdb=" C   MET R 137 "
      ideal   model   delta    sigma   weight residual
     113.88  111.12    2.76 1.23e+00 6.61e-01 5.04e+00
  angle pdb=" CA  THR B 181 "
        pdb=" C   THR B 181 "
        pdb=" O   THR B 181 "
      ideal   model   delta    sigma   weight residual
     121.89  119.03    2.86 1.29e+00 6.01e-01 4.90e+00
  ... (remaining 11326 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 4638
       17.73 -    35.47: 284
       35.47 -    53.20: 44
       53.20 -    70.93: 13
       70.93 -    88.67: 9
  Dihedral angle restraints: 4988
    sinusoidal: 1985
      harmonic: 3003
  Sorted by residual:
  dihedral pdb=" CA  LEU A 291 "
           pdb=" C   LEU A 291 "
           pdb=" N   ASN A 292 "
           pdb=" CA  ASN A 292 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -149.30  -30.70     0      5.00e+00 4.00e-02 3.77e+01
  dihedral pdb=" CA  ARG A 231 "
           pdb=" C   ARG A 231 "
           pdb=" N   ARG A 232 "
           pdb=" CA  ARG A 232 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.64  -23.36     0      5.00e+00 4.00e-02 2.18e+01
  dihedral pdb=" CA  PHE N 108 "
           pdb=" C   PHE N 108 "
           pdb=" N   ASP N 109 "
           pdb=" CA  ASP N 109 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.23  -22.77     0      5.00e+00 4.00e-02 2.07e+01
  ... (remaining 4985 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 1121
       0.064 -    0.128: 139
       0.128 -    0.192: 15
       0.192 -    0.256: 2
       0.256 -    0.320: 1
  Chirality restraints: 1278
  Sorted by residual:
  chirality pdb=" C14 CLR R 601 "
            pdb=" C13 CLR R 601 "
            pdb=" C15 CLR R 601 "
            pdb=" C8  CLR R 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.64    0.32 2.00e-01 2.50e+01 2.56e+00
  chirality pdb=" C10 CLR R 601 "
            pdb=" C1  CLR R 601 "
            pdb=" C5  CLR R 601 "
            pdb=" C9  CLR R 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -2.61   -0.24 2.00e-01 2.50e+01 1.40e+00
  chirality pdb=" C20 CLR R 601 "
            pdb=" C17 CLR R 601 "
            pdb=" C21 CLR R 601 "
            pdb=" C22 CLR R 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.59    2.80   -0.20 2.00e-01 2.50e+01 1.04e+00
  ... (remaining 1275 not shown)

  Planarity restraints: 1426
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG G  13 "   -0.010 2.00e-02 2.50e+03   1.99e-02 3.98e+00
        pdb=" C   ARG G  13 "    0.035 2.00e-02 2.50e+03
        pdb=" O   ARG G  13 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   LYS G  14 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.031 5.00e-02 4.00e+02   4.64e-02 3.44e+00
        pdb=" N   PRO B 236 "   -0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP R 311 "   -0.014 2.00e-02 2.50e+03   1.17e-02 3.41e+00
        pdb=" CG  TRP R 311 "    0.031 2.00e-02 2.50e+03
        pdb=" CD1 TRP R 311 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 TRP R 311 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP R 311 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP R 311 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP R 311 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP R 311 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP R 311 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP R 311 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1423 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 206
        2.71 -     3.26: 7905
        3.26 -     3.80: 11827
        3.80 -     4.35: 15594
        4.35 -     4.90: 27219
  Nonbonded interactions: 62751
  Sorted by model distance:
  nonbonded pdb=" O   ASN B 313 "
            pdb=" OG  SER B 331 "
     model   vdw
     2.162 3.040
  nonbonded pdb=" O   ASP B 163 "
            pdb=" OG1 THR B 164 "
     model   vdw
     2.171 3.040
  nonbonded pdb=" OD1 ASN B  16 "
            pdb=" NH2 ARG B  19 "
     model   vdw
     2.199 3.120
  nonbonded pdb=" OD1 ASN B 110 "
            pdb=" NZ  LYS B 127 "
     model   vdw
     2.203 3.120
  nonbonded pdb=" OE1 GLU R 170 "
            pdb=" NH2 ARG R 184 "
     model   vdw
     2.252 3.120
  ... (remaining 62746 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.170
  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:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     19.710
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  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:             0.010
