Starting phenix.real_space_refine
on Mon May 12 07:43:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fus_50776/05_2025/9fus_50776.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fus_50776/05_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_50776/05_2025/9fus_50776.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fus_50776/05_2025/9fus_50776.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fus_50776/05_2025/9fus_50776.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fus_50776/05_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 5.95, per 1000 atoms: 0.67
  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: 2.40
  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: 0.94
  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: 2.52

  Time building geometry restraints manager: 2.77 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: 0.05
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:             3.230
  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:          0.440
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     23.700
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.670
-------------------------------------------------------------------------------
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  : 1.006 
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: 0.2044
  time to fit residues: 51.3186
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  : 1.019 
-------------------------------------------------------------------------------
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 = 0.144718 restraints weight = 11238.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.141241 restraints weight = 23062.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.139202 restraints weight = 29509.340|
|-----------------------------------------------------------------------------|
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
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       5.29757 ( 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  : 0.920 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 ARG cc_start: 0.6196 (OUTLIER) cc_final: 0.5656 (ptp-170)
REVERT: A   40 SER cc_start: 0.9261 (t) cc_final: 0.9005 (m)
REVERT: A   41 ASP cc_start: 0.7336 (t0) cc_final: 0.7112 (t0)
REVERT: A   44 MET cc_start: 0.8712 (ttt) cc_final: 0.8499 (ttt)
REVERT: A  111 MET cc_start: 0.7853 (ptp) cc_final: 0.7540 (ptp)
REVERT: A  144 ILE cc_start: 0.8549 (pt) cc_final: 0.8038 (mt)
  outliers start: 28
  outliers final: 15
  residues processed: 163
  average time/residue: 0.1844
  time to fit residues: 42.6762
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  : 0.889 
-------------------------------------------------------------------------------
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:    0.0970
   chunk 46 optimal weight:    0.3980
   chunk 27 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0010
   chunk 52 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   overall best weight:    0.3584

-------------------------------------------------------------------------------
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 449 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.180630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.154861 restraints weight = 11116.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.149666 restraints weight = 22180.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.148150 restraints weight = 26300.646|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.2493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8950  Z= 0.118
  Angle     :  0.577   8.195  12092  Z= 0.300
  Chirality :  0.040   0.138   1440
  Planarity :  0.004   0.043   1532
  Dihedral  :  5.231  57.244   1240
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 13.74 %
    Favored  : 83.78 %
  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: -0.97 (0.24), residues: 1134
  helix: -0.26 (0.19), residues: 706
  sheet:  0.95 (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   0.001   HIS A 576 
 PHE   0.013   0.001   PHE A 115 
 TYR   0.014   0.001   TYR B 410 
 ARG   0.002   0.000   ARG B 497 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03634 (  458)
  hydrogen bonds       : angle       4.84154 ( 1362)
  covalent geometry    : bond        0.00256 ( 8950)
  covalent geometry    : angle       0.57742 (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
  157 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 133
  time to evaluate  : 0.947 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 ARG cc_start: 0.6228 (OUTLIER) cc_final: 0.5788 (ptp-170)
REVERT: A  111 MET cc_start: 0.7290 (ptp) cc_final: 0.6948 (ptp)
REVERT: B   67 MET cc_start: 0.9018 (tpp) cc_final: 0.8693 (tpp)
  outliers start: 24
  outliers final: 15
  residues processed: 146
  average time/residue: 0.1864
  time to fit residues: 38.8954
Evaluate side-chains
  134 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
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  284 ILE
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:    1.9990
   chunk 5 optimal weight:    0.0770
   chunk 23 optimal weight:    0.9990
   chunk 98 optimal weight:    0.5980
   chunk 39 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   chunk 92 optimal weight:    9.9990
   chunk 99 optimal weight:    2.9990
   chunk 107 optimal weight:    7.9990
   chunk 2 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   overall best weight:    0.6140

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.179263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.152643 restraints weight = 11026.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 64)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.147393 restraints weight = 18970.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.147304 restraints weight = 25593.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.2712

