Starting phenix.real_space_refine
on Wed Feb  4 02:34:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9oq1_70733/02_2026/9oq1_70733.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9oq1_70733/02_2026/9oq1_70733.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9oq1_70733/02_2026/9oq1_70733.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9oq1_70733/02_2026/9oq1_70733.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9oq1_70733/02_2026/9oq1_70733.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9oq1_70733/02_2026/9oq1_70733.cif"
  }
  resolution = 2.98
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.004 sd=   0.098
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: 5
    Type Number    sf(0)   Gaussians
     S      60      5.16       5
     Cl      3      4.86       5
     C    5250      2.51       5
     N    1404      2.21       5
     O    1534      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8251
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4141
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 514, 4141
          Classifications: {'peptide': 514}
          Link IDs: {'PTRANS': 23, 'TRANS': 490}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 4087
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 523, 4087
          Classifications: {'peptide': 523}
          Link IDs: {'PTRANS': 26, 'TRANS': 496}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 23
          Unusual residues: {'RRJ': 1, 'RRY': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.39, per 1000 atoms: 0.17
  Number of scatterers: 8251
  At special positions: 0
  Unit cell: (93.456, 84.37, 123.31, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      3     17.00
     S      60     16.00
     O    1534      8.00
     N    1404      7.00
     C    5250      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=16, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  59 " - pdb=" SG  CYS A 102 " distance=1.30
    Simple disulfide: pdb=" SG  CYS A 233 " - pdb=" SG  CYS A 513 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 363 " - pdb=" SG  CYS A 366 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 405 " - pdb=" SG  CYS A 410 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 495 " - pdb=" SG  CYS A 514 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 499 " - pdb=" SG  CYS A 517 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 520 " - pdb=" SG  CYS A 535 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 538 " - pdb=" SG  CYS A 551 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  62 " - pdb=" SG  CYS B 103 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 236 " - pdb=" SG  CYS B 522 " distance=1.47
    Simple disulfide: pdb=" SG  CYS B 369 " - pdb=" SG  CYS B 372 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 417 " - pdb=" SG  CYS B 422 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 504 " - pdb=" SG  CYS B 523 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 508 " - pdb=" SG  CYS B 526 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 529 " - pdb=" SG  CYS B 543 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 546 " - pdb=" SG  CYS B 559 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ?1-2
      " RRY C   1 " - " RRJ C   2 "
  Time building additional restraints: 0.59
  Conformation dependent library (CDL) restraints added in 261.0 milliseconds
  

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1970

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 13 sheets defined
      38.3% alpha, 15.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 58 through 62
      removed outlier: 4.067A  pdb=" N   GLU A  61 " --> pdb=" O   MET A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 85
    Processing helix  chain 'A' and resid 108 through 116
    Processing helix  chain 'A' and resid 143 through 158
      removed outlier: 4.231A  pdb=" N   PHE A 153 " --> pdb=" O   THR A 149 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   LEU A 156 " --> pdb=" O   ASN A 152 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   PHE A 157 " --> pdb=" O   PHE A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 173
    Processing helix  chain 'A' and resid 186 through 202
      removed outlier: 3.591A  pdb=" N   HIS A 190 " --> pdb=" O   SER A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 231
      removed outlier: 3.725A  pdb=" N   ALA A 228 " --> pdb=" O   GLY A 224 " (cutoff:3.500A)
      removed outlier: 4.845A  pdb=" N   ARG A 229 " --> pdb=" O   GLU A 225 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ARG A 230 " --> pdb=" O   ARG A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 267
      removed outlier: 3.590A  pdb=" N   SER A 267 " --> pdb=" O   LYS A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 291
      removed outlier: 4.204A  pdb=" N   PHE A 284 " --> pdb=" O   THR A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
    Processing helix  chain 'A' and resid 313 through 318
    Processing helix  chain 'A' and resid 334 through 339
    Processing helix  chain 'A' and resid 365 through 380
      removed outlier: 3.891A  pdb=" N   SER A 372 " --> pdb=" O   ASN A 368 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   PHE A 373 " --> pdb=" O   ALA A 369 " (cutoff:3.500A)
      removed outlier: 5.216A  pdb=" N   THR A 375 " --> pdb=" O   LEU A 371 " (cutoff:3.500A)
      removed outlier: 5.727A  pdb=" N   ILE A 376 " --> pdb=" O   SER A 372 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   SER A 380 " --> pdb=" O   ILE A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 403
    Processing helix  chain 'A' and resid 416 through 425
      removed outlier: 3.697A  pdb=" N   LEU A 420 " --> pdb=" O   TYR A 416 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 28
    Processing helix  chain 'B' and resid 47 through 51
    Processing helix  chain 'B' and resid 66 through 86
      removed outlier: 4.352A  pdb=" N   LEU B  70 " --> pdb=" O   SER B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 117
    Processing helix  chain 'B' and resid 146 through 158
      removed outlier: 4.144A  pdb=" N   PHE B 156 " --> pdb=" O   ILE B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 171 through 176
      removed outlier: 3.681A  pdb=" N   LEU B 174 " --> pdb=" O   MET B 171 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 204
      removed outlier: 3.631A  pdb=" N   GLN B 193 " --> pdb=" O   SER B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 233
      removed outlier: 3.504A  pdb=" N   SER B 228 " --> pdb=" O   SER B 224 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 266
      removed outlier: 3.794A  pdb=" N   LYS B 255 " --> pdb=" O   GLN B 251 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   LEU B 260 " --> pdb=" O   VAL B 256 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ASN B 264 " --> pdb=" O   LEU B 260 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 291