  Load rotamer database and sin/cos tables:12.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.093   8351  Z= 0.232
  Angle     :  0.648   5.932  11331  Z= 0.359
  Chirality :  0.045   0.320   1278
  Planarity :  0.004   0.046   1426
  Dihedral  : 12.716  88.667   3039
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 1.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.27), residues: 1020
  helix:  1.64 (0.28), residues: 374
  sheet:  0.68 (0.35), residues: 214
  loop : -0.99 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP R 311 
 HIS   0.006   0.001   HIS R 154 
 PHE   0.009   0.001   PHE B 151 
 TYR   0.009   0.001   TYR R 324 
 ARG   0.004   0.001   ARG B 214 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.897 
Fit side-chains
REVERT: A  214 VAL cc_start: 0.8988 (p) cc_final: 0.8734 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 155
  average time/residue: 1.4111
  time to fit residues: 229.9340
Evaluate side-chains
  115 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.918 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:   10.0000
   chunk 76 optimal weight:    0.9990
   chunk 42 optimal weight:    0.5980
   chunk 26 optimal weight:    8.9990
   chunk 51 optimal weight:    0.9980
   chunk 40 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9990
   chunk 30 optimal weight:    0.0980
   chunk 48 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9990
   chunk 91 optimal weight:    6.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
G  59 ASN
N   3 GLN
N 120 GLN
A 220 HIS
B  75 GLN
B 175 GLN
B 176 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.147216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.122076 restraints weight = 10780.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 1.79
r_work: 0.3329 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3218 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8602
moved from start:          0.1597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8351  Z= 0.154
  Angle     :  0.544   5.938  11331  Z= 0.296
  Chirality :  0.044   0.163   1278
  Planarity :  0.004   0.045   1426
  Dihedral  :  4.667  28.056   1189
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  :  9.34 %
    Favored  : 88.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.26), residues: 1020
  helix:  1.64 (0.27), residues: 398
  sheet:  0.87 (0.35), residues: 215
  loop : -0.91 (0.29), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP R 311 
 HIS   0.004   0.001   HIS R 154 
 PHE   0.014   0.001   PHE A 212 
 TYR   0.011   0.001   TYR R 135 
 ARG   0.005   0.000   ARG A 347 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 139
  time to evaluate  : 0.895 
Fit side-chains
REVERT: G   47 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7378 (mp0)
REVERT: A   17 LYS cc_start: 0.7836 (mptt) cc_final: 0.7567 (ttpt)
REVERT: A   19 GLN cc_start: 0.7623 (tt0) cc_final: 0.7313 (pt0)
REVERT: B   76 ASP cc_start: 0.8315 (p0) cc_final: 0.8095 (p0)
REVERT: B  134 ARG cc_start: 0.7443 (mtm180) cc_final: 0.7100 (mtm-85)
REVERT: B  188 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.7185 (mtm)
  outliers start: 20
  outliers final: 2
  residues processed: 147
  average time/residue: 1.4683
  time to fit residues: 227.3189
Evaluate side-chains
  121 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 117
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  243 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 25 optimal weight:    0.2980
   chunk 2 optimal weight:    6.9990
   chunk 67 optimal weight:    7.9990
   chunk 77 optimal weight:    3.9990
   chunk 91 optimal weight:    0.9980
   chunk 61 optimal weight:    0.6980
   chunk 95 optimal weight:    5.9990
   chunk 36 optimal weight:    0.4980
   chunk 31 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
G  59 ASN
N  35 ASN
N 120 GLN
A 220 HIS
B 175 GLN
B 259 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.149223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.124212 restraints weight = 10778.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.3530 rms_B_bonded: 1.79
r_work: 0.3439 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3327 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8598
moved from start:          0.1915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8351  Z= 0.142
  Angle     :  0.507   6.066  11331  Z= 0.276
