Starting phenix.real_space_refine
on Fri Aug 22 22:17:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8h4l_34480/08_2025/8h4l_34480_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8h4l_34480/08_2025/8h4l_34480.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.07
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8h4l_34480/08_2025/8h4l_34480_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8h4l_34480/08_2025/8h4l_34480_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8h4l_34480/08_2025/8h4l_34480.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8h4l_34480/08_2025/8h4l_34480.map"
  }
  resolution = 3.07
  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=   0.034 sd=   0.130
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      48      5.16       5
     C    5212      2.51       5
     N    1409      2.21       5
     O    1502      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 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: 8171
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1904
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1904
          Classifications: {'peptide': 234}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 6, 'TRANS': 227}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "B"
      Number of atoms: 2547
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2547
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 53
          Unresolved non-hydrogen angles: 62
          Unresolved non-hydrogen dihedrals: 44
          Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 41
    Chain: "G"
      Number of atoms: 408
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 408
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 25
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 14
    Chain: "N"
      Number of atoms: 963
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 963
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "R"
      Number of atoms: 2325
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 302, 2325
          Classifications: {'peptide': 302}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 13, 'TRANS': 288}
          Unresolved non-hydrogen bonds: 71
          Unresolved non-hydrogen angles: 86
          Unresolved non-hydrogen dihedrals: 58
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 4, 'GLU:plan': 2, 'GLN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 55
    Chain: "R"
      Number of atoms: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 24
          Unusual residues: {'HXA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.34, per 1000 atoms: 0.16
  Number of scatterers: 8171
  At special positions: 0
  Unit cell: (78.1, 103.4, 139.7, 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      48     16.00
     O    1502      8.00
     N    1409      7.00
     C    5212      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 111 " - pdb=" SG  CYS R 194 " distance=2.04

  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: 0.62
  Conformation dependent library (CDL) restraints added in 262.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1998

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 11 sheets defined
      41.8% alpha, 21.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 38
      removed outlier: 4.174A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 61
    Processing helix  chain 'A' and resid 235 through 239
      removed outlier: 3.760A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
      removed outlier: 3.561A  pdb=" N   ALA A 269 " --> pdb=" O   ARG A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 283
      removed outlier: 4.080A  pdb=" N   ARG A 283 " --> pdb=" O   ARG A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 3.568A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   GLY A 304 " --> pdb=" O   LYS A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 311
    Processing helix  chain 'A' and resid 312 through 317
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 3.813A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 4 through 25
      removed outlier: 3.849A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.748A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 7 through 23
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.728A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   HIS G  44 " --> pdb=" O   TYR G  40 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.751A  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 'G' and resid 55 through 59
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.562A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.641A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 35 through 68
      removed outlier: 3.957A  pdb=" N   ARG R  68 " --> pdb=" O   LEU R  64 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 72 through 89
      removed outlier: 3.985A  pdb=" N   CYS R  76 " --> pdb=" O   GLY R  72 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 91 through 102
      removed outlier: 3.765A  pdb=" N   VAL R  95 " --> pdb=" O   ALA R  91 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 107 through 145
      removed outlier: 5.661A  pdb=" N   PHE R 115 " --> pdb=" O   CYS R 111 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   TYR R 116 " --> pdb=" O   HIS R 112 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 151 through 170
    Processing helix  chain 'R' and resid 171 through 176
      removed outlier: 4.029A  pdb=" N   VAL R 175 " --> pdb=" O   LEU R 171 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 200 through 214
      removed outlier: 3.602A  pdb=" N   GLU R 204 " --> pdb=" O   THR R 200 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 216 through 244
      removed outlier: 4.212A  pdb=" N   LEU R 241 " --> pdb=" O   SER R 237 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   THR R 242 " --> pdb=" O   ARG R 238 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 251 through 256
    Processing helix  chain 'R' and resid 258 through 270
      removed outlier: 3.966A  pdb=" N   LEU R 262 " --> pdb=" O   GLN R 258 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   PHE R 267 " --> pdb=" O   PHE R 263 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 271 through 277
    Processing helix  chain 'R' and resid 277 through 293
      removed outlier: 3.988A  pdb=" N   ILE R 281 " --> pdb=" O   TRP R 277 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 299 through 311
    Processing helix  chain 'R' and resid 312 through 321
      Proline residue:  R 318  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 4.911A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.475A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.270A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.965A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.677A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.831A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.142A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.385A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.757A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.784A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.090A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.219A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 5.016A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.085A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ASN B 125 " --> pdb=" O   ARG B 134 " (cutoff:3.500A)
      removed outlier: 3.940A  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: 6.947A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.201A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.722A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192
      removed outlier: 3.903A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.113A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.576A  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: 6.833A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.828A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.210A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.719A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.989A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 6.207A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.629A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 177 through 183

    409 hydrogen bonds defined for protein.
