Starting phenix.real_space_refine
on Wed Feb  4 03:04:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9u9f_63962/02_2026/9u9f_63962.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9u9f_63962/02_2026/9u9f_63962.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.77
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9u9f_63962/02_2026/9u9f_63962.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9u9f_63962/02_2026/9u9f_63962.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9u9f_63962/02_2026/9u9f_63962.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9u9f_63962/02_2026/9u9f_63962.cif"
  }
  resolution = 2.77
  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=   0.003 sd=   0.152
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      54      5.16       5
     C    5458      2.51       5
     N    1388      2.21       5
     O    1498      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8400
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4195
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 559, 4195
          Classifications: {'peptide': 559}
          Link IDs: {'PTRANS': 23, 'TRANS': 535}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 5
          Unusual residues: {'PO4': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.01, per 1000 atoms: 0.24
  Number of scatterers: 8400
  At special positions: 0
  Unit cell: (99.724, 129.548, 89.472, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      54     16.00
     P       2     15.00
     O    1498      8.00
     N    1388      7.00
     C    5458      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: 0.51
  Conformation dependent library (CDL) restraints added in 333.3 milliseconds
  

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2068

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 4 sheets defined
      57.4% alpha, 4.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 99 through 104
    Processing helix  chain 'A' and resid 109 through 121
      removed outlier: 3.505A  pdb=" N   SER A 114 " --> pdb=" O   ARG A 110 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   VAL A 117 " --> pdb=" O   ARG A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 137
      removed outlier: 3.593A  pdb=" N   GLN A 129 " --> pdb=" O   LEU A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 147
    Processing helix  chain 'A' and resid 149 through 159
      removed outlier: 3.681A  pdb=" N   LEU A 157 " --> pdb=" O   LEU A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 180
    Processing helix  chain 'A' and resid 189 through 213
      removed outlier: 3.540A  pdb=" N   GLN A 195 " --> pdb=" O   ILE A 191 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   LEU A 196 " --> pdb=" O   LEU A 192 " (cutoff:3.500A)
      removed outlier: 5.273A  pdb=" N   PHE A 198 " --> pdb=" O   LEU A 194 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   SER A 210 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLY A 212 " --> pdb=" O   GLN A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 246
      removed outlier: 3.564A  pdb=" N   GLY A 230 " --> pdb=" O   ALA A 226 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   MET A 232 " --> pdb=" O   LEU A 228 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   GLY A 233 " --> pdb=" O   THR A 229 " (cutoff:3.500A)
      removed outlier: 5.902A  pdb=" N   ALA A 236 " --> pdb=" O   MET A 232 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   ILE A 237 " --> pdb=" O   GLY A 233 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   ILE A 238 " --> pdb=" O   GLY A 234 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   SER A 240 " --> pdb=" O   ALA A 236 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLY A 246 " --> pdb=" O   GLN A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 298
      removed outlier: 3.740A  pdb=" N   PHE A 284 " --> pdb=" O   MET A 280 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   LEU A 285 " --> pdb=" O   GLY A 281 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LEU A 289 " --> pdb=" O   LEU A 285 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   THR A 290 " --> pdb=" O   ALA A 286 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   THR A 291 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ARG A 292 " --> pdb=" O   LEU A 288 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   HIS A 293 " --> pdb=" O   LEU A 289 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ALA A 296 " --> pdb=" O   ARG A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 322
      Proline residue:  A 309  - end of helix
    Processing helix  chain 'A' and resid 354 through 359
    Processing helix  chain 'A' and resid 367 through 375
      removed outlier: 4.417A  pdb=" N   ALA A 373 " --> pdb=" O   THR A 369 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLY A 375 " --> pdb=" O   GLY A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 382
      removed outlier: 3.591A  pdb=" N   SER A 380 " --> pdb=" O   ARG A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 403
      removed outlier: 4.355A  pdb=" N   GLY A 396 " --> pdb=" O   MET A 392 " (cutoff:3.500A)
      removed outlier: 5.838A  pdb=" N   ASN A 399 " --> pdb=" O   ILE A 395 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   MET A 400 " --> pdb=" O   GLY A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 406
      No H-bonds generated for 'chain 'A' and resid 404 through 406'
    Processing helix  chain 'A' and resid 413 through 421
      removed outlier: 3.525A  pdb=" N   ALA A 418 " --> pdb=" O   PHE A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 442
      removed outlier: 3.661A  pdb=" N   ALA A 435 " --> pdb=" O   ASN A 431 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LEU A 439 " --> pdb=" O   ALA A 435 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   VAL A 440 " --> pdb=" O   SER A 436 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   THR A 441 " --> pdb=" O   ALA A 437 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 450
      removed outlier: 3.609A  pdb=" N   HIS A 450 " --> pdb=" O   PRO A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 466
      removed outlier: 3.986A  pdb=" N   ILE A 461 " --> pdb=" O   LEU A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 480
      removed outlier: 3.861A  pdb=" N   TRP A 478 " --> pdb=" O   ALA A 474 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   LYS A 479 " --> pdb=" O   ALA A 475 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   VAL A 480 " --> pdb=" O   ARG A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 496
      removed outlier: 3.516A  pdb=" N   LEU A 496 " --> pdb=" O   PHE A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 520
      removed outlier: 3.665A  pdb=" N   LYS A 514 " --> pdb=" O   ILE A 510 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   ILE A 515 " --> pdb=" O   SER A 511 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   GLN A 518 " --> pdb=" O   LYS A 514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 571
      removed outlier: 3.559A  pdb=" N   GLU A 570 " --> pdb=" O   MET A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 571 through 583
    Processing helix  chain 'A' and resid 605 through 617
      removed outlier: 3.507A  pdb=" N   LYS A 617 " --> pdb=" O   ALA A 613 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 617 through 622
      removed outlier: 3.542A  pdb=" N   LYS A 621 " --> pdb=" O   LYS A 617 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ARG A 622 " --> pdb=" O   VAL A 618 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 617 through 622'
    Processing helix  chain 'A' and resid 635 through 640
    Processing helix  chain 'A' and resid 656 through 664
