Starting phenix.real_space_refine
on Wed Mar 12 12:01:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vvo_32146/03_2025/7vvo_32146.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vvo_32146/03_2025/7vvo_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_2025/7vvo_32146.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vvo_32146/03_2025/7vvo_32146.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vvo_32146/03_2025/7vvo_32146.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vvo_32146/03_2025/7vvo_32146.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'PHE:plan': 1, 'ARG:plan': 2}
          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: {'GLN:plan1': 2, 'ASN%COO:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 3}
          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: {'GLN:plan1': 3, 'HIS:plan': 5, 'TYR:plan': 9, 'ASN:plan1': 5, 'TRP:plan': 5, 'ASP:plan': 4, 'PHE:plan': 7, 'GLU:plan': 7, 'ARG:plan': 12}
          Unresolved non-hydrogen planarities: 302
  Time building chain proxies: 4.61, per 1000 atoms: 0.58
  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: 1.75
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 0.91
  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: 2.11

  Time building geometry restraints manager: 2.10 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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     20.770
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.580
-------------------------------------------------------------------------------
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   0.073   8090  Z= 0.924
  Angle     :  1.879  10.863  10991  Z= 1.360
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.84 (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
 TRP   0.063   0.009   TRP R 298 
 HIS   0.021   0.006   HIS B  54 
 PHE   0.043   0.007   PHE R 238 
 TYR   0.038   0.009   TYR A 381 
 ARG   0.024   0.003   ARG N  67 

*********************** 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  : 0.866 
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: 0.8004 (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: 0.8810 (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: 0.2263
  time to fit residues: 69.2560
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  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 78 optimal weight:   40.0000
   chunk 43 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 41 optimal weight:    7.9990
   chunk 80 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   chunk 60 optimal weight:   20.0000
   chunk 93 optimal weight:    0.8980
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
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
B 176 GLN
G  44 HIS
N  31 ASN
N  84 ASN
** R 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 295 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.113006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.097561 restraints weight = 19845.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.099256 restraints weight = 13289.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.100275 restraints weight = 9947.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6918
moved from start:          0.2369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8090  Z= 0.236
  Angle     :  0.648   8.780  10991  Z= 0.342
  Chirality :  0.044   0.163   1268
  Planarity :  0.005   0.072   1418
  Dihedral  :  4.509  19.424   1135
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.10 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  4.45 %
    Favored  : 95.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.25), residues: 1033
  helix:  0.79 (0.27), residues: 368
  sheet: -1.33 (0.31), residues: 223
  loop : -0.80 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 234 
 HIS   0.005   0.001   HIS R 420 
 PHE   0.033   0.002   PHE R 230 
 TYR   0.059   0.002   TYR B  59 
 ARG   0.004   0.001   ARG N  19 

*********************** 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
  184 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 183
  time to evaluate  : 0.727 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 ILE cc_start: 0.7873 (mt) cc_final: 0.6955 (mt)
REVERT: A   60 MET cc_start: 0.5728 (mpp) cc_final: 0.4540 (mtm)
REVERT: A  304 GLU cc_start: 0.6872 (mm-30) cc_final: 0.6585 (pm20)
REVERT: B   75 GLN cc_start: 0.7578 (mt0) cc_final: 0.6856 (pp30)
REVERT: B   78 LYS cc_start: 0.8013 (mmmt) cc_final: 0.7788 (tptt)
REVERT: N    3 GLN cc_start: 0.5672 (mp10) cc_final: 0.5239 (mm110)
REVERT: N   32 TYR cc_start: 0.7510 (m-80) cc_final: 0.7072 (m-10)
REVERT: N   47 TRP cc_start: 0.7268 (t60) cc_final: 0.6993 (t60)
REVERT: R  219 ARG cc_start: 0.7529 (tmm160) cc_final: 0.7132 (ptt90)
REVERT: R  376 ILE cc_start: 0.8810 (mt) cc_final: 0.8521 (tt)
REVERT: R  405 LYS cc_start: 0.8282 (tppp) cc_final: 0.7794 (tppt)
  outliers start: 1
  outliers final: 0
  residues processed: 184
  average time/residue: 0.3367
  time to fit residues: 83.4213
Evaluate side-chains
  134 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 1.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 9 optimal weight:    9.9990
   chunk 70 optimal weight:    6.9990
   chunk 19 optimal weight:    5.9990
   chunk 99 optimal weight:    5.9990
   chunk 46 optimal weight:    7.9990
   chunk 42 optimal weight:    5.9990
   chunk 12 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 13 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9990
   overall best weight:    2.5188