      removed outlier: 3.581A  pdb=" N   VAL B 280 " --> pdb=" O   SER B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 300 through 305
    Processing helix  chain 'B' and resid 308 through 312
      removed outlier: 3.575A  pdb=" N   THR B 311 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 314 through 318
    Processing helix  chain 'B' and resid 333 through 347
      removed outlier: 3.654A  pdb=" N   ASP B 347 " --> pdb=" O   ALA B 343 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 348 through 353
      removed outlier: 3.556A  pdb=" N   CYS B 351 " --> pdb=" O   PRO B 348 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 388
      removed outlier: 4.296A  pdb=" N   LEU B 385 " --> pdb=" O   SER B 381 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 393 through 415
      removed outlier: 3.675A  pdb=" N   ILE B 397 " --> pdb=" O   LEU B 393 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   VAL B 404 " --> pdb=" O   THR B 400 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   TYR B 405 " --> pdb=" O   TYR B 401 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 429 through 435
    Processing helix  chain 'B' and resid 489 through 492
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29
      removed outlier: 6.156A  pdb=" N   TYR A  33 " --> pdb=" O   GLY A  95 " (cutoff:3.500A)
      removed outlier: 7.540A  pdb=" N   GLU A  97 " --> pdb=" O   TYR A  33 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   LEU A  35 " --> pdb=" O   GLU A  97 " (cutoff:3.500A)
      removed outlier: 7.708A  pdb=" N   VAL A  99 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
      removed outlier: 5.959A  pdb=" N   GLY A  37 " --> pdb=" O   VAL A  99 " (cutoff:3.500A)
      removed outlier: 7.233A  pdb=" N   LEU A  34 " --> pdb=" O   ALA A 137 " (cutoff:3.500A)
      removed outlier: 8.248A  pdb=" N   ILE A 139 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   GLY A  36 " --> pdb=" O   ILE A 139 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   VAL A 138 " --> pdb=" O   ILE A 162 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 123
    Processing sheet with id=AA3, first strand: chain 'A' and resid 233 through 240
      removed outlier: 7.327A  pdb=" N   ILE A 206 " --> pdb=" O   PHE A 236 " (cutoff:3.500A)
      removed outlier: 8.979A  pdb=" N   GLU A 238 " --> pdb=" O   ILE A 206 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   VAL A 208 " --> pdb=" O   GLU A 238 " (cutoff:3.500A)
      removed outlier: 7.556A  pdb=" N   LEU A 240 " --> pdb=" O   VAL A 208 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   VAL A 210 " --> pdb=" O   LEU A 240 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   VAL A 271 " --> pdb=" O   TRP A 205 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   VAL A 272 " --> pdb=" O   ILE A 299 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   ALA A 296 " --> pdb=" O   THR A 321 " (cutoff:3.500A)
      removed outlier: 7.671A  pdb=" N   LEU A 323 " --> pdb=" O   ALA A 296 " (cutoff:3.500A)
      removed outlier: 5.919A  pdb=" N   TRP A 298 " --> pdb=" O   LEU A 323 " (cutoff:3.500A)
      removed outlier: 7.689A  pdb=" N   ILE A 325 " --> pdb=" O   TRP A 298 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   ALA A 300 " --> pdb=" O   ILE A 325 " (cutoff:3.500A)
      removed outlier: 9.119A  pdb=" N   ILE A 327 " --> pdb=" O   ALA A 300 " (cutoff:3.500A)
      removed outlier: 5.437A  pdb=" N   PHE A 322 " --> pdb=" O   TRP A 453 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   LEU A 448 " --> pdb=" O   SER A 467 " (cutoff:3.500A)
      removed outlier: 4.895A  pdb=" N   SER A 467 " --> pdb=" O   LEU A 448 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ILE A 450 " --> pdb=" O   VAL A 465 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 428 through 430
    Processing sheet with id=AA5, first strand: chain 'A' and resid 503 through 507
    Processing sheet with id=AA6, first strand: chain 'A' and resid 524 through 525
    Processing sheet with id=AA7, first strand: chain 'A' and resid 542 through 543
    Processing sheet with id=AA8, first strand: chain 'B' and resid 30 through 31
      removed outlier: 6.368A  pdb=" N   TYR B  35 " --> pdb=" O   GLY B  96 " (cutoff:3.500A)
      removed outlier: 7.910A  pdb=" N   ASP B  98 " --> pdb=" O   TYR B  35 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   LEU B  37 " --> pdb=" O   ASP B  98 " (cutoff:3.500A)
      removed outlier: 7.612A  pdb=" N   PHE B 100 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 5.817A  pdb=" N   GLY B  39 " --> pdb=" O   PHE B 100 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   ILE B  36 " --> pdb=" O   ALA B 140 " (cutoff:3.500A)
      removed outlier: 8.179A  pdb=" N   ILE B 142 " --> pdb=" O   ILE B  36 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   GLY B  38 " --> pdb=" O   ILE B 142 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   VAL B 141 " --> pdb=" O   VAL B 165 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 44 through 45
    Processing sheet with id=AB1, first strand: chain 'B' and resid 236 through 243
      removed outlier: 7.461A  pdb=" N   VAL B 209 " --> pdb=" O   ALA B 238 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   GLU B 240 " --> pdb=" O   VAL B 209 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   ALA B 211 " --> pdb=" O   GLU B 240 " (cutoff:3.500A)
      removed outlier: 5.367A  pdb=" N   LEU B 242 " --> pdb=" O   ALA B 211 " (cutoff:3.500A)
      removed outlier: 5.840A  pdb=" N   GLY B 213 " --> pdb=" O   LEU B 242 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   TRP B 208 " --> pdb=" O   VAL B 270 " (cutoff:3.500A)
      removed outlier: 8.556A  pdb=" N   VAL B 272 " --> pdb=" O   TRP B 208 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   ALA B 210 " --> pdb=" O   VAL B 272 " (cutoff:3.500A)
      removed outlier: 8.151A  pdb=" N   PHE B 274 " --> pdb=" O   ALA B 210 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   LEU B 212 " --> pdb=" O   PHE B 274 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   PHE B 324 " --> pdb=" O   ALA B 299 " (cutoff:3.500A)
      removed outlier: 4.943A  pdb=" N   VAL B 321 " --> pdb=" O   TRP B 466 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLY B 479 " --> pdb=" O   LEU B 463 " (cutoff:3.500A)
      removed outlier: 6.222A  pdb=" N   MET B 465 " --> pdb=" O   THR B 477 " (cutoff:3.500A)
      removed outlier: 5.523A  pdb=" N   THR B 477 " --> pdb=" O   MET B 465 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   VAL B 467 " --> pdb=" O   LEU B 475 " (cutoff:3.500A)
      removed outlier: 5.341A  pdb=" N   LEU B 475 " --> pdb=" O   VAL B 467 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 441 through 444
    Processing sheet with id=AB3, first strand: chain 'B' and resid 512 through 517
      removed outlier: 3.668A  pdb=" N   CYS B 523 " --> pdb=" O   LYS B 517 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 533 through 534

    304 hydrogen bonds defined for protein.
