Starting phenix.real_space_refine
on Wed Sep 17 13:11:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fus_50776/09_2025/9fus_50776.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fus_50776/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fus_50776/09_2025/9fus_50776.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fus_50776/09_2025/9fus_50776.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fus_50776/09_2025/9fus_50776.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fus_50776/09_2025/9fus_50776.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.013
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.36, per 1000 atoms: 0.27
  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: 0.85
  Conformation dependent library (CDL) restraints added in 330.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.23
  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: 1.51

  Time building geometry restraints manager: 1.12 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: 0.01
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:             3.970
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     9.890
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.550
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.004   0.000   ARG B 101 
 TYR   0.009   0.001   TYR A 163 
 PHE   0.010   0.001   PHE A 105 
 TRP   0.013   0.001   TRP B  66 
 HIS   0.005   0.001   HIS A 576 

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

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

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 180
  time to evaluate  : 0.362 
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: 0.0930
  time to fit residues: 23.6481
Evaluate side-chains
  137 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 136
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
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 108 optimal weight:    5.9990
   chunk 49 optimal weight:   10.0000
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:    3.9990
   chunk 106 optimal weight:    3.9990
   overall best weight:    1.5386

-------------------------------------------------------------------------------
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 = 0.3945 r_free = 0.3945 target = 0.171679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.143418 restraints weight = 11394.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.141142 restraints weight = 25748.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.140090 restraints weight = 28609.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.139342 restraints weight = 21179.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.138739 restraints weight = 22776.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.1971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   8950  Z= 0.233
  Angle     :  0.684   7.144  12092  Z= 0.360
  Chirality :  0.045   0.174   1440
  Planarity :  0.005   0.045   1532
  Dihedral  :  5.640  50.665   1240
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 11.47 %
    Favored  : 85.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.59 (0.24), residues: 1134
  helix: -0.79 (0.19), residues: 692
  sheet:  0.56 (0.84), residues: 32
  loop : -1.44 (0.29), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 493 
 TYR   0.015   0.001   TYR B 410 
 PHE   0.014   0.002   PHE B 308 
 TRP   0.015   0.002   TRP B  66 
 HIS   0.003   0.001   HIS B 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00545 ( 8950)
  covalent geometry    : angle       0.68414 (12092)
  hydrogen bonds       : bond        0.04508 (  458)
  hydrogen bonds       : angle       5.39988 ( 1362)

*********************** 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
  174 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 145
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ARG cc_start: 0.6152 (OUTLIER) cc_final: 0.5624 (ptp-170)
REVERT: A   40 SER cc_start: 0.9246 (t) cc_final: 0.9008 (m)
REVERT: A  111 MET cc_start: 0.7920 (ptp) cc_final: 0.7611 (ptp)
REVERT: A  127 ARG cc_start: 0.7635 (mmt-90) cc_final: 0.7428 (tpp-160)
REVERT: A  144 ILE cc_start: 0.8614 (pt) cc_final: 0.8070 (mt)
  outliers start: 29
  outliers final: 15
  residues processed: 163
  average time/residue: 0.0822
  time to fit residues: 19.2238
Evaluate side-chains
  142 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 126
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
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  169 ILE
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 51 optimal weight:    9.9990
   chunk 32 optimal weight:    4.9990
   chunk 17 optimal weight:    0.5980
   chunk 83 optimal weight:    0.6980
   chunk 73 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0050
   chunk 55 optimal weight:   20.0000
   chunk 38 optimal weight:    0.8980
   chunk 96 optimal weight:    0.7980
   chunk 79 optimal weight:    0.5980
   overall best weight:    0.5194

-------------------------------------------------------------------------------
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**
** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 430 ASN
B 449 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.175067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.147131 restraints weight = 11207.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.143802 restraints weight = 21871.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.142716 restraints weight = 25001.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.141754 restraints weight = 18793.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.141094 restraints weight = 19604.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.2470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8950  Z= 0.128
  Angle     :  0.581   6.384  12092  Z= 0.305
  Chirality :  0.041   0.139   1440
  Planarity :  0.004   0.043   1532
  Dihedral  :  5.313  56.949   1240
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 13.53 %
    Favored  : 83.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.05 (0.24), residues: 1134
  helix: -0.30 (0.19), residues: 692
  sheet:  0.91 (0.89), residues: 32
  loop : -1.36 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 455 
 TYR   0.017   0.001   TYR B 410 
 PHE   0.013   0.001   PHE A 115 
 TRP   0.016   0.001   TRP B  66 
 HIS   0.004   0.001   HIS A 576 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 8950)
  covalent geometry    : angle       0.58109 (12092)
  hydrogen bonds       : bond        0.03716 (  458)
  hydrogen bonds       : angle       4.92954 ( 1362)