    1167 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: 1.10

  Time building geometry restraints manager: 0.82 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2673
        1.34 -     1.47: 2024
        1.47 -     1.59: 3572
        1.59 -     1.72: 0
        1.72 -     1.84: 66
  Bond restraints: 8335
  Sorted by residual:
  bond pdb=" N   HIS A 357 "
       pdb=" CA  HIS A 357 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.034 1.21e-02 6.83e+03 8.07e+00
  bond pdb=" N   ILE A 348 "
       pdb=" CA  ILE A 348 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.25e-02 6.40e+03 7.98e+00
  bond pdb=" N   ARG A 389 "
       pdb=" CA  ARG A 389 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.033 1.32e-02 5.74e+03 6.15e+00
  bond pdb=" N   GLY A 353 "
       pdb=" CA  GLY A 353 "
    ideal  model  delta    sigma   weight residual
    1.448  1.475 -0.028 1.13e-02 7.83e+03 6.01e+00
  bond pdb=" N   GLU A 390 "
       pdb=" CA  GLU A 390 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.27e-02 6.20e+03 5.94e+00
  ... (remaining 8330 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.24: 10980
        2.24 -     4.49: 300
        4.49 -     6.73: 36
        6.73 -     8.98: 9
        8.98 -    11.22: 3
  Bond angle restraints: 11328
  Sorted by residual:
  angle pdb=" CA  TRP B  82 "
        pdb=" CB  TRP B  82 "
        pdb=" CG  TRP B  82 "
      ideal   model   delta    sigma   weight residual
     113.60  121.12   -7.52 1.90e+00 2.77e-01 1.57e+01
  angle pdb=" N   ASP N 109 "
        pdb=" CA  ASP N 109 "
        pdb=" C   ASP N 109 "
      ideal   model   delta    sigma   weight residual
     110.06  115.63   -5.57 1.43e+00 4.89e-01 1.51e+01
  angle pdb=" N   ALA B 309 "
        pdb=" CA  ALA B 309 "
        pdb=" C   ALA B 309 "
      ideal   model   delta    sigma   weight residual
     107.48  116.05   -8.57 2.29e+00 1.91e-01 1.40e+01
  angle pdb=" N   ALA B 203 "
        pdb=" CA  ALA B 203 "
        pdb=" C   ALA B 203 "
      ideal   model   delta    sigma   weight residual
     110.06  115.39   -5.33 1.43e+00 4.89e-01 1.39e+01
  angle pdb=" N   THR A 350 "
        pdb=" CA  THR A 350 "
        pdb=" C   THR A 350 "
      ideal   model   delta    sigma   weight residual
     114.04  109.46    4.58 1.24e+00 6.50e-01 1.36e+01
  ... (remaining 11323 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.71: 4584
       17.71 -    35.41: 292
       35.41 -    53.12: 47
       53.12 -    70.83: 10
       70.83 -    88.54: 10
  Dihedral angle restraints: 4943
    sinusoidal: 1863
      harmonic: 3080
  Sorted by residual:
  dihedral pdb=" CA  ASP N 109 "
           pdb=" C   ASP N 109 "
           pdb=" N   VAL N 110 "
           pdb=" CA  VAL N 110 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.13   19.87     0      5.00e+00 4.00e-02 1.58e+01
  dihedral pdb=" CA  ALA B 203 "
           pdb=" C   ALA B 203 "
           pdb=" N   CYS B 204 "
           pdb=" CA  CYS B 204 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.36   19.64     0      5.00e+00 4.00e-02 1.54e+01
  dihedral pdb=" CA  GLY B 202 "
           pdb=" C   GLY B 202 "
           pdb=" N   ALA B 203 "
           pdb=" CA  ALA B 203 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.52  -19.48     0      5.00e+00 4.00e-02 1.52e+01
  ... (remaining 4940 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 1017
       0.059 -    0.118: 264
       0.118 -    0.177: 36
       0.177 -    0.236: 4
       0.236 -    0.295: 1
  Chirality restraints: 1322
  Sorted by residual:
  chirality pdb=" CA  THR R 101 "
            pdb=" N   THR R 101 "
            pdb=" C   THR R 101 "
            pdb=" CB  THR R 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.23    0.30 2.00e-01 2.50e+01 2.18e+00
  chirality pdb=" CA  SER A 251 "
            pdb=" N   SER A 251 "
            pdb=" C   SER A 251 "
            pdb=" CB  SER A 251 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.24e+00
  chirality pdb=" CA  PRO R  93 "
            pdb=" N   PRO R  93 "
            pdb=" C   PRO R  93 "
            pdb=" CB  PRO R  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.53    0.19 2.00e-01 2.50e+01 9.29e-01
  ... (remaining 1319 not shown)

  Planarity restraints: 1442
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE R  92 "   -0.073 5.00e-02 4.00e+02   1.08e-01 1.86e+01
        pdb=" N   PRO R  93 "    0.187 5.00e-02 4.00e+02
        pdb=" CA  PRO R  93 "   -0.054 5.00e-02 4.00e+02
        pdb=" CD  PRO R  93 "   -0.060 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP G  48 "   -0.045 5.00e-02 4.00e+02   6.78e-02 7.36e+00
        pdb=" N   PRO G  49 "    0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO G  49 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO G  49 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  82 "    0.025 2.00e-02 2.50e+03   1.47e-02 5.37e+00