    834 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.26

  Time building geometry restraints manager: 0.79 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2697
        1.34 -     1.46: 1909
        1.46 -     1.58: 3761
        1.58 -     1.70: 0
        1.70 -     1.82: 87
  Bond restraints: 8454
  Sorted by residual:
  bond pdb=" N   VAL A 414 "
       pdb=" CA  VAL A 414 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.036 1.30e-02 5.92e+03 7.54e+00
  bond pdb=" N   SER B 276 "
       pdb=" CA  SER B 276 "
    ideal  model  delta    sigma   weight residual
    1.453  1.486 -0.033 1.31e-02 5.83e+03 6.40e+00
  bond pdb=" N   LYS A 412 "
       pdb=" CA  LYS A 412 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.031 1.25e-02 6.40e+03 6.26e+00
  bond pdb=" CA  ILE A 332 "
       pdb=" C   ILE A 332 "
    ideal  model  delta    sigma   weight residual
    1.528  1.546 -0.018 7.70e-03 1.69e+04 5.72e+00
  bond pdb=" C2  RRY C   1 "
       pdb=" O2  RRY C   1 "
    ideal  model  delta    sigma   weight residual
    1.383  1.430 -0.047 2.00e-02 2.50e+03 5.59e+00
  ... (remaining 8449 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 11114
        1.61 -     3.22: 337
        3.22 -     4.83: 47
        4.83 -     6.44: 6
        6.44 -     8.05: 1
  Bond angle restraints: 11505
  Sorted by residual:
  angle pdb=" N   SER B 282 "
        pdb=" CA  SER B 282 "
        pdb=" C   SER B 282 "
      ideal   model   delta    sigma   weight residual
     111.07  106.16    4.91 1.07e+00 8.73e-01 2.11e+01
  angle pdb=" CA  SER B 276 "
        pdb=" C   SER B 276 "
        pdb=" O   SER B 276 "
      ideal   model   delta    sigma   weight residual
     121.81  117.44    4.37 1.18e+00 7.18e-01 1.37e+01
  angle pdb=" C   ARG B 445 "
        pdb=" CA  ARG B 445 "
        pdb=" CB  ARG B 445 "
      ideal   model   delta    sigma   weight residual
     116.54  112.47    4.07 1.15e+00 7.56e-01 1.25e+01
  angle pdb=" N   ALA B 277 "
        pdb=" CA  ALA B 277 "
        pdb=" C   ALA B 277 "
      ideal   model   delta    sigma   weight residual
     111.07  114.79   -3.72 1.07e+00 8.73e-01 1.21e+01
  angle pdb=" CA  LYS A 412 "
        pdb=" C   LYS A 412 "
        pdb=" O   LYS A 412 "
      ideal   model   delta    sigma   weight residual
     121.55  117.89    3.66 1.06e+00 8.90e-01 1.19e+01
  ... (remaining 11500 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.41: 4865
       23.41 -    46.81: 193
       46.81 -    70.22: 27
       70.22 -    93.63: 5
       93.63 -   117.03: 6
  Dihedral angle restraints: 5096
    sinusoidal: 2057
      harmonic: 3039
  Sorted by residual:
  dihedral pdb=" CB  CYS B 529 "
           pdb=" SG  CYS B 529 "
           pdb=" SG  CYS B 543 "
           pdb=" CB  CYS B 543 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -142.17   56.17     1      1.00e+01 1.00e-02 4.26e+01
  dihedral pdb=" CA  ILE B 142 "
           pdb=" C   ILE B 142 "
           pdb=" N   GLY B 143 "
           pdb=" CA  GLY B 143 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.91  -26.09     0      5.00e+00 4.00e-02 2.72e+01
  dihedral pdb=" CA  THR B 305 "
           pdb=" C   THR B 305 "
           pdb=" N   SER B 306 "
           pdb=" CA  SER B 306 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.45  -25.55     0      5.00e+00 4.00e-02 2.61e+01
  ... (remaining 5093 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 1082
       0.055 -    0.110: 174
       0.110 -    0.164: 29
       0.164 -    0.219: 3
       0.219 -    0.274: 1
  Chirality restraints: 1289
  Sorted by residual:
  chirality pdb=" CA  ILE A 481 "
            pdb=" N   ILE A 481 "
            pdb=" C   ILE A 481 "
            pdb=" CB  ILE A 481 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.71   -0.27 2.00e-01 2.50e+01 1.87e+00
  chirality pdb=" CA  TYR B 281 "
            pdb=" N   TYR B 281 "
            pdb=" C   TYR B 281 "
            pdb=" CB  TYR B 281 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.18 2.00e-01 2.50e+01 7.68e-01
  chirality pdb=" CA  VAL A 414 "
            pdb=" N   VAL A 414 "
            pdb=" C   VAL A 414 "
            pdb=" CB  VAL A 414 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 7.52e-01
  ... (remaining 1286 not shown)

  Planarity restraints: 1482
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 401 "   -0.008 2.00e-02 2.50e+03   1.65e-02 2.72e+00
        pdb=" C   TYR B 401 "    0.029 2.00e-02 2.50e+03
        pdb=" O   TYR B 401 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ALA B 402 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 413 "    0.140 9.50e-02 1.11e+02   6.28e-02 2.48e+00
        pdb=" NE  ARG A 413 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 413 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 413 "    0.000 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 413 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 480 "   -0.008 2.00e-02 2.50e+03   1.54e-02 2.39e+00
        pdb=" C   ASP A 480 "    0.027 2.00e-02 2.50e+03
        pdb=" O   ASP A 480 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ILE A 481 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1479 not shown)

  Histogram of nonbonded interaction distances:
        2.37 -     2.88: 3145
        2.88 -     3.38: 7933
        3.38 -     3.89: 13283
        3.89 -     4.39: 15822
        4.39 -     4.90: 26436
  Nonbonded interactions: 66619
  Sorted by model distance:
  nonbonded pdb=" N   GLN B 469 "
            pdb=" OE1 GLN B 469 "
     model   vdw
     2.373 3.120
  nonbonded pdb=" OE1 GLU A  81 "
            pdb=" OH  TYR A 389 "
     model   vdw
     2.389 3.040
  nonbonded pdb=" N   GLN B 498 "
            pdb=" OE1 GLN B 498 "
     model   vdw
     2.389 3.120
  nonbonded pdb=" OD1 ASP A 169 "
            pdb=" OG  SER A 186 "
     model   vdw
     2.395 3.040
  nonbonded pdb=" OD1 ASP A 100 "
            pdb=" O   ASN A 360 "
     model   vdw
     2.395 3.040
  ... (remaining 66614 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.810
  Set stop_for_unknowns flag:              0.010
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.980
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
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      :  0.011   0.730   8471  Z= 0.538
  Angle     :  0.935  53.337  11540  Z= 0.500
  Chirality :  0.043   0.274   1289
  Planarity :  0.005   0.063   1482
  Dihedral  : 13.776 117.032   3078
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 2.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.04 (0.25), residues: 1027
  helix: -0.43 (0.26), residues: 349
  sheet: -0.74 (0.39), residues: 167
  loop : -0.74 (0.27), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 413 
 TYR   0.018   0.001   TYR A 389 
 PHE   0.012   0.001   PHE B 226 
 TRP   0.011   0.001   TRP B 208 
 HIS   0.004   0.001   HIS B 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 8454)
