Starting phenix.real_space_refine
on Tue Apr 29 17:51:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fus_50776/04_2025/9fus_50776.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fus_50776/04_2025/9fus_50776.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fus_50776/04_2025/9fus_50776.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fus_50776/04_2025/9fus_50776.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fus_50776/04_2025/9fus_50776.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fus_50776/04_2025/9fus_50776.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      54      5.16       5
     C    5590      2.51       5
     N    1536      2.21       5
     O    1642      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 8822
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 569, 4411
          Classifications: {'peptide': 569}
          Link IDs: {'PTRANS': 13, 'TRANS': 555}
    Chain: "B"
      Number of atoms: 4411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 569, 4411
          Classifications: {'peptide': 569}
          Link IDs: {'PTRANS': 13, 'TRANS': 555}
  Time building chain proxies: 6.30, per 1000 atoms: 0.71
  Number of scatterers: 8822
  At special positions: 0
  Unit cell: (111.52, 107.44, 133.28, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      54     16.00
     O    1642      8.00
     N    1536      7.00
     C    5590      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.39
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2128

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 4 sheets defined
      65.1% alpha, 5.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.85
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 15
      No H-bonds generated for 'chain 'A' and resid 13 through 15'
    Processing helix  chain 'A' and resid 16 through 21
      removed outlier: 3.637A  pdb=" N   ILE A  20 " --> pdb=" O   LEU A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 28 through 43
      removed outlier: 3.908A  pdb=" N   LEU A  34 " --> pdb=" O   ALA A  30 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LEU A  36 " --> pdb=" O   VAL A  32 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   ASN A  37 " --> pdb=" O   ALA A  33 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 53
    Processing helix  chain 'A' and resid 62 through 91
      Proline residue:  A  68  - end of helix
      removed outlier: 3.645A  pdb=" N   LEU A  77 " --> pdb=" O   GLY A  73 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ARG A  78 " --> pdb=" O   LEU A  74 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   SER A  85 " --> pdb=" O   THR A  81 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   SER A  86 " --> pdb=" O   SER A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 105
      removed outlier: 4.269A  pdb=" N   VAL A  97 " --> pdb=" O   SER A  93 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ARG A 103 " --> pdb=" O   THR A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 117
      removed outlier: 4.315A  pdb=" N   PHE A 116 " --> pdb=" O   PRO A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 130
      removed outlier: 4.000A  pdb=" N   SER A 126 " --> pdb=" O   GLY A 122 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   ILE A 128 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 138
    Processing helix  chain 'A' and resid 147 through 163
      removed outlier: 4.939A  pdb=" N   ILE A 153 " --> pdb=" O   GLU A 149 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   ILE A 154 " --> pdb=" O   GLY A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 213
      removed outlier: 4.163A  pdb=" N   ILE A 170 " --> pdb=" O   GLN A 166 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ALA A 175 " --> pdb=" O   LEU A 171 " (cutoff:3.500A)
      Proline residue:  A 176  - end of helix
      removed outlier: 3.757A  pdb=" N   SER A 193 " --> pdb=" O   PHE A 189 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   MET A 210 " --> pdb=" O   SER A 206 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LEU A 211 " --> pdb=" O   ALA A 207 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   GLY A 213 " --> pdb=" O   GLN A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 221
      removed outlier: 3.772A  pdb=" N   ILE A 219 " --> pdb=" O   LYS A 215 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   PHE A 220 " --> pdb=" O   GLU A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 249
      removed outlier: 3.700A  pdb=" N   ASN A 235 " --> pdb=" O   ASP A 231 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   GLN A 240 " --> pdb=" O   ARG A 236 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLY A 241 " --> pdb=" O   MET A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 270
      removed outlier: 3.626A  pdb=" N   ILE A 254 " --> pdb=" O   ILE A 250 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ALA A 262 " --> pdb=" O   ILE A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 277
      removed outlier: 3.786A  pdb=" N   ASP A 277 " --> pdb=" O   PRO A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 280
      No H-bonds generated for 'chain 'A' and resid 278 through 280'
    Processing helix  chain 'A' and resid 281 through 303
      removed outlier: 3.608A  pdb=" N   VAL A 286 " --> pdb=" O   GLY A 282 " (cutoff:3.500A)
      removed outlier: 5.177A  pdb=" N   VAL A 287 " --> pdb=" O   THR A 283 " (cutoff:3.500A)
      removed outlier: 4.695A  pdb=" N   ARG A 296 " --> pdb=" O   ILE A 292 " (cutoff:3.500A)
      Proline residue:  A 297  - end of helix
      removed outlier: 4.045A  pdb=" N   ASN A 303 " --> pdb=" O   LYS A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 323
      removed outlier: 3.739A  pdb=" N   ALA A 314 " --> pdb=" O   ARG A 310 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   CYS A 315 " --> pdb=" O   GLY A 311 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LEU A 318 " --> pdb=" O   ALA A 314 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ILE A 321 " --> pdb=" O   THR A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 390
      removed outlier: 4.182A  pdb=" N   ALA A 386 " --> pdb=" O   LYS A 382 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   SER A 387 " --> pdb=" O   SER A 383 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   LEU A 388 " --> pdb=" O   THR A 384 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   ILE A 389 " --> pdb=" O   ILE A 385 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   THR A 390 " --> pdb=" O   ALA A 386 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 382 through 390'
    Processing helix  chain 'A' and resid 411 through 417
      removed outlier: 3.654A  pdb=" N   ASN A 417 " --> pdb=" O   ALA A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 457
    Processing helix  chain 'A' and resid 459 through 466
      removed outlier: 3.543A  pdb=" N   ILE A 463 " --> pdb=" O   ALA A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 498
    Processing helix  chain 'A' and resid 515 through 527
    Processing helix  chain 'A' and resid 538 through 545