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 295 ASN
** N   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  84 ASN
** 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 = 0.3803 r_free = 0.3803 target = 0.111649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.096525 restraints weight = 20469.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.098194 restraints weight = 13772.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.099223 restraints weight = 10223.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6958
moved from start:          0.3117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8090  Z= 0.240
  Angle     :  0.620   9.142  10991  Z= 0.327
  Chirality :  0.044   0.157   1268
  Planarity :  0.005   0.057   1418
  Dihedral  :  4.385  18.233   1135
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.48 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  5.21 %
    Favored  : 94.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.26), residues: 1033
  helix:  1.02 (0.27), residues: 363
  sheet: -1.06 (0.33), residues: 211
  loop : -0.76 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.003   TRP R 339 
 HIS   0.007   0.001   HIS B 225 
 PHE   0.035   0.002   PHE R 238 
 TYR   0.020   0.002   TYR A 381 
 ARG   0.005   0.001   ARG R 404 

*********************** 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
  163 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 162
  time to evaluate  : 0.974 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 MET cc_start: 0.5440 (mpp) cc_final: 0.4176 (mtm)
REVERT: B   75 GLN cc_start: 0.7198 (mt0) cc_final: 0.6694 (pp30)
REVERT: B  111 TYR cc_start: 0.7003 (m-80) cc_final: 0.6735 (m-80)
REVERT: B  130 GLU cc_start: 0.4139 (pt0) cc_final: 0.3935 (pt0)
REVERT: B  143 THR cc_start: 0.8174 (p) cc_final: 0.7699 (t)
REVERT: N    2 VAL cc_start: 0.6508 (t) cc_final: 0.6080 (t)
REVERT: N   47 TRP cc_start: 0.7244 (t60) cc_final: 0.6856 (t60)
REVERT: N   83 MET cc_start: 0.6628 (mpp) cc_final: 0.6343 (mpp)
REVERT: R  219 ARG cc_start: 0.7652 (tmm160) cc_final: 0.7225 (ptt90)
REVERT: R  339 TRP cc_start: 0.7061 (t60) cc_final: 0.6652 (t60)
REVERT: R  371 ILE cc_start: 0.8029 (mm) cc_final: 0.7610 (mt)
REVERT: R  376 ILE cc_start: 0.8801 (mt) cc_final: 0.8557 (tt)
  outliers start: 1
  outliers final: 0
  residues processed: 162
  average time/residue: 0.2713
  time to fit residues: 61.0182
Evaluate side-chains
  123 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 94 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 2 optimal weight:    5.9990
   chunk 70 optimal weight:    7.9990
   chunk 102 optimal weight:    4.9990
   chunk 80 optimal weight:    0.7980
   chunk 69 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9980
   chunk 85 optimal weight:    9.9990
   chunk 1 optimal weight:    3.9990
   chunk 79 optimal weight:   50.0000
   overall best weight:    2.5586

-------------------------------------------------------------------------------
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  91 HIS
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  18 GLN
** N   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 295 ASN
R 420 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.111395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.096015 restraints weight = 20434.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.097723 restraints weight = 13788.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.098701 restraints weight = 10267.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6969
moved from start:          0.3563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8090  Z= 0.242
  Angle     :  0.605   9.164  10991  Z= 0.316
  Chirality :  0.043   0.178   1268
  Planarity :  0.004   0.051   1418
  Dihedral  :  4.452  20.629   1135
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 12.47
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.48 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  4.19 %
    Favored  : 95.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.26), residues: 1033
  helix:  1.13 (0.27), residues: 357
  sheet: -0.92 (0.32), residues: 231
  loop : -0.70 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP R 339 
 HIS   0.005   0.001   HIS A 347 
 PHE   0.019   0.002   PHE N  68 
 TYR   0.016   0.002   TYR N  95 
 ARG   0.007   0.001   ARG A 307 