      removed outlier: 3.576A  pdb=" N   ALA A 664 " --> pdb=" O   ALA A 660 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 99 through 104
    Processing helix  chain 'B' and resid 109 through 121
      removed outlier: 3.504A  pdb=" N   SER B 114 " --> pdb=" O   ARG B 110 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   VAL B 117 " --> pdb=" O   ARG B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 137
      removed outlier: 3.592A  pdb=" N   GLN B 129 " --> pdb=" O   LEU B 125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 147
    Processing helix  chain 'B' and resid 149 through 159
      removed outlier: 3.681A  pdb=" N   LEU B 157 " --> pdb=" O   LEU B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 169 through 180
    Processing helix  chain 'B' and resid 189 through 213
      removed outlier: 3.541A  pdb=" N   GLN B 195 " --> pdb=" O   ILE B 191 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   LEU B 196 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 5.272A  pdb=" N   PHE B 198 " --> pdb=" O   LEU B 194 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   SER B 210 " --> pdb=" O   VAL B 206 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLY B 212 " --> pdb=" O   GLN B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 226 through 246
      removed outlier: 3.564A  pdb=" N   GLY B 230 " --> pdb=" O   ALA B 226 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   MET B 232 " --> pdb=" O   LEU B 228 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   GLY B 233 " --> pdb=" O   THR B 229 " (cutoff:3.500A)
      removed outlier: 5.902A  pdb=" N   ALA B 236 " --> pdb=" O   MET B 232 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   ILE B 237 " --> pdb=" O   GLY B 233 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   ILE B 238 " --> pdb=" O   GLY B 234 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   SER B 240 " --> pdb=" O   ALA B 236 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLY B 246 " --> pdb=" O   GLN B 242 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 275 through 298
      removed outlier: 3.741A  pdb=" N   PHE B 284 " --> pdb=" O   MET B 280 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   LEU B 285 " --> pdb=" O   GLY B 281 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LEU B 289 " --> pdb=" O   LEU B 285 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   THR B 290 " --> pdb=" O   ALA B 286 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   THR B 291 " --> pdb=" O   VAL B 287 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ARG B 292 " --> pdb=" O   LEU B 288 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   HIS B 293 " --> pdb=" O   LEU B 289 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ALA B 296 " --> pdb=" O   ARG B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 322
      Proline residue:  B 309  - end of helix
    Processing helix  chain 'B' and resid 354 through 359
    Processing helix  chain 'B' and resid 367 through 375
      removed outlier: 4.417A  pdb=" N   ALA B 373 " --> pdb=" O   THR B 369 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLY B 375 " --> pdb=" O   GLY B 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 382
      removed outlier: 3.591A  pdb=" N   SER B 380 " --> pdb=" O   ARG B 376 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 388 through 403
      removed outlier: 4.355A  pdb=" N   GLY B 396 " --> pdb=" O   MET B 392 " (cutoff:3.500A)
      removed outlier: 5.838A  pdb=" N   ASN B 399 " --> pdb=" O   ILE B 395 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   MET B 400 " --> pdb=" O   GLY B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 406
      No H-bonds generated for 'chain 'B' and resid 404 through 406'
    Processing helix  chain 'B' and resid 413 through 421
      removed outlier: 3.525A  pdb=" N   ALA B 418 " --> pdb=" O   PHE B 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 429 through 442
      removed outlier: 3.661A  pdb=" N   ALA B 435 " --> pdb=" O   ASN B 431 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   LEU B 439 " --> pdb=" O   ALA B 435 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   VAL B 440 " --> pdb=" O   SER B 436 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   THR B 441 " --> pdb=" O   ALA B 437 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 445 through 450
      removed outlier: 3.610A  pdb=" N   HIS B 450 " --> pdb=" O   PRO B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 466
      removed outlier: 3.986A  pdb=" N   ILE B 461 " --> pdb=" O   LEU B 457 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 471 through 480
      removed outlier: 3.861A  pdb=" N   TRP B 478 " --> pdb=" O   ALA B 474 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   LYS B 479 " --> pdb=" O   ALA B 475 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   VAL B 480 " --> pdb=" O   ARG B 476 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 484 through 496
      removed outlier: 3.516A  pdb=" N   LEU B 496 " --> pdb=" O   PHE B 492 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 510 through 520
      removed outlier: 3.665A  pdb=" N   LYS B 514 " --> pdb=" O   ILE B 510 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   ILE B 515 " --> pdb=" O   SER B 511 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   GLN B 518 " --> pdb=" O   LYS B 514 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 566 through 571
      removed outlier: 3.559A  pdb=" N   GLU B 570 " --> pdb=" O   MET B 566 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 571 through 583
    Processing helix  chain 'B' and resid 605 through 617
      removed outlier: 3.507A  pdb=" N   LYS B 617 " --> pdb=" O   ALA B 613 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 617 through 622
      removed outlier: 3.543A  pdb=" N   LYS B 621 " --> pdb=" O   LYS B 617 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ARG B 622 " --> pdb=" O   VAL B 618 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 617 through 622'
    Processing helix  chain 'B' and resid 635 through 640
    Processing helix  chain 'B' and resid 656 through 664
      removed outlier: 3.577A  pdb=" N   ALA B 664 " --> pdb=" O   ALA B 660 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 166 through 168
    Processing sheet with id=AA2, first strand: chain 'A' and resid 536 through 538
      removed outlier: 4.556A  pdb=" N   ASN A 523 " --> pdb=" O   GLU A 557 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   VAL A 553 " --> pdb=" O   LYS A 527 " (cutoff:3.500A)
      removed outlier: 9.078A  pdb=" N   VAL A 529 " --> pdb=" O   PHE A 551 " (cutoff:3.500A)
      removed outlier: 12.296A  pdb=" N   PHE A 551 " --> pdb=" O   VAL A 529 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   VAL A 556 " --> pdb=" O   ASP A 597 " (cutoff:3.500A)
      removed outlier: 9.352A  pdb=" N   PHE A 654 " --> pdb=" O   LEU A 626 " (cutoff:3.500A)
      removed outlier: 7.417A  pdb=" N   LEU A 628 " --> pdb=" O   PHE A 654 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 166 through 168
    Processing sheet with id=AA4, first strand: chain 'B' and resid 536 through 538
      removed outlier: 4.556A  pdb=" N   ASN B 523 " --> pdb=" O   GLU B 557 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   VAL B 553 " --> pdb=" O   LYS B 527 " (cutoff:3.500A)
      removed outlier: 9.078A  pdb=" N   VAL B 529 " --> pdb=" O   PHE B 551 " (cutoff:3.500A)
      removed outlier: 12.297A  pdb=" N   PHE B 551 " --> pdb=" O   VAL B 529 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   VAL B 556 " --> pdb=" O   ASP B 597 " (cutoff:3.500A)
      removed outlier: 9.352A  pdb=" N   PHE B 654 " --> pdb=" O   LEU B 626 " (cutoff:3.500A)
      removed outlier: 7.417A  pdb=" N   LEU B 628 " --> pdb=" O   PHE B 654 " (cutoff:3.500A)

    346 hydrogen bonds defined for protein.
