Starting phenix.real_space_refine
on Tue Mar  3 18:03:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vvo_32146/03_2026/7vvo_32146.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vvo_32146/03_2026/7vvo_32146.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vvo_32146/03_2026/7vvo_32146.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vvo_32146/03_2026/7vvo_32146.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vvo_32146/03_2026/7vvo_32146.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vvo_32146/03_2026/7vvo_32146.cif"
  }
  resolution = 4.1
  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=   0.000 sd=   0.004
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      39      5.16       5
     C    5019      2.51       5
     N    1393      2.21       5
     O    1491      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7942
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1895
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1895
          Classifications: {'peptide': 230}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 6, 'TRANS': 223}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 25
          Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "B"
      Number of atoms: 2551
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2551
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 50
          Unresolved non-hydrogen angles: 59
          Unresolved non-hydrogen dihedrals: 41
          Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 3, 'ASN%COO:plan1': 1}
          Unresolved non-hydrogen planarities: 35
    Chain: "G"
      Number of atoms: 420
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 420
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "N"
      Number of atoms: 964
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 964
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 8
          Unresolved non-hydrogen chiralities: 1
    Chain: "P"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 36
          Classifications: {'peptide': 5}
          Link IDs: {'TRANS': 4}
    Chain: "R"
      Number of atoms: 2076
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 302, 2076
          Classifications: {'peptide': 302}
          Incomplete info: {'truncation_to_alanine': 100}
          Link IDs: {'PTRANS': 7, 'TRANS': 294}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 460
          Unresolved non-hydrogen angles: 588
          Unresolved non-hydrogen dihedrals: 418
          Unresolved non-hydrogen chiralities: 21
          Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 3, 'PHE:plan': 7, 'HIS:plan': 5, 'ARG:plan': 12, 'ASP:plan': 4, 'TYR:plan': 9, 'ASN:plan1': 5, 'TRP:plan': 5}
          Unresolved non-hydrogen planarities: 302
  Time building chain proxies: 1.88, per 1000 atoms: 0.24
  Number of scatterers: 7942
  At special positions: 0
  Unit cell: (126.16, 102.92, 128.374, 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      39     16.00
     O    1491      8.00
     N    1393      7.00
     C    5019      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 121 " - pdb=" SG  CYS B 149 " distance=2.11
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " 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: 0.77
  Conformation dependent library (CDL) restraints added in 280.2 milliseconds
  

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1992

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 12 sheets defined
      38.3% alpha, 18.2% 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 13 through 40
      removed outlier: 3.736A  pdb=" N   LYS A  17 " --> pdb=" O   ARG A  13 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 60
      removed outlier: 3.605A  pdb=" N   ILE A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   VAL A  57 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   GLN A  59 " --> pdb=" O   THR A  55 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   MET A  60 " --> pdb=" O   ILE A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 238
    Processing helix  chain 'A' and resid 252 through 268
      removed outlier: 4.345A  pdb=" N   GLN A 257 " --> pdb=" O   TYR A 253 " (cutoff:3.500A)
      removed outlier: 4.817A  pdb=" N   GLU A 258 " --> pdb=" O   ASN A 254 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ASN A 268 " --> pdb=" O   LYS A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 294
      removed outlier: 3.517A  pdb=" N   LEU A 287 " --> pdb=" O   LYS A 283 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ALA A 293 " --> pdb=" O   GLU A 289 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   GLY A 294 " --> pdb=" O   LYS A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 301
      removed outlier: 3.506A  pdb=" N   ASP A 300 " --> pdb=" O   LYS A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 308
    Processing helix  chain 'A' and resid 321 through 343
      removed outlier: 3.805A  pdb=" N   THR A 325 " --> pdb=" O   ASP A 321 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ARG A 332 " --> pdb=" O   LYS A 328 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   ILE A 338 " --> pdb=" O   GLU A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 381
      removed outlier: 3.811A  pdb=" N   TYR A 381 " --> pdb=" O   HIS A 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 26
      removed outlier: 3.524A  pdb=" N   GLN B  17 " --> pdb=" O   GLN B  13 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.778A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 8 through 23
      removed outlier: 3.771A  pdb=" N   ARG G  13 " --> pdb=" O   ILE G   9 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   LYS G  14 " --> pdb=" O   ALA G  10 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 4.027A  pdb=" N   LEU G  37 " --> pdb=" O   ALA G  33 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.545A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 34 through 52
    Processing helix  chain 'R' and resid 187 through 211
    Processing helix  chain 'R' and resid 217 through 241
      removed outlier: 3.584A  pdb=" N   ILE R 222 " --> pdb=" O   THR R 218 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   HIS R 223 " --> pdb=" O   ARG R 219 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 281 through 285
    Processing helix  chain 'R' and resid 287 through 309
      removed outlier: 3.684A  pdb=" N   ASN R 295 " --> pdb=" O   PHE R 291 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 321 through 328
      removed outlier: 3.541A  pdb=" N   THR R 325 " --> pdb=" O   LEU R 321 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 332 through 345
      removed outlier: 3.511A  pdb=" N   ALA R 337 " --> pdb=" O   ALA R 333 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   VAL R 338 " --> pdb=" O   VAL R 334 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 360 through 391
      Proline residue:  R 366  - end of helix
      removed outlier: 3.645A  pdb=" N   VAL R 384 " --> pdb=" O   ASN R 380 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 399 through 418
      removed outlier: 3.624A  pdb=" N   LEU R 407 " --> pdb=" O   TYR R 403 " (cutoff:3.500A)
      Proline residue:  R 415  - end of helix
    Processing helix  chain 'R' and resid 419 through 423
      removed outlier: 3.833A  pdb=" N   VAL R 423 " --> pdb=" O   HIS R 420 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 443 through 460
      removed outlier: 4.559A  pdb=" N   PHE R 450 " --> pdb=" O   LEU R 446 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   GLY R 452 " --> pdb=" O   ASN R 448 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   PHE R 453 " --> pdb=" O   SER R 449 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   TYR R 459 " --> pdb=" O   VAL R 455 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   CYS R 460 " --> pdb=" O   ALA R 456 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 463 through 477
      removed outlier: 3.653A  pdb=" N   TRP R 477 " --> pdb=" O   SER R 473 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 210
    Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 210
      removed outlier: 6.252A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.315A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.046A  pdb=" N   ASP A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
      removed outlier: 7.063A  pdb=" N   PHE A 280 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 280 " (cutoff:3.500A)
      removed outlier: 6.876A  pdb=" N   ASN A 282 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 282 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.053A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.396A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.097A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.403A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 3.511A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 7.116A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151
      removed outlier: 3.805A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.196A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.792A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.249A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.842A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.101A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.371A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ALA B 203 " --> pdb=" O   SER B 207 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.489A  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: 6.902A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.920A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 7.310A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 5.106A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.391A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.183A  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: 6.255A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.321A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 315 through 320
      removed outlier: 3.537A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 5
    Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12
      removed outlier: 3.515A  pdb=" N   ALA N  92 " --> pdb=" O   VAL N 124 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'R' and resid 127 through 130

    363 hydrogen bonds defined for protein.