*********************** 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  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ARG cc_start: 0.6246 (OUTLIER) cc_final: 0.5827 (ptp-170)
REVERT: A   67 MET cc_start: 0.8861 (tpp) cc_final: 0.8603 (mmp)
REVERT: A  111 MET cc_start: 0.7358 (ptp) cc_final: 0.7032 (ptp)
REVERT: B   67 MET cc_start: 0.9060 (tpp) cc_final: 0.8695 (tpp)
  outliers start: 24
  outliers final: 13
  residues processed: 148
  average time/residue: 0.0881
  time to fit residues: 18.5282
Evaluate side-chains
  133 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
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  279 LEU
Chi-restraints excluded: chain A residue  280 THR
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  172 ILE
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 13 optimal weight:    0.0270
   chunk 89 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 45 optimal weight:    5.9990
   chunk 71 optimal weight:    0.5980
   chunk 66 optimal weight:    8.9990
   chunk 36 optimal weight:   10.0000
   chunk 81 optimal weight:    0.5980
   chunk 53 optimal weight:    8.9990
   chunk 85 optimal weight:    0.9990
   overall best weight:    0.6438

-------------------------------------------------------------------------------
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 = 0.4009 r_free = 0.4009 target = 0.178187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.151756 restraints weight = 11211.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.146319 restraints weight = 21185.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.145729 restraints weight = 28352.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.144283 restraints weight = 22010.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.144029 restraints weight = 21470.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
moved from start:          0.2740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8950  Z= 0.132
  Angle     :  0.586   8.462  12092  Z= 0.303
  Chirality :  0.041   0.137   1440
  Planarity :  0.004   0.043   1532
  Dihedral  :  5.232  57.326   1240
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 14.15 %
    Favored  : 82.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.82 (0.25), residues: 1134
  helix: -0.07 (0.20), residues: 692
  sheet:  1.08 (0.93), residues: 32
  loop : -1.36 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 455 
 TYR   0.016   0.001   TYR B 410 
 PHE   0.011   0.001   PHE A 115 
 TRP   0.015   0.001   TRP B  66 
 HIS   0.002   0.000   HIS B 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 8950)
  covalent geometry    : angle       0.58617 (12092)
  hydrogen bonds       : bond        0.03570 (  458)
  hydrogen bonds       : angle       4.72987 ( 1362)

*********************** 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
  159 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 126
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ARG cc_start: 0.6256 (OUTLIER) cc_final: 0.5856 (ptp-170)
REVERT: A  111 MET cc_start: 0.7510 (ptp) cc_final: 0.7144 (ptp)
REVERT: B   67 MET cc_start: 0.9039 (tpp) cc_final: 0.8647 (tpp)
  outliers start: 33
  outliers final: 18
  residues processed: 149
  average time/residue: 0.0872
  time to fit residues: 18.3647
Evaluate side-chains
  135 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 116
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ARG
Chi-restraints excluded: chain A residue   23 PHE
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   66 TRP
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  295 MET
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain B residue   23 PHE
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  576 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 96 optimal weight:    7.9990
   chunk 111 optimal weight:   20.0000
   chunk 44 optimal weight:    8.9990
   chunk 83 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 81 optimal weight:    0.6980
   chunk 72 optimal weight:    0.0970
   chunk 47 optimal weight:    7.9990
   chunk 24 optimal weight:    0.6980
   chunk 99 optimal weight:    0.5980
   chunk 49 optimal weight:    6.9990
   overall best weight:    0.5978