    1026 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: 1.03

  Time building geometry restraints manager: 0.72 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2106
        1.33 -     1.45: 1537
        1.45 -     1.57: 4819
        1.57 -     1.69: 0
        1.69 -     1.81: 94
  Bond restraints: 8556
  Sorted by residual:
  bond pdb=" C   ILE B 127 "
       pdb=" N   PRO B 128 "
    ideal  model  delta    sigma   weight residual
    1.336  1.381 -0.045 1.23e-02 6.61e+03 1.35e+01
  bond pdb=" C   ILE A 127 "
       pdb=" N   PRO A 128 "
    ideal  model  delta    sigma   weight residual
    1.336  1.380 -0.044 1.23e-02 6.61e+03 1.29e+01
  bond pdb=" CA  SER B 329 "
       pdb=" CB  SER B 329 "
    ideal  model  delta    sigma   weight residual
    1.528  1.476  0.052 1.54e-02 4.22e+03 1.15e+01
  bond pdb=" CA  SER A 329 "
       pdb=" CB  SER A 329 "
    ideal  model  delta    sigma   weight residual
    1.528  1.477  0.052 1.54e-02 4.22e+03 1.13e+01
  bond pdb=" CA  ALA B 540 "
       pdb=" CB  ALA B 540 "
    ideal  model  delta    sigma   weight residual
    1.531  1.479  0.052 1.57e-02 4.06e+03 1.11e+01
  ... (remaining 8551 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.75: 11496
        4.75 -     9.50: 120
        9.50 -    14.24: 4
       14.24 -    18.99: 4
       18.99 -    23.74: 2
  Bond angle restraints: 11626
  Sorted by residual:
  angle pdb=" N   LYS B 324 "
        pdb=" CA  LYS B 324 "
        pdb=" C   LYS B 324 "
      ideal   model   delta    sigma   weight residual
     111.28   87.54   23.74 1.35e+00 5.49e-01 3.09e+02
  angle pdb=" N   LYS A 324 "
        pdb=" CA  LYS A 324 "
        pdb=" C   LYS A 324 "
      ideal   model   delta    sigma   weight residual
     111.28   87.57   23.71 1.35e+00 5.49e-01 3.08e+02
  angle pdb=" N   GLN A 541 "
        pdb=" CA  GLN A 541 "
        pdb=" C   GLN A 541 "
      ideal   model   delta    sigma   weight residual
     110.53   97.35   13.18 1.32e+00 5.74e-01 9.97e+01
  angle pdb=" N   GLN B 541 "
        pdb=" CA  GLN B 541 "
        pdb=" C   GLN B 541 "
      ideal   model   delta    sigma   weight residual
     110.53   97.38   13.15 1.32e+00 5.74e-01 9.93e+01
  angle pdb=" N   TYR B 542 "
        pdb=" CA  TYR B 542 "
        pdb=" C   TYR B 542 "
      ideal   model   delta    sigma   weight residual
     111.28  123.33  -12.05 1.35e+00 5.49e-01 7.97e+01
  ... (remaining 11621 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 4678
       17.84 -    35.68: 352
       35.68 -    53.52: 62
       53.52 -    71.37: 6
       71.37 -    89.21: 2
  Dihedral angle restraints: 5100
    sinusoidal: 1888
      harmonic: 3212
  Sorted by residual:
  dihedral pdb=" C   VAL A 322 "
           pdb=" N   VAL A 322 "
           pdb=" CA  VAL A 322 "
           pdb=" CB  VAL A 322 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -139.47   17.47     0      2.50e+00 1.60e-01 4.88e+01
  dihedral pdb=" C   VAL B 322 "
           pdb=" N   VAL B 322 "
           pdb=" CA  VAL B 322 "
           pdb=" CB  VAL B 322 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -139.43   17.43     0      2.50e+00 1.60e-01 4.86e+01
  dihedral pdb=" CA  LEU B 457 "
           pdb=" C   LEU B 457 "
           pdb=" N   SER B 458 "
           pdb=" CA  SER B 458 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.73   26.27     0      5.00e+00 4.00e-02 2.76e+01
  ... (remaining 5097 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.107: 1314
       0.107 -    0.214: 96
       0.214 -    0.321: 10
       0.321 -    0.429: 2
       0.429 -    0.536: 2
  Chirality restraints: 1424
  Sorted by residual:
  chirality pdb=" CA  VAL A 322 "
            pdb=" N   VAL A 322 "
            pdb=" C   VAL A 322 "
            pdb=" CB  VAL A 322 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    1.91    0.54 2.00e-01 2.50e+01 7.17e+00
  chirality pdb=" CA  VAL B 322 "
            pdb=" N   VAL B 322 "
            pdb=" C   VAL B 322 "
            pdb=" CB  VAL B 322 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    1.91    0.53 2.00e-01 2.50e+01 7.14e+00
  chirality pdb=" CA  ILE A 319 "
            pdb=" N   ILE A 319 "
            pdb=" C   ILE A 319 "
            pdb=" CB  ILE A 319 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.82   -0.39 2.00e-01 2.50e+01 3.71e+00
  ... (remaining 1421 not shown)

  Planarity restraints: 1436
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 319 "   -0.020 2.00e-02 2.50e+03   3.98e-02 1.58e+01
        pdb=" C   ILE A 319 "    0.069 2.00e-02 2.50e+03
        pdb=" O   ILE A 319 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   SER A 320 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 319 "    0.020 2.00e-02 2.50e+03   3.96e-02 1.57e+01
        pdb=" C   ILE B 319 "   -0.068 2.00e-02 2.50e+03
        pdb=" O   ILE B 319 "    0.025 2.00e-02 2.50e+03
        pdb=" N   SER B 320 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 548 "    0.049 5.00e-02 4.00e+02   7.54e-02 9.09e+00
        pdb=" N   PRO A 549 "   -0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO A 549 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A 549 "    0.041 5.00e-02 4.00e+02
  ... (remaining 1433 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2059
        2.78 -     3.31: 7177
        3.31 -     3.84: 14052
        3.84 -     4.37: 17610
        4.37 -     4.90: 29261
  Nonbonded interactions: 70159
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 155 "
            pdb=" OE2 GLU A 391 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" OH  TYR B 155 "
            pdb=" OE2 GLU B 391 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O   PHE A 198 "
            pdb=" OG  SER A 403 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" O   PHE B 198 "
            pdb=" OG  SER B 403 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" N   GLN A 541 "
            pdb=" O   GLN A 541 "
     model   vdw
     2.277 2.496
  ... (remaining 70154 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: 0.02
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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.110
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
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      :  0.007   0.085   8556  Z= 0.341
  Angle     :  1.198  23.741  11626  Z= 0.734
  Chirality :  0.064   0.536   1424
  Planarity :  0.008   0.075   1436
  Dihedral  : 12.995  89.206   3032
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Cbeta Deviations :  0.58 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -6.49 (0.15), residues: 1106
  helix: -4.70 (0.07), residues: 762
  sheet: -2.94 (0.70), residues: 36
  loop : -2.50 (0.30), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 622 
 TYR   0.015   0.002   TYR B 408 
 PHE   0.009   0.002   PHE A 378 
 TRP   0.016   0.002   TRP B 103 
 HIS   0.004   0.001   HIS B 450 

Details of bonding type rmsd
  covalent geometry    : bond        0.00675 ( 8556)
  covalent geometry    : angle       1.19752 (11626)
  hydrogen bonds       : bond        0.29855 (  346)
  hydrogen bonds       : angle      11.57519 ( 1026)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.202 
Fit side-chains