  covalent geometry    : angle       0.65438 (11505)
  SS BOND              : bond        0.22977 (   16)
  SS BOND              : angle      12.61509 (   32)
  hydrogen bonds       : bond        0.16184 (  304)
  hydrogen bonds       : angle       6.59150 (  834)
  glycosidic custom    : bond        0.02341 (    1)
  glycosidic custom    : angle       5.06322 (    3)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 MET cc_start: 0.8720 (ttt) cc_final: 0.8323 (ttt)
REVERT: A  117 HIS cc_start: 0.7467 (m-70) cc_final: 0.6828 (m170)
REVERT: A  173 ASP cc_start: 0.7384 (m-30) cc_final: 0.7184 (m-30)
REVERT: A  282 TYR cc_start: 0.8194 (t80) cc_final: 0.7206 (m-80)
REVERT: A  290 ARG cc_start: 0.7972 (mmt-90) cc_final: 0.7729 (mmt-90)
REVERT: A  414 VAL cc_start: 0.8956 (t) cc_final: 0.8608 (p)
REVERT: A  477 ASN cc_start: 0.8273 (t0) cc_final: 0.7868 (t0)
REVERT: A  492 MET cc_start: 0.8168 (pmm) cc_final: 0.7787 (tpt)
REVERT: A  506 LYS cc_start: 0.8141 (mmmt) cc_final: 0.7923 (ttpt)
REVERT: A  532 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7298 (mm-30)
REVERT: B  317 ARG cc_start: 0.7156 (ttm-80) cc_final: 0.6404 (tmm160)
REVERT: B  435 GLU cc_start: 0.7976 (tt0) cc_final: 0.7682 (mt-10)
REVERT: B  465 MET cc_start: 0.6699 (ttp) cc_final: 0.6248 (ttt)
REVERT: B  466 TRP cc_start: 0.7230 (t60) cc_final: 0.6652 (t-100)
REVERT: B  492 MET cc_start: 0.7552 (mmm) cc_final: 0.6794 (mpt)
REVERT: B  493 TYR cc_start: 0.6281 (m-80) cc_final: 0.6029 (m-80)
REVERT: B  551 TRP cc_start: 0.6582 (p-90) cc_final: 0.5666 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.5316
  time to fit residues: 94.4842
Evaluate side-chains
  93 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:    9.9990
   chunk 53 optimal weight:    0.4980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    7.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    3.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A  55 GLN
A 536 GLN
B  58 ASN
B 392 GLN
B 482 ASN
B 486 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.165830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.114164 restraints weight = 11660.960|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 3.02
r_work: 0.3333 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.1940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8471  Z= 0.159
  Angle     :  0.631   8.786  11540  Z= 0.331
  Chirality :  0.045   0.305   1289
  Planarity :  0.005   0.034   1482
  Dihedral  :  6.683  56.113   1156
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 11.48 %
    Favored  : 85.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.29 (0.26), residues: 1027
  helix:  0.65 (0.27), residues: 353
  sheet: -0.46 (0.40), residues: 166
  loop : -0.63 (0.28), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 256 
 TYR   0.026   0.002   TYR B 281 
 PHE   0.014   0.001   PHE A 275 
 TRP   0.015   0.002   TRP B 208 
 HIS   0.010   0.001   HIS B 290 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 8454)
  covalent geometry    : angle       0.62929 (11505)
  SS BOND              : bond        0.00397 (   16)
  SS BOND              : angle       0.83755 (   32)
  hydrogen bonds       : bond        0.05130 (  304)
  hydrogen bonds       : angle       4.73953 (  834)
  glycosidic custom    : bond        0.00318 (    1)
  glycosidic custom    : angle       1.82421 (    3)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 100
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 HIS cc_start: 0.7331 (m-70) cc_final: 0.6538 (m170)
REVERT: A  238 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7874 (tt0)
REVERT: A  414 VAL cc_start: 0.9121 (t) cc_final: 0.8813 (p)
REVERT: A  477 ASN cc_start: 0.8131 (t0) cc_final: 0.7589 (t0)
REVERT: A  492 MET cc_start: 0.8397 (pmm) cc_final: 0.8138 (tpt)
REVERT: A  504 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.6987 (pttp)
REVERT: A  532 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7297 (mm-30)
REVERT: B  155 LYS cc_start: 0.8683 (mttt) cc_final: 0.8189 (mtmt)
REVERT: B  317 ARG cc_start: 0.7054 (ttm-80) cc_final: 0.6291 (tmm160)
REVERT: B  394 HIS cc_start: 0.7654 (OUTLIER) cc_final: 0.7417 (t-90)
REVERT: B  435 GLU cc_start: 0.8060 (tt0) cc_final: 0.7709 (mt-10)
REVERT: B  466 TRP cc_start: 0.7034 (t60) cc_final: 0.6722 (t-100)
REVERT: B  551 TRP cc_start: 0.6596 (p-90) cc_final: 0.5767 (p90)
  outliers start: 26
  outliers final: 9
  residues processed: 115
  average time/residue: 0.4822
  time to fit residues: 59.1998
Evaluate side-chains
  101 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue   59 CYS
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  504 LYS
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  394 HIS
Chi-restraints excluded: chain B residue  397 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 78 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 72 optimal weight:    0.8980
   chunk 66 optimal weight:    0.5980
   chunk 95 optimal weight:    3.9990
   chunk 84 optimal weight:   20.0000
   chunk 61 optimal weight:    0.7980
   chunk 73 optimal weight:   10.0000
   chunk 52 optimal weight:    3.9990
   chunk 79 optimal weight:    2.9990
   overall best weight:    1.8584

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

Flipped N/Q/H residues before XYZ refinement:
A 536 GLN
B 145 HIS
B 290 HIS
B 503 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.164930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.112472 restraints weight = 11671.904|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 2.98
r_work: 0.3283 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.2494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   8471  Z= 0.222
  Angle     :  0.626   7.997  11540  Z= 0.328
  Chirality :  0.046   0.286   1289
  Planarity :  0.005   0.036   1482
  Dihedral  :  5.933  58.540   1156
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 13.54 %
    Favored  : 82.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.42 (0.26), residues: 1027
  helix:  0.72 (0.27), residues: 353
  sheet: -0.73 (0.38), residues: 166
  loop : -0.77 (0.28), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 256 
 TYR   0.026   0.002   TYR A 389 
 PHE   0.020   0.002   PHE A 275 
 TRP   0.013   0.002   TRP B 303 
 HIS   0.009   0.001   HIS B 290 

Details of bonding type rmsd
  covalent geometry    : bond        0.00534 ( 8454)
  covalent geometry    : angle       0.62291 (11505)
  SS BOND              : bond        0.00324 (   16)
  SS BOND              : angle       1.06306 (   32)
  hydrogen bonds       : bond        0.05008 (  304)
  hydrogen bonds       : angle       4.63603 (  834)
  glycosidic custom    : bond        0.00491 (    1)
  glycosidic custom    : angle       2.79093 (    3)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 93
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