    1002 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: 1.13

  Time building geometry restraints manager: 1.03 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1375
        1.32 -     1.45: 2165
        1.45 -     1.58: 4496
        1.58 -     1.71: 0
        1.71 -     1.84: 54
  Bond restraints: 8090
  Sorted by residual:
  bond pdb=" N   VAL R 157 "
       pdb=" CA  VAL R 157 "
    ideal  model  delta    sigma   weight residual
    1.460  1.493 -0.034 7.50e-03 1.78e+04 2.05e+01
  bond pdb=" C   THR B 329 "
       pdb=" O   THR B 329 "
    ideal  model  delta    sigma   weight residual
    1.235  1.188  0.047 1.14e-02 7.69e+03 1.72e+01
  bond pdb=" CG  HIS B 142 "
       pdb=" ND1 HIS B 142 "
    ideal  model  delta    sigma   weight residual
    1.378  1.333  0.045 1.10e-02 8.26e+03 1.70e+01
  bond pdb=" N   VAL N  64 "
       pdb=" CA  VAL N  64 "
    ideal  model  delta    sigma   weight residual
    1.455  1.496 -0.041 1.04e-02 9.25e+03 1.55e+01
  bond pdb=" C   SER R 449 "
       pdb=" O   SER R 449 "
    ideal  model  delta    sigma   weight residual
    1.235  1.186  0.049 1.26e-02 6.30e+03 1.54e+01
  ... (remaining 8085 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.17: 8214
        2.17 -     4.35: 2571
        4.35 -     6.52: 197
        6.52 -     8.69: 8
        8.69 -    10.86: 1
  Bond angle restraints: 10991
  Sorted by residual:
  angle pdb=" CA  ASP B 186 "
        pdb=" CB  ASP B 186 "
        pdb=" CG  ASP B 186 "
      ideal   model   delta    sigma   weight residual
     112.60  118.03   -5.43 1.00e+00 1.00e+00 2.95e+01
  angle pdb=" C   TYR R 211 "
        pdb=" CA  TYR R 211 "
        pdb=" CB  TYR R 211 "
      ideal   model   delta    sigma   weight residual
     111.17  119.09   -7.92 1.53e+00 4.27e-01 2.68e+01
  angle pdb=" N   TYR A 381 "
        pdb=" CA  TYR A 381 "
        pdb=" CB  TYR A 381 "
      ideal   model   delta    sigma   weight residual
     110.35  115.99   -5.64 1.15e+00 7.56e-01 2.41e+01
  angle pdb=" CA  MET R 445 "
        pdb=" C   MET R 445 "
        pdb=" O   MET R 445 "
      ideal   model   delta    sigma   weight residual
     120.70  115.77    4.93 1.03e+00 9.43e-01 2.29e+01
  angle pdb=" N   VAL R 204 "
        pdb=" CA  VAL R 204 "
        pdb=" CB  VAL R 204 "
      ideal   model   delta    sigma   weight residual
     110.55  116.05   -5.50 1.17e+00 7.31e-01 2.21e+01
  ... (remaining 10986 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.21: 4229
       17.21 -    34.41: 431
       34.41 -    51.62: 91
       51.62 -    68.83: 24
       68.83 -    86.03: 8
  Dihedral angle restraints: 4783
    sinusoidal: 1712
      harmonic: 3071
  Sorted by residual:
  dihedral pdb=" CA  TYR R 429 "
           pdb=" C   TYR R 429 "
           pdb=" N   THR R 430 "
           pdb=" CA  THR R 430 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.28   24.72     0      5.00e+00 4.00e-02 2.44e+01
  dihedral pdb=" CA  THR A 359 "
           pdb=" C   THR A 359 "
           pdb=" N   GLU A 360 "
           pdb=" CA  GLU A 360 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.19  -23.81     0      5.00e+00 4.00e-02 2.27e+01
  dihedral pdb=" CA  PHE B 278 "
           pdb=" C   PHE B 278 "
           pdb=" N   SER B 279 "
           pdb=" CA  SER B 279 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.08   22.92     0      5.00e+00 4.00e-02 2.10e+01
  ... (remaining 4780 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 680
       0.069 -    0.137: 412
       0.137 -    0.206: 149
       0.206 -    0.274: 24
       0.274 -    0.343: 3
  Chirality restraints: 1268
  Sorted by residual:
  chirality pdb=" CA  ILE N  51 "
            pdb=" N   ILE N  51 "
            pdb=" C   ILE N  51 "
            pdb=" CB  ILE N  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.78   -0.34 2.00e-01 2.50e+01 2.94e+00
  chirality pdb=" CB  VAL A 324 "
            pdb=" CA  VAL A 324 "
            pdb=" CG1 VAL A 324 "
            pdb=" CG2 VAL A 324 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.35   -0.28 2.00e-01 2.50e+01 1.98e+00
  chirality pdb=" CB  VAL B 200 "
            pdb=" CA  VAL B 200 "
            pdb=" CG1 VAL B 200 "
            pdb=" CG2 VAL B 200 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.35   -0.28 2.00e-01 2.50e+01 1.91e+00
  ... (remaining 1265 not shown)

  Planarity restraints: 1418
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP R 298 "    0.048 2.00e-02 2.50e+03   2.65e-02 1.76e+01
        pdb=" CG  TRP R 298 "   -0.063 2.00e-02 2.50e+03
        pdb=" CD1 TRP R 298 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 TRP R 298 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP R 298 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP R 298 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE3 TRP R 298 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ2 TRP R 298 "    0.018 2.00e-02 2.50e+03
        pdb=" CZ3 TRP R 298 "   -0.008 2.00e-02 2.50e+03
        pdb=" CH2 TRP R 298 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 378 "   -0.017 2.00e-02 2.50e+03   3.60e-02 1.30e+01
        pdb=" C   LEU A 378 "    0.062 2.00e-02 2.50e+03
        pdb=" O   LEU A 378 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   ARG A 379 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 105 "    0.034 2.00e-02 2.50e+03   2.53e-02 1.28e+01
        pdb=" CG  TYR B 105 "    0.017 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 105 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 105 "   -0.027 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 105 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 105 "   -0.019 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 105 "    0.010 2.00e-02 2.50e+03