-------------------------------------------------------------------------------
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 = 0.3994 r_free = 0.3994 target = 0.176023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.148563 restraints weight = 11214.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.144708 restraints weight = 19990.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.143885 restraints weight = 25591.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.142626 restraints weight = 19982.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.142123 restraints weight = 19087.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.2938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8950  Z= 0.127
  Angle     :  0.594  11.769  12092  Z= 0.304
  Chirality :  0.041   0.136   1440
  Planarity :  0.004   0.042   1532
  Dihedral  :  5.159  58.237   1240
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 15.29 %
    Favored  : 81.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.65 (0.25), residues: 1134
  helix:  0.02 (0.20), residues: 708
  sheet:  1.28 (0.95), residues: 32
  loop : -1.26 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 455 
 TYR   0.014   0.001   TYR B 410 
 PHE   0.032   0.001   PHE B 115 
 TRP   0.016   0.001   TRP A  66 
 HIS   0.002   0.000   HIS A 576 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 8950)
  covalent geometry    : angle       0.59355 (12092)
  hydrogen bonds       : bond        0.03468 (  458)
  hydrogen bonds       : angle       4.61443 ( 1362)

*********************** 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
  156 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 126
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 MET cc_start: 0.7447 (ptp) cc_final: 0.7067 (ptp)
REVERT: B   67 MET cc_start: 0.9035 (tpp) cc_final: 0.8652 (tpp)
  outliers start: 30
  outliers final: 20
  residues processed: 146
  average time/residue: 0.0858
  time to fit residues: 18.0451
Evaluate side-chains
  137 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 117
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  263 LEU
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  295 MET
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain B residue   23 PHE
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  576 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 109 optimal weight:    7.9990
   chunk 95 optimal weight:    7.9990
   chunk 7 optimal weight:    0.5980
   chunk 108 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 79 optimal weight:    0.9980
   chunk 53 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 58 optimal weight:    0.6980
   chunk 45 optimal weight:    5.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 468 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.174198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.146469 restraints weight = 11154.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.142629 restraints weight = 23004.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.141587 restraints weight = 25791.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.140196 restraints weight = 20852.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.140154 restraints weight = 18025.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.3092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8950  Z= 0.142
  Angle     :  0.605  10.980  12092  Z= 0.310
  Chirality :  0.041   0.153   1440
  Planarity :  0.004   0.041   1532
  Dihedral  :  5.160  59.701   1240
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 16.32 %
    Favored  : 79.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.59 (0.25), residues: 1134
  helix:  0.08 (0.20), residues: 706
  sheet: -0.16 (0.71), residues: 60
  loop : -1.16 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 455 
 TYR   0.013   0.001   TYR B 410 
 PHE   0.018   0.001   PHE B 115 
 TRP   0.017   0.001   TRP A  66 
 HIS   0.002   0.000   HIS B 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 8950)
  covalent geometry    : angle       0.60477 (12092)
  hydrogen bonds       : bond        0.03516 (  458)
  hydrogen bonds       : angle       4.57750 ( 1362)

*********************** 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
  158 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 121
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  304 VAL cc_start: 0.8140 (OUTLIER) cc_final: 0.7906 (p)
REVERT: B   67 MET cc_start: 0.9035 (tpp) cc_final: 0.8635 (tpp)
  outliers start: 37
  outliers final: 26
  residues processed: 146
  average time/residue: 0.0838
  time to fit residues: 17.7387
Evaluate side-chains
  142 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 115
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
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  113 VAL
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  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  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  468 ASN
Chi-restraints excluded: chain B residue  576 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0770
   chunk 104 optimal weight:    0.9990
   chunk 37 optimal weight:    7.9990
   chunk 88 optimal weight:   10.0000
   chunk 65 optimal weight:    0.3980
   chunk 109 optimal weight:    5.9990
   chunk 36 optimal weight:    7.9990
   chunk 93 optimal weight:    0.0570
   overall best weight:    0.5058