      removed outlier: 3.904A  pdb=" N   ILE A 542 " --> pdb=" O   ARG A 538 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLU A 543 " --> pdb=" O   LEU A 539 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   LYS A 544 " --> pdb=" O   SER A 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 561 through 568
      removed outlier: 3.760A  pdb=" N   GLU A 567 " --> pdb=" O   ASN A 563 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   HIS A 568 " --> pdb=" O   ASP A 564 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 571 through 580
    Processing helix  chain 'B' and resid 16 through 21
      removed outlier: 3.565A  pdb=" N   ILE B  20 " --> pdb=" O   LEU B  16 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 46
      removed outlier: 3.826A  pdb=" N   LEU B  34 " --> pdb=" O   ALA B  30 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   ASN B  37 " --> pdb=" O   ALA B  33 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 55
    Processing helix  chain 'B' and resid 62 through 91
      Proline residue:  B  68  - end of helix
      removed outlier: 3.689A  pdb=" N   ILE B  89 " --> pdb=" O   SER B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 91 through 105
      removed outlier: 4.192A  pdb=" N   VAL B  97 " --> pdb=" O   SER B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 118
      removed outlier: 4.030A  pdb=" N   PHE B 116 " --> pdb=" O   PRO B 112 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   LYS B 118 " --> pdb=" O   SER B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 130
      removed outlier: 3.772A  pdb=" N   SER B 126 " --> pdb=" O   GLY B 122 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   ILE B 128 " --> pdb=" O   LEU B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 150
      removed outlier: 4.459A  pdb=" N   ALA B 136 " --> pdb=" O   SER B 132 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLY B 141 " --> pdb=" O   SER B 137 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 151 through 164
      removed outlier: 3.505A  pdb=" N   MET B 160 " --> pdb=" O   LEU B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 213
      removed outlier: 3.687A  pdb=" N   ILE B 170 " --> pdb=" O   GLN B 166 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU B 174 " --> pdb=" O   ILE B 170 " (cutoff:3.500A)
      Proline residue:  B 176  - end of helix
      removed outlier: 4.065A  pdb=" N   GLY B 213 " --> pdb=" O   GLN B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 221
    Processing helix  chain 'B' and resid 222 through 249
      removed outlier: 3.781A  pdb=" N   LYS B 232 " --> pdb=" O   LYS B 228 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LYS B 243 " --> pdb=" O   LEU B 239 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 272
      removed outlier: 3.802A  pdb=" N   ILE B 254 " --> pdb=" O   ILE B 250 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   PHE B 272 " --> pdb=" O   TYR B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 294
    Processing helix  chain 'B' and resid 295 through 300
    Processing helix  chain 'B' and resid 303 through 323
      removed outlier: 3.832A  pdb=" N   ALA B 314 " --> pdb=" O   ARG B 310 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   CYS B 315 " --> pdb=" O   GLY B 311 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 390
      removed outlier: 3.578A  pdb=" N   ILE B 385 " --> pdb=" O   GLY B 381 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ALA B 386 " --> pdb=" O   LYS B 382 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LEU B 388 " --> pdb=" O   THR B 384 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   ILE B 389 " --> pdb=" O   ILE B 385 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   THR B 390 " --> pdb=" O   ALA B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 417
      removed outlier: 3.764A  pdb=" N   ASN B 417 " --> pdb=" O   ALA B 413 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 438
      removed outlier: 3.518A  pdb=" N   ALA B 438 " --> pdb=" O   ALA B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 446 through 457
    Processing helix  chain 'B' and resid 459 through 466
      removed outlier: 3.536A  pdb=" N   LYS B 465 " --> pdb=" O   ASP B 461 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 498
    Processing helix  chain 'B' and resid 514 through 527
      removed outlier: 3.983A  pdb=" N   ALA B 521 " --> pdb=" O   ARG B 517 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 538 through 544
    Processing helix  chain 'B' and resid 563 through 568
    Processing helix  chain 'B' and resid 571 through 580
    Processing sheet with id=AA1, first strand: chain 'A' and resid 365 through 366
      removed outlier: 3.594A  pdb=" N   VAL A 342 " --> pdb=" O   ILE A 366 " (cutoff:3.500A)
      removed outlier: 4.950A  pdb=" N   PHE A 344 " --> pdb=" O   LEU A 401 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   LEU A 401 " --> pdb=" O   PHE A 344 " (cutoff:3.500A)
      removed outlier: 4.993A  pdb=" N   ASN A 346 " --> pdb=" O   GLU A 399 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   GLU A 399 " --> pdb=" O   ASN A 346 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 419 through 422
      removed outlier: 6.734A  pdb=" N   ALA A 420 " --> pdb=" O   ILE A 503 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   LEU A 502 " --> pdb=" O   LEU A 533 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   THR A 371 " --> pdb=" O   GLU A 547 " (cutoff:3.500A)
      removed outlier: 8.214A  pdb=" N   VAL A 549 " --> pdb=" O   THR A 371 " (cutoff:3.500A)
      removed outlier: 6.071A  pdb=" N   ALA A 373 " --> pdb=" O   VAL A 549 " (cutoff:3.500A)
      removed outlier: 7.564A  pdb=" N   VAL A 551 " --> pdb=" O   ALA A 373 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   ILE A 548 " --> pdb=" O   ARG A 559 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   ARG A 559 " --> pdb=" O   ILE A 548 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   VAL A 550 " --> pdb=" O   VAL A 557 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 359 through 364
      removed outlier: 6.984A  pdb=" N   ARG B 360 " --> pdb=" O   THR B 348 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   THR B 348 " --> pdb=" O   ARG B 360 " (cutoff:3.500A)
      removed outlier: 5.045A  pdb=" N   ILE B 362 " --> pdb=" O   ASN B 346 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ARG B 345 " --> pdb=" O   GLU B 399 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   GLU B 399 " --> pdb=" O   ARG B 345 " (cutoff:3.500A)
      removed outlier: 5.098A  pdb=" N   VAL B 347 " --> pdb=" O   GLU B 397 " (cutoff:3.500A)
      removed outlier: 7.320A  pdb=" N   GLU B 397 " --> pdb=" O   VAL B 347 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 419 through 422
      removed outlier: 6.729A  pdb=" N   ALA B 420 " --> pdb=" O   ILE B 503 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   LEU B 502 " --> pdb=" O   LEU B 533 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   ILE B 535 " --> pdb=" O   LEU B 502 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   LEU B 504 " --> pdb=" O   ILE B 535 " (cutoff:3.500A)