*********************** 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
  158 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 157
  time to evaluate  : 0.938 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 MET cc_start: 0.5614 (mpp) cc_final: 0.4364 (mtm)
REVERT: A  304 GLU cc_start: 0.7062 (mm-30) cc_final: 0.6550 (pm20)
REVERT: B   19 ARG cc_start: 0.6719 (mtm-85) cc_final: 0.6459 (mtm-85)
REVERT: B   32 GLN cc_start: 0.6674 (pm20) cc_final: 0.6317 (pp30)
REVERT: B   75 GLN cc_start: 0.7210 (mt0) cc_final: 0.6607 (pp30)
REVERT: B  111 TYR cc_start: 0.7054 (m-80) cc_final: 0.6789 (m-10)
REVERT: B  130 GLU cc_start: 0.4063 (pt0) cc_final: 0.3859 (pt0)
REVERT: B  145 TYR cc_start: 0.8303 (p90) cc_final: 0.8029 (p90)
REVERT: G   27 ARG cc_start: 0.7089 (mtm-85) cc_final: 0.6845 (mtm-85)
REVERT: N   32 TYR cc_start: 0.7928 (m-10) cc_final: 0.7503 (m-80)
REVERT: N  109 ASP cc_start: 0.6285 (m-30) cc_final: 0.5520 (p0)
REVERT: R  215 LEU cc_start: 0.5969 (pt) cc_final: 0.5530 (pt)
REVERT: R  219 ARG cc_start: 0.7646 (tmm160) cc_final: 0.7286 (ptt90)
REVERT: R  339 TRP cc_start: 0.6916 (t60) cc_final: 0.6518 (t60)
REVERT: R  376 ILE cc_start: 0.8859 (mt) cc_final: 0.8625 (tt)
REVERT: R  448 ASN cc_start: 0.7413 (m-40) cc_final: 0.6653 (m110)
  outliers start: 1
  outliers final: 1
  residues processed: 158
  average time/residue: 0.2091
  time to fit residues: 44.3971
Evaluate side-chains
  122 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 121
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 102 optimal weight:    6.9990
   chunk 19 optimal weight:    5.9990
   chunk 73 optimal weight:    1.9990
   chunk 82 optimal weight:    5.9990
   chunk 96 optimal weight:    8.9990
   chunk 31 optimal weight:    0.4980
   chunk 88 optimal weight:    0.8980
   chunk 85 optimal weight:    8.9990
   chunk 94 optimal weight:    5.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.6786

-------------------------------------------------------------------------------
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**
N   3 GLN
R 220 ASN
R 295 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.113288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.097880 restraints weight = 19862.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.099527 restraints weight = 13400.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.100700 restraints weight = 10051.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6918
moved from start:          0.3801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8090  Z= 0.195
  Angle     :  0.577   8.857  10991  Z= 0.302
  Chirality :  0.042   0.145   1268
  Planarity :  0.004   0.046   1418
  Dihedral  :  4.312  18.981   1135
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.26), residues: 1033
  helix:  1.29 (0.28), residues: 357
  sheet: -1.00 (0.31), residues: 234
  loop : -0.58 (0.31), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP R 339 
 HIS   0.005   0.001   HIS A 347 
 PHE   0.035   0.002   PHE R 238 
 TYR   0.016   0.002   TYR A 381 
 ARG   0.003   0.000   ARG N  67 

*********************** 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
  163 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 162
  time to evaluate  : 0.836 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 MET cc_start: 0.5654 (mpp) cc_final: 0.4400 (mtm)
REVERT: A  304 GLU cc_start: 0.7002 (mm-30) cc_final: 0.6550 (pm20)
REVERT: B   32 GLN cc_start: 0.6726 (pm20) cc_final: 0.6359 (pp30)
REVERT: B   75 GLN cc_start: 0.7152 (mt0) cc_final: 0.6512 (pp30)
REVERT: B  145 TYR cc_start: 0.8296 (p90) cc_final: 0.7943 (p90)
REVERT: G   27 ARG cc_start: 0.7067 (mtm-85) cc_final: 0.6842 (mtm-85)
REVERT: N   32 TYR cc_start: 0.7637 (m-10) cc_final: 0.7326 (m-80)
REVERT: N   47 TRP cc_start: 0.7225 (t60) cc_final: 0.6729 (t60)
REVERT: N   87 LYS cc_start: 0.7206 (tttp) cc_final: 0.6944 (tttm)
REVERT: N  109 ASP cc_start: 0.6266 (m-30) cc_final: 0.5568 (p0)
REVERT: R  215 LEU cc_start: 0.5760 (pt) cc_final: 0.5251 (pt)
REVERT: R  219 ARG cc_start: 0.7611 (tmm160) cc_final: 0.7278 (ptt90)
REVERT: R  376 ILE cc_start: 0.8850 (mt) cc_final: 0.8646 (tt)
REVERT: R  405 LYS cc_start: 0.8356 (tppp) cc_final: 0.7965 (tppt)
  outliers start: 1
  outliers final: 0
  residues processed: 162
  average time/residue: 0.2106
  time to fit residues: 45.7971
Evaluate side-chains
  120 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 72 optimal weight:    0.0770
   chunk 18 optimal weight:    6.9990
   chunk 90 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   chunk 34 optimal weight:   10.0000
   chunk 7 optimal weight:    4.9990
   overall best weight:    2.2144