REVERT: A  117 HIS cc_start: 0.7706 (m-70) cc_final: 0.6670 (m-70)
REVERT: A  238 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7790 (tt0)
REVERT: A  477 ASN cc_start: 0.8141 (t0) cc_final: 0.7577 (t0)
REVERT: A  492 MET cc_start: 0.8434 (pmm) cc_final: 0.8169 (mmp)
REVERT: A  504 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.7228 (ptmm)
REVERT: B  155 LYS cc_start: 0.8813 (mttt) cc_final: 0.8390 (mtmt)
REVERT: B  317 ARG cc_start: 0.6973 (ttm-80) cc_final: 0.6195 (tmm160)
REVERT: B  435 GLU cc_start: 0.8039 (tt0) cc_final: 0.7578 (mt-10)
REVERT: B  466 TRP cc_start: 0.7132 (t60) cc_final: 0.6673 (t-100)
REVERT: B  551 TRP cc_start: 0.6681 (p-90) cc_final: 0.5986 (p90)
  outliers start: 32
  outliers final: 12
  residues processed: 115
  average time/residue: 0.4821
  time to fit residues: 59.3657
Evaluate side-chains
  93 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  504 LYS
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain B residue  303 TRP
Chi-restraints excluded: chain B residue  397 ILE
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  501 VAL
Chi-restraints excluded: chain B residue  522 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 30 optimal weight:    0.3980
   chunk 15 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 76 optimal weight:    7.9990
   chunk 60 optimal weight:    0.9990
   chunk 63 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 536 GLN
B 503 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.168173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.114894 restraints weight = 11842.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.3478 rms_B_bonded: 3.13
r_work: 0.3328 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.2857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8471  Z= 0.125
  Angle     :  0.561   9.517  11540  Z= 0.289
  Chirality :  0.043   0.300   1289
  Planarity :  0.004   0.052   1482
  Dihedral  :  5.571  58.482   1156
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 15.71 %
    Favored  : 81.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.26), residues: 1027
  helix:  1.00 (0.27), residues: 356
  sheet: -0.65 (0.39), residues: 169
  loop : -0.70 (0.28), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 498 
 TYR   0.021   0.001   TYR B 281 
 PHE   0.012   0.001   PHE A 552 
 TRP   0.012   0.001   TRP B 303 
 HIS   0.003   0.001   HIS B 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 8454)
  covalent geometry    : angle       0.55980 (11505)
  SS BOND              : bond        0.00171 (   16)
  SS BOND              : angle       0.80976 (   32)
  hydrogen bonds       : bond        0.03955 (  304)
  hydrogen bonds       : angle       4.26906 (  834)
  glycosidic custom    : bond        0.00098 (    1)
  glycosidic custom    : angle       1.58507 (    3)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 94
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
REVERT: A  238 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7938 (tt0)
REVERT: A  278 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8219 (p0)
REVERT: A  477 ASN cc_start: 0.8017 (t0) cc_final: 0.7495 (OUTLIER)
REVERT: A  492 MET cc_start: 0.8399 (pmm) cc_final: 0.8108 (mmp)
REVERT: A  504 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.7236 (ptmm)
REVERT: B   98 ASP cc_start: 0.8230 (p0) cc_final: 0.7968 (p0)
REVERT: B  155 LYS cc_start: 0.8644 (mttt) cc_final: 0.8145 (mtmt)
REVERT: B  204 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.7742 (m-10)
REVERT: B  274 PHE cc_start: 0.5855 (t80) cc_final: 0.4998 (t80)
REVERT: B  317 ARG cc_start: 0.7114 (ttm-80) cc_final: 0.6302 (tmm160)
REVERT: B  435 GLU cc_start: 0.8092 (tt0) cc_final: 0.7629 (mt-10)
REVERT: B  466 TRP cc_start: 0.7120 (t60) cc_final: 0.6719 (t-100)
REVERT: B  478 VAL cc_start: 0.7861 (m) cc_final: 0.7625 (p)
REVERT: B  551 TRP cc_start: 0.6710 (p-90) cc_final: 0.6013 (p90)
  outliers start: 26
  outliers final: 12
  residues processed: 111
  average time/residue: 0.4620
  time to fit residues: 54.6334
Evaluate side-chains
  99 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  278 ASP
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  504 LYS
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  204 PHE
Chi-restraints excluded: chain B residue  303 TRP
Chi-restraints excluded: chain B residue  394 HIS
Chi-restraints excluded: chain B residue  397 ILE
Chi-restraints excluded: chain B residue  501 VAL
Chi-restraints excluded: chain B residue  559 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0770
   chunk 50 optimal weight:    7.9990
   chunk 90 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 87 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 53 optimal weight:    6.9990
   chunk 32 optimal weight:    8.9990
   overall best weight:    1.1142

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

Flipped N/Q/H residues before XYZ refinement:
A 536 GLN
B 503 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.165284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.113759 restraints weight = 11724.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 3.00
r_work: 0.3327 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.3011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8471  Z= 0.153
  Angle     :  0.584  10.195  11540  Z= 0.300
  Chirality :  0.044   0.350   1289
  Planarity :  0.004   0.041   1482
  Dihedral  :  5.509  63.975   1156
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 15.71 %
    Favored  : 80.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.16 (0.26), residues: 1027
  helix:  1.06 (0.28), residues: 356
  sheet: -0.74 (0.38), residues: 169
  loop : -0.66 (0.28), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 498 
 TYR   0.022   0.002   TYR B 281 
 PHE   0.014   0.001   PHE A 275 
 TRP   0.012   0.001   TRP B 303 
 HIS   0.005   0.001   HIS B 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 8454)
  covalent geometry    : angle       0.57352 (11505)
  SS BOND              : bond        0.00314 (   16)
  SS BOND              : angle       2.10310 (   32)
  hydrogen bonds       : bond        0.04108 (  304)
  hydrogen bonds       : angle       4.27622 (  834)
  glycosidic custom    : bond        0.00255 (    1)
  glycosidic custom    : angle       1.46291 (    3)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 90
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  225 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7126 (pp20)
REVERT: A  238 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7927 (tt0)
REVERT: A  477 ASN cc_start: 0.8073 (t0) cc_final: 0.7553 (t0)
REVERT: A  492 MET cc_start: 0.8410 (pmm) cc_final: 0.8132 (mmp)
REVERT: A  504 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.7196 (ptmm)
REVERT: A  532 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8344 (pm20)
REVERT: B  155 LYS cc_start: 0.8715 (mttt) cc_final: 0.8221 (mtmt)