        pdb=" CG  TRP B  82 "   -0.038 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  82 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  82 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  82 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  82 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  82 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  82 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  82 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  82 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1439 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 72
        2.64 -     3.20: 7036
        3.20 -     3.77: 11220
        3.77 -     4.33: 15666
        4.33 -     4.90: 27374
  Nonbonded interactions: 61368
  Sorted by model distance:
  nonbonded pdb=" O   PRO R 108 "
            pdb=" ND1 HIS R 112 "
     model   vdw
     2.069 3.120
  nonbonded pdb=" OG1 THR R  74 "
            pdb=" OE1 GLU R 135 "
     model   vdw
     2.194 3.040
  nonbonded pdb=" OE2 GLU A  27 "
            pdb=" NZ  LYS B  89 "
     model   vdw
     2.230 3.120
  nonbonded pdb=" O   CYS A 359 "
            pdb=" OH  TYR R 247 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" O   ALA R  66 "
            pdb=" NH2 ARG R  71 "
     model   vdw
     2.236 3.120
  ... (remaining 61363 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.050
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.400
  Find NCS groups from input model:        0.040
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
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      :  0.007   0.059   8336  Z= 0.327
  Angle     :  0.900  11.221  11330  Z= 0.522
  Chirality :  0.052   0.295   1322
  Planarity :  0.006   0.108   1442
  Dihedral  : 12.790  88.536   2942
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  0.92 %
    Favored  : 98.85 %
  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: -0.34 (0.26), residues: 1047
  helix:  0.74 (0.27), residues: 393
  sheet:  0.50 (0.33), residues: 237
  loop : -1.61 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG N  72 
 TYR   0.021   0.003   TYR B  59 
 PHE   0.023   0.003   PHE B 199 
 TRP   0.038   0.003   TRP B  82 
 HIS   0.008   0.002   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00727 ( 8335)
  covalent geometry    : angle       0.89972 (11328)
  SS BOND              : bond        0.00646 (    1)
  SS BOND              : angle       2.78139 (    2)
  hydrogen bonds       : bond        0.15188 (  409)
  hydrogen bonds       : angle       5.73862 ( 1167)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 98
  time to evaluate  : 0.317 
Fit side-chains
REVERT: N   46 GLU cc_start: 0.7509 (tt0) cc_final: 0.7183 (tt0)
  outliers start: 2
  outliers final: 1
  residues processed: 100
  average time/residue: 0.0933
  time to fit residues: 12.5994
Evaluate side-chains
  92 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 91
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  388 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 49 optimal weight:    0.0020
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.2980
   chunk 51 optimal weight:    0.8980
   chunk 100 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   overall best weight:    0.5388

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.124542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.094999 restraints weight = 12755.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 2.21
r_work: 0.3124 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2971 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.1096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8336  Z= 0.131
  Angle     :  0.564   6.723  11330  Z= 0.308
  Chirality :  0.043   0.144   1322
  Planarity :  0.005   0.056   1442
  Dihedral  :  5.607  53.407   1159
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 2.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  3.92 %
    Favored  : 95.50 %
  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:  0.35 (0.26), residues: 1047
  helix:  1.58 (0.27), residues: 397
  sheet:  0.93 (0.34), residues: 233
  loop : -1.57 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 280 
 TYR   0.013   0.001   TYR R 247 
 PHE   0.020   0.002   PHE R 263 
 TRP   0.024   0.001   TRP B  82 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 8335)
  covalent geometry    : angle       0.56309 (11328)
  SS BOND              : bond        0.00462 (    1)
  SS BOND              : angle       1.96964 (    2)
  hydrogen bonds       : bond        0.06124 (  409)
  hydrogen bonds       : angle       4.26793 ( 1167)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 98
  time to evaluate  : 0.300 
Fit side-chains
REVERT: A  229 ASP cc_start: 0.7860 (m-30) cc_final: 0.7641 (m-30)
REVERT: N  106 ASP cc_start: 0.8002 (p0) cc_final: 0.7783 (p0)
REVERT: R  239 LYS cc_start: 0.7893 (tttt) cc_final: 0.7678 (tptt)
  outliers start: 5
  outliers final: 1
  residues processed: 101
  average time/residue: 0.0716
  time to fit residues: 10.0255
Evaluate side-chains
  88 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 87