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= 0.130
  Angle     :  0.584   7.165  12092  Z= 0.300
  Chirality :  0.040   0.138   1440
  Planarity :  0.004   0.042   1532
  Dihedral  :  5.161  58.065   1240
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 14.98 %
    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: -0.73 (0.25), residues: 1134
  helix: -0.04 (0.20), residues: 706
  sheet:  1.09 (0.95), residues: 32
  loop : -1.27 (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   0.011   0.001   TYR B 410 
 ARG   0.003   0.000   ARG A 455 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03520 (  458)
  hydrogen bonds       : angle       4.66222 ( 1362)
  covalent geometry    : bond        0.00289 ( 8950)
  covalent geometry    : angle       0.58362 (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
  153 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 122
  time to evaluate  : 1.006 
Fit side-chains
REVERT: A   14 ARG cc_start: 0.6254 (OUTLIER) cc_final: 0.5912 (ptp-170)
REVERT: B   67 MET cc_start: 0.9041 (tpp) cc_final: 0.8645 (tpp)
  outliers start: 31
  outliers final: 16
  residues processed: 142
  average time/residue: 0.1952
  time to fit residues: 39.8946
Evaluate side-chains
  134 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
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  169 ILE
Chi-restraints excluded: chain A residue  279 LEU
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:    0.6980
   chunk 35 optimal weight:    6.9990
   chunk 89 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 70 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.4012 r_free = 0.4012 target = 0.178432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.150592 restraints weight = 11007.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.147885 restraints weight = 20674.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.146803 restraints weight = 21803.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.2950

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= 0.145
  Angle     :  0.605  11.271  12092  Z= 0.311
  Chirality :  0.041   0.134   1440
  Planarity :  0.004   0.042   1532
  Dihedral  :  5.177  59.484   1240
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 14.67 %
    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: -0.66 (0.25), residues: 1134
  helix:  0.01 (0.20), residues: 706
  sheet:  1.31 (0.97), residues: 32
  loop : -1.26 (0.30), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  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   0.002   0.000   ARG A 455 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03547 (  458)
  hydrogen bonds       : angle       4.66223 ( 1362)
  covalent geometry    : bond        0.00330 ( 8950)
  covalent geometry    : angle       0.60525 (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
  157 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 123
  time to evaluate  : 0.989 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   67 MET cc_start: 0.9049 (tpp) cc_final: 0.8664 (tpp)
  outliers start: 34
  outliers final: 23
  residues processed: 145
  average time/residue: 0.1952
  time to fit residues: 40.5457
Evaluate side-chains
  136 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
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   85 SER
Chi-restraints excluded: chain A residue   89 ILE
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  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   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:    0.6980
   chunk 4 optimal weight:    0.1980
   chunk 86 optimal weight:    0.5980
   chunk 51 optimal weight:    8.9990
   chunk 55 optimal weight:    8.9990
   chunk 33 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 101 optimal weight:    0.6980
   chunk 106 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   chunk 29 optimal weight:    0.4980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 309 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.176678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.149455 restraints weight = 10994.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.144620 restraints weight = 20088.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.143955 restraints weight = 26065.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7517
moved from start:          0.3111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8950  Z= 0.128
  Angle     :  0.613  10.893  12092  Z= 0.314
  Chirality :  0.041   0.147   1440
  Planarity :  0.004   0.041   1532
  Dihedral  :  5.099  59.154   1240
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 17.05 %
    Favored  : 79.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.53 (0.25), residues: 1134
  helix:  0.20 (0.20), residues: 692
  sheet: -0.24 (0.70), residues: 60
  loop : -1.25 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  66 
 HIS   0.002   0.000   HIS B 214 
 PHE   0.016   0.001   PHE B  56 
 TYR   0.008   0.001   TYR B 410 
 ARG   0.003   0.000   ARG A 455 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03401 (  458)
  hydrogen bonds       : angle       4.62002 ( 1362)
  covalent geometry    : bond        0.00284 ( 8950)
  covalent geometry    : angle       0.61269 (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
  147 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 116
  time to evaluate  : 1.079 
Fit side-chains
   revert: symmetry clash
REVERT: B   67 MET cc_start: 0.9034 (tpp) cc_final: 0.8640 (tpp)
  outliers start: 31
  outliers final: 22
  residues processed: 138
  average time/residue: 0.1939
  time to fit residues: 38.1770
Evaluate side-chains
  134 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  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   66 TRP
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  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   97 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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 103 optimal weight:    7.9990
   chunk 100 optimal weight:    3.9990
   chunk 57 optimal weight:    0.0670
   chunk 104 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   chunk 74 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9990
   chunk 59 optimal weight:    0.3980
   chunk 30 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   overall best weight:    0.6318