    458 hydrogen bonds defined for protein.
    1362 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.56

  Time building geometry restraints manager: 2.86 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2578
        1.33 -     1.45: 1227
        1.45 -     1.57: 5040
        1.57 -     1.69: 1
        1.69 -     1.81: 104
  Bond restraints: 8950
  Sorted by residual:
  bond pdb=" N   VAL A 555 "
       pdb=" CA  VAL A 555 "
    ideal  model  delta    sigma   weight residual
    1.458  1.497 -0.039 1.17e-02 7.31e+03 1.12e+01
  bond pdb=" N   ILE A 556 "
       pdb=" CA  ILE A 556 "
    ideal  model  delta    sigma   weight residual
    1.457  1.496 -0.039 1.19e-02 7.06e+03 1.06e+01
  bond pdb=" N   VAL B 479 "
       pdb=" CA  VAL B 479 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.036 1.12e-02 7.97e+03 1.05e+01
  bond pdb=" N   THR A 280 "
       pdb=" CA  THR A 280 "
    ideal  model  delta    sigma   weight residual
    1.457  1.498 -0.041 1.29e-02 6.01e+03 9.91e+00
  bond pdb=" N   VAL A 550 "
       pdb=" CA  VAL A 550 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 1.14e-02 7.69e+03 9.48e+00
  ... (remaining 8945 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.24: 11900
        2.24 -     4.48: 167
        4.48 -     6.71: 19
        6.71 -     8.95: 5
        8.95 -    11.19: 1
  Bond angle restraints: 12092
  Sorted by residual:
  angle pdb=" N   LEU A 279 "
        pdb=" CA  LEU A 279 "
        pdb=" C   LEU A 279 "
      ideal   model   delta    sigma   weight residual
     112.59  101.40   11.19 1.22e+00 6.72e-01 8.41e+01
  angle pdb=" N   ASN B 529 "
        pdb=" CA  ASN B 529 "
        pdb=" C   ASN B 529 "
      ideal   model   delta    sigma   weight residual
     113.19  104.45    8.74 1.58e+00 4.01e-01 3.06e+01
  angle pdb=" N   ILE A  89 "
        pdb=" CA  ILE A  89 "
        pdb=" C   ILE A  89 "
      ideal   model   delta    sigma   weight residual
     111.81  107.47    4.34 8.60e-01 1.35e+00 2.55e+01
  angle pdb=" C   LEU A 279 "
        pdb=" CA  LEU A 279 "
        pdb=" CB  LEU A 279 "
      ideal   model   delta    sigma   weight residual
     111.02  117.91   -6.89 1.61e+00 3.86e-01 1.83e+01
  angle pdb=" C   MET B 276 "
        pdb=" N   ASP B 277 "
        pdb=" CA  ASP B 277 "
      ideal   model   delta    sigma   weight residual
     121.54  128.84   -7.30 1.91e+00 2.74e-01 1.46e+01
  ... (remaining 12087 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.44: 5045
       17.44 -    34.88: 324
       34.88 -    52.32: 72
       52.32 -    69.77: 7
       69.77 -    87.21: 6
  Dihedral angle restraints: 5454
    sinusoidal: 2164
      harmonic: 3290
  Sorted by residual:
  dihedral pdb=" CA  VAL A 433 "
           pdb=" C   VAL A 433 "
           pdb=" N   ALA A 434 "
           pdb=" CA  ALA A 434 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.30   26.70     0      5.00e+00 4.00e-02 2.85e+01
  dihedral pdb=" CA  ASP B 277 "
           pdb=" C   ASP B 277 "
           pdb=" N   SER B 278 "
           pdb=" CA  SER B 278 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.69   22.31     0      5.00e+00 4.00e-02 1.99e+01
  dihedral pdb=" CA  PHE B 105 "
           pdb=" C   PHE B 105 "
           pdb=" N   GLY B 106 "
           pdb=" CA  GLY B 106 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.43   21.57     0      5.00e+00 4.00e-02 1.86e+01
  ... (remaining 5451 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1156
       0.050 -    0.099: 225
       0.099 -    0.149: 49
       0.149 -    0.199: 7
       0.199 -    0.248: 3
  Chirality restraints: 1440
  Sorted by residual:
  chirality pdb=" CA  VAL A 550 "
            pdb=" N   VAL A 550 "
            pdb=" C   VAL A 550 "
            pdb=" CB  VAL A 550 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.69   -0.25 2.00e-01 2.50e+01 1.54e+00
  chirality pdb=" CA  ILE A 556 "
            pdb=" N   ILE A 556 "
            pdb=" C   ILE A 556 "
            pdb=" CB  ILE A 556 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.23 2.00e-01 2.50e+01 1.35e+00
  chirality pdb=" CB  VAL B 479 "
            pdb=" CA  VAL B 479 "
            pdb=" CG1 VAL B 479 "
            pdb=" CG2 VAL B 479 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.18e+00
  ... (remaining 1437 not shown)