  Chirality :  0.043   0.153   1278
  Planarity :  0.004   0.045   1426
  Dihedral  :  4.357  27.155   1189
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 11.50 %
    Favored  : 85.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.26), residues: 1020
  helix:  1.85 (0.27), residues: 399
  sheet:  0.94 (0.34), residues: 215
  loop : -0.96 (0.29), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP R 311 
 HIS   0.003   0.001   HIS R 154 
 PHE   0.012   0.001   PHE A 212 
 TYR   0.009   0.001   TYR R 135 
 ARG   0.004   0.000   ARG A 347 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 126
  time to evaluate  : 0.969 
Fit side-chains
REVERT: R  185 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7815 (mt-10)
REVERT: N   19 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7498 (ptm160)
REVERT: A   17 LYS cc_start: 0.7761 (mptt) cc_final: 0.7534 (ttpt)
REVERT: A   19 GLN cc_start: 0.7630 (tt0) cc_final: 0.7331 (pt0)
REVERT: A   28 LYS cc_start: 0.8158 (mtpt) cc_final: 0.7919 (ptpt)
REVERT: B   23 LYS cc_start: 0.7942 (tptt) cc_final: 0.7350 (tppt)
REVERT: B   46 ARG cc_start: 0.8659 (mtm180) cc_final: 0.7692 (ptp90)
REVERT: B  134 ARG cc_start: 0.7463 (mtm180) cc_final: 0.7152 (mtm-85)
REVERT: B  270 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8228 (mp)
  outliers start: 24
  outliers final: 8
  residues processed: 137
  average time/residue: 1.4216
  time to fit residues: 205.4419
Evaluate side-chains
  127 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 116
  time to evaluate  : 0.869 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   89 ILE
Chi-restraints excluded: chain R residue  185 GLU
Chi-restraints excluded: chain R residue  281 VAL
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  270 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 82 optimal weight:    0.5980
   chunk 91 optimal weight:    0.9980
   chunk 46 optimal weight:    3.9990
   chunk 2 optimal weight:    6.9990
   chunk 10 optimal weight:    0.0370
   chunk 1 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 35 optimal weight:    0.3980
   chunk 42 optimal weight:    8.9990
   chunk 59 optimal weight:    0.9980
   overall best weight:    0.6058

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

Flipped N/Q/H residues before XYZ refinement:
G  59 ASN
N 120 GLN
A 220 HIS
B 259 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.149966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.124954 restraints weight = 10743.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 1.81
r_work: 0.3444 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3331 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.2132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8351  Z= 0.132
  Angle     :  0.488   6.003  11331  Z= 0.266
  Chirality :  0.042   0.159   1278
  Planarity :  0.004   0.044   1426
  Dihedral  :  4.182  26.449   1189
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 13.10 %
    Favored  : 84.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.26), residues: 1020
  helix:  1.94 (0.27), residues: 400
  sheet:  1.06 (0.34), residues: 212
  loop : -1.04 (0.28), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP N  47 
 HIS   0.003   0.001   HIS R 154 
 PHE   0.013   0.001   PHE A 212 
 TYR   0.009   0.001   TYR R 135 
 ARG   0.006   0.000   ARG R  91 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 126
  time to evaluate  : 0.973 
Fit side-chains
REVERT: R  185 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7823 (mt-10)
REVERT: A   17 LYS cc_start: 0.7867 (mptt) cc_final: 0.7646 (ttpt)
REVERT: A   19 GLN cc_start: 0.7784 (tt0) cc_final: 0.7486 (pt0)
REVERT: A   28 LYS cc_start: 0.8192 (mtpt) cc_final: 0.7978 (ptpt)
REVERT: B   23 LYS cc_start: 0.8165 (tptt) cc_final: 0.7568 (tppt)
REVERT: B   46 ARG cc_start: 0.8637 (mtm180) cc_final: 0.7860 (ptp90)
REVERT: B  134 ARG cc_start: 0.7464 (mtm180) cc_final: 0.7213 (mtm-85)
REVERT: B  270 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8173 (mp)
  outliers start: 22
  outliers final: 8
  residues processed: 137
  average time/residue: 1.3730
  time to fit residues: 198.4611
Evaluate side-chains
  126 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 116
  time to evaluate  : 1.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   89 ILE
Chi-restraints excluded: chain R residue  185 GLU