-------------------------------------------------------------------------------
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**
B 142 HIS
N   5 GLN
R 295 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.112184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.096999 restraints weight = 20178.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.098647 restraints weight = 13601.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.099600 restraints weight = 10213.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6951
moved from start:          0.4024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8090  Z= 0.215
  Angle     :  0.586  10.641  10991  Z= 0.306
  Chirality :  0.043   0.167   1268
  Planarity :  0.004   0.044   1418
  Dihedral  :  4.381  22.394   1135
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  3.18 %
    Favored  : 96.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.00 (0.26), residues: 1033
  helix:  1.42 (0.28), residues: 357
  sheet: -0.87 (0.32), residues: 226
  loop : -0.59 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP R 339 
 HIS   0.009   0.001   HIS A 220 
 PHE   0.011   0.002   PHE R 335 
 TYR   0.016   0.001   TYR N  95 
 ARG   0.008   0.001   ARG A 307 

*********************** 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
  153 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 152
  time to evaluate  : 0.882 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 MET cc_start: 0.5732 (mpp) cc_final: 0.4383 (mtm)
REVERT: A  304 GLU cc_start: 0.7117 (mm-30) cc_final: 0.6578 (pm20)
REVERT: B   32 GLN cc_start: 0.6748 (pm20) cc_final: 0.6385 (pp30)
REVERT: B   75 GLN cc_start: 0.7301 (mt0) cc_final: 0.6798 (pp30)
REVERT: B  130 GLU cc_start: 0.3986 (pt0) cc_final: 0.3780 (pt0)
REVERT: B  145 TYR cc_start: 0.8298 (p90) cc_final: 0.8021 (p90)
REVERT: B  300 LEU cc_start: 0.7650 (mm) cc_final: 0.7256 (mm)
REVERT: B  325 MET cc_start: 0.7161 (mtp) cc_final: 0.6937 (mtp)
REVERT: N   32 TYR cc_start: 0.7632 (m-10) cc_final: 0.7295 (m-80)
REVERT: N   39 GLN cc_start: 0.6542 (tp40) cc_final: 0.6114 (tt0)
REVERT: N   89 GLU cc_start: 0.6997 (mp0) cc_final: 0.6754 (mp0)
REVERT: N  109 ASP cc_start: 0.6327 (m-30) cc_final: 0.5607 (p0)
REVERT: R  215 LEU cc_start: 0.6041 (pt) cc_final: 0.5561 (pt)
REVERT: R  219 ARG cc_start: 0.7767 (tmm160) cc_final: 0.7373 (ptt90)
REVERT: R  339 TRP cc_start: 0.7126 (t60) cc_final: 0.6856 (t60)
REVERT: R  376 ILE cc_start: 0.8881 (mt) cc_final: 0.8668 (tt)
  outliers start: 1
  outliers final: 0
  residues processed: 152
  average time/residue: 0.1959
  time to fit residues: 40.7613
Evaluate side-chains
  126 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 64 optimal weight:    7.9990
   chunk 89 optimal weight:    0.0970
   chunk 32 optimal weight:    3.9990
   chunk 55 optimal weight:   20.0000
   chunk 98 optimal weight:    9.9990
   chunk 35 optimal weight:    5.9990
   chunk 16 optimal weight:    0.4980
   chunk 63 optimal weight:    7.9990
   chunk 14 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 99 optimal weight:    3.9990
   overall best weight:    1.5182