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue   50 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 39 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 81 optimal weight:    7.9990
   chunk 65 optimal weight:    0.7980
   chunk 97 optimal weight:    3.9990
   chunk 7 optimal weight:    5.9990
   chunk 86 optimal weight:    7.9990
   chunk 48 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   overall best weight:    1.0382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.123294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.094063 restraints weight = 12689.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 2.12
r_work: 0.3106 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2953 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.1316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8336  Z= 0.154
  Angle     :  0.580   7.595  11330  Z= 0.313
  Chirality :  0.044   0.145   1322
  Planarity :  0.004   0.043   1442
  Dihedral  :  5.479  58.230   1157
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 2.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  6.00 %
    Favored  : 92.85 %
  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:  0.58 (0.26), residues: 1047
  helix:  1.80 (0.27), residues: 397
  sheet:  1.05 (0.34), residues: 228
  loop : -1.45 (0.28), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N  72 
 TYR   0.013   0.001   TYR N  95 
 PHE   0.017   0.002   PHE B 199 
 TRP   0.020   0.002   TRP B  82 
 HIS   0.007   0.002   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 8335)
  covalent geometry    : angle       0.57930 (11328)
  SS BOND              : bond        0.00562 (    1)
  SS BOND              : angle       2.28946 (    2)
  hydrogen bonds       : bond        0.06170 (  409)
  hydrogen bonds       : angle       4.12264 ( 1167)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 0.310 
Fit side-chains
REVERT: N  106 ASP cc_start: 0.8076 (p0) cc_final: 0.7808 (p0)
  outliers start: 10
  outliers final: 6
  residues processed: 98
  average time/residue: 0.0790
  time to fit residues: 10.6760
Evaluate side-chains
  94 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 88
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain N residue   50 ASP
Chi-restraints excluded: chain R residue   42 VAL
Chi-restraints excluded: chain R residue  138 VAL
Chi-restraints excluded: chain R residue  247 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 64 optimal weight:    0.8980
   chunk 7 optimal weight:    4.9990
   chunk 99 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 41 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 19 optimal weight:    0.4980
   chunk 97 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 86 optimal weight:    4.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.125067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.095366 restraints weight = 12955.294|
|-----------------------------------------------------------------------------|
r_work (start): 0.3252 rms_B_bonded: 2.22
r_work: 0.3128 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2976 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.1600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8336  Z= 0.122
  Angle     :  0.528   6.047  11330  Z= 0.286
  Chirality :  0.043   0.139   1322
  Planarity :  0.004   0.040   1442
  Dihedral  :  5.208  58.010   1157
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 2.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  :  8.19 %
    Favored  : 90.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.81 (0.26), residues: 1047
  helix:  1.99 (0.27), residues: 401
  sheet:  1.11 (0.34), residues: 229
  loop : -1.31 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 280 
 TYR   0.010   0.001   TYR N  95 
 PHE   0.014   0.002   PHE B 199 
 TRP   0.020   0.001   TRP B  82 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 8335)
  covalent geometry    : angle       0.52761 (11328)
  SS BOND              : bond        0.00386 (    1)
  SS BOND              : angle       1.99489 (    2)
  hydrogen bonds       : bond        0.05263 (  409)
  hydrogen bonds       : angle       3.90219 ( 1167)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.295 
Fit side-chains
REVERT: N  106 ASP cc_start: 0.7976 (p0) cc_final: 0.7723 (p0)
  outliers start: 8
  outliers final: 7
  residues processed: 96
  average time/residue: 0.0782
  time to fit residues: 10.4428
Evaluate side-chains
  96 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  317 ARG
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain N residue   50 ASP
Chi-restraints excluded: chain R residue  247 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 73 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9990
   chunk 25 optimal weight:    8.9990
   chunk 38 optimal weight:    0.5980
   chunk 3 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 32 optimal weight:    3.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.124269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.094438 restraints weight = 12843.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 2.21