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  336 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 40 optimal weight:    5.9990
   chunk 7 optimal weight:    7.9990
   chunk 91 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 80 optimal weight:   10.0000
   chunk 56 optimal weight:    5.9990
   chunk 48 optimal weight:    0.6980
   chunk 49 optimal weight:    0.4980
   chunk 15 optimal weight:    0.9980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
G  59 ASN
N 120 GLN
A 220 HIS
B 259 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.144755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.119268 restraints weight = 10688.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 1.80
r_work: 0.3400 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3288 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8639
moved from start:          0.2120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8351  Z= 0.170
  Angle     :  0.528   6.037  11331  Z= 0.287
  Chirality :  0.043   0.156   1278
  Planarity :  0.004   0.044   1426
  Dihedral  :  4.325  28.229   1189
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 13.33 %
    Favored  : 83.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.26), residues: 1020
  helix:  1.96 (0.27), residues: 399
  sheet:  1.09 (0.33), residues: 216
  loop : -1.04 (0.28), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP R 311 
 HIS   0.004   0.001   HIS R 154 
 PHE   0.012   0.001   PHE A 212 
 TYR   0.012   0.001   TYR R 135 
 ARG   0.005   0.000   ARG R  91 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 123
  time to evaluate  : 0.947 
Fit side-chains
REVERT: R  185 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7905 (mt-10)
REVERT: N   19 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7554 (ptm160)
REVERT: A   17 LYS cc_start: 0.7800 (mptt) cc_final: 0.7530 (ttpt)
REVERT: A   19 GLN cc_start: 0.7727 (tt0) cc_final: 0.7429 (pt0)
REVERT: A   28 LYS cc_start: 0.8224 (mtpt) cc_final: 0.7978 (ptpt)
REVERT: B   14 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7185 (mm)
REVERT: B   17 GLN cc_start: 0.6717 (tm-30) cc_final: 0.6513 (tm-30)
REVERT: B   23 LYS cc_start: 0.8071 (tptt) cc_final: 0.7465 (tppt)
REVERT: B   46 ARG cc_start: 0.8565 (mtm180) cc_final: 0.7730 (ptp90)
REVERT: B  134 ARG cc_start: 0.7477 (mtm180) cc_final: 0.7204 (mtm-85)
  outliers start: 26
  outliers final: 11
  residues processed: 137
  average time/residue: 1.3263
  time to fit residues: 192.0379
Evaluate side-chains
  132 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   56 SER
Chi-restraints excluded: chain R residue   89 ILE
Chi-restraints excluded: chain R residue  185 GLU
Chi-restraints excluded: chain R residue  281 VAL
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  336 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 33 optimal weight:    0.2980
   chunk 31 optimal weight:    2.9990
   chunk 68 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 61 optimal weight:    0.8980
   chunk 48 optimal weight:    6.9990
   chunk 72 optimal weight:    0.9990
   chunk 56 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 88 optimal weight:    2.9990
   overall best weight:    1.0386

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

Flipped N/Q/H residues before XYZ refinement:
G  59 ASN
N 120 GLN
A 220 HIS
B 259 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.144177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.118693 restraints weight = 10831.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 1.82
r_work: 0.3320 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3209 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8640
moved from start:          0.2203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8351  Z= 0.171
  Angle     :  0.526   6.098  11331  Z= 0.285
  Chirality :  0.043   0.167   1278
  Planarity :  0.004   0.044   1426
  Dihedral  :  4.329  28.198   1189
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 14.35 %
    Favored  : 82.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.26), residues: 1020
  helix:  1.90 (0.27), residues: 399
  sheet:  1.10 (0.33), residues: 215
  loop : -1.07 (0.29), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP R 311 
 HIS   0.003   0.001   HIS R 154 
 PHE   0.012   0.001   PHE A 212 
 TYR   0.026   0.001   TYR R 150 
 ARG   0.006   0.000   ARG R  91 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 121