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

Flipped N/Q/H residues before XYZ refinement:
** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 436 ASN
A 576 HIS
A 579 GLN
** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 309 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.179477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.153028 restraints weight = 11066.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.149063 restraints weight = 20624.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.148604 restraints weight = 25045.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.146859 restraints weight = 19832.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.145846 restraints weight = 22200.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.3243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   8950  Z= 0.125
  Angle     :  0.596   9.672  12092  Z= 0.303
  Chirality :  0.041   0.134   1440
  Planarity :  0.004   0.046   1532
  Dihedral  :  5.108  59.744   1240
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 17.05 %
    Favored  : 79.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.44 (0.25), residues: 1134
  helix:  0.27 (0.20), residues: 692
  sheet: -0.03 (0.72), residues: 60
  loop : -1.24 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  61 
 TYR   0.006   0.001   TYR A 572 
 PHE   0.021   0.001   PHE B 349 
 TRP   0.017   0.001   TRP A  66 
 HIS   0.002   0.000   HIS B 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 8950)
  covalent geometry    : angle       0.59594 (12092)
  hydrogen bonds       : bond        0.03384 (  458)
  hydrogen bonds       : angle       4.53131 ( 1362)

*********************** 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
  155 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 123
  time to evaluate  : 0.291 
Fit side-chains
REVERT: A   67 MET cc_start: 0.8643 (tpp) cc_final: 0.8391 (mmp)
REVERT: B  208 GLU cc_start: 0.7056 (tm-30) cc_final: 0.6373 (tm-30)
  outliers start: 32
  outliers final: 29
  residues processed: 145
  average time/residue: 0.0898
  time to fit residues: 18.5264
Evaluate side-chains
  142 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 113
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
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  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  412 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   23 PHE
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  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 18 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   chunk 88 optimal weight:    8.9990
   chunk 33 optimal weight:    2.9990
   chunk 58 optimal weight:    0.2980
   chunk 37 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 99 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 28 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
A 574 GLN
A 576 HIS
B 209 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.178699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.152088 restraints weight = 11063.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.147458 restraints weight = 20008.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.147080 restraints weight = 25778.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.146389 restraints weight = 18776.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.145836 restraints weight = 19729.010|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.3350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8950  Z= 0.141
  Angle     :  0.641  12.018  12092  Z= 0.324
  Chirality :  0.042   0.174   1440
  Planarity :  0.004   0.043   1532
  Dihedral  :  5.141  58.746   1240
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 17.05 %
    Favored  : 79.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.51 (0.25), residues: 1134
  helix:  0.14 (0.20), residues: 706
  sheet:  0.01 (0.73), residues: 60
  loop : -1.15 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 530 
 TYR   0.005   0.001   TYR B 163 
 PHE   0.044   0.002   PHE B 115 
 TRP   0.022   0.002   TRP B  66 
 HIS   0.001   0.000   HIS A 576 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 8950)
  covalent geometry    : angle       0.64055 (12092)
  hydrogen bonds       : bond        0.03496 (  458)
  hydrogen bonds       : angle       4.62909 ( 1362)

*********************** 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
  150 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 115
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.8652 (tpp) cc_final: 0.8440 (mmp)
REVERT: A  304 VAL cc_start: 0.8153 (OUTLIER) cc_final: 0.7925 (p)
REVERT: A  530 ARG cc_start: 0.7318 (mmm-85) cc_final: 0.6957 (tpp80)
  outliers start: 35
  outliers final: 29
  residues processed: 142
  average time/residue: 0.0865
  time to fit residues: 17.7153
Evaluate side-chains
  144 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 114
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
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  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   16 LEU
Chi-restraints excluded: chain B residue   23 PHE
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  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  284 ILE
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 109 optimal weight:    4.9990
   chunk 26 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 105 optimal weight:    6.9990
   chunk 9 optimal weight:    2.9990
   chunk 57 optimal weight:    0.0370
   chunk 33 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 83 optimal weight:    0.0040
   chunk 89 optimal weight:    2.9990
   overall best weight:    0.7474

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

Flipped N/Q/H residues before XYZ refinement:
A 107 HIS
A 576 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.174055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.145918 restraints weight = 11079.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.144135 restraints weight = 23333.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.142604 restraints weight = 22044.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.140292 restraints weight = 22176.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.139670 restraints weight = 23505.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.3424