REVERT: B  204 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.7767 (m-10)
REVERT: B  274 PHE cc_start: 0.5997 (t80) cc_final: 0.5212 (t80)
REVERT: B  292 LEU cc_start: 0.6970 (OUTLIER) cc_final: 0.6610 (tt)
REVERT: B  317 ARG cc_start: 0.7187 (ttm-80) cc_final: 0.6449 (tmm160)
REVERT: B  435 GLU cc_start: 0.8102 (tt0) cc_final: 0.7662 (mt-10)
REVERT: B  466 TRP cc_start: 0.7288 (t60) cc_final: 0.6785 (t-100)
REVERT: B  551 TRP cc_start: 0.6745 (p-90) cc_final: 0.6036 (p90)
  outliers start: 36
  outliers final: 16
  residues processed: 118
  average time/residue: 0.4806
  time to fit residues: 61.2167
Evaluate side-chains
  104 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 83
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  504 LYS
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   83 ILE
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  204 PHE
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  303 TRP
Chi-restraints excluded: chain B residue  305 THR
Chi-restraints excluded: chain B residue  394 HIS
Chi-restraints excluded: chain B residue  397 ILE
Chi-restraints excluded: chain B residue  501 VAL
Chi-restraints excluded: chain B residue  559 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 89 optimal weight:    6.9990
   chunk 84 optimal weight:   20.0000
   chunk 98 optimal weight:    8.9990
   chunk 50 optimal weight:    6.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 536 GLN
B 503 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.162355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.109849 restraints weight = 11856.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 3.01
r_work: 0.3268 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.3204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.055   8471  Z= 0.296
  Angle     :  0.691   9.178  11540  Z= 0.356
  Chirality :  0.048   0.327   1289
  Planarity :  0.005   0.040   1482
  Dihedral  :  5.901  84.950   1156
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 17.01 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.54 (0.26), residues: 1027
  helix:  0.69 (0.27), residues: 354
  sheet: -1.03 (0.38), residues: 169
  loop : -0.81 (0.28), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 498 
 TYR   0.026   0.002   TYR A 389 
 PHE   0.024   0.002   PHE A 275 
 TRP   0.017   0.002   TRP B 303 
 HIS   0.009   0.001   HIS B 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00717 ( 8454)
  covalent geometry    : angle       0.68857 (11505)
  SS BOND              : bond        0.00589 (   16)
  SS BOND              : angle       1.24875 (   32)
  hydrogen bonds       : bond        0.05123 (  304)
  hydrogen bonds       : angle       4.67945 (  834)
  glycosidic custom    : bond        0.00732 (    1)
  glycosidic custom    : angle       1.98920 (    3)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 87
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
REVERT: A  117 HIS cc_start: 0.7968 (m-70) cc_final: 0.6789 (m-70)
REVERT: A  154 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8250 (mp)
REVERT: A  225 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7064 (pp20)
REVERT: A  238 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7894 (tt0)
REVERT: A  477 ASN cc_start: 0.8216 (t0) cc_final: 0.7593 (t0)
REVERT: A  492 MET cc_start: 0.8522 (pmm) cc_final: 0.8210 (OUTLIER)
REVERT: A  532 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8239 (pm20)
REVERT: B  155 LYS cc_start: 0.8866 (mttt) cc_final: 0.8391 (mtmt)
REVERT: B  204 PHE cc_start: 0.8574 (OUTLIER) cc_final: 0.7741 (m-10)
REVERT: B  274 PHE cc_start: 0.6203 (t80) cc_final: 0.5419 (t80)
REVERT: B  292 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6696 (tt)
REVERT: B  317 ARG cc_start: 0.7253 (ttm-80) cc_final: 0.6323 (tmm160)
REVERT: B  435 GLU cc_start: 0.8059 (tt0) cc_final: 0.7644 (mt-10)
REVERT: B  466 TRP cc_start: 0.7401 (t60) cc_final: 0.6760 (t-100)
REVERT: B  519 PHE cc_start: 0.7328 (t80) cc_final: 0.6783 (t80)
REVERT: B  551 TRP cc_start: 0.6751 (p-90) cc_final: 0.6130 (p90)
  outliers start: 39
  outliers final: 21
  residues processed: 118
  average time/residue: 0.3973
  time to fit residues: 50.5849
Evaluate side-chains
  107 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 82
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain A residue  535 CYS
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  204 PHE
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  303 TRP
Chi-restraints excluded: chain B residue  305 THR
Chi-restraints excluded: chain B residue  394 HIS
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  501 VAL
Chi-restraints excluded: chain B residue  559 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 70 optimal weight:    0.5980
   chunk 95 optimal weight:    4.9990
   chunk 96 optimal weight:    0.0970
   chunk 14 optimal weight:    0.9980
   chunk 77 optimal weight:    5.9990
   chunk 94 optimal weight:    0.3980
   chunk 11 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9980
   chunk 99 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 22 optimal weight:    7.9990
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
A 361 GLN
A 536 GLN
B 503 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.167884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.117469 restraints weight = 11852.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 3.31
r_work: 0.3335 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.3351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8471  Z= 0.117
  Angle     :  0.578  10.632  11540  Z= 0.296
  Chirality :  0.043   0.337   1289
  Planarity :  0.004   0.036   1482
  Dihedral  :  5.594  84.586   1156
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 18.74 %
    Favored  : 78.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.27), residues: 1027
  helix:  1.34 (0.28), residues: 340
  sheet: -0.87 (0.39), residues: 169
  loop : -0.69 (0.28), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 498 
 TYR   0.022   0.001   TYR B 281 
 PHE   0.009   0.001   PHE A 153 
 TRP   0.012   0.001   TRP B 208 
 HIS   0.004   0.001   HIS B 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 8454)
  covalent geometry    : angle       0.57592 (11505)
  SS BOND              : bond        0.00416 (   16)
  SS BOND              : angle       0.99240 (   32)
  hydrogen bonds       : bond        0.03813 (  304)
  hydrogen bonds       : angle       4.22744 (  834)
  glycosidic custom    : bond        0.00140 (    1)
  glycosidic custom    : angle       1.08385 (    3)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 86
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
REVERT: A  225 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7159 (pp20)
REVERT: A  238 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7969 (tt0)
REVERT: A  477 ASN cc_start: 0.8137 (t0) cc_final: 0.7584 (t0)