-------------------------------------------------------------------------------
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 = 0.176303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.148963 restraints weight = 11137.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.145221 restraints weight = 20529.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.144445 restraints weight = 26353.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.3233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8950  Z= 0.131
  Angle     :  0.610   8.881  12092  Z= 0.311
  Chirality :  0.041   0.144   1440
  Planarity :  0.004   0.041   1532
  Dihedral  :  5.087  58.737   1240
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 17.15 %
    Favored  : 79.44 %
  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: -0.52 (0.25), residues: 1134
  helix:  0.15 (0.20), residues: 706
  sheet: -0.02 (0.72), residues: 60
  loop : -1.17 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A  66 
 HIS   0.002   0.000   HIS B 214 
 PHE   0.012   0.001   PHE B  56 
 TYR   0.007   0.001   TYR B 410 
 ARG   0.004   0.000   ARG A 530 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03463 (  458)
  hydrogen bonds       : angle       4.60738 ( 1362)
  covalent geometry    : bond        0.00296 ( 8950)
  covalent geometry    : angle       0.61007 (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
  150 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 117
  time to evaluate  : 0.950 
Fit side-chains
   revert: symmetry clash
REVERT: A  304 VAL cc_start: 0.8147 (OUTLIER) cc_final: 0.7892 (p)
REVERT: B   67 MET cc_start: 0.9003 (tpp) cc_final: 0.8633 (tpp)
  outliers start: 33
  outliers final: 25
  residues processed: 141
  average time/residue: 0.1974
  time to fit residues: 39.7183
Evaluate side-chains
  138 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 112
  time to evaluate  : 1.022 
-------------------------------------------------------------------------------
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   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  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  135 VAL
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  242 MET
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:    8.9990
   chunk 51 optimal weight:   10.0000
   chunk 85 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 102 optimal weight:    0.0970
   chunk 99 optimal weight:    1.9990
   chunk 37 optimal weight:    5.9990
   chunk 86 optimal weight:    0.9980
   chunk 41 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
A 209 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 = 0.3943 r_free = 0.3943 target = 0.171064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.142994 restraints weight = 11338.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.140982 restraints weight = 24592.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.138101 restraints weight = 26892.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.3299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   8950  Z= 0.210
  Angle     :  0.672  10.170  12092  Z= 0.343
  Chirality :  0.044   0.139   1440
  Planarity :  0.004   0.055   1532
  Dihedral  :  5.309  56.551   1240
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 17.46 %
    Favored  : 79.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.81 (0.24), residues: 1134
  helix: -0.11 (0.19), residues: 712
  sheet:  1.42 (1.01), residues: 32
  loop : -1.35 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A  66 
 HIS   0.002   0.000   HIS A 214 
 PHE   0.022   0.002   PHE B 349 
 TYR   0.009   0.001   TYR A  87 
 ARG   0.008   0.000   ARG A 530 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03894 (  458)
  hydrogen bonds       : angle       4.79171 ( 1362)
  covalent geometry    : bond        0.00486 ( 8950)
  covalent geometry    : angle       0.67237 (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
  149 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 117
  time to evaluate  : 0.935 
Fit side-chains
   revert: symmetry clash
REVERT: A  144 ILE cc_start: 0.8558 (pt) cc_final: 0.7944 (mt)
REVERT: A  304 VAL cc_start: 0.8180 (OUTLIER) cc_final: 0.7970 (p)
  outliers start: 32
  outliers final: 26
  residues processed: 142
  average time/residue: 0.1916
  time to fit residues: 39.2462
Evaluate side-chains
  135 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 108
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
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   85 SER
Chi-restraints excluded: chain A residue  113 VAL
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   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  242 MET
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 74 optimal weight:    0.5980
   chunk 27 optimal weight:    0.8980
   chunk 3 optimal weight:    0.8980
   chunk 78 optimal weight:    0.5980
   chunk 6 optimal weight:    0.6980
   chunk 79 optimal weight:    0.0670
   chunk 16 optimal weight:    0.1980
   chunk 87 optimal weight:    6.9990
   chunk 77 optimal weight:    0.7980
   chunk 49 optimal weight:    3.9990
   chunk 32 optimal weight:    0.1980
   overall best weight:    0.3318