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= 0.140
  Angle     :  0.632  11.007  12092  Z= 0.320
  Chirality :  0.041   0.169   1440
  Planarity :  0.004   0.048   1532
  Dihedral  :  5.117  57.964   1240
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 17.25 %
    Favored  : 79.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.47 (0.25), residues: 1134
  helix:  0.27 (0.20), residues: 692
  sheet:  0.03 (0.72), residues: 60
  loop : -1.31 (0.30), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 530 
 TYR   0.005   0.001   TYR B 163 
 PHE   0.038   0.002   PHE B 115 
 TRP   0.026   0.002   TRP B  66 
 HIS   0.002   0.000   HIS B 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 8950)
  covalent geometry    : angle       0.63244 (12092)
  hydrogen bonds       : bond        0.03498 (  458)
  hydrogen bonds       : angle       4.61414 ( 1362)

*********************** 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: 33
    poor density    : 112
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
REVERT: A  304 VAL cc_start: 0.8175 (OUTLIER) cc_final: 0.7944 (p)
  outliers start: 33
  outliers final: 30
  residues processed: 137
  average time/residue: 0.0862
  time to fit residues: 16.9979
Evaluate side-chains
  142 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 111
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
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  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   16 LEU
Chi-restraints excluded: chain B residue   23 PHE
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  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  284 ILE
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 47 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 81 optimal weight:    0.5980
   chunk 82 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 76 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 92 optimal weight:   10.0000
   chunk 108 optimal weight:    6.9990
   chunk 44 optimal weight:    0.7980
   chunk 109 optimal weight:    5.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 576 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.174222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.146489 restraints weight = 11148.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.142596 restraints weight = 20242.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.141031 restraints weight = 24321.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.138429 restraints weight = 25058.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.138683 restraints weight = 25301.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.3500

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= 0.146
  Angle     :  0.635  10.648  12092  Z= 0.321
  Chirality :  0.042   0.168   1440
  Planarity :  0.004   0.042   1532
  Dihedral  :  5.158  58.275   1240
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.48 (0.25), residues: 1134
  helix:  0.25 (0.20), residues: 698
  sheet:  0.05 (0.71), residues: 60
  loop : -1.31 (0.30), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 530 
 TYR   0.005   0.001   TYR A 163 
 PHE   0.032   0.002   PHE B 115 
 TRP   0.026   0.002   TRP B  66 
 HIS   0.002   0.000   HIS B 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 8950)
  covalent geometry    : angle       0.63538 (12092)
  hydrogen bonds       : bond        0.03547 (  458)
  hydrogen bonds       : angle       4.61899 ( 1362)

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

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 116
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
REVERT: A  304 VAL cc_start: 0.8179 (OUTLIER) cc_final: 0.7958 (p)
  outliers start: 32
  outliers final: 28
  residues processed: 140
  average time/residue: 0.0827
  time to fit residues: 16.7686
Evaluate side-chains
  142 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 113
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
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  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  284 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 80 optimal weight:    0.8980
   chunk 104 optimal weight:    7.9990
   chunk 84 optimal weight:    0.9990
   chunk 49 optimal weight:    7.9990
   chunk 29 optimal weight:    0.8980
   chunk 50 optimal weight:    0.8980
   chunk 59 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0000
   chunk 65 optimal weight:    0.7980
   chunk 94 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.6384

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

Flipped N/Q/H residues before XYZ refinement:
A 468 ASN
A 576 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.175547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.147328 restraints weight = 10964.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 66)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.141989 restraints weight = 20804.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.141235 restraints weight = 28117.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.139452 restraints weight = 22207.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.139035 restraints weight = 24591.149|
|-----------------------------------------------------------------------------|
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.3603

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= 0.132
  Angle     :  0.630  10.661  12092  Z= 0.318
  Chirality :  0.041   0.161   1440
  Planarity :  0.004   0.054   1532
  Dihedral  :  5.094  57.565   1240
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 17.98 %
    Favored  : 78.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.41 (0.25), residues: 1134
  helix:  0.32 (0.20), residues: 698
  sheet:  0.05 (0.71), residues: 60
  loop : -1.33 (0.30), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 530 
 TYR   0.005   0.001   TYR A 163 
 PHE   0.031   0.002   PHE B 115 
 TRP   0.026   0.002   TRP B  66 
 HIS   0.002   0.000   HIS A 576 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 8950)
  covalent geometry    : angle       0.63022 (12092)
  hydrogen bonds       : bond        0.03464 (  458)
  hydrogen bonds       : angle       4.58524 ( 1362)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1620.04 seconds
wall clock time: 28 minutes 40.99 seconds (1720.99 seconds total)