        pdb=" OH  TYR B 105 "    0.032 2.00e-02 2.50e+03
  ... (remaining 1415 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 290
        2.71 -     3.25: 7979
        3.25 -     3.80: 12603
        3.80 -     4.35: 16517
        4.35 -     4.90: 26859
  Nonbonded interactions: 64248
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 215 "
            pdb=" NH1 ARG A 363 "
     model   vdw
     2.158 3.120
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" O   TYR R 305 "
            pdb=" OG  SER R 308 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" OG  SER N  52 "
            pdb=" OG  SER N  57 "
     model   vdw
     2.376 3.040
  ... (remaining 64243 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.200
  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:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.670
  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:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7343
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      :  0.014   0.082   8092  Z= 1.009
  Angle     :  1.882  10.863  10995  Z= 1.361
  Chirality :  0.092   0.343   1268
  Planarity :  0.008   0.038   1418
  Dihedral  : 15.541  86.034   2785
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.45 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  :  8.13 %
    Favored  : 88.06 %
  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 are not related in a simple way.
  whole: -1.84 (0.24), residues: 1033
  helix: -0.35 (0.25), residues: 348
  sheet: -1.73 (0.33), residues: 186
  loop : -1.59 (0.26), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.024   0.003   ARG N  67 
 TYR   0.038   0.009   TYR A 381 
 PHE   0.043   0.007   PHE R 238 
 TRP   0.063   0.009   TRP R 298 
 HIS   0.021   0.006   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.01398 ( 8090)
  covalent geometry    : angle       1.87905 (10991)
  SS BOND              : bond        0.05789 (    2)
  SS BOND              : angle       5.70452 (    4)
  hydrogen bonds       : bond        0.25576 (  359)
  hydrogen bonds       : angle       8.35887 ( 1002)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 208
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8624 (tm-30)
REVERT: A   56 ILE cc_start: 0.8423 (mt) cc_final: 0.8003 (mt)
REVERT: A   60 MET cc_start: 0.7060 (mpp) cc_final: 0.5341 (mtm)
REVERT: A  379 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.8003 (ptm-80)
REVERT: B   52 ARG cc_start: 0.7454 (ttm-80) cc_final: 0.7186 (mtp-110)
REVERT: B   68 ARG cc_start: 0.8631 (ttt-90) cc_final: 0.8293 (ttt90)
REVERT: B   75 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8453 (mt0)
REVERT: B  111 TYR cc_start: 0.8784 (m-80) cc_final: 0.8556 (m-80)
REVERT: B  130 GLU cc_start: 0.4808 (pt0) cc_final: 0.4561 (pt0)
REVERT: B  137 ARG cc_start: 0.6309 (mmm-85) cc_final: 0.5991 (mmt90)
REVERT: B  145 TYR cc_start: 0.8242 (p90) cc_final: 0.7926 (p90)
REVERT: B  172 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7447 (mm-30)
REVERT: B  217 MET cc_start: 0.7587 (tpp) cc_final: 0.7123 (tmm)
REVERT: B  255 LEU cc_start: 0.8073 (mt) cc_final: 0.7829 (tt)
REVERT: B  284 LEU cc_start: 0.9171 (mt) cc_final: 0.8965 (mt)
REVERT: B  325 MET cc_start: 0.6982 (mmp) cc_final: 0.6487 (mtt)
REVERT: G   11 GLN cc_start: 0.6607 (OUTLIER) cc_final: 0.6373 (pp30)
REVERT: G   61 PHE cc_start: 0.7397 (m-80) cc_final: 0.7154 (m-80)
REVERT: N   19 ARG cc_start: 0.6915 (ttm-80) cc_final: 0.6619 (ttm-80)
REVERT: N   32 TYR cc_start: 0.8628 (m-80) cc_final: 0.8402 (m-10)
REVERT: N   34 MET cc_start: 0.8790 (mpp) cc_final: 0.8357 (mmm)
REVERT: N   47 TRP cc_start: 0.7729 (t60) cc_final: 0.6341 (t60)
REVERT: N   61 THR cc_start: 0.7940 (t) cc_final: 0.7409 (t)
REVERT: N   73 ASP cc_start: 0.8486 (t70) cc_final: 0.8087 (t70)
REVERT: N   82 GLN cc_start: 0.8475 (tm-30) cc_final: 0.7864 (tp-100)
REVERT: N   83 MET cc_start: 0.8259 (mpp) cc_final: 0.7507 (mpp)
REVERT: N   89 GLU cc_start: 0.8793 (tt0) cc_final: 0.8162 (mp0)
REVERT: R  219 ARG cc_start: 0.7550 (tmm160) cc_final: 0.7191 (ptt90)
REVERT: R  302 GLU cc_start: 0.8451 (tm-30) cc_final: 0.7876 (tp30)
REVERT: R  339 TRP cc_start: 0.6908 (t60) cc_final: 0.6518 (t60)
REVERT: R  371 ILE cc_start: 0.8308 (mm) cc_final: 0.7767 (mt)
REVERT: R  383 ARG cc_start: 0.8467 (tmm-80) cc_final: 0.8164 (ttp-170)
REVERT: R  401 GLN cc_start: 0.8086 (mm-40) cc_final: 0.7574 (mp10)
REVERT: R  404 ARG cc_start: 0.8103 (ttp80) cc_final: 0.7668 (tpt90)
REVERT: R  405 LYS cc_start: 0.7903 (tppp) cc_final: 0.7531 (tppt)
REVERT: R  422 ILE cc_start: 0.8595 (tp) cc_final: 0.8311 (mm)
REVERT: R  444 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8299 (mm-30)
REVERT: R  448 ASN cc_start: 0.8129 (m-40) cc_final: 0.7904 (m110)
  outliers start: 30
  outliers final: 11
  residues processed: 232
  average time/residue: 0.0931
  time to fit residues: 28.5611
Evaluate side-chains
  156 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 142
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    5.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    6.9990
   overall best weight:    3.5388

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
A 257 GLN
A 261 ASN
** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 176 GLN
G  44 HIS
N  31 ASN
N  84 ASN