REVERT: A  300 LYS cc_start: 0.7718 (tptp) cc_final: 0.7479 (tptp)
REVERT: A  392 MET cc_start: 0.8200 (mtp) cc_final: 0.7889 (mtt)
REVERT: A  592 ARG cc_start: 0.7413 (mtt180) cc_final: 0.7150 (mmp80)
REVERT: A  637 GLU cc_start: 0.7618 (pp20) cc_final: 0.7058 (pp20)
REVERT: A  641 ASN cc_start: 0.7377 (m110) cc_final: 0.7001 (p0)
REVERT: A  652 ARG cc_start: 0.7610 (mtt180) cc_final: 0.7381 (mtt90)
REVERT: B  113 ARG cc_start: 0.7498 (tmt170) cc_final: 0.7284 (ttp80)
REVERT: B  300 LYS cc_start: 0.7852 (tptp) cc_final: 0.7610 (tptp)
REVERT: B  392 MET cc_start: 0.8316 (mtp) cc_final: 0.7897 (mtt)
REVERT: B  393 MET cc_start: 0.7961 (mtp) cc_final: 0.7726 (mtt)
REVERT: B  502 MET cc_start: 0.7263 (mmp) cc_final: 0.6931 (tpt)
REVERT: B  592 ARG cc_start: 0.7375 (mtt180) cc_final: 0.6951 (mmp80)
  outliers start: 0
  outliers final: 0
  residues processed: 179
  average time/residue: 0.4680
  time to fit residues: 89.0997
Evaluate side-chains
  132 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.5980
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.3980
   chunk 65 optimal weight:    0.2980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.3980
   chunk 100 optimal weight:    2.9990
   chunk 106 optimal weight:    2.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A  50 HIS
A 382 ASN
A 389 ASN
A 501 GLN
A 641 ASN
B  50 HIS
B 242 GLN
B 382 ASN
B 389 ASN
B 641 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.164357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.135890 restraints weight = 9529.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3748 rms_B_bonded: 2.01
r_work: 0.3667 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3564 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7371
moved from start:          0.1816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8556  Z= 0.129
  Angle     :  0.614   5.638  11626  Z= 0.336
  Chirality :  0.042   0.160   1424
  Planarity :  0.006   0.059   1436
  Dihedral  :  6.290  27.157   1190
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 14.04 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.86 (0.20), residues: 1106
  helix: -3.47 (0.13), residues: 768
  sheet: -3.01 (0.72), residues: 36
  loop : -1.74 (0.34), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 652 
 TYR   0.013   0.001   TYR B 408 
 PHE   0.012   0.001   PHE A 321 
 TRP   0.015   0.002   TRP A 275 
 HIS   0.002   0.001   HIS A 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 8556)
  covalent geometry    : angle       0.61387 (11626)
  hydrogen bonds       : bond        0.03656 (  346)
  hydrogen bonds       : angle       5.44926 ( 1026)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 146
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
REVERT: A  300 LYS cc_start: 0.7890 (tptp) cc_final: 0.7586 (tptp)
REVERT: A  392 MET cc_start: 0.8189 (mtp) cc_final: 0.7838 (mtt)
REVERT: A  502 MET cc_start: 0.7363 (mmp) cc_final: 0.7085 (mmm)
REVERT: A  524 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8412 (mtm)
REVERT: A  543 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7220 (mtm110)
REVERT: A  592 ARG cc_start: 0.7744 (mtt180) cc_final: 0.6828 (mmp80)
REVERT: A  637 GLU cc_start: 0.7466 (pp20) cc_final: 0.6889 (pp20)
REVERT: A  641 ASN cc_start: 0.7413 (m-40) cc_final: 0.6796 (p0)
REVERT: A  652 ARG cc_start: 0.7583 (mtt180) cc_final: 0.7360 (mtt90)
REVERT: B  106 ASP cc_start: 0.7540 (m-30) cc_final: 0.7313 (m-30)
REVERT: B  113 ARG cc_start: 0.7599 (tmt170) cc_final: 0.7239 (ttp80)
REVERT: B  300 LYS cc_start: 0.7880 (tptp) cc_final: 0.7647 (tptp)
REVERT: B  392 MET cc_start: 0.8299 (mtp) cc_final: 0.7880 (mtt)
REVERT: B  393 MET cc_start: 0.8140 (mtp) cc_final: 0.7883 (mtt)
REVERT: B  400 MET cc_start: 0.8661 (ptt) cc_final: 0.8244 (ptt)
REVERT: B  446 MET cc_start: 0.7976 (mmt) cc_final: 0.7744 (mmm)
REVERT: B  502 MET cc_start: 0.7447 (mmp) cc_final: 0.7148 (tpt)
REVERT: B  592 ARG cc_start: 0.7568 (mtt180) cc_final: 0.6591 (mmp80)
  outliers start: 24
  outliers final: 8
  residues processed: 158
  average time/residue: 0.4439
  time to fit residues: 75.1623
Evaluate side-chains
  140 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 130
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 SER
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  160 SER
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  523 ASN
Chi-restraints excluded: chain A residue  524 MET
Chi-restraints excluded: chain A residue  543 ARG
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  523 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 81 optimal weight:    0.6980
   chunk 40 optimal weight:    0.8980
   chunk 75 optimal weight:    0.9980
   chunk 44 optimal weight:    0.6980
   chunk 100 optimal weight:    1.9990
   chunk 55 optimal weight:    0.2980
   chunk 12 optimal weight:    2.9990
   chunk 95 optimal weight:    3.9990
   chunk 15 optimal weight:    0.6980
   chunk 87 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 358 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.163578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.134913 restraints weight = 9420.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.3744 rms_B_bonded: 2.00
r_work: 0.3660 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3558 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7395
moved from start:          0.2201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8556  Z= 0.124
  Angle     :  0.582   6.042  11626  Z= 0.309
  Chirality :  0.041   0.165   1424
  Planarity :  0.005   0.059   1436
  Dihedral  :  5.801  24.650   1190
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 15.46 %
    Favored  : 81.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.67 (0.22), residues: 1106
  helix: -2.52 (0.16), residues: 768
  sheet: -2.85 (0.72), residues: 36
  loop : -1.40 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 215 
 TYR   0.013   0.001   TYR A 408 
 PHE   0.008   0.001   PHE B 378 
 TRP   0.012   0.001   TRP B 103 
 HIS   0.001   0.000   HIS A 450 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 8556)
  covalent geometry    : angle       0.58214 (11626)
  hydrogen bonds       : bond        0.03348 (  346)
  hydrogen bonds       : angle       4.54894 ( 1026)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 134
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
REVERT: A  300 LYS cc_start: 0.7840 (tptp) cc_final: 0.7510 (tptp)
REVERT: A  392 MET cc_start: 0.8235 (mtp) cc_final: 0.7891 (mtt)
REVERT: A  489 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.7320 (mmp)
REVERT: A  502 MET cc_start: 0.7579 (mmp) cc_final: 0.7303 (mmm)
REVERT: A  592 ARG cc_start: 0.7782 (mtt180) cc_final: 0.6874 (mmp80)
REVERT: B  106 ASP cc_start: 0.7538 (m-30) cc_final: 0.7316 (m-30)
REVERT: B  113 ARG cc_start: 0.7428 (tmt170) cc_final: 0.7186 (ttp80)
REVERT: B  300 LYS cc_start: 0.7864 (tptp) cc_final: 0.7575 (tptp)
REVERT: B  385 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7227 (tm-30)
REVERT: B  392 MET cc_start: 0.8307 (mtp) cc_final: 0.7952 (mtt)
REVERT: B  393 MET cc_start: 0.8034 (mtp) cc_final: 0.7801 (mtt)
REVERT: B  400 MET cc_start: 0.8433 (ptt) cc_final: 0.8129 (ptt)