r_work: 0.3118 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2964 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.1704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8336  Z= 0.130
  Angle     :  0.539   6.311  11330  Z= 0.289
  Chirality :  0.043   0.137   1322
  Planarity :  0.004   0.038   1442
  Dihedral  :  5.176  59.160   1157
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 2.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  9.00 %
    Favored  : 89.73 %
  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:  0.90 (0.27), residues: 1047
  helix:  2.10 (0.27), residues: 402
  sheet:  1.09 (0.34), residues: 231
  loop : -1.27 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG N  72 
 TYR   0.011   0.001   TYR N  95 
 PHE   0.015   0.002   PHE B 199 
 TRP   0.020   0.001   TRP B  82 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 8335)
  covalent geometry    : angle       0.53875 (11328)
  SS BOND              : bond        0.00506 (    1)
  SS BOND              : angle       2.17477 (    2)
  hydrogen bonds       : bond        0.05325 (  409)
  hydrogen bonds       : angle       3.88526 ( 1167)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.323 
Fit side-chains
REVERT: B  333 ASP cc_start: 0.7399 (p0) cc_final: 0.7095 (p0)
REVERT: N   80 TYR cc_start: 0.8771 (m-80) cc_final: 0.8486 (m-80)
REVERT: N  106 ASP cc_start: 0.7982 (p0) cc_final: 0.7716 (p0)
  outliers start: 11
  outliers final: 8
  residues processed: 101
  average time/residue: 0.1020
  time to fit residues: 13.9125
Evaluate side-chains
  97 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 89
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  317 ARG
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain N residue   50 ASP
Chi-restraints excluded: chain R residue  233 ILE
Chi-restraints excluded: chain R residue  247 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 80 optimal weight:    5.9990
   chunk 101 optimal weight:    0.8980
   chunk 2 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 94 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 86 optimal weight:    0.3980
   chunk 53 optimal weight:    0.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.123762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.094166 restraints weight = 12780.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 2.20
r_work: 0.3105 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2953 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.1700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8336  Z= 0.146
  Angle     :  0.560   7.092  11330  Z= 0.301
  Chirality :  0.043   0.141   1322
  Planarity :  0.004   0.037   1442
  Dihedral  :  5.224  59.692   1157
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 2.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  :  9.46 %
    Favored  : 89.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.27), residues: 1047
  helix:  2.05 (0.27), residues: 402
  sheet:  1.18 (0.34), residues: 230
  loop : -1.29 (0.29), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N  72 
 TYR   0.012   0.001   TYR N  95 
 PHE   0.016   0.002   PHE B 199 
 TRP   0.020   0.002   TRP B  82 
 HIS   0.007   0.002   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 8335)
  covalent geometry    : angle       0.55927 (11328)
  SS BOND              : bond        0.00561 (    1)
  SS BOND              : angle       2.18384 (    2)
  hydrogen bonds       : bond        0.05662 (  409)
  hydrogen bonds       : angle       3.93112 ( 1167)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.321 
Fit side-chains
REVERT: N   80 TYR cc_start: 0.8765 (m-80) cc_final: 0.8476 (m-80)
  outliers start: 12
  outliers final: 9
  residues processed: 96
  average time/residue: 0.1057
  time to fit residues: 13.7769
Evaluate side-chains
  95 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain N residue   50 ASP
Chi-restraints excluded: chain R residue   56 LEU
Chi-restraints excluded: chain R residue  233 ILE
Chi-restraints excluded: chain R residue  247 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 20 optimal weight:    0.4980
   chunk 46 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.122155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.092372 restraints weight = 12880.694|
|-----------------------------------------------------------------------------|
r_work (start): 0.3209 rms_B_bonded: 2.21
r_work: 0.3084 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2933 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.1686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8336  Z= 0.172
  Angle     :  0.596   8.031  11330  Z= 0.319
  Chirality :  0.044   0.145   1322
  Planarity :  0.004   0.036   1442
  Dihedral  :  5.334  57.709   1157
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 2.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  :  9.92 %