** R 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 307 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.110309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.094809 restraints weight = 20489.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.096461 restraints weight = 13850.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.097597 restraints weight = 10382.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.098037 restraints weight = 8447.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.098613 restraints weight = 7582.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6971
moved from start:          0.2538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   8092  Z= 0.213
  Angle     :  0.697   8.174  10995  Z= 0.370
  Chirality :  0.046   0.170   1268
  Planarity :  0.005   0.078   1418
  Dihedral  :  4.720  24.836   1135
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 12.53
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.48 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  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 are not related in a simple way.
  whole: -0.76 (0.25), residues: 1033
  helix:  0.67 (0.26), residues: 357
  sheet: -1.48 (0.31), residues: 221
  loop : -0.83 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG N  98 
 TYR   0.056   0.003   TYR B  59 
 PHE   0.029   0.003   PHE R 230 
 TRP   0.019   0.002   TRP A 234 
 HIS   0.007   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 ( 8090)
  covalent geometry    : angle       0.69658 (10991)
  SS BOND              : bond        0.00704 (    2)
  SS BOND              : angle       1.82331 (    4)
  hydrogen bonds       : bond        0.05628 (  359)
  hydrogen bonds       : angle       5.23935 ( 1002)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
REVERT: A  304 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6500 (pm20)
REVERT: B   61 MET cc_start: 0.8557 (ppp) cc_final: 0.8241 (ppp)
REVERT: B   75 GLN cc_start: 0.7342 (mt0) cc_final: 0.6703 (pp30)
REVERT: B  145 TYR cc_start: 0.8335 (p90) cc_final: 0.8062 (p90)
REVERT: N    1 GLN cc_start: 0.6657 (pm20) cc_final: 0.6331 (tp40)
REVERT: N   47 TRP cc_start: 0.7434 (t60) cc_final: 0.7234 (t60)
REVERT: R  219 ARG cc_start: 0.7559 (tmm160) cc_final: 0.7152 (ptt90)
REVERT: R  376 ILE cc_start: 0.8881 (mt) cc_final: 0.8596 (tt)
REVERT: R  383 ARG cc_start: 0.8249 (tmm-80) cc_final: 0.7995 (ttp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.0849
  time to fit residues: 20.0715
Evaluate side-chains
  122 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 90 optimal weight:    6.9990
   chunk 78 optimal weight:   20.0000
   chunk 44 optimal weight:    5.9990
   chunk 34 optimal weight:    0.7980
   chunk 85 optimal weight:    0.0870
   chunk 11 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 76 optimal weight:    7.9990
   chunk 3 optimal weight:    6.9990
   chunk 59 optimal weight:    0.0670
   overall best weight:    0.5900

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 367 ASN
B  91 HIS
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 295 ASN
G  18 GLN
** R 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 295 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.114112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.098893 restraints weight = 20094.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.100597 restraints weight = 13427.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.101457 restraints weight = 9956.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 54)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.102590 restraints weight = 8256.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.103171 restraints weight = 6959.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6849
moved from start:          0.3173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8092  Z= 0.126
  Angle     :  0.585   8.907  10995  Z= 0.307
  Chirality :  0.043   0.173   1268
  Planarity :  0.004   0.054   1418
  Dihedral  :  4.275  19.384   1135
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.19 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  2.92 %
    Favored  : 96.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.23 (0.26), residues: 1033
  helix:  1.21 (0.27), residues: 363
  sheet: -0.99 (0.33), residues: 222
  loop : -0.75 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  68 
 TYR   0.027   0.002   TYR A 381 
 PHE   0.039   0.002   PHE R 238 
 TRP   0.032   0.002   TRP R 339 
 HIS   0.006   0.001   HIS R 420 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 8090)
  covalent geometry    : angle       0.58458 (10991)
  SS BOND              : bond        0.00358 (    2)
  SS BOND              : angle       1.10292 (    4)
  hydrogen bonds       : bond        0.04653 (  359)
  hydrogen bonds       : angle       4.69273 ( 1002)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 183
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  302 PHE cc_start: 0.6015 (m-80) cc_final: 0.5725 (m-10)
REVERT: A  378 LEU cc_start: 0.8694 (mt) cc_final: 0.8437 (mt)
REVERT: B   61 MET cc_start: 0.8403 (ppp) cc_final: 0.8150 (ppp)
REVERT: B   75 GLN cc_start: 0.7182 (mt0) cc_final: 0.6596 (pp30)
REVERT: B  111 TYR cc_start: 0.6805 (m-80) cc_final: 0.6596 (m-80)
REVERT: N   47 TRP cc_start: 0.7312 (t60) cc_final: 0.6986 (t60)
REVERT: N  109 ASP cc_start: 0.6258 (m-30) cc_final: 0.5529 (p0)
REVERT: R  219 ARG cc_start: 0.7630 (tmm160) cc_final: 0.7342 (ptt90)
REVERT: R  339 TRP cc_start: 0.7041 (t60) cc_final: 0.6628 (t60)
REVERT: R  376 ILE cc_start: 0.8827 (mt) cc_final: 0.8570 (tt)
REVERT: R  383 ARG cc_start: 0.8234 (tmm-80) cc_final: 0.7984 (ttp-170)
REVERT: R  405 LYS cc_start: 0.8261 (tppp) cc_final: 0.7910 (tppt)
REVERT: R  448 ASN cc_start: 0.7195 (m-40) cc_final: 0.6950 (m110)