  Planarity restraints: 1532
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 529 "    0.022 2.00e-02 2.50e+03   4.56e-02 2.08e+01
        pdb=" C   ASN A 529 "   -0.079 2.00e-02 2.50e+03
        pdb=" O   ASN A 529 "    0.030 2.00e-02 2.50e+03
        pdb=" N   ARG A 530 "    0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 279 "   -0.018 2.00e-02 2.50e+03   3.48e-02 1.21e+01
        pdb=" C   LEU A 279 "    0.060 2.00e-02 2.50e+03
        pdb=" O   LEU A 279 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   THR A 280 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 280 "    0.014 2.00e-02 2.50e+03   2.86e-02 8.16e+00
        pdb=" C   THR A 280 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   THR A 280 "    0.018 2.00e-02 2.50e+03
        pdb=" N   ALA A 281 "    0.017 2.00e-02 2.50e+03
  ... (remaining 1529 not shown)

  Histogram of nonbonded interaction distances:
        1.82 -     2.43: 22
        2.43 -     3.05: 5719
        3.05 -     3.67: 13170
        3.67 -     4.28: 19902
        4.28 -     4.90: 32673
  Nonbonded interactions: 71486
  Sorted by model distance:
  nonbonded pdb=" O   ASP A 564 "
            pdb=" OD1 ASP A 564 "
     model   vdw
     1.817 3.040
  nonbonded pdb=" OG  SER A 246 "
            pdb=" OH  TYR B  83 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" OG  SER A 446 "
            pdb=" OE1 GLN A 449 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" O   THR A 320 "
            pdb=" OG  SER A 324 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" O   THR A 285 "
            pdb=" OG  SER A 289 "
     model   vdw
     2.297 3.040
  ... (remaining 71481 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             23.010
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     24.430
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   51.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8950  Z= 0.227
  Angle     :  0.719  11.190  12092  Z= 0.429
  Chirality :  0.044   0.248   1440
  Planarity :  0.005   0.046   1532
  Dihedral  : 12.685  87.208   3326
  Min Nonbonded Distance : 1.817