    Favored  : 88.24 %
  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:  0.91 (0.26), residues: 1047
  helix:  2.11 (0.27), residues: 396
  sheet:  1.17 (0.34), residues: 228
  loop : -1.25 (0.29), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N  72 
 TYR   0.013   0.001   TYR N  95 
 PHE   0.018   0.002   PHE R 273 
 TRP   0.022   0.002   TRP B  82 
 HIS   0.006   0.002   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 8335)
  covalent geometry    : angle       0.59541 (11328)
  SS BOND              : bond        0.00645 (    1)
  SS BOND              : angle       2.34210 (    2)
  hydrogen bonds       : bond        0.06143 (  409)
  hydrogen bonds       : angle       3.99481 ( 1167)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.368 
Fit side-chains
REVERT: N   80 TYR cc_start: 0.8789 (m-80) cc_final: 0.8485 (m-80)
  outliers start: 16
  outliers final: 14
  residues processed: 99
  average time/residue: 0.1096
  time to fit residues: 14.6761
Evaluate side-chains
  103 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  317 ARG
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain N residue   50 ASP
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain R residue   42 VAL
Chi-restraints excluded: chain R residue   56 LEU
Chi-restraints excluded: chain R residue  233 ILE
Chi-restraints excluded: chain R residue  247 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 88 optimal weight:    0.1980
   chunk 74 optimal weight:   20.0000
   chunk 28 optimal weight:    1.9990
   chunk 56 optimal weight:    6.9990
   chunk 92 optimal weight:    0.0470
   chunk 25 optimal weight:   10.0000
   chunk 58 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.8280

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.123530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.093920 restraints weight = 12676.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 2.18
r_work: 0.3105 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2953 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.1815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8336  Z= 0.133
  Angle     :  0.552   6.884  11330  Z= 0.295
  Chirality :  0.043   0.138   1322
  Planarity :  0.004   0.036   1442
  Dihedral  :  5.153  59.198   1157
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 2.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 10.61 %
    Favored  : 88.12 %
  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:  1.02 (0.27), residues: 1047
  helix:  2.24 (0.27), residues: 396
  sheet:  1.20 (0.34), residues: 231
  loop : -1.23 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG N  72 
 TYR   0.011   0.001   TYR N  95 
 PHE   0.017   0.002   PHE R 177 
 TRP   0.025   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 8335)
  covalent geometry    : angle       0.55073 (11328)
  SS BOND              : bond        0.00463 (    1)
  SS BOND              : angle       2.30649 (    2)
  hydrogen bonds       : bond        0.05389 (  409)
  hydrogen bonds       : angle       3.87287 ( 1167)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.361 
Fit side-chains
REVERT: N   80 TYR cc_start: 0.8737 (m-80) cc_final: 0.8424 (m-80)
REVERT: R  161 LEU cc_start: 0.6192 (tt) cc_final: 0.5926 (tp)
  outliers start: 11
  outliers final: 9
  residues processed: 97
  average time/residue: 0.1003
  time to fit residues: 13.2291
Evaluate side-chains
  98 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  317 ARG
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain N residue   50 ASP
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain R residue   42 VAL
Chi-restraints excluded: chain R residue  247 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 53 optimal weight:    0.8980
   chunk 66 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9980
   chunk 78 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9990
   chunk 95 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9980
   chunk 96 optimal weight:    8.9990
   chunk 6 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.124669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.095002 restraints weight = 12719.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 2.19
r_work: 0.3129 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2979 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.1999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8336  Z= 0.120
  Angle     :  0.530   6.993  11330  Z= 0.284
  Chirality :  0.042   0.141   1322
  Planarity :  0.004   0.035   1442
  Dihedral  :  4.993  59.226   1157
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 2.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 11.30 %
    Favored  : 87.54 %
  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:  1.11 (0.27), residues: 1047
  helix:  2.36 (0.27), residues: 397
  sheet:  1.01 (0.34), residues: 239
  loop : -1.13 (0.29), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  39 