  outliers start: 1
  outliers final: 1
  residues processed: 184
  average time/residue: 0.0836
  time to fit residues: 21.0294
Evaluate side-chains
  134 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 133
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 52 optimal weight:    9.9990
   chunk 49 optimal weight:    2.9990
   chunk 44 optimal weight:    7.9990
   chunk 39 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 29 optimal weight:    7.9990
   chunk 33 optimal weight:    8.9990
   chunk 51 optimal weight:    5.9990
   chunk 27 optimal weight:   10.0000
   chunk 91 optimal weight:    0.7980
   chunk 96 optimal weight:    5.9990
   overall best weight:    4.7588

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 295 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.108184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.093177 restraints weight = 21083.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.094740 restraints weight = 14208.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.095704 restraints weight = 10676.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.096624 restraints weight = 8762.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.097038 restraints weight = 7480.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7025
moved from start:          0.3828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   8092  Z= 0.251
  Angle     :  0.733  10.011  10995  Z= 0.385
  Chirality :  0.048   0.251   1268
  Planarity :  0.005   0.052   1418
  Dihedral  :  4.981  28.335   1135
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 16.10
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.87 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  6.35 %
    Favored  : 93.52 %
  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 are not related in a simple way.
  whole: -0.59 (0.25), residues: 1033
  helix:  0.76 (0.26), residues: 360
  sheet: -1.07 (0.33), residues: 221
  loop : -0.87 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 307 
 TYR   0.020   0.002   TYR B 111 
 PHE   0.023   0.003   PHE B 234 
 TRP   0.027   0.003   TRP R 339 
 HIS   0.010   0.001   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00563 ( 8090)
  covalent geometry    : angle       0.73109 (10991)
  SS BOND              : bond        0.00581 (    2)
  SS BOND              : angle       2.64210 (    4)
  hydrogen bonds       : bond        0.05117 (  359)
  hydrogen bonds       : angle       4.91245 ( 1002)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 145
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  304 GLU cc_start: 0.7270 (mm-30) cc_final: 0.6513 (tm-30)
REVERT: B   19 ARG cc_start: 0.6748 (mtm-85) cc_final: 0.6378 (mtm-85)
REVERT: B   61 MET cc_start: 0.8656 (ppp) cc_final: 0.8446 (ppp)
REVERT: B  284 LEU cc_start: 0.7981 (mt) cc_final: 0.7692 (mt)
REVERT: B  300 LEU cc_start: 0.7699 (mm) cc_final: 0.7413 (mm)
REVERT: G   27 ARG cc_start: 0.7066 (mtm-85) cc_final: 0.6797 (mtm-85)
REVERT: R  215 LEU cc_start: 0.6986 (pt) cc_final: 0.6719 (pt)
REVERT: R  219 ARG cc_start: 0.7702 (tmm160) cc_final: 0.7398 (ptt90)
REVERT: R  376 ILE cc_start: 0.8954 (mt) cc_final: 0.8671 (tt)
REVERT: R  383 ARG cc_start: 0.8430 (tmm-80) cc_final: 0.7738 (ptt90)
  outliers start: 1
  outliers final: 1
  residues processed: 146
  average time/residue: 0.0867
  time to fit residues: 17.3350
Evaluate side-chains
  117 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 116
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 21 optimal weight:    3.9990
   chunk 13 optimal weight:   10.0000
   chunk 79 optimal weight:   20.0000
   chunk 12 optimal weight:    0.9990
   chunk 64 optimal weight:    6.9990
   chunk 68 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   chunk 87 optimal weight:    6.9990
   chunk 84 optimal weight:    0.9990
   overall best weight:    2.1388

-------------------------------------------------------------------------------
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**
A 268 ASN
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N   5 GLN
** R 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 295 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.111668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.096676 restraints weight = 20418.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.098358 restraints weight = 13649.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.099348 restraints weight = 10196.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.100265 restraints weight = 8324.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.100588 restraints weight = 7121.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6928
moved from start:          0.3988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8092  Z= 0.149
  Angle     :  0.616   9.123  10995  Z= 0.321
  Chirality :  0.043   0.154   1268
  Planarity :  0.004   0.049   1418
  Dihedral  :  4.574  27.491   1135
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 13.25
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.78 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  2.67 %
    Favored  : 97.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.36 (0.26), residues: 1033
  helix:  1.09 (0.27), residues: 360
  sheet: -1.05 (0.32), residues: 231
  loop : -0.79 (0.30), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 307 
 TYR   0.021   0.002   TYR B  59 
 PHE   0.032   0.002   PHE R 238 
 TRP   0.026   0.002   TRP R 339 
 HIS   0.005   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 8090)
  covalent geometry    : angle       0.61473 (10991)