  time to evaluate  : 0.978 
Fit side-chains
REVERT: R  185 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7939 (mt-10)
REVERT: G   17 GLU cc_start: 0.6958 (mp0) cc_final: 0.6642 (pm20)
REVERT: N   19 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7601 (ptm160)
REVERT: A   17 LYS cc_start: 0.7835 (mptt) cc_final: 0.7527 (ttpt)
REVERT: A   19 GLN cc_start: 0.7717 (tt0) cc_final: 0.7430 (pt0)
REVERT: A   28 LYS cc_start: 0.8239 (mtpt) cc_final: 0.7970 (ptpt)
REVERT: B   23 LYS cc_start: 0.8030 (tptt) cc_final: 0.7806 (tptt)
REVERT: B   46 ARG cc_start: 0.8575 (mtm180) cc_final: 0.7682 (ptp90)
REVERT: B  188 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7326 (mtm)
  outliers start: 26
  outliers final: 13
  residues processed: 133
  average time/residue: 1.3520
  time to fit residues: 189.9827
Evaluate side-chains
  132 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   56 SER
Chi-restraints excluded: chain R residue   89 ILE
Chi-restraints excluded: chain R residue  185 GLU
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  336 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 84 optimal weight:    3.9990
   chunk 26 optimal weight:   20.0000
   chunk 80 optimal weight:    4.9990
   chunk 71 optimal weight:    5.9990
   chunk 43 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0270
   chunk 34 optimal weight:    5.9990
   chunk 76 optimal weight:    1.9990
   chunk 53 optimal weight:    0.2980
   chunk 85 optimal weight:    5.9990
   overall best weight:    1.8644

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

Flipped N/Q/H residues before XYZ refinement:
G  59 ASN
N 120 GLN
A 220 HIS
B 175 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.140089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.114462 restraints weight = 10874.294|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 1.84
r_work: 0.3255 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3140 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8719
moved from start:          0.2257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8351  Z= 0.263
  Angle     :  0.619   7.569  11331  Z= 0.331
  Chirality :  0.046   0.162   1278
  Planarity :  0.004   0.045   1426
  Dihedral  :  4.712  30.975   1189
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 14.81 %
    Favored  : 82.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.26), residues: 1020
  helix:  1.67 (0.26), residues: 399
  sheet:  1.09 (0.34), residues: 217
  loop : -1.12 (0.28), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP R 311 
 HIS   0.005   0.001   HIS R 154 
 PHE   0.014   0.002   PHE A 363 
 TYR   0.016   0.002   TYR R 135 
 ARG   0.006   0.000   ARG R  91 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 122
  time to evaluate  : 1.016 
Fit side-chains
REVERT: R   61 LEU cc_start: 0.9187 (tt) cc_final: 0.8935 (tt)
REVERT: R  185 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8087 (mt-10)
REVERT: N   19 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7861 (ptm160)
REVERT: N   43 LYS cc_start: 0.8225 (mtpt) cc_final: 0.7762 (mtmt)
REVERT: A   19 GLN cc_start: 0.7694 (tt0) cc_final: 0.7426 (pt0)
REVERT: B   17 GLN cc_start: 0.6709 (tm-30) cc_final: 0.6502 (tm-30)
REVERT: B   23 LYS cc_start: 0.8082 (tptt) cc_final: 0.7515 (tppt)
REVERT: B  188 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7452 (mtm)
  outliers start: 28
  outliers final: 12
  residues processed: 137
  average time/residue: 1.4484
  time to fit residues: 209.2907
Evaluate side-chains
  132 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   59 LEU
Chi-restraints excluded: chain R residue  185 GLU
Chi-restraints excluded: chain R residue  281 VAL
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  336 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 84 optimal weight:    3.9990
   chunk 28 optimal weight:    8.9990
   chunk 90 optimal weight:    0.8980
   chunk 7 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 66 optimal weight:    0.0980
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
G  59 ASN
N 120 GLN
A 220 HIS
B 175 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.138780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.112987 restraints weight = 10728.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 1.83
r_work: 0.3308 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3190 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8672