 TYR   0.010   0.001   TYR N  95 
 PHE   0.014   0.001   PHE B 199 
 TRP   0.025   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 8335)
  covalent geometry    : angle       0.52954 (11328)
  SS BOND              : bond        0.00463 (    1)
  SS BOND              : angle       2.30582 (    2)
  hydrogen bonds       : bond        0.04945 (  409)
  hydrogen bonds       : angle       3.78569 ( 1167)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 0.364 
Fit side-chains
REVERT: N   80 TYR cc_start: 0.8747 (m-80) cc_final: 0.8387 (m-80)
REVERT: R  161 LEU cc_start: 0.6221 (tt) cc_final: 0.5938 (tp)
  outliers start: 10
  outliers final: 9
  residues processed: 101
  average time/residue: 0.1028
  time to fit residues: 14.1844
Evaluate side-chains
  96 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain N residue   50 ASP
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain R residue   42 VAL
Chi-restraints excluded: chain R residue  233 ILE
Chi-restraints excluded: chain R residue  247 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 99 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 57 optimal weight:    6.9990
   chunk 3 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9980
   chunk 81 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** 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 = 0.3688 r_free = 0.3688 target = 0.123285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.093936 restraints weight = 12738.690|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 2.11
r_work: 0.3108 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2958 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.1853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8336  Z= 0.160
  Angle     :  0.586   7.480  11330  Z= 0.312
  Chirality :  0.044   0.143   1322
  Planarity :  0.004   0.035   1442
  Dihedral  :  5.188  58.806   1157
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 2.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 11.19 %
    Favored  : 87.54 %
  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:  1.08 (0.27), residues: 1047
  helix:  2.33 (0.27), residues: 396
  sheet:  1.14 (0.34), residues: 231
  loop : -1.17 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  39 
 TYR   0.012   0.001   TYR N  95 
 PHE   0.017   0.002   PHE R 273 
 TRP   0.019   0.002   TRP B  82 
 HIS   0.006   0.002   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 8335)
  covalent geometry    : angle       0.58519 (11328)
  SS BOND              : bond        0.00522 (    1)
  SS BOND              : angle       2.41894 (    2)
  hydrogen bonds       : bond        0.05759 (  409)
  hydrogen bonds       : angle       3.90114 ( 1167)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.339 
Fit side-chains
REVERT: N   80 TYR cc_start: 0.8741 (m-80) cc_final: 0.8416 (m-80)
REVERT: R  161 LEU cc_start: 0.6187 (tt) cc_final: 0.5940 (tp)
  outliers start: 11
  outliers final: 11
  residues processed: 91
  average time/residue: 0.1104
  time to fit residues: 13.5191
Evaluate side-chains
  94 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  317 ARG
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain N residue   50 ASP
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain R residue   42 VAL
Chi-restraints excluded: chain R residue  233 ILE
Chi-restraints excluded: chain R residue  247 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   chunk 86 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 55 optimal weight:    4.9990
   chunk 17 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.124307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.095073 restraints weight = 12651.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 2.11
r_work: 0.3127 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2977 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.1993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8336  Z= 0.131
  Angle     :  0.546   7.141  11330  Z= 0.291
  Chirality :  0.043   0.139   1322
  Planarity :  0.004   0.035   1442
  Dihedral  :  5.053  59.921   1157
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 2.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 11.42 %
    Favored  : 87.43 %
  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:  1.19 (0.27), residues: 1047
  helix:  2.41 (0.27), residues: 399
  sheet:  1.19 (0.34), residues: 231
  loop : -1.14 (0.29), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  39 
 TYR   0.011   0.001   TYR N  95 
 PHE   0.015   0.002   PHE B 199 
 TRP   0.025   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 8335)
  covalent geometry    : angle       0.54568 (11328)
  SS BOND              : bond        0.00456 (    1)
  SS BOND              : angle       2.18977 (    2)
  hydrogen bonds       : bond        0.05212 (  409)
  hydrogen bonds       : angle       3.80947 ( 1167)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2378.48 seconds
wall clock time: 41 minutes 22.58 seconds (2482.58 seconds total)