  SS BOND              : bond        0.00673 (    2)
  SS BOND              : angle       2.03572 (    4)
  hydrogen bonds       : bond        0.04352 (  359)
  hydrogen bonds       : angle       4.59218 ( 1002)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 154
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
REVERT: A  304 GLU cc_start: 0.7242 (mm-30) cc_final: 0.6559 (pm20)
REVERT: B  300 LEU cc_start: 0.7485 (mm) cc_final: 0.7094 (mm)
REVERT: R  219 ARG cc_start: 0.7628 (tmm160) cc_final: 0.7196 (ptt90)
REVERT: R  339 TRP cc_start: 0.6891 (t60) cc_final: 0.6577 (t60)
REVERT: R  376 ILE cc_start: 0.8916 (mt) cc_final: 0.8626 (tt)
REVERT: R  383 ARG cc_start: 0.8453 (tmm-80) cc_final: 0.7759 (ptt90)
REVERT: R  405 LYS cc_start: 0.8240 (tppp) cc_final: 0.7870 (tppt)
  outliers start: 1
  outliers final: 0
  residues processed: 154
  average time/residue: 0.0824
  time to fit residues: 17.5195
Evaluate side-chains
  116 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 33 optimal weight:   10.0000
   chunk 75 optimal weight:    4.9990
   chunk 15 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 95 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 56 optimal weight:    0.3980
   chunk 32 optimal weight:    0.1980
   chunk 25 optimal weight:    6.9990
   chunk 27 optimal weight:    9.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N   5 GLN
N  13 GLN
** R 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 295 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.112746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.097985 restraints weight = 20136.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.099661 restraints weight = 13334.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.100795 restraints weight = 9853.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.101628 restraints weight = 7938.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.101869 restraints weight = 6778.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6902
moved from start:          0.4153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8092  Z= 0.130
  Angle     :  0.592   9.430  10995  Z= 0.306
  Chirality :  0.043   0.180   1268
  Planarity :  0.004   0.044   1418
  Dihedral  :  4.429  26.688   1135
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  1.91 %
    Favored  : 97.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.14 (0.26), residues: 1033
  helix:  1.39 (0.28), residues: 353
  sheet: -0.94 (0.31), residues: 236
  loop : -0.75 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 404 
 TYR   0.028   0.002   TYR A 381 
 PHE   0.014   0.002   PHE B 234 
 TRP   0.020   0.002   TRP R 339 
 HIS   0.005   0.001   HIS R 420 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 8090)
  covalent geometry    : angle       0.59081 (10991)
  SS BOND              : bond        0.00547 (    2)
  SS BOND              : angle       1.73055 (    4)
  hydrogen bonds       : bond        0.04074 (  359)
  hydrogen bonds       : angle       4.40392 ( 1002)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 154
  time to evaluate  : 0.279 
Fit side-chains
REVERT: A  304 GLU cc_start: 0.7067 (mm-30) cc_final: 0.6579 (pm20)
REVERT: B   75 GLN cc_start: 0.7201 (mt0) cc_final: 0.6252 (pp30)
REVERT: B  300 LEU cc_start: 0.7512 (mm) cc_final: 0.7108 (mm)
REVERT: N   39 GLN cc_start: 0.6483 (tp40) cc_final: 0.6053 (tt0)
REVERT: R  215 LEU cc_start: 0.6764 (pt) cc_final: 0.6410 (pt)
REVERT: R  219 ARG cc_start: 0.7621 (tmm160) cc_final: 0.7255 (ptt90)
REVERT: R  376 ILE cc_start: 0.8898 (mt) cc_final: 0.8664 (tt)
REVERT: R  383 ARG cc_start: 0.8425 (tmm-80) cc_final: 0.7783 (ptt90)
REVERT: R  404 ARG cc_start: 0.7684 (ttp80) cc_final: 0.7475 (ttp80)
REVERT: R  405 LYS cc_start: 0.8169 (tppp) cc_final: 0.7922 (tptm)
  outliers start: 1
  outliers final: 0
  residues processed: 154
  average time/residue: 0.0872
  time to fit residues: 18.3319
Evaluate side-chains
  118 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 99 optimal weight:    7.9990
   chunk 49 optimal weight:    0.9990
   chunk 52 optimal weight:    0.2980
   chunk 83 optimal weight:   10.0000
   chunk 7 optimal weight:    6.9990
   chunk 14 optimal weight:    3.9990
   chunk 10 optimal weight:    0.5980
   chunk 55 optimal weight:    8.9990
   chunk 45 optimal weight:    5.9990
   chunk 58 optimal weight:    8.9990
   chunk 40 optimal weight:    8.9990
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 380 GLN
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 156 GLN
N   5 GLN
** R 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 295 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.112558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.097541 restraints weight = 20546.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.099190 restraints weight = 13685.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.100380 restraints weight = 10154.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.101093 restraints weight = 8144.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.101717 restraints weight = 7016.239|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6927
moved from start:          0.4326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8092  Z= 0.151
  Angle     :  0.608   8.701  10995  Z= 0.317
  Chirality :  0.043   0.184   1268
  Planarity :  0.004   0.041   1418
  Dihedral  :  4.499  28.489   1135
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  1.52 %
    Favored  : 98.35 %
  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 are not related in a simple way.