REVERT: B  446 MET cc_start: 0.8024 (mmt) cc_final: 0.7799 (mmm)
REVERT: B  489 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.7119 (mmp)
REVERT: B  502 MET cc_start: 0.7495 (mmp) cc_final: 0.7209 (tpt)
REVERT: B  592 ARG cc_start: 0.7575 (mtt180) cc_final: 0.6635 (mmp80)
  outliers start: 31
  outliers final: 10
  residues processed: 155
  average time/residue: 0.4287
  time to fit residues: 71.1166
Evaluate side-chains
  139 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 126
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 SER
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  489 MET
Chi-restraints excluded: chain A residue  523 ASN
Chi-restraints excluded: chain A residue  524 MET
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  185 SER
Chi-restraints excluded: chain B residue  385 GLN
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  489 MET
Chi-restraints excluded: chain B residue  523 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 59 optimal weight:    0.0970
   chunk 99 optimal weight:    1.9990
   chunk 96 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 29 optimal weight:    0.4980
   chunk 52 optimal weight:    3.9990
   overall best weight:    0.8780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.159595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.131030 restraints weight = 9556.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.3715 rms_B_bonded: 1.95
r_work: 0.3584 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3460 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.2396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8556  Z= 0.140
  Angle     :  0.581   5.885  11626  Z= 0.307
  Chirality :  0.042   0.158   1424
  Planarity :  0.005   0.059   1436
  Dihedral  :  5.675  25.496   1190
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 15.57 %
    Favored  : 80.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.11 (0.23), residues: 1106
  helix: -2.08 (0.17), residues: 768
  sheet: -2.75 (0.72), residues: 36
  loop : -1.25 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 622 
 TYR   0.013   0.001   TYR A 408 
 PHE   0.009   0.001   PHE B 378 
 TRP   0.013   0.001   TRP B 103 
 HIS   0.001   0.001   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 8556)
  covalent geometry    : angle       0.58066 (11626)
  hydrogen bonds       : bond        0.03077 (  346)
  hydrogen bonds       : angle       4.36608 ( 1026)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 137
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
REVERT: A  300 LYS cc_start: 0.7893 (tptp) cc_final: 0.7631 (tptp)
REVERT: A  385 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.7821 (tm-30)
REVERT: A  392 MET cc_start: 0.8523 (mtp) cc_final: 0.8279 (mtt)
REVERT: A  489 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7645 (mmp)
REVERT: A  502 MET cc_start: 0.8030 (mmp) cc_final: 0.7818 (mmm)
REVERT: A  592 ARG cc_start: 0.8038 (mtt180) cc_final: 0.7267 (mmp80)
REVERT: A  625 GLU cc_start: 0.8156 (tp30) cc_final: 0.7525 (tp30)
REVERT: A  641 ASN cc_start: 0.7505 (m-40) cc_final: 0.7029 (p0)
REVERT: A  646 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7798 (mptm)
REVERT: A  652 ARG cc_start: 0.7632 (mtt90) cc_final: 0.6959 (mtt90)
REVERT: B  300 LYS cc_start: 0.7939 (tptp) cc_final: 0.7705 (tptp)
REVERT: B  385 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7623 (tm-30)
REVERT: B  392 MET cc_start: 0.8533 (mtp) cc_final: 0.8270 (mtt)
REVERT: B  400 MET cc_start: 0.8587 (ptt) cc_final: 0.8309 (ptt)
REVERT: B  489 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7656 (mmp)
REVERT: B  502 MET cc_start: 0.8000 (mmp) cc_final: 0.7756 (tpt)
REVERT: B  592 ARG cc_start: 0.7852 (mtt180) cc_final: 0.7024 (mmp80)
REVERT: B  625 GLU cc_start: 0.8174 (tp30) cc_final: 0.7761 (tp30)
REVERT: B  652 ARG cc_start: 0.7528 (mtt90) cc_final: 0.6808 (mmt90)
  outliers start: 36
  outliers final: 21
  residues processed: 163
  average time/residue: 0.4581
  time to fit residues: 79.7854
Evaluate side-chains
  153 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 127
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  160 SER
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  385 GLN
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  489 MET
Chi-restraints excluded: chain A residue  523 ASN
Chi-restraints excluded: chain A residue  524 MET
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  627 VAL
Chi-restraints excluded: chain A residue  646 LYS
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  185 SER
Chi-restraints excluded: chain B residue  385 GLN
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  482 LYS
Chi-restraints excluded: chain B residue  489 MET
Chi-restraints excluded: chain B residue  523 ASN
Chi-restraints excluded: chain B residue  548 VAL
Chi-restraints excluded: chain B residue  556 VAL
Chi-restraints excluded: chain B residue  579 GLU
Chi-restraints excluded: chain B residue  627 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 87 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9980
   chunk 75 optimal weight:    0.0060
   chunk 104 optimal weight:    3.9990
   overall best weight:    1.2002

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.157268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.128244 restraints weight = 9498.365|
|-----------------------------------------------------------------------------|
r_work (start): 0.3684 rms_B_bonded: 1.95
r_work: 0.3549 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3419 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.2569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8556  Z= 0.171
  Angle     :  0.599   6.240  11626  Z= 0.315
  Chirality :  0.043   0.161   1424
  Planarity :  0.005   0.059   1436
  Dihedral  :  5.694  25.865   1190
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 16.45 %
    Favored  : 79.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.80 (0.24), residues: 1106
  helix: -1.84 (0.17), residues: 770
  sheet: -2.77 (0.72), residues: 36
  loop : -1.12 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 622 
 TYR   0.015   0.002   TYR A 408 
 PHE   0.011   0.001   PHE A 378 
 TRP   0.012   0.001   TRP A 103 
 HIS   0.002   0.001   HIS A 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 8556)
  covalent geometry    : angle       0.59878 (11626)
  hydrogen bonds       : bond        0.03162 (  346)
  hydrogen bonds       : angle       4.31049 ( 1026)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 132
  time to evaluate  : 0.219 
Fit side-chains
REVERT: A  300 LYS cc_start: 0.7930 (tptp) cc_final: 0.7638 (tptp)
REVERT: A  385 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.7691 (tm-30)
REVERT: A  392 MET cc_start: 0.8519 (mtp) cc_final: 0.8253 (mtt)
REVERT: A  489 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7548 (mmp)
REVERT: A  502 MET cc_start: 0.7973 (mmp) cc_final: 0.7754 (tpt)
REVERT: A  592 ARG cc_start: 0.7971 (mtt180) cc_final: 0.7123 (mmp80)
REVERT: A  637 GLU cc_start: 0.7802 (pp20) cc_final: 0.7188 (pp20)
REVERT: A  641 ASN cc_start: 0.7466 (m-40) cc_final: 0.6953 (p0)
REVERT: A  652 ARG cc_start: 0.7616 (mtt90) cc_final: 0.7346 (mtt90)