-------------------------------------------------------------------------------
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**
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  13 GLN
R 295 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.113480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.098315 restraints weight = 20445.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.100027 restraints weight = 13728.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.101233 restraints weight = 10227.647|
|-----------------------------------------------------------------------------|
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6905
moved from start:          0.4196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8090  Z= 0.187
  Angle     :  0.586   9.479  10991  Z= 0.304
  Chirality :  0.042   0.200   1268
  Planarity :  0.004   0.042   1418
  Dihedral  :  4.305  19.784   1135
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.27), residues: 1033
  helix:  1.51 (0.28), residues: 359
  sheet: -0.84 (0.32), residues: 236
  loop : -0.65 (0.31), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP R 339 
 HIS   0.005   0.001   HIS A 220 
 PHE   0.014   0.001   PHE B 234 
 TYR   0.023   0.001   TYR A 381 
 ARG   0.006   0.000   ARG A 307 

*********************** 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
  165 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.942 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 MET cc_start: 0.5550 (mpp) cc_final: 0.4872 (mtm)
REVERT: A  304 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6597 (pm20)
REVERT: A  378 LEU cc_start: 0.8562 (mt) cc_final: 0.8332 (mt)
REVERT: B   32 GLN cc_start: 0.6695 (pm20) cc_final: 0.6350 (pp30)
REVERT: B   75 GLN cc_start: 0.7342 (mt0) cc_final: 0.6760 (pp30)
REVERT: B  145 TYR cc_start: 0.8309 (p90) cc_final: 0.7928 (p90)
REVERT: B  325 MET cc_start: 0.7124 (mtp) cc_final: 0.6920 (mtp)
REVERT: N   32 TYR cc_start: 0.7581 (m-10) cc_final: 0.7340 (m-10)
REVERT: N   47 TRP cc_start: 0.7251 (t60) cc_final: 0.6962 (t60)
REVERT: N  109 ASP cc_start: 0.6151 (m-30) cc_final: 0.5445 (p0)
REVERT: R  215 LEU cc_start: 0.6077 (pt) cc_final: 0.5588 (pt)
REVERT: R  219 ARG cc_start: 0.7755 (tmm160) cc_final: 0.7274 (ptt90)
REVERT: R  339 TRP cc_start: 0.7191 (t60) cc_final: 0.6973 (t60)
REVERT: R  376 ILE cc_start: 0.8863 (mt) cc_final: 0.8649 (tt)
REVERT: R  383 ARG cc_start: 0.8024 (ttp80) cc_final: 0.7476 (ptt90)
REVERT: R  405 LYS cc_start: 0.8256 (tppp) cc_final: 0.7760 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 0.2157
  time to fit residues: 47.6290
Evaluate side-chains
  123 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 50 optimal weight:    6.9990
   chunk 101 optimal weight:    3.9990
   chunk 87 optimal weight:    2.9990
   chunk 99 optimal weight:    0.4980
   chunk 2 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 69 optimal weight:    0.8980
   chunk 46 optimal weight:    4.9990
   chunk 90 optimal weight:    0.8980
   chunk 72 optimal weight:    6.9990
   chunk 62 optimal weight:    9.9990
   overall best weight:    1.2382

-------------------------------------------------------------------------------
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 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 216 HIS
R 295 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.114836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.099513 restraints weight = 20291.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.101257 restraints weight = 13571.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.102455 restraints weight = 10039.623|
|-----------------------------------------------------------------------------|
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6892
moved from start:          0.4300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8090  Z= 0.175
  Angle     :  0.574   8.737  10991  Z= 0.297
  Chirality :  0.041   0.164   1268
  Planarity :  0.004   0.040   1418
  Dihedral  :  4.245  19.509   1135
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.27), residues: 1033
  helix:  1.64 (0.28), residues: 358
  sheet: -0.64 (0.33), residues: 231
  loop : -0.59 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B  82 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.011   0.001   PHE R 327 
 TYR   0.020   0.001   TYR A 381 
 ARG   0.008   0.000   ARG R 404 