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.61 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  7.85 %
    Favored  : 92.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.08 (0.23), residues: 1134
  helix: -1.26 (0.19), residues: 670
  sheet: -1.27 (0.63), residues: 52
  loop : -1.32 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  66 
 HIS   0.005   0.001   HIS A 576 
 PHE   0.010   0.001   PHE A 105 
 TYR   0.009   0.001   TYR A 163 
 ARG   0.004   0.000   ARG B 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.23134 (  458)
  hydrogen bonds       : angle       8.79136 ( 1362)
  covalent geometry    : bond        0.00430 ( 8950)
  covalent geometry    : angle       0.71948 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 180
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.8702 (tpp) cc_final: 0.8411 (mmp)
REVERT: A  144 ILE cc_start: 0.8596 (pt) cc_final: 0.8357 (pt)
REVERT: A  268 TYR cc_start: 0.8315 (t80) cc_final: 0.7977 (t80)
REVERT: B   67 MET cc_start: 0.8410 (ttm) cc_final: 0.8107 (tpp)
REVERT: B  405 HIS cc_start: 0.7215 (m90) cc_final: 0.6899 (m90)
REVERT: B  466 MET cc_start: 0.6343 (mmm) cc_final: 0.5794 (mtp)
  outliers start: 1
  outliers final: 1
  residues processed: 181
  average time/residue: 0.1984
  time to fit residues: 50.0107
Evaluate side-chains
  137 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 136
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  279 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.8980
   chunk 84 optimal weight:    1.9990
   chunk 47 optimal weight:    0.6980
   chunk 28 optimal weight:    4.9990
   chunk 57 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 87 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 101 optimal weight:    1.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 436 ASN
** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 361 ASN
B 449 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.172669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.144710 restraints weight = 11238.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.141218 restraints weight = 23267.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.139376 restraints weight = 29262.050|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.2024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   8950  Z= 0.208
  Angle     :  0.669   7.025  12092  Z= 0.352
  Chirality :  0.044   0.144   1440
  Planarity :  0.005   0.044   1532
  Dihedral  :  5.574  51.105   1240
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 11.78 %
    Favored  : 85.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.24), residues: 1134
  helix: -0.73 (0.19), residues: 692
  sheet:  0.60 (0.85), residues: 32
  loop : -1.43 (0.29), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  66 
 HIS   0.003   0.001   HIS B 405 
 PHE   0.013   0.002   PHE B 308 
 TYR   0.016   0.001   TYR B 410 
 ARG   0.003   0.000   ARG B 493 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04235 (  458)
  hydrogen bonds       : angle       5.29756 ( 1362)
  covalent geometry    : bond        0.00482 ( 8950)
  covalent geometry    : angle       0.66885 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 143
  time to evaluate  : 0.897 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 ARG cc_start: 0.6195 (OUTLIER) cc_final: 0.5656 (ptp-170)
REVERT: A   40 SER cc_start: 0.9261 (t) cc_final: 0.9003 (m)
REVERT: A   41 ASP cc_start: 0.7338 (t0) cc_final: 0.7111 (t0)
REVERT: A   44 MET cc_start: 0.8706 (ttt) cc_final: 0.8492 (ttt)
REVERT: A  111 MET cc_start: 0.7852 (ptp) cc_final: 0.7539 (ptp)
REVERT: A  144 ILE cc_start: 0.8547 (pt) cc_final: 0.8037 (mt)
  outliers start: 28
  outliers final: 15
  residues processed: 163
  average time/residue: 0.1910
  time to fit residues: 44.4119
Evaluate side-chains
  141 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 125
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ARG
Chi-restraints excluded: chain A residue   23 PHE
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  295 MET
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain B residue   20 ILE
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  172 ILE
Chi-restraints excluded: chain B residue  279 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 79 optimal weight:    0.6980
   chunk 62 optimal weight:    0.5980
   chunk 4 optimal weight:    0.0270
   chunk 46 optimal weight:    2.9990
   chunk 27 optimal weight:    0.5980
   chunk 10 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 48 optimal weight:    5.9990
   chunk 82 optimal weight:    1.9990
   overall best weight:    0.5638

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

Flipped N/Q/H residues before XYZ refinement:
** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 576 HIS
** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 430 ASN
B 449 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.175355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.147499 restraints weight = 11214.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.143415 restraints weight = 21171.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.141512 restraints weight = 25362.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.2459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8950  Z= 0.129
  Angle     :  0.585   8.309  12092  Z= 0.304
  Chirality :  0.041   0.135   1440
  Planarity :  0.004   0.043   1532
  Dihedral  :  5.294  57.400   1240
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 13.64 %
    Favored  : 83.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.03 (0.24), residues: 1134
  helix: -0.32 (0.19), residues: 706
  sheet:  0.92 (0.92), residues: 32
  loop : -1.30 (0.30), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  66 
 HIS   0.002   0.000   HIS A 562 
 PHE   0.014   0.001   PHE A 115 
 TYR   0.013   0.001   TYR B 410 
 ARG   0.002   0.000   ARG B 530 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03732 (  458)
  hydrogen bonds       : angle       4.88596 ( 1362)
  covalent geometry    : bond        0.00288 ( 8950)
  covalent geometry    : angle       0.58509 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 132
  time to evaluate  : 0.948 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 ARG cc_start: 0.6252 (OUTLIER) cc_final: 0.5858 (ptp-170)
REVERT: A  111 MET cc_start: 0.7358 (ptp) cc_final: 0.7028 (ptp)
REVERT: A  210 MET cc_start: 0.7610 (mmm) cc_final: 0.7369 (mmt)
REVERT: B   67 MET cc_start: 0.9031 (tpp) cc_final: 0.8697 (tpp)
  outliers start: 23
  outliers final: 14
  residues processed: 144
  average time/residue: 0.1858
  time to fit residues: 38.3103
Evaluate side-chains
  133 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ARG
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   66 TRP
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  295 MET
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain B residue   20 ILE
Chi-restraints excluded: chain B residue   23 PHE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  279 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 87 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0980
   chunk 23 optimal weight:    2.9990
   chunk 98 optimal weight:    0.6980
   chunk 39 optimal weight:    0.0570
   chunk 16 optimal weight:    0.9980
   chunk 92 optimal weight:    9.9990
   chunk 99 optimal weight:    0.9990
   chunk 107 optimal weight:    8.9990
   chunk 2 optimal weight:    2.9990
   chunk 77 optimal weight:    0.6980
   overall best weight:    0.4298