REVERT: A  492 MET cc_start: 0.8461 (pmm) cc_final: 0.8190 (mmp)
REVERT: A  532 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8190 (pm20)
REVERT: A  536 GLN cc_start: 0.6021 (mt0) cc_final: 0.5505 (pt0)
REVERT: B   36 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8110 (mm)
REVERT: B  155 LYS cc_start: 0.8726 (mttt) cc_final: 0.8241 (mtmt)
REVERT: B  274 PHE cc_start: 0.5683 (t80) cc_final: 0.4906 (t80)
REVERT: B  292 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6567 (tp)
REVERT: B  317 ARG cc_start: 0.7179 (ttm-80) cc_final: 0.6460 (tmm160)
REVERT: B  435 GLU cc_start: 0.7930 (tt0) cc_final: 0.7540 (mt-10)
REVERT: B  466 TRP cc_start: 0.7410 (t60) cc_final: 0.6789 (t-100)
REVERT: B  519 PHE cc_start: 0.7192 (t80) cc_final: 0.6634 (t80)
REVERT: B  551 TRP cc_start: 0.6751 (p-90) cc_final: 0.6039 (p90)
  outliers start: 27
  outliers final: 13
  residues processed: 104
  average time/residue: 0.4396
  time to fit residues: 49.0733
Evaluate side-chains
  94 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  303 TRP
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  501 VAL
Chi-restraints excluded: chain B residue  559 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 89 optimal weight:    4.9990
   chunk 6 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 96 optimal weight:   10.0000
   chunk 98 optimal weight:   10.0000
   chunk 93 optimal weight:    4.9990
   chunk 8 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   chunk 47 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
B 503 GLN
B 520 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.163030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.111301 restraints weight = 11840.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 2.94
r_work: 0.3279 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.3442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.060   8471  Z= 0.269
  Angle     :  0.666   9.808  11540  Z= 0.343
  Chirality :  0.047   0.343   1289
  Planarity :  0.005   0.038   1482
  Dihedral  :  5.713  77.170   1156
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 18.42 %
    Favored  : 77.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.53 (0.26), residues: 1027
  helix:  0.75 (0.27), residues: 357
  sheet: -1.07 (0.39), residues: 168
  loop : -0.84 (0.29), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 498 
 TYR   0.024   0.002   TYR A 389 
 PHE   0.021   0.002   PHE A 275 
 TRP   0.017   0.002   TRP B 303 
 HIS   0.009   0.001   HIS B 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00656 ( 8454)
  covalent geometry    : angle       0.66458 (11505)
  SS BOND              : bond        0.00534 (   16)
  SS BOND              : angle       0.93456 (   32)
  hydrogen bonds       : bond        0.04817 (  304)
  hydrogen bonds       : angle       4.61551 (  834)
  glycosidic custom    : bond        0.00604 (    1)
  glycosidic custom    : angle       1.40467 (    3)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 77
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
REVERT: A  117 HIS cc_start: 0.7949 (m-70) cc_final: 0.6790 (m-70)
REVERT: A  225 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7231 (pp20)
REVERT: A  229 ARG cc_start: 0.8455 (mtm110) cc_final: 0.8202 (mtp180)
REVERT: A  238 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7923 (tt0)
REVERT: A  362 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8120 (pm20)
REVERT: A  477 ASN cc_start: 0.8209 (t0) cc_final: 0.7607 (t0)
REVERT: A  492 MET cc_start: 0.8552 (pmm) cc_final: 0.8218 (mmp)
REVERT: A  532 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8159 (pm20)
REVERT: B  155 LYS cc_start: 0.8860 (mttt) cc_final: 0.8429 (mtmt)
REVERT: B  274 PHE cc_start: 0.5879 (t80) cc_final: 0.5226 (t80)
REVERT: B  292 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6509 (tp)
REVERT: B  317 ARG cc_start: 0.7436 (ttm-80) cc_final: 0.6536 (tmm160)
REVERT: B  435 GLU cc_start: 0.8032 (tt0) cc_final: 0.7629 (mt-10)
REVERT: B  448 THR cc_start: 0.7809 (OUTLIER) cc_final: 0.7463 (m)
REVERT: B  466 TRP cc_start: 0.7502 (t60) cc_final: 0.6862 (t-100)
REVERT: B  519 PHE cc_start: 0.7302 (t80) cc_final: 0.6799 (t80)
REVERT: B  551 TRP cc_start: 0.6848 (p-90) cc_final: 0.6119 (p90)
  outliers start: 36
  outliers final: 15
  residues processed: 105
  average time/residue: 0.4681
  time to fit residues: 52.7498
Evaluate side-chains
  95 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 75
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  362 GLU
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  524 THR
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  303 TRP
Chi-restraints excluded: chain B residue  397 ILE
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  448 THR
Chi-restraints excluded: chain B residue  501 VAL
Chi-restraints excluded: chain B residue  559 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 4 optimal weight:    0.5980
   chunk 17 optimal weight:    0.7980
   chunk 65 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9980
   chunk 92 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 503 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.167001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.115867 restraints weight = 11677.730|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 2.94
r_work: 0.3350 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.3536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   8471  Z= 0.130
  Angle     :  0.598  12.518  11540  Z= 0.304
  Chirality :  0.043   0.347   1289
  Planarity :  0.004   0.037   1482
  Dihedral  :  5.397  73.150   1156
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 19.93 %
    Favored  : 77.57 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.27), residues: 1027
  helix:  1.15 (0.27), residues: 352
  sheet: -0.92 (0.40), residues: 168
  loop : -0.74 (0.29), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 498 
 TYR   0.022   0.001   TYR B 286 
 PHE   0.010   0.001   PHE A 153 
 TRP   0.013   0.001   TRP B 303 
 HIS   0.006   0.001   HIS A  42 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 8454)
  covalent geometry    : angle       0.59645 (11505)
  SS BOND              : bond        0.00416 (   16)
  SS BOND              : angle       0.86898 (   32)
  hydrogen bonds       : bond        0.03843 (  304)
  hydrogen bonds       : angle       4.27670 (  834)
  glycosidic custom    : bond        0.00164 (    1)
  glycosidic custom    : angle       0.96572 (    3)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 77
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
REVERT: A  225 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7150 (pp20)
REVERT: A  238 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7968 (tt0)
REVERT: A  477 ASN cc_start: 0.8113 (t0) cc_final: 0.7556 (t0)
REVERT: A  492 MET cc_start: 0.8458 (pmm) cc_final: 0.8203 (mmp)