*********************** 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
  150 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.972 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 MET cc_start: 0.5520 (mpp) cc_final: 0.4880 (mtm)
REVERT: B   22 ARG cc_start: 0.6391 (ttm170) cc_final: 0.5806 (ttt180)
REVERT: B   75 GLN cc_start: 0.7243 (mt0) cc_final: 0.6424 (pp30)
REVERT: B  255 LEU cc_start: 0.7406 (tt) cc_final: 0.7086 (mt)
REVERT: N   32 TYR cc_start: 0.7597 (m-10) cc_final: 0.7288 (m-80)
REVERT: N   47 TRP cc_start: 0.7245 (t60) cc_final: 0.6990 (t60)
REVERT: N   65 LYS cc_start: 0.6977 (pttm) cc_final: 0.6737 (ptpt)
REVERT: N   89 GLU cc_start: 0.7032 (mp0) cc_final: 0.6821 (mp0)
REVERT: N  109 ASP cc_start: 0.6531 (m-30) cc_final: 0.5592 (p0)
REVERT: R  215 LEU cc_start: 0.6280 (pt) cc_final: 0.5814 (pt)
REVERT: R  219 ARG cc_start: 0.7774 (tmm160) cc_final: 0.7300 (ptt90)
REVERT: R  339 TRP cc_start: 0.7141 (t60) cc_final: 0.6869 (t60)
REVERT: R  371 ILE cc_start: 0.7908 (mm) cc_final: 0.7383 (mt)
REVERT: R  376 ILE cc_start: 0.8905 (mt) cc_final: 0.8575 (tt)
REVERT: R  383 ARG cc_start: 0.8030 (ttp80) cc_final: 0.7524 (ptt90)
  outliers start: 0
  outliers final: 0
  residues processed: 150
  average time/residue: 0.2003
  time to fit residues: 41.0704
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  : 0.831 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 83 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 53 optimal weight:    9.9990
   chunk 18 optimal weight:    6.9990
   chunk 23 optimal weight:   20.0000
   chunk 20 optimal weight:    5.9990
   chunk 8 optimal weight:    0.8980
   chunk 70 optimal weight:    7.9990
   chunk 7 optimal weight:    4.9990
   overall best weight:    3.7788

-------------------------------------------------------------------------------
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**
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 216 HIS
R 295 ASN
R 307 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.110707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.095284 restraints weight = 20883.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.096861 restraints weight = 13871.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.098177 restraints weight = 10357.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6993
moved from start:          0.4438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   8090  Z= 0.311
  Angle     :  0.673   8.334  10991  Z= 0.355
  Chirality :  0.045   0.191   1268
  Planarity :  0.005   0.050   1418
  Dihedral  :  4.801  28.373   1135
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 13.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.26), residues: 1033
  helix:  1.11 (0.27), residues: 367
  sheet: -0.76 (0.33), residues: 223
  loop : -0.91 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP R 339 
 HIS   0.007   0.001   HIS R 216 
 PHE   0.014   0.002   PHE N 108 
 TYR   0.017   0.002   TYR N  95 
 ARG   0.017   0.001   ARG N  67 

*********************** 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
  156 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.970 
Fit side-chains
   revert: symmetry clash
REVERT: A  376 MET cc_start: 0.7447 (tpt) cc_final: 0.7074 (tpt)
REVERT: B   32 GLN cc_start: 0.6745 (pm20) cc_final: 0.5624 (pp30)
REVERT: B   75 GLN cc_start: 0.7244 (mt0) cc_final: 0.6646 (pp30)
REVERT: B  130 GLU cc_start: 0.4137 (pt0) cc_final: 0.3920 (pt0)
REVERT: B  300 LEU cc_start: 0.7850 (mm) cc_final: 0.7521 (mm)
REVERT: N   32 TYR cc_start: 0.7738 (m-80) cc_final: 0.7492 (m-10)
REVERT: N   65 LYS cc_start: 0.7188 (pttm) cc_final: 0.6947 (ptmt)
REVERT: N   91 THR cc_start: 0.7207 (p) cc_final: 0.6976 (p)
REVERT: R  215 LEU cc_start: 0.6445 (pt) cc_final: 0.6071 (pt)
REVERT: R  219 ARG cc_start: 0.7775 (tmm160) cc_final: 0.7347 (ptt90)
REVERT: R  376 ILE cc_start: 0.8911 (mt) cc_final: 0.8639 (tt)
REVERT: R  422 ILE cc_start: 0.7743 (mm) cc_final: 0.7521 (tp)
REVERT: R  444 GLU cc_start: 0.7982 (tp30) cc_final: 0.7693 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 156
  average time/residue: 0.2010
  time to fit residues: 42.2809
Evaluate side-chains
  126 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 61 optimal weight:    8.9990
   chunk 80 optimal weight:    2.9990
   chunk 81 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9980
   chunk 98 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 101 optimal weight:    0.8980
   chunk 78 optimal weight:    0.0020
   chunk 33 optimal weight:    0.0770
   overall best weight:    0.5546