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

Flipped N/Q/H residues before XYZ refinement:
** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 576 HIS
** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.176155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.148431 restraints weight = 11073.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.143366 restraints weight = 19877.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.142888 restraints weight = 27635.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7513
moved from start:          0.2779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8950  Z= 0.115
  Angle     :  0.573   7.142  12092  Z= 0.296
  Chirality :  0.040   0.137   1440
  Planarity :  0.004   0.043   1532
  Dihedral  :  5.120  57.623   1240
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 14.26 %
    Favored  : 82.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.70 (0.25), residues: 1134
  helix: -0.01 (0.20), residues: 706
  sheet: -0.47 (0.69), residues: 60
  loop : -1.15 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  66 
 HIS   0.002   0.000   HIS B 214 
 PHE   0.011   0.001   PHE A 115 
 TYR   0.012   0.001   TYR B 410 
 ARG   0.002   0.000   ARG A 455 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03431 (  458)
  hydrogen bonds       : angle       4.60968 ( 1362)
  covalent geometry    : bond        0.00252 ( 8950)
  covalent geometry    : angle       0.57308 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 131
  time to evaluate  : 0.900 
Fit side-chains
REVERT: A   14 ARG cc_start: 0.6274 (OUTLIER) cc_final: 0.5950 (ptp-170)
REVERT: A  111 MET cc_start: 0.7453 (ptp) cc_final: 0.7091 (ptp)
REVERT: A  210 MET cc_start: 0.7490 (mmm) cc_final: 0.7283 (mmt)
REVERT: B   67 MET cc_start: 0.9033 (tpp) cc_final: 0.8678 (tpp)
  outliers start: 32
  outliers final: 17
  residues processed: 153
  average time/residue: 0.1788
  time to fit residues: 39.3004
Evaluate side-chains
  136 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ARG
Chi-restraints excluded: chain A residue   23 PHE
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   66 TRP
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain B residue   23 PHE
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  576 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 78 optimal weight:    0.9990
   chunk 35 optimal weight:    9.9990
   chunk 89 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0770
   chunk 11 optimal weight:    0.9990
   chunk 70 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 40 optimal weight:    8.9990
   chunk 9 optimal weight:    1.9990
   chunk 60 optimal weight:    0.5980
   chunk 66 optimal weight:    8.9990
   overall best weight:    0.6742

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

Flipped N/Q/H residues before XYZ refinement:
** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 576 HIS
A 579 GLN
** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.175273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.148269 restraints weight = 11072.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.144410 restraints weight = 22341.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.143857 restraints weight = 25787.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7504
moved from start:          0.2962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8950  Z= 0.134
  Angle     :  0.597  10.742  12092  Z= 0.306
  Chirality :  0.041   0.136   1440
  Planarity :  0.004   0.042   1532
  Dihedral  :  5.133  59.817   1240
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 14.88 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.25), residues: 1134
  helix:  0.09 (0.20), residues: 706
  sheet:  1.31 (0.97), residues: 32
  loop : -1.32 (0.30), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  66 
 HIS   0.001   0.000   HIS B 214 
 PHE   0.012   0.001   PHE B 105 
 TYR   0.009   0.001   TYR B 410 
 ARG   0.004   0.000   ARG B  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03492 (  458)
  hydrogen bonds       : angle       4.59870 ( 1362)
  covalent geometry    : bond        0.00303 ( 8950)
  covalent geometry    : angle       0.59670 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 127
  time to evaluate  : 0.909 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ARG cc_start: 0.6348 (OUTLIER) cc_final: 0.5992 (ptp-170)
REVERT: A  210 MET cc_start: 0.7496 (mmm) cc_final: 0.7221 (mmt)
REVERT: B   67 MET cc_start: 0.9032 (tpp) cc_final: 0.8656 (tpp)
  outliers start: 32
  outliers final: 20
  residues processed: 148
  average time/residue: 0.1976
  time to fit residues: 42.0286
Evaluate side-chains
  135 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 114
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ARG
Chi-restraints excluded: chain A residue   23 PHE
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   66 TRP
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain B residue   23 PHE
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  576 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 63 optimal weight:    0.3980
   chunk 4 optimal weight:    0.0030
   chunk 86 optimal weight:    0.9990
   chunk 51 optimal weight:    0.7980
   chunk 55 optimal weight:   30.0000
   chunk 33 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 101 optimal weight:    6.9990
   chunk 106 optimal weight:    4.9990
   chunk 7 optimal weight:    0.3980
   chunk 29 optimal weight:    0.0010
   overall best weight:    0.3196