-------------------------------------------------------------------------------
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 = 0.4023 r_free = 0.4023 target = 0.179610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.151805 restraints weight = 11014.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.145783 restraints weight = 18010.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.143164 restraints weight = 23106.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.3425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8950  Z= 0.120
  Angle     :  0.630  10.960  12092  Z= 0.320
  Chirality :  0.041   0.177   1440
  Planarity :  0.004   0.050   1532
  Dihedral  :  5.148  59.229   1240
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 18.80 %
    Favored  : 78.31 %
  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: -0.54 (0.25), residues: 1134
  helix:  0.21 (0.20), residues: 694
  sheet: -0.02 (0.72), residues: 60
  loop : -1.33 (0.30), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B  66 
 HIS   0.002   0.000   HIS A 576 
 PHE   0.011   0.001   PHE B  56 
 TYR   0.006   0.001   TYR B 410 
 ARG   0.010   0.000   ARG B 447 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03470 (  458)
  hydrogen bonds       : angle       4.66316 ( 1362)
  covalent geometry    : bond        0.00262 ( 8950)
  covalent geometry    : angle       0.62983 (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
  145 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 117
  time to evaluate  : 1.062 
Fit side-chains
REVERT: A  304 VAL cc_start: 0.8179 (OUTLIER) cc_final: 0.7939 (p)
  outliers start: 28
  outliers final: 25
  residues processed: 138
  average time/residue: 0.2010
  time to fit residues: 39.4393
Evaluate side-chains
  139 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 113
  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   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  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  135 VAL
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  242 MET
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:    0.6980
   chunk 95 optimal weight:    0.4980
   chunk 72 optimal weight:    0.8980
   chunk 70 optimal weight:    1.9990
   chunk 87 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 88 optimal weight:   10.0000
   chunk 100 optimal weight:    0.9980
   chunk 68 optimal weight:    0.7980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4005 r_free = 0.4005 target = 0.177764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.151593 restraints weight = 11041.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.146671 restraints weight = 23179.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.145373 restraints weight = 28580.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.3495

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= 0.142
  Angle     :  0.639  11.024  12092  Z= 0.324
  Chirality :  0.042   0.168   1440
  Planarity :  0.004   0.041   1532
  Dihedral  :  5.162  58.300   1240
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 18.70 %
    Favored  : 78.10 %
  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:  0.17 (0.20), residues: 698
  sheet:  0.16 (0.73), residues: 60
  loop : -1.33 (0.30), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B  66 
 HIS   0.003   0.000   HIS A 576 
 PHE   0.012   0.001   PHE B 105 
 TYR   0.006   0.001   TYR B 410 
 ARG   0.006   0.000   ARG A 455 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03581 (  458)
  hydrogen bonds       : angle       4.64929 ( 1362)
  covalent geometry    : bond        0.00324 ( 8950)
  covalent geometry    : angle       0.63908 (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
  149 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 118
  time to evaluate  : 1.027 
Fit side-chains
   revert: symmetry clash
REVERT: A  144 ILE cc_start: 0.8589 (pt) cc_final: 0.8021 (mt)
REVERT: A  304 VAL cc_start: 0.8145 (OUTLIER) cc_final: 0.7916 (p)
  outliers start: 31
  outliers final: 28
  residues processed: 139
  average time/residue: 0.1999
  time to fit residues: 40.1180
Evaluate side-chains
  147 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 118
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
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   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  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  242 MET
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  405 HIS
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:    0.7980
   chunk 37 optimal weight:    0.4980
   chunk 12 optimal weight:    4.9990
   chunk 40 optimal weight:    6.9990
   chunk 53 optimal weight:    7.9990
   chunk 86 optimal weight:    0.7980
   chunk 54 optimal weight:    7.9990
   chunk 111 optimal weight:    8.9990
   chunk 102 optimal weight:    8.9990
   chunk 84 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.4004 r_free = 0.4004 target = 0.177712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.150708 restraints weight = 11080.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.146347 restraints weight = 18892.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.145774 restraints weight = 23824.173|
|-----------------------------------------------------------------------------|
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.3570

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= 0.147
  Angle     :  0.640  10.977  12092  Z= 0.325
  Chirality :  0.042   0.170   1440
  Planarity :  0.004   0.044   1532
  Dihedral  :  5.188  58.726   1240
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 18.80 %
    Favored  : 77.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.52 (0.25), residues: 1134
  helix:  0.22 (0.20), residues: 692
  sheet:  0.23 (0.72), residues: 60
  loop : -1.36 (0.30), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B  66 
 HIS   0.003   0.000   HIS A 576 
 PHE   0.011   0.001   PHE B  56 
 TYR   0.005   0.001   TYR A  87 
 ARG   0.010   0.000   ARG A 455 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03584 (  458)
  hydrogen bonds       : angle       4.64088 ( 1362)
  covalent geometry    : bond        0.00336 ( 8950)
  covalent geometry    : angle       0.63989 (12092)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3051.43 seconds
wall clock time: 54 minutes 28.89 seconds (3268.89 seconds total)