REVERT: A  525 PHE cc_start: 0.7110 (p90) cc_final: 0.6809 (p90)
REVERT: A  532 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8187 (pm20)
REVERT: B   74 MET cc_start: 0.8440 (mmm) cc_final: 0.8160 (mmp)
REVERT: B  155 LYS cc_start: 0.8721 (mttt) cc_final: 0.8236 (mtmt)
REVERT: B  274 PHE cc_start: 0.5541 (t80) cc_final: 0.4984 (t80)
REVERT: B  292 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6648 (tp)
REVERT: B  317 ARG cc_start: 0.7314 (ttm-80) cc_final: 0.6603 (tmm160)
REVERT: B  466 TRP cc_start: 0.7484 (t60) cc_final: 0.6887 (t-100)
REVERT: B  519 PHE cc_start: 0.7151 (t80) cc_final: 0.6601 (t80)
REVERT: B  551 TRP cc_start: 0.6852 (p-90) cc_final: 0.6109 (p90)
  outliers start: 23
  outliers final: 16
  residues processed: 93
  average time/residue: 0.5376
  time to fit residues: 53.5366
Evaluate side-chains
  94 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 75
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  524 THR
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  303 TRP
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  501 VAL
Chi-restraints excluded: chain B residue  559 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 99 optimal weight:    4.9990
   chunk 57 optimal weight:    0.0070
   chunk 52 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   chunk 33 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 90 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9990
   chunk 80 optimal weight:    6.9990
   chunk 76 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.6998

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

Flipped N/Q/H residues before XYZ refinement:
A 536 GLN
B 265 GLN
B 503 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.167877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.116405 restraints weight = 11692.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3497 rms_B_bonded: 2.96
r_work: 0.3348 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.3648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8471  Z= 0.124
  Angle     :  0.587  11.356  11540  Z= 0.297
  Chirality :  0.042   0.141   1289
  Planarity :  0.004   0.037   1482
  Dihedral  :  5.211  72.545   1156
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 19.72 %
    Favored  : 77.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.27), residues: 1027
  helix:  1.30 (0.27), residues: 353
  sheet: -0.86 (0.40), residues: 169
  loop : -0.72 (0.29), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 498 
 TYR   0.020   0.001   TYR B 281 
 PHE   0.010   0.001   PHE A 275 
 TRP   0.014   0.001   TRP B 303 
 HIS   0.007   0.001   HIS A  42 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 8454)
  covalent geometry    : angle       0.58619 (11505)
  SS BOND              : bond        0.00418 (   16)
  SS BOND              : angle       0.75272 (   32)
  hydrogen bonds       : bond        0.03718 (  304)
  hydrogen bonds       : angle       4.13062 (  834)
  glycosidic custom    : bond        0.00155 (    1)
  glycosidic custom    : angle       0.97089 (    3)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 83
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  238 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7950 (tt0)
REVERT: A  362 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8197 (pm20)
REVERT: A  477 ASN cc_start: 0.8103 (t0) cc_final: 0.7428 (t0)
REVERT: A  492 MET cc_start: 0.8437 (pmm) cc_final: 0.8198 (mmp)
REVERT: A  525 PHE cc_start: 0.7184 (p90) cc_final: 0.6930 (p90)
REVERT: A  532 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8194 (pm20)
REVERT: A  536 GLN cc_start: 0.6147 (OUTLIER) cc_final: 0.5887 (pt0)
REVERT: B   64 ARG cc_start: 0.6459 (ttt180) cc_final: 0.6059 (tmt-80)
REVERT: B   74 MET cc_start: 0.8436 (mmm) cc_final: 0.8173 (mmp)
REVERT: B  155 LYS cc_start: 0.8708 (mttt) cc_final: 0.8213 (mtmt)
REVERT: B  274 PHE cc_start: 0.5485 (t80) cc_final: 0.4944 (t80)
REVERT: B  292 LEU cc_start: 0.6915 (OUTLIER) cc_final: 0.6703 (tp)
REVERT: B  317 ARG cc_start: 0.7248 (ttm-80) cc_final: 0.6472 (tmm160)
REVERT: B  466 TRP cc_start: 0.7522 (t60) cc_final: 0.6835 (t-100)
REVERT: B  530 LYS cc_start: 0.8481 (tppt) cc_final: 0.8049 (mtmm)
REVERT: B  551 TRP cc_start: 0.6761 (p-90) cc_final: 0.6058 (p90)
  outliers start: 25
  outliers final: 14
  residues processed: 99
  average time/residue: 0.5439
  time to fit residues: 57.4351
Evaluate side-chains
  97 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  362 GLU
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  524 THR
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain A residue  536 GLN
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  303 TRP
Chi-restraints excluded: chain B residue  397 ILE
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  501 VAL
Chi-restraints excluded: chain B residue  559 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 83 optimal weight:   10.0000
   chunk 84 optimal weight:    8.9990
   chunk 61 optimal weight:    0.2980
   chunk 72 optimal weight:    6.9990
   chunk 7 optimal weight:    0.6980
   chunk 0 optimal weight:    0.9990
   chunk 95 optimal weight:    5.9990
   chunk 41 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 77 optimal weight:    6.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
A 536 GLN
B 503 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.167715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.116132 restraints weight = 11703.703|
|-----------------------------------------------------------------------------|
r_work (start): 0.3510 rms_B_bonded: 2.96
r_work: 0.3365 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.3666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.228   8471  Z= 0.236
  Angle     :  0.929  59.200  11540  Z= 0.532
  Chirality :  0.043   0.335   1289
  Planarity :  0.004   0.037   1482
  Dihedral  :  5.234  72.543   1156
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 20.26 %
    Favored  : 77.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.27), residues: 1027
  helix:  1.30 (0.27), residues: 353
  sheet: -0.86 (0.40), residues: 169
  loop : -0.72 (0.29), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 515 
 TYR   0.021   0.001   TYR B 281 
 PHE   0.010   0.001   PHE A 275 
 TRP   0.014   0.001   TRP B 303 
 HIS   0.006   0.001   HIS A  42 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 ( 8454)
  covalent geometry    : angle       0.92930 (11505)
  SS BOND              : bond        0.00395 (   16)
  SS BOND              : angle       0.72287 (   32)
  hydrogen bonds       : bond        0.03937 (  304)
  hydrogen bonds       : angle       4.12992 (  834)
  glycosidic custom    : bond        0.00187 (    1)
  glycosidic custom    : angle       0.98152 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2459.09 seconds
wall clock time: 42 minutes 34.75 seconds (2554.75 seconds total)