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

Flipped N/Q/H residues before XYZ refinement:
** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 436 ASN
A 576 HIS
** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 309 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.178797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.151544 restraints weight = 10951.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.146864 restraints weight = 18098.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.145631 restraints weight = 22656.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7488
moved from start:          0.3223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   8950  Z= 0.112
  Angle     :  0.589  11.525  12092  Z= 0.300
  Chirality :  0.040   0.156   1440
  Planarity :  0.004   0.041   1532
  Dihedral  :  5.001  59.738   1240
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 15.81 %
    Favored  : 80.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.25), residues: 1134
  helix:  0.36 (0.20), residues: 684
  sheet: -0.24 (0.70), residues: 60
  loop : -1.30 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  66 
 HIS   0.002   0.000   HIS B 214 
 PHE   0.038   0.001   PHE B 115 
 TYR   0.009   0.001   TYR B 410 
 ARG   0.003   0.000   ARG A 455 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03253 (  458)
  hydrogen bonds       : angle       4.49395 ( 1362)
  covalent geometry    : bond        0.00244 ( 8950)
  covalent geometry    : angle       0.58884 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 122
  time to evaluate  : 0.982 
Fit side-chains
   revert: symmetry clash
REVERT: A  210 MET cc_start: 0.7257 (mmm) cc_final: 0.7034 (mmt)
REVERT: A  502 LEU cc_start: 0.7736 (mp) cc_final: 0.7441 (mp)
  outliers start: 39
  outliers final: 24
  residues processed: 150
  average time/residue: 0.1983
  time to fit residues: 41.9287
Evaluate side-chains
  146 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 122
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   66 TRP
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  295 MET
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   23 PHE
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  114 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  279 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 103 optimal weight:    0.9990
   chunk 100 optimal weight:    6.9990
   chunk 57 optimal weight:    0.5980
   chunk 104 optimal weight:    3.9990
   chunk 40 optimal weight:    6.9990
   chunk 70 optimal weight:    0.6980
   chunk 74 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 59 optimal weight:    0.1980
   chunk 30 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 576 HIS
** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.179443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.151520 restraints weight = 11124.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 71)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.146140 restraints weight = 20225.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.145468 restraints weight = 26516.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.3309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8950  Z= 0.135
  Angle     :  0.600  10.047  12092  Z= 0.305
  Chirality :  0.041   0.133   1440
  Planarity :  0.003   0.041   1532
  Dihedral  :  5.027  58.332   1240
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 17.15 %
    Favored  : 79.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.25), residues: 1134
  helix:  0.28 (0.20), residues: 694
  sheet: -0.05 (0.72), residues: 60
  loop : -1.37 (0.30), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  66 
 HIS   0.002   0.000   HIS B 214 
 PHE   0.022   0.001   PHE B 115 
 TYR   0.007   0.001   TYR B 410 
 ARG   0.003   0.000   ARG A 455 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03426 (  458)
  hydrogen bonds       : angle       4.51057 ( 1362)
  covalent geometry    : bond        0.00306 ( 8950)
  covalent geometry    : angle       0.60005 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 122
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
  outliers start: 29
  outliers final: 24
  residues processed: 143
  average time/residue: 0.1866
  time to fit residues: 38.0522
Evaluate side-chains
  142 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 118
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ARG
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   66 TRP
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  295 MET
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   23 PHE
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  576 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 96 optimal weight:    0.5980
   chunk 51 optimal weight:    8.9990
   chunk 85 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 102 optimal weight:    4.9990
   chunk 99 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9980
   chunk 41 optimal weight:    4.9990
   chunk 49 optimal weight:    0.0030
   overall best weight:    1.7194

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

Flipped N/Q/H residues before XYZ refinement:
** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 576 HIS
** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.173406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.146254 restraints weight = 11372.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.143472 restraints weight = 24323.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.141254 restraints weight = 29740.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.3350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   8950  Z= 0.241
  Angle     :  0.701  11.413  12092  Z= 0.358
  Chirality :  0.045   0.174   1440
  Planarity :  0.004   0.042   1532
  Dihedral  :  5.389  56.202   1240
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 17.56 %
    Favored  : 79.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.24), residues: 1134
  helix: -0.14 (0.19), residues: 710
  sheet:  0.12 (0.74), residues: 60
  loop : -1.29 (0.31), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B  66 
 HIS   0.002   0.001   HIS A 214 
 PHE   0.019   0.002   PHE B 349 
 TYR   0.011   0.001   TYR A  87 
 ARG   0.006   0.000   ARG A 455 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04005 (  458)
  hydrogen bonds       : angle       4.83839 ( 1362)
  covalent geometry    : bond        0.00562 ( 8950)
  covalent geometry    : angle       0.70129 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 123
  time to evaluate  : 0.914 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 ILE cc_start: 0.8711 (pt) cc_final: 0.8124 (mt)
REVERT: A  304 VAL cc_start: 0.8202 (OUTLIER) cc_final: 0.7989 (p)
  outliers start: 33
  outliers final: 27
  residues processed: 148
  average time/residue: 0.1937
  time to fit residues: 41.0917
Evaluate side-chains
  144 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 116
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ARG
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   66 TRP
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  295 MET
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain B residue   23 PHE
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  349 PHE
Chi-restraints excluded: chain B residue  531 THR
Chi-restraints excluded: chain B residue  576 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 74 optimal weight:    0.9980
   chunk 27 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9980
   chunk 6 optimal weight:    0.5980
   chunk 79 optimal weight:    0.7980
   chunk 16 optimal weight:    0.2980
   chunk 87 optimal weight:    3.9990
   chunk 77 optimal weight:    0.0470
   chunk 49 optimal weight:    6.9990
   chunk 32 optimal weight:    0.5980
   overall best weight:    0.4278