  whole: -0.14 (0.26), residues: 1033
  helix:  1.37 (0.28), residues: 357
  sheet: -0.85 (0.33), residues: 224
  loop : -0.82 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG R 404 
 TYR   0.026   0.002   TYR A 381 
 PHE   0.014   0.002   PHE B 234 
 TRP   0.030   0.002   TRP R 339 
 HIS   0.005   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 8090)
  covalent geometry    : angle       0.60698 (10991)
  SS BOND              : bond        0.00543 (    2)
  SS BOND              : angle       1.56972 (    4)
  hydrogen bonds       : bond        0.04110 (  359)
  hydrogen bonds       : angle       4.40508 ( 1002)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 146
  time to evaluate  : 0.309 
Fit side-chains
REVERT: A   34 LYS cc_start: 0.7781 (tptt) cc_final: 0.7510 (tptt)
REVERT: B  300 LEU cc_start: 0.7751 (mm) cc_final: 0.7406 (mm)
REVERT: B  325 MET cc_start: 0.6529 (mtp) cc_final: 0.6108 (mpp)
REVERT: N   47 TRP cc_start: 0.7336 (t60) cc_final: 0.7068 (t60)
REVERT: R  215 LEU cc_start: 0.6949 (pt) cc_final: 0.6630 (pt)
REVERT: R  219 ARG cc_start: 0.7634 (tmm160) cc_final: 0.7386 (ptt90)
REVERT: R  339 TRP cc_start: 0.7390 (t60) cc_final: 0.7118 (t60)
REVERT: R  376 ILE cc_start: 0.8908 (mt) cc_final: 0.8610 (tt)
REVERT: R  405 LYS cc_start: 0.8236 (tppp) cc_final: 0.7849 (tppt)
  outliers start: 1
  outliers final: 0
  residues processed: 146
  average time/residue: 0.0812
  time to fit residues: 16.7142
Evaluate side-chains
  118 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 25 optimal weight:    9.9990
   chunk 43 optimal weight:    3.9990
   chunk 22 optimal weight:   10.0000
   chunk 9 optimal weight:    0.0970
   chunk 7 optimal weight:    3.9990
   chunk 79 optimal weight:    0.0770
   chunk 28 optimal weight:    6.9990
   chunk 18 optimal weight:    6.9990
   chunk 83 optimal weight:    1.9990
   chunk 61 optimal weight:    9.9990
   chunk 39 optimal weight:    5.9990
   overall best weight:    2.0342

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 380 GLN
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N   5 GLN
** R 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 295 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.112914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.097839 restraints weight = 20434.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.099482 restraints weight = 13690.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.100660 restraints weight = 10219.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.101398 restraints weight = 8249.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.102106 restraints weight = 7102.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.3653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6911
moved from start:          0.4483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8092  Z= 0.141
  Angle     :  0.600   8.743  10995  Z= 0.313
  Chirality :  0.043   0.191   1268
  Planarity :  0.004   0.044   1418
  Dihedral  :  4.494  29.364   1135
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.38 %
    Favored  : 99.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.09 (0.26), residues: 1033
  helix:  1.37 (0.28), residues: 358
  sheet: -0.70 (0.33), residues: 223
  loop : -0.81 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG B 314 
 TYR   0.015   0.001   TYR N  95 
 PHE   0.012   0.002   PHE N  27 
 TRP   0.027   0.002   TRP R 339 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 8090)
  covalent geometry    : angle       0.59965 (10991)
  SS BOND              : bond        0.00551 (    2)
  SS BOND              : angle       1.56098 (    4)
  hydrogen bonds       : bond        0.04028 (  359)
  hydrogen bonds       : angle       4.38245 ( 1002)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 145
  time to evaluate  : 0.287 
Fit side-chains
REVERT: B   32 GLN cc_start: 0.6913 (pm20) cc_final: 0.6134 (pp30)
REVERT: B   59 TYR cc_start: 0.7417 (m-80) cc_final: 0.7119 (m-80)
REVERT: B   75 GLN cc_start: 0.7111 (mt0) cc_final: 0.5693 (mt0)
REVERT: B  300 LEU cc_start: 0.7746 (mm) cc_final: 0.7433 (mm)
REVERT: B  325 MET cc_start: 0.6515 (mtp) cc_final: 0.6127 (mpp)
REVERT: N   47 TRP cc_start: 0.7324 (t60) cc_final: 0.7078 (t60)
REVERT: R  215 LEU cc_start: 0.6896 (pt) cc_final: 0.6595 (pt)
REVERT: R  219 ARG cc_start: 0.7591 (tmm160) cc_final: 0.7136 (ptt90)
REVERT: R  339 TRP cc_start: 0.7407 (t60) cc_final: 0.7135 (t60)
REVERT: R  376 ILE cc_start: 0.8867 (mt) cc_final: 0.8614 (tt)
REVERT: R  405 LYS cc_start: 0.8152 (tppp) cc_final: 0.7858 (tppt)
  outliers start: 1
  outliers final: 0
  residues processed: 145
  average time/residue: 0.0830
  time to fit residues: 16.8245
Evaluate side-chains
  118 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 69 optimal weight:   10.0000
   chunk 29 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   chunk 71 optimal weight:    6.9990
   chunk 48 optimal weight:    5.9990
   chunk 56 optimal weight:    9.9990
   chunk 17 optimal weight:    0.8980
   chunk 85 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 55 optimal weight:    6.9990
   overall best weight:    3.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N   5 GLN
** R 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 295 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.110908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.095879 restraints weight = 20627.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.097493 restraints weight = 13945.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.098493 restraints weight = 10433.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.099377 restraints weight = 8540.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.099815 restraints weight = 7304.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6963
moved from start:          0.4605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8092  Z= 0.186
  Angle     :  0.655   8.669  10995  Z= 0.345
  Chirality :  0.045   0.208   1268
  Planarity :  0.004   0.043   1418
  Dihedral  :  4.749  34.168   1135
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 13.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  1.52 %
    Favored  : 98.35 %
  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 are not related in a simple way.