REVERT: B  300 LYS cc_start: 0.7938 (tptp) cc_final: 0.7659 (tptp)
REVERT: B  392 MET cc_start: 0.8514 (mtp) cc_final: 0.8225 (mtt)
REVERT: B  400 MET cc_start: 0.8529 (ptt) cc_final: 0.8195 (ptt)
REVERT: B  489 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7533 (mmp)
REVERT: B  502 MET cc_start: 0.7973 (mmp) cc_final: 0.7749 (tpt)
REVERT: B  592 ARG cc_start: 0.7916 (mtt180) cc_final: 0.7067 (mmp80)
REVERT: B  625 GLU cc_start: 0.8077 (tp30) cc_final: 0.7473 (tp30)
REVERT: B  652 ARG cc_start: 0.7516 (mtt90) cc_final: 0.7105 (mtt90)
  outliers start: 38
  outliers final: 21
  residues processed: 164
  average time/residue: 0.4281
  time to fit residues: 75.0618
Evaluate side-chains
  151 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 127
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  160 SER
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  385 GLN
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  489 MET
Chi-restraints excluded: chain A residue  523 ASN
Chi-restraints excluded: chain A residue  524 MET
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  624 ILE
Chi-restraints excluded: chain A residue  627 VAL
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  185 SER
Chi-restraints excluded: chain B residue  357 LEU
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  489 MET
Chi-restraints excluded: chain B residue  523 ASN
Chi-restraints excluded: chain B residue  548 VAL
Chi-restraints excluded: chain B residue  627 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 102 optimal weight:    6.9990
   chunk 22 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 90 optimal weight:    1.9990
   chunk 76 optimal weight:    0.0870
   chunk 69 optimal weight:    0.5980
   chunk 94 optimal weight:    2.9990
   chunk 87 optimal weight:    0.7980
   chunk 68 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   overall best weight:    0.6958

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.164044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.135617 restraints weight = 9348.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.3675 rms_B_bonded: 1.92
r_work: 0.3548 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3426 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start:          0.2754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8556  Z= 0.122
  Angle     :  0.556   6.197  11626  Z= 0.295
  Chirality :  0.042   0.178   1424
  Planarity :  0.004   0.059   1436
  Dihedral  :  5.469  24.593   1190
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 18.09 %
    Favored  : 78.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.34 (0.24), residues: 1106
  helix: -1.48 (0.18), residues: 768
  sheet: -2.70 (0.73), residues: 36
  loop : -0.99 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 622 
 TYR   0.013   0.001   TYR B 408 
 PHE   0.007   0.001   PHE A 378 
 TRP   0.013   0.001   TRP B 103 
 HIS   0.002   0.001   HIS A 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 8556)
  covalent geometry    : angle       0.55613 (11626)
  hydrogen bonds       : bond        0.02881 (  346)
  hydrogen bonds       : angle       4.12760 ( 1026)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 129
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
REVERT: A  300 LYS cc_start: 0.7921 (tptp) cc_final: 0.7685 (tptp)
REVERT: A  392 MET cc_start: 0.8484 (mtp) cc_final: 0.8230 (mtt)
REVERT: A  400 MET cc_start: 0.8757 (ptt) cc_final: 0.8446 (ptt)
REVERT: A  489 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7581 (mmp)
REVERT: A  592 ARG cc_start: 0.7995 (mtt180) cc_final: 0.7189 (mmp80)
REVERT: A  641 ASN cc_start: 0.7477 (m-40) cc_final: 0.6991 (p0)
REVERT: A  652 ARG cc_start: 0.7576 (mtt90) cc_final: 0.7247 (mtt90)
REVERT: B  300 LYS cc_start: 0.7866 (tptp) cc_final: 0.7634 (tptp)
REVERT: B  390 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8247 (tttp)
REVERT: B  392 MET cc_start: 0.8569 (mtp) cc_final: 0.8308 (mtt)
REVERT: B  400 MET cc_start: 0.8485 (ptt) cc_final: 0.8284 (ptp)
REVERT: B  489 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7589 (mmp)
REVERT: B  592 ARG cc_start: 0.7967 (mtt180) cc_final: 0.7161 (mmp80)
REVERT: B  625 GLU cc_start: 0.8072 (tp30) cc_final: 0.7560 (tp30)
REVERT: B  652 ARG cc_start: 0.7555 (mtt90) cc_final: 0.7197 (mtt90)
  outliers start: 30
  outliers final: 20
  residues processed: 152
  average time/residue: 0.4023
  time to fit residues: 65.7544
Evaluate side-chains
  143 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  160 SER
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  489 MET
Chi-restraints excluded: chain A residue  523 ASN
Chi-restraints excluded: chain A residue  524 MET
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  579 GLU
Chi-restraints excluded: chain A residue  627 VAL
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  185 SER
Chi-restraints excluded: chain B residue  232 MET
Chi-restraints excluded: chain B residue  390 LYS
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  489 MET
Chi-restraints excluded: chain B residue  523 ASN
Chi-restraints excluded: chain B residue  548 VAL
Chi-restraints excluded: chain B residue  556 VAL
Chi-restraints excluded: chain B residue  627 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 21 optimal weight:   10.0000
   chunk 19 optimal weight:    0.0970
   chunk 13 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0980
   chunk 17 optimal weight:    0.6980
   chunk 44 optimal weight:    0.7980
   chunk 32 optimal weight:    0.5980
   chunk 63 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.4578

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.166257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.137836 restraints weight = 9397.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3743 rms_B_bonded: 1.94
r_work: 0.3605 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3481 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.2924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8556  Z= 0.105
  Angle     :  0.537   6.204  11626  Z= 0.283
  Chirality :  0.041   0.190   1424
  Planarity :  0.004   0.058   1436
  Dihedral  :  5.208  23.891   1190
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 19.63 %
    Favored  : 77.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.81 (0.25), residues: 1106
  helix: -1.08 (0.18), residues: 768
  sheet: -2.50 (0.75), residues: 36
  loop : -0.80 (0.37), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 622 
 TYR   0.012   0.001   TYR A 408 
 PHE   0.006   0.001   PHE A 284 
 TRP   0.011   0.001   TRP B 103 
 HIS   0.001   0.000   HIS A 450 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 8556)
  covalent geometry    : angle       0.53656 (11626)
  hydrogen bonds       : bond        0.02724 (  346)
  hydrogen bonds       : angle       3.94075 ( 1026)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 126
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A  191 ILE cc_start: 0.8349 (mp) cc_final: 0.8130 (mm)
REVERT: A  300 LYS cc_start: 0.7922 (tptp) cc_final: 0.7577 (tptp)
REVERT: A  392 MET cc_start: 0.8467 (mtp) cc_final: 0.8220 (mtt)