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

Flipped N/Q/H residues before XYZ refinement:
** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 576 HIS
** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.179111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.152370 restraints weight = 11027.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.147418 restraints weight = 21109.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.147357 restraints weight = 24692.584|
|-----------------------------------------------------------------------------|
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.3444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8950  Z= 0.120
  Angle     :  0.619  11.256  12092  Z= 0.315
  Chirality :  0.041   0.190   1440
  Planarity :  0.004   0.041   1532
  Dihedral  :  5.183  59.163   1240
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 18.80 %
    Favored  : 78.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.25), residues: 1134
  helix:  0.24 (0.20), residues: 690
  sheet:  0.08 (0.73), residues: 60
  loop : -1.25 (0.30), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B  66 
 HIS   0.002   0.000   HIS A 214 
 PHE   0.035   0.001   PHE B 115 
 TYR   0.006   0.001   TYR B 410 
 ARG   0.004   0.000   ARG A 455 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03454 (  458)
  hydrogen bonds       : angle       4.62322 ( 1362)
  covalent geometry    : bond        0.00264 ( 8950)
  covalent geometry    : angle       0.61859 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 122
  time to evaluate  : 0.976 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  210 MET cc_start: 0.7427 (mmm) cc_final: 0.7150 (mmt)
REVERT: A  304 VAL cc_start: 0.8154 (OUTLIER) cc_final: 0.7924 (p)
  outliers start: 26
  outliers final: 23
  residues processed: 143
  average time/residue: 0.1954
  time to fit residues: 40.1090
Evaluate side-chains
  143 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 119
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ARG
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   66 TRP
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  295 MET
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain B residue   23 PHE
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  133 GLU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  576 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 95 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   chunk 70 optimal weight:    0.7980
   chunk 87 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9980
   chunk 73 optimal weight:    0.8980
   chunk 8 optimal weight:    0.6980
   chunk 88 optimal weight:   20.0000
   chunk 100 optimal weight:    5.9990
   chunk 68 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 424 GLN
** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 576 HIS
** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.173564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.145963 restraints weight = 11147.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.142992 restraints weight = 24125.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.141495 restraints weight = 27282.777|
|-----------------------------------------------------------------------------|
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.3490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8950  Z= 0.151
  Angle     :  0.638  11.174  12092  Z= 0.327
  Chirality :  0.042   0.169   1440
  Planarity :  0.004   0.050   1532
  Dihedral  :  5.210  58.269   1240
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 19.52 %
    Favored  : 77.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.25), residues: 1134
  helix:  0.15 (0.20), residues: 692
  sheet:  0.05 (0.72), residues: 60
  loop : -1.23 (0.30), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B  66 
 HIS   0.002   0.000   HIS B 214 
 PHE   0.032   0.002   PHE B 115 
 TYR   0.005   0.001   TYR A  87 
 ARG   0.017   0.000   ARG A 455 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03629 (  458)
  hydrogen bonds       : angle       4.69178 ( 1362)
  covalent geometry    : bond        0.00346 ( 8950)
  covalent geometry    : angle       0.63783 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 123
  time to evaluate  : 0.948 
Fit side-chains
   revert: symmetry clash
REVERT: A  144 ILE cc_start: 0.8638 (pt) cc_final: 0.7988 (mt)
REVERT: A  210 MET cc_start: 0.7458 (mmm) cc_final: 0.7192 (mmt)
REVERT: A  304 VAL cc_start: 0.8125 (OUTLIER) cc_final: 0.7887 (p)
  outliers start: 25
  outliers final: 24
  residues processed: 141
  average time/residue: 0.1877
  time to fit residues: 38.0026
Evaluate side-chains
  145 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 120
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ARG
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   66 TRP
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  295 MET
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain B residue   23 PHE
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  133 GLU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  412 LEU
Chi-restraints excluded: chain B residue  576 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 78 optimal weight:    0.9980
   chunk 37 optimal weight:    0.6980
   chunk 12 optimal weight:    4.9990
   chunk 40 optimal weight:    7.9990
   chunk 53 optimal weight:   10.0000
   chunk 86 optimal weight:    0.7980
   chunk 54 optimal weight:   20.0000
   chunk 111 optimal weight:    8.9990
   chunk 102 optimal weight:    1.9990
   chunk 84 optimal weight:    0.8980
   chunk 87 optimal weight:   10.0000
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 576 HIS
** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.176361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.150025 restraints weight = 11130.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.146704 restraints weight = 23985.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.145306 restraints weight = 27282.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.3550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8950  Z= 0.173
  Angle     :  0.656  11.080  12092  Z= 0.335
  Chirality :  0.043   0.167   1440
  Planarity :  0.004   0.049   1532
  Dihedral  :  5.281  58.431   1240
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 19.32 %
    Favored  : 77.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (0.25), residues: 1134
  helix:  0.06 (0.20), residues: 692
  sheet: -0.17 (0.79), residues: 52
  loop : -1.38 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B  66 
 HIS   0.001   0.000   HIS A 427 
 PHE   0.031   0.002   PHE B 115 
 TYR   0.007   0.001   TYR A  87 
 ARG   0.013   0.000   ARG A 455 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03764 (  458)
  hydrogen bonds       : angle       4.75510 ( 1362)
  covalent geometry    : bond        0.00399 ( 8950)
  covalent geometry    : angle       0.65620 (12092)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3253.24 seconds
wall clock time: 57 minutes 23.63 seconds (3443.63 seconds total)