moved from start:          0.2341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8351  Z= 0.164
  Angle     :  0.539   6.676  11331  Z= 0.291
  Chirality :  0.044   0.183   1278
  Planarity :  0.004   0.045   1426
  Dihedral  :  4.382  28.767   1189
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 15.49 %
    Favored  : 82.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.26), residues: 1020
  helix:  1.67 (0.26), residues: 406
  sheet:  1.08 (0.34), residues: 217
  loop : -1.10 (0.29), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP R 311 
 HIS   0.004   0.001   HIS R 154 
 PHE   0.012   0.001   PHE A 212 
 TYR   0.009   0.001   TYR R 135 
 ARG   0.007   0.000   ARG R  91 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 120
  time to evaluate  : 0.909 
Fit side-chains
REVERT: R   61 LEU cc_start: 0.9145 (tt) cc_final: 0.8872 (tt)
REVERT: R  195 TRP cc_start: 0.8466 (OUTLIER) cc_final: 0.6532 (t60)
REVERT: G   17 GLU cc_start: 0.6945 (mp0) cc_final: 0.6655 (pm20)
REVERT: N   19 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7729 (ptm160)
REVERT: A   17 LYS cc_start: 0.7967 (mptt) cc_final: 0.7591 (pttt)
REVERT: A   19 GLN cc_start: 0.7794 (tt0) cc_final: 0.7538 (pt0)
REVERT: B   46 ARG cc_start: 0.8573 (mtm180) cc_final: 0.7744 (ptp90)
REVERT: B  188 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.7260 (mtm)
  outliers start: 22
  outliers final: 13
  residues processed: 130
  average time/residue: 1.4572
  time to fit residues: 199.8010
Evaluate side-chains
  133 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   59 LEU
Chi-restraints excluded: chain R residue   89 ILE
Chi-restraints excluded: chain R residue  195 TRP
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  336 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 48 optimal weight:    5.9990
   chunk 40 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0270
   chunk 0 optimal weight:    6.9990
   chunk 50 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 89 optimal weight:    3.9990
   chunk 5 optimal weight:    0.6980
   overall best weight:    1.1242

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

Flipped N/Q/H residues before XYZ refinement:
G  59 ASN
N 120 GLN
A 220 HIS
B 175 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.138495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.112930 restraints weight = 10804.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 1.83
r_work: 0.3253 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3134 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8688
moved from start:          0.2372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8351  Z= 0.182
  Angle     :  0.549   6.396  11331  Z= 0.296
  Chirality :  0.044   0.167   1278
  Planarity :  0.004   0.045   1426
  Dihedral  :  4.384  28.725   1189
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 15.72 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.26), residues: 1020
  helix:  1.70 (0.26), residues: 405
  sheet:  1.10 (0.34), residues: 218
  loop : -1.13 (0.29), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP R 311 
 HIS   0.004   0.001   HIS R 154 
 PHE   0.012   0.001   PHE A 212 
 TYR   0.011   0.001   TYR R 135 
 ARG   0.006   0.000   ARG R  91 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 118
  time to evaluate  : 0.892 
Fit side-chains
REVERT: R   61 LEU cc_start: 0.9098 (tt) cc_final: 0.8818 (tt)
REVERT: R  195 TRP cc_start: 0.8476 (OUTLIER) cc_final: 0.6604 (t60)
REVERT: N   19 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7741 (ptm160)
REVERT: A   17 LYS cc_start: 0.7974 (mptt) cc_final: 0.7566 (pttt)
REVERT: A   19 GLN cc_start: 0.7796 (tt0) cc_final: 0.7549 (pt0)
REVERT: A  204 THR cc_start: 0.2729 (OUTLIER) cc_final: 0.2371 (p)
REVERT: B   17 GLN cc_start: 0.6680 (tm-30) cc_final: 0.6142 (tm-30)
REVERT: B   23 LYS cc_start: 0.7895 (tptt) cc_final: 0.7476 (tppt)
REVERT: B   46 ARG cc_start: 0.8587 (mtm180) cc_final: 0.7870 (ptp90)
REVERT: B  188 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.7335 (mtm)
  outliers start: 25
  outliers final: 14
  residues processed: 131
  average time/residue: 1.2967
  time to fit residues: 179.3826
Evaluate side-chains
  132 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   59 LEU
Chi-restraints excluded: chain R residue   89 ILE
Chi-restraints excluded: chain R residue  195 TRP