REVERT: A  489 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7529 (mmp)
REVERT: A  592 ARG cc_start: 0.7931 (mtt180) cc_final: 0.7134 (mmp80)
REVERT: A  623 ASN cc_start: 0.7751 (m110) cc_final: 0.7316 (m-40)
REVERT: A  641 ASN cc_start: 0.7424 (m-40) cc_final: 0.7028 (p0)
REVERT: A  652 ARG cc_start: 0.7517 (mtt90) cc_final: 0.7188 (mtt90)
REVERT: B  300 LYS cc_start: 0.7951 (tptp) cc_final: 0.7725 (tptp)
REVERT: B  392 MET cc_start: 0.8570 (mtp) cc_final: 0.8323 (mtt)
REVERT: B  470 ASP cc_start: 0.8091 (t70) cc_final: 0.7835 (t0)
REVERT: B  489 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7590 (mmp)
REVERT: B  592 ARG cc_start: 0.7969 (mtt180) cc_final: 0.7150 (mmp80)
REVERT: B  623 ASN cc_start: 0.7536 (m110) cc_final: 0.7145 (m-40)
  outliers start: 25
  outliers final: 14
  residues processed: 145
  average time/residue: 0.4921
  time to fit residues: 76.3362
Evaluate side-chains
  136 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 SER
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  434 MET
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  489 MET
Chi-restraints excluded: chain A residue  523 ASN
Chi-restraints excluded: chain A residue  524 MET
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain B residue  185 SER
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  489 MET
Chi-restraints excluded: chain B residue  523 ASN
Chi-restraints excluded: chain B residue  548 VAL
Chi-restraints excluded: chain B residue  556 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 84 optimal weight:    0.5980
   chunk 43 optimal weight:    4.9990
   chunk 92 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 65 optimal weight:    0.1980
   chunk 48 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B 276 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.165797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.137417 restraints weight = 9303.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.3733 rms_B_bonded: 1.93
r_work: 0.3595 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3471 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.3027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8556  Z= 0.112
  Angle     :  0.540   6.363  11626  Z= 0.285
  Chirality :  0.041   0.180   1424
  Planarity :  0.004   0.058   1436
  Dihedral  :  5.184  23.452   1190
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 19.30 %
    Favored  : 77.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.52 (0.25), residues: 1106
  helix: -0.87 (0.19), residues: 764
  sheet: -2.41 (0.76), residues: 36
  loop : -0.68 (0.36), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 652 
 TYR   0.013   0.001   TYR A 408 
 PHE   0.007   0.001   PHE A 378 
 TRP   0.012   0.001   TRP B 103 
 HIS   0.001   0.000   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 8556)
  covalent geometry    : angle       0.54030 (11626)
  hydrogen bonds       : bond        0.02734 (  346)
  hydrogen bonds       : angle       3.93869 ( 1026)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 121
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  191 ILE cc_start: 0.8383 (mp) cc_final: 0.8158 (mm)
REVERT: A  300 LYS cc_start: 0.7934 (tptp) cc_final: 0.7581 (tptp)
REVERT: A  385 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7669 (tm-30)
REVERT: A  392 MET cc_start: 0.8460 (mtp) cc_final: 0.8232 (mtt)
REVERT: A  489 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7597 (mmp)
REVERT: A  592 ARG cc_start: 0.7929 (mtt180) cc_final: 0.7133 (mmp80)
REVERT: A  623 ASN cc_start: 0.7760 (m110) cc_final: 0.7344 (m-40)
REVERT: A  641 ASN cc_start: 0.7438 (m-40) cc_final: 0.7030 (p0)
REVERT: A  652 ARG cc_start: 0.7499 (mtt90) cc_final: 0.7178 (mtt90)
REVERT: B  300 LYS cc_start: 0.7968 (tptp) cc_final: 0.7737 (tptp)
REVERT: B  390 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8209 (tttp)
REVERT: B  392 MET cc_start: 0.8577 (mtp) cc_final: 0.8349 (mtt)
REVERT: B  470 ASP cc_start: 0.8101 (t70) cc_final: 0.7873 (t0)
REVERT: B  489 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7600 (mmp)
REVERT: B  592 ARG cc_start: 0.7983 (mtt180) cc_final: 0.7164 (mmp80)
  outliers start: 32
  outliers final: 20
  residues processed: 145
  average time/residue: 0.4651
  time to fit residues: 72.2978
Evaluate side-chains
  145 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 121
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  160 SER
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  385 GLN
Chi-restraints excluded: chain A residue  434 MET
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  489 MET
Chi-restraints excluded: chain A residue  523 ASN
Chi-restraints excluded: chain A residue  524 MET
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  627 VAL
Chi-restraints excluded: chain B residue  185 SER
Chi-restraints excluded: chain B residue  390 LYS
Chi-restraints excluded: chain B residue  434 MET
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  489 MET
Chi-restraints excluded: chain B residue  523 ASN
Chi-restraints excluded: chain B residue  548 VAL
Chi-restraints excluded: chain B residue  556 VAL
Chi-restraints excluded: chain B residue  579 GLU
Chi-restraints excluded: chain B residue  627 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 93 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 107 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   chunk 24 optimal weight:    0.8980
   chunk 86 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   overall best weight:    1.1584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.163012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.134228 restraints weight = 9362.020|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 1.93
r_work: 0.3521 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3402 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.3021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8556  Z= 0.170
  Angle     :  0.597   7.033  11626  Z= 0.312
  Chirality :  0.044   0.197   1424
  Planarity :  0.005   0.058   1436
  Dihedral  :  5.406  23.390   1190
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 19.63 %
    Favored  : 77.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.61 (0.25), residues: 1106
  helix: -0.97 (0.18), residues: 768
  sheet: -2.57 (0.74), residues: 36
  loop : -0.59 (0.37), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 652 
 TYR   0.013   0.002   TYR B 408 
 PHE   0.013   0.001   PHE A 378 
 TRP   0.014   0.001   TRP B 103 
 HIS   0.002   0.001   HIS A 450 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 8556)
  covalent geometry    : angle       0.59715 (11626)
  hydrogen bonds       : bond        0.03100 (  346)
  hydrogen bonds       : angle       4.13716 ( 1026)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 130
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  300 LYS cc_start: 0.7995 (tptp) cc_final: 0.7642 (tptp)
REVERT: A  385 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7589 (tm-30)
REVERT: A  392 MET cc_start: 0.8522 (mtp) cc_final: 0.8282 (mtt)
REVERT: A  489 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7552 (mmp)
REVERT: A  592 ARG cc_start: 0.7993 (mtt180) cc_final: 0.7157 (mmp80)