  whole: -0.22 (0.26), residues: 1033
  helix:  1.36 (0.28), residues: 353
  sheet: -0.79 (0.33), residues: 228
  loop : -0.96 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG R 404 
 TYR   0.015   0.002   TYR N  95 
 PHE   0.015   0.002   PHE B 234 
 TRP   0.038   0.003   TRP B  63 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 ( 8090)
  covalent geometry    : angle       0.65466 (10991)
  SS BOND              : bond        0.00651 (    2)
  SS BOND              : angle       1.77548 (    4)
  hydrogen bonds       : bond        0.04277 (  359)
  hydrogen bonds       : angle       4.49793 ( 1002)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 145
  time to evaluate  : 0.307 
Fit side-chains
REVERT: B   32 GLN cc_start: 0.7053 (pm20) cc_final: 0.6164 (pp30)
REVERT: B   59 TYR cc_start: 0.7472 (m-80) cc_final: 0.7180 (m-80)
REVERT: B   75 GLN cc_start: 0.7230 (mt0) cc_final: 0.6948 (mt0)
REVERT: B  145 TYR cc_start: 0.8336 (p90) cc_final: 0.8089 (p90)
REVERT: B  300 LEU cc_start: 0.7798 (mm) cc_final: 0.7478 (mm)
REVERT: B  325 MET cc_start: 0.6463 (mtp) cc_final: 0.6088 (mpp)
REVERT: N   91 THR cc_start: 0.7028 (p) cc_final: 0.6731 (p)
REVERT: R  215 LEU cc_start: 0.6974 (pt) cc_final: 0.6638 (pt)
REVERT: R  219 ARG cc_start: 0.7727 (tmm160) cc_final: 0.7269 (ptt90)
REVERT: R  339 TRP cc_start: 0.7477 (t60) cc_final: 0.7152 (t60)
REVERT: R  376 ILE cc_start: 0.8896 (mt) cc_final: 0.8667 (tt)
REVERT: R  422 ILE cc_start: 0.7801 (mm) cc_final: 0.7551 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 145
  average time/residue: 0.0783
  time to fit residues: 16.1614
Evaluate side-chains
  115 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 66 optimal weight:    6.9990
   chunk 48 optimal weight:    3.9990
   chunk 61 optimal weight:   20.0000
   chunk 31 optimal weight:    0.8980
   chunk 57 optimal weight:    0.8980
   chunk 91 optimal weight:    6.9990
   chunk 25 optimal weight:   10.0000
   chunk 98 optimal weight:    0.9990
   chunk 81 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N   5 GLN
** R 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 295 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.113742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.098777 restraints weight = 20249.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.100460 restraints weight = 13405.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.101739 restraints weight = 9937.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.102348 restraints weight = 7942.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.103069 restraints weight = 6945.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6884
moved from start:          0.4742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8092  Z= 0.132
  Angle     :  0.627   8.832  10995  Z= 0.327
  Chirality :  0.043   0.199   1268
  Planarity :  0.004   0.042   1418
  Dihedral  :  4.594  32.979   1135
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 12.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.25 %
    Favored  : 99.62 %
  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 are not related in a simple way.
  whole: -0.14 (0.26), residues: 1033
  helix:  1.43 (0.28), residues: 358
  sheet: -0.69 (0.33), residues: 224
  loop : -0.98 (0.30), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG R 404 
 TYR   0.026   0.002   TYR A 381 
 PHE   0.014   0.002   PHE N  27 
 TRP   0.031   0.003   TRP B  63 
 HIS   0.004   0.001   HIS R 420 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 8090)
  covalent geometry    : angle       0.62633 (10991)
  SS BOND              : bond        0.00594 (    2)
  SS BOND              : angle       1.46934 (    4)
  hydrogen bonds       : bond        0.04046 (  359)
  hydrogen bonds       : angle       4.41098 ( 1002)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 150
  time to evaluate  : 0.331 
Fit side-chains
REVERT: B  145 TYR cc_start: 0.8245 (p90) cc_final: 0.7964 (p90)
REVERT: B  284 LEU cc_start: 0.7949 (mt) cc_final: 0.7414 (mt)
REVERT: B  300 LEU cc_start: 0.7731 (mm) cc_final: 0.7405 (mm)
REVERT: B  325 MET cc_start: 0.6515 (mtp) cc_final: 0.6039 (mpp)
REVERT: N   91 THR cc_start: 0.7122 (p) cc_final: 0.6886 (p)
REVERT: N  117 TYR cc_start: 0.6307 (m-80) cc_final: 0.4931 (m-80)
REVERT: R  215 LEU cc_start: 0.6982 (pt) cc_final: 0.6700 (pt)
REVERT: R  219 ARG cc_start: 0.7755 (tmm160) cc_final: 0.7217 (ptt90)
REVERT: R  339 TRP cc_start: 0.7422 (t60) cc_final: 0.7080 (t60)
REVERT: R  376 ILE cc_start: 0.8884 (mt) cc_final: 0.8608 (tt)
REVERT: R  405 LYS cc_start: 0.8150 (tppp) cc_final: 0.7770 (tppt)
REVERT: R  422 ILE cc_start: 0.7682 (mm) cc_final: 0.7440 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 150
  average time/residue: 0.0737
  time to fit residues: 15.8636
Evaluate side-chains
  112 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 93 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 76 optimal weight:    8.9990
   chunk 8 optimal weight:    0.6980
   chunk 87 optimal weight:    1.9990
   chunk 72 optimal weight:    5.9990
   chunk 96 optimal weight:    6.9990
   chunk 44 optimal weight:    0.4980
   chunk 10 optimal weight:    1.9990
   chunk 92 optimal weight:    7.9990
   chunk 77 optimal weight:    0.7980
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N   5 GLN
** R 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 295 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.114247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.099430 restraints weight = 20226.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.101143 restraints weight = 13365.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.102363 restraints weight = 9875.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.103075 restraints weight = 7929.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.103836 restraints weight = 6855.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6863
moved from start:          0.4808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8092  Z= 0.124
  Angle     :  0.609   8.631  10995  Z= 0.318
  Chirality :  0.042   0.196   1268
  Planarity :  0.004   0.041   1418
  Dihedral  :  4.469  30.641   1135
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.13 %
    Favored  : 99.75 %
  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 are not related in a simple way.
  whole:  0.04 (0.27), residues: 1033
  helix:  1.57 (0.28), residues: 359
  sheet: -0.62 (0.33), residues: 228
  loop : -0.86 (0.31), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG R 404 
 TYR   0.026   0.002   TYR A 381 
 PHE   0.011   0.001   PHE N  27 
 TRP   0.029   0.002   TRP B  63 
 HIS   0.005   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 8090)
  covalent geometry    : angle       0.60882 (10991)
  SS BOND              : bond        0.00563 (    2)
  SS BOND              : angle       1.39699 (    4)
  hydrogen bonds       : bond        0.03913 (  359)
  hydrogen bonds       : angle       4.30853 ( 1002)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1257.00 seconds
wall clock time: 22 minutes 27.06 seconds (1347.06 seconds total)