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  336 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 96 optimal weight:    5.9990
   chunk 58 optimal weight:    0.7980
   chunk 1 optimal weight:    5.9990
   chunk 94 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 64 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 73 optimal weight:    6.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
G  59 ASN
N 120 GLN
A 220 HIS
B 175 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.132131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.106475 restraints weight = 11121.448|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 1.83
r_work: 0.3108 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2999 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8679
moved from start:          0.2405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8351  Z= 0.247
  Angle     :  0.613   8.320  11331  Z= 0.329
  Chirality :  0.046   0.187   1278
  Planarity :  0.004   0.045   1426
  Dihedral  :  4.667  30.569   1189
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 16.06 %
    Favored  : 81.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.26), residues: 1020
  helix:  1.52 (0.26), residues: 405
  sheet:  1.11 (0.34), residues: 217
  loop : -1.19 (0.29), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.054   0.002   TRP R 311 
 HIS   0.005   0.001   HIS R 154 
 PHE   0.013   0.001   PHE A 363 
 TYR   0.014   0.001   TYR R 135 
 ARG   0.006   0.000   ARG R  91 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 121
  time to evaluate  : 1.040 
Fit side-chains
REVERT: R   61 LEU cc_start: 0.9136 (tt) cc_final: 0.8838 (tt)
REVERT: R  195 TRP cc_start: 0.8522 (OUTLIER) cc_final: 0.6546 (t60)
REVERT: N   19 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7766 (ptm160)
REVERT: N   43 LYS cc_start: 0.8146 (mtpt) cc_final: 0.7671 (mtmt)
REVERT: A   17 LYS cc_start: 0.7870 (mptt) cc_final: 0.7424 (pttt)
REVERT: A   19 GLN cc_start: 0.7765 (tt0) cc_final: 0.7481 (pt0)
REVERT: A  204 THR cc_start: 0.2744 (OUTLIER) cc_final: 0.2383 (p)
REVERT: B   17 GLN cc_start: 0.6558 (tm-30) cc_final: 0.6005 (tm-30)
REVERT: B   23 LYS cc_start: 0.7742 (tptt) cc_final: 0.7163 (tppt)
REVERT: B  188 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7410 (mtm)
  outliers start: 23
  outliers final: 12
  residues processed: 133
  average time/residue: 1.3815
  time to fit residues: 193.8038
Evaluate side-chains
  134 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   59 LEU
Chi-restraints excluded: chain R residue  195 TRP
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  336 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 47 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 87 optimal weight:    3.9990
   chunk 53 optimal weight:    0.0870
   chunk 8 optimal weight:    2.9990
   chunk 40 optimal weight:    8.9990
   chunk 95 optimal weight:    1.9990
   chunk 76 optimal weight:    0.5980
   chunk 84 optimal weight:    0.1980
   chunk 64 optimal weight:    0.4980
   chunk 38 optimal weight:    6.9990
   overall best weight:    0.4558

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

Flipped N/Q/H residues before XYZ refinement:
G  59 ASN
N 120 GLN
A 220 HIS
B  35 ASN
B 175 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.142406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.117242 restraints weight = 10742.241|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 1.82
r_work: 0.3321 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3203 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8627
moved from start:          0.2562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8351  Z= 0.127
  Angle     :  0.500   6.496  11331  Z= 0.273
  Chirality :  0.042   0.182   1278
  Planarity :  0.004   0.046   1426
  Dihedral  :  4.156  26.688   1189
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 16.86 %
    Favored  : 81.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.26), residues: 1020
  helix:  1.71 (0.26), residues: 405
  sheet:  1.11 (0.33), residues: 223
  loop : -1.08 (0.29), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.001   TRP R 311 
 HIS   0.004   0.001   HIS R 154 
 PHE   0.012   0.001   PHE A 212 
 TYR   0.008   0.001   TYR A 391 
 ARG   0.006   0.000   ARG R  91 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6807.97 seconds
wall clock time: 120 minutes 26.35 seconds (7226.35 seconds total)