REVERT: A  641 ASN cc_start: 0.7506 (m-40) cc_final: 0.6967 (p0)
REVERT: A  652 ARG cc_start: 0.7549 (mtt90) cc_final: 0.7173 (mtt90)
REVERT: B  300 LYS cc_start: 0.8009 (tptp) cc_final: 0.7662 (tptp)
REVERT: B  390 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8207 (tttp)
REVERT: B  392 MET cc_start: 0.8586 (mtp) cc_final: 0.8335 (mtt)
REVERT: B  470 ASP cc_start: 0.8115 (t70) cc_final: 0.7887 (t0)
REVERT: B  489 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7612 (mmp)
REVERT: B  592 ARG cc_start: 0.7981 (mtt180) cc_final: 0.7113 (mmp80)
  outliers start: 30
  outliers final: 21
  residues processed: 152
  average time/residue: 0.4579
  time to fit residues: 74.7740
Evaluate side-chains
  151 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 126
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  160 SER
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  385 GLN
Chi-restraints excluded: chain A residue  434 MET
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  489 MET
Chi-restraints excluded: chain A residue  523 ASN
Chi-restraints excluded: chain A residue  524 MET
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  627 VAL
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  185 SER
Chi-restraints excluded: chain B residue  390 LYS
Chi-restraints excluded: chain B residue  434 MET
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  489 MET
Chi-restraints excluded: chain B residue  523 ASN
Chi-restraints excluded: chain B residue  548 VAL
Chi-restraints excluded: chain B residue  556 VAL
Chi-restraints excluded: chain B residue  579 GLU
Chi-restraints excluded: chain B residue  627 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 38 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9990
   chunk 79 optimal weight:    4.9990
   chunk 58 optimal weight:    3.9990
   chunk 7 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 56 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   chunk 19 optimal weight:    0.6980
   chunk 9 optimal weight:    0.5980
   chunk 69 optimal weight:    0.9980
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.164649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.136011 restraints weight = 9377.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.3741 rms_B_bonded: 1.94
r_work: 0.3667 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3564 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.3094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8556  Z= 0.129
  Angle     :  0.567   6.392  11626  Z= 0.296
  Chirality :  0.042   0.187   1424
  Planarity :  0.004   0.058   1436
  Dihedral  :  5.326  23.693   1190
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 20.29 %
    Favored  : 76.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.43 (0.25), residues: 1106
  helix: -0.83 (0.19), residues: 768
  sheet: -2.53 (0.75), residues: 36
  loop : -0.52 (0.37), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 652 
 TYR   0.013   0.001   TYR A 408 
 PHE   0.009   0.001   PHE A 378 
 TRP   0.012   0.001   TRP B 103 
 HIS   0.001   0.000   HIS A 450 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 8556)
  covalent geometry    : angle       0.56695 (11626)
  hydrogen bonds       : bond        0.02925 (  346)
  hydrogen bonds       : angle       4.04436 ( 1026)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 128
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  191 ILE cc_start: 0.8160 (mp) cc_final: 0.7919 (mm)
REVERT: A  300 LYS cc_start: 0.7962 (tptp) cc_final: 0.7597 (tptp)
REVERT: A  385 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7422 (tm-30)
REVERT: A  392 MET cc_start: 0.8403 (mtp) cc_final: 0.8124 (mtt)
REVERT: A  489 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.7277 (mmp)
REVERT: A  592 ARG cc_start: 0.7849 (mtt180) cc_final: 0.7009 (mmp80)
REVERT: A  641 ASN cc_start: 0.7394 (m-40) cc_final: 0.6879 (p0)
REVERT: A  652 ARG cc_start: 0.7327 (mtt90) cc_final: 0.6923 (mtt90)
REVERT: B  300 LYS cc_start: 0.7963 (tptp) cc_final: 0.7605 (tptp)
REVERT: B  392 MET cc_start: 0.8448 (mtp) cc_final: 0.8176 (mtt)
REVERT: B  470 ASP cc_start: 0.8026 (t70) cc_final: 0.7771 (t0)
REVERT: B  489 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7379 (mmp)
REVERT: B  592 ARG cc_start: 0.7836 (mtt180) cc_final: 0.6936 (mmp80)
  outliers start: 25
  outliers final: 20
  residues processed: 147
  average time/residue: 0.3981
  time to fit residues: 62.9267
Evaluate side-chains
  147 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 124
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  160 SER
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  385 GLN
Chi-restraints excluded: chain A residue  434 MET
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  489 MET
Chi-restraints excluded: chain A residue  523 ASN
Chi-restraints excluded: chain A residue  524 MET
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  627 VAL
Chi-restraints excluded: chain B residue  185 SER
Chi-restraints excluded: chain B residue  434 MET
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  489 MET
Chi-restraints excluded: chain B residue  523 ASN
Chi-restraints excluded: chain B residue  548 VAL
Chi-restraints excluded: chain B residue  556 VAL
Chi-restraints excluded: chain B residue  579 GLU
Chi-restraints excluded: chain B residue  627 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 86 optimal weight:    0.9990
   chunk 107 optimal weight:    0.1980
   chunk 15 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9990
   chunk 71 optimal weight:    8.9990
   chunk 91 optimal weight:    4.9990
   chunk 90 optimal weight:    0.6980
   chunk 109 optimal weight:    0.6980
   chunk 22 optimal weight:    4.9990
   chunk 23 optimal weight:    0.3980
   chunk 79 optimal weight:    1.9990
   overall best weight:    0.5982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.165619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.137042 restraints weight = 9325.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3761 rms_B_bonded: 1.93
r_work: 0.3689 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3587 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.3172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8556  Z= 0.117
  Angle     :  0.552   6.353  11626  Z= 0.290
  Chirality :  0.042   0.191   1424
  Planarity :  0.004   0.058   1436
  Dihedral  :  5.213  23.368   1190
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 19.96 %
    Favored  : 76.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.22 (0.25), residues: 1106
  helix: -0.66 (0.19), residues: 768
  sheet: -2.45 (0.75), residues: 36
  loop : -0.47 (0.37), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 652 
 TYR   0.013   0.001   TYR A 408 
 PHE   0.007   0.001   PHE A 378 
 TRP   0.012   0.001   TRP B 103 
 HIS   0.001   0.000   HIS A 450 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 8556)
  covalent geometry    : angle       0.55161 (11626)
  hydrogen bonds       : bond        0.02878 (  346)
  hydrogen bonds       : angle       3.98668 ( 1026)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2722.43 seconds
wall clock time: 47 minutes 5.81 seconds (2825.81 seconds total)