-------------------------------------------------------------------------------
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**
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N   5 GLN ** 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 = 0.3862 r_free = 0.3862 target = 0.115560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.100386 restraints weight = 20116.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.102129 restraints weight = 13390.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.103084 restraints weight = 9942.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6874
moved from start:          0.4646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8090  Z= 0.165
  Angle     :  0.608   8.526  10991  Z= 0.313
  Chirality :  0.042   0.154   1268
  Planarity :  0.004   0.042   1418
  Dihedral  :  4.437  23.690   1135
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.27), residues: 1033
  helix:  1.52 (0.28), residues: 358
  sheet: -0.69 (0.33), residues: 228
  loop : -0.80 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP R 339 
 HIS   0.003   0.001   HIS R 216 
 PHE   0.014   0.001   PHE N  27 
 TYR   0.026   0.002   TYR B 145 
 ARG   0.007   0.001   ARG R 404 

********************** 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
  158 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.861 
Fit side-chains
   revert: symmetry clash
REVERT: B   75 GLN cc_start: 0.7008 (mt0) cc_final: 0.6185 (pp30)
REVERT: B  284 LEU cc_start: 0.7929 (mt) cc_final: 0.7341 (mt)
REVERT: B  314 ARG cc_start: 0.7087 (ttp80) cc_final: 0.6733 (ttp80)
REVERT: N   32 TYR cc_start: 0.7426 (m-80) cc_final: 0.7214 (m-10)
REVERT: N   65 LYS cc_start: 0.7031 (pttm) cc_final: 0.6646 (ptpt)
REVERT: R  215 LEU cc_start: 0.6640 (pt) cc_final: 0.6160 (pt)
REVERT: R  219 ARG cc_start: 0.7695 (tmm160) cc_final: 0.7234 (ptt90)
REVERT: R  339 TRP cc_start: 0.7325 (t60) cc_final: 0.7068 (t60)
REVERT: R  376 ILE cc_start: 0.8895 (mt) cc_final: 0.8596 (tt)
REVERT: R  383 ARG cc_start: 0.8107 (ttp80) cc_final: 0.7533 (ptt90)
REVERT: R  422 ILE cc_start: 0.7686 (mm) cc_final: 0.7437 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 158
  average time/residue: 0.2083
  time to fit residues: 45.3203
Evaluate side-chains
  120 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 52 optimal weight:    4.9990
   chunk 83 optimal weight:    1.9990
   chunk 47 optimal weight:    9.9990
   chunk 97 optimal weight:    2.9990
   chunk 76 optimal weight:   20.0000
   chunk 20 optimal weight:    9.9990
   chunk 102 optimal weight:    4.9990
   chunk 21 optimal weight:    0.5980
   chunk 70 optimal weight:    7.9990
   chunk 35 optimal weight:    7.9990
   chunk 7 optimal weight:    0.0060
   overall best weight:    2.1202

-------------------------------------------------------------------------------
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**
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N   5 GLN ** 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 = 0.3828 r_free = 0.3828 target = 0.113305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.098383 restraints weight = 20665.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.100057 restraints weight = 13760.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.100923 restraints weight = 10237.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6928
moved from start:          0.4732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8090  Z= 0.227
  Angle     :  0.625   9.816  10991  Z= 0.324
  Chirality :  0.043   0.174   1268
  Planarity :  0.004   0.042   1418
  Dihedral  :  4.480  26.081   1135
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.27), residues: 1033
  helix:  1.42 (0.28), residues: 360
  sheet: -0.75 (0.33), residues: 237
  loop : -0.72 (0.31), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.003   TRP B  63 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.015   0.002   PHE A 335 
 TYR   0.023   0.002   TYR B 145 
 ARG   0.007   0.001   ARG R 404 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2873.20 seconds
wall clock time: 53 minutes 4.29 seconds (3184.29 seconds total)