Starting phenix.real_space_refine
on Wed Mar  4 09:19:51 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9vbm_64927/03_2026/9vbm_64927.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9vbm_64927/03_2026/9vbm_64927.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.19
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9vbm_64927/03_2026/9vbm_64927.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9vbm_64927/03_2026/9vbm_64927.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9vbm_64927/03_2026/9vbm_64927.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9vbm_64927/03_2026/9vbm_64927.map"
  }
  resolution = 3.19
  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=   0.001 sd=   0.030
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      52      5.16       5
     C    7738      2.51       5
     N    2000      2.21       5
     O    2312      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12104
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 6052
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 751, 6052
          Classifications: {'peptide': 751}
          Link IDs: {'PTRANS': 20, 'TRANS': 730}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'LLP:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
  Restraints were copied for chains:
    B
  Time building chain proxies: 4.46, per 1000 atoms: 0.37
  Number of scatterers: 12104
  At special positions: 0
  Unit cell: (143.59, 87.15, 89.64, 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      52     16.00
     P       2     15.00
     O    2312      8.00
     N    2000      7.00
     C    7738      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: 0.92
  Conformation dependent library (CDL) restraints added in 436.1 milliseconds
  

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2836

  Finding SS restraints...
    Secondary structure from input PDB file:
      66 helices and 12 sheets defined
      52.2% alpha, 10.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 13
    Processing helix  chain 'A' and resid 20 through 40
      removed outlier: 3.946A  pdb=" N   GLY A  40 " --> pdb=" O   ALA A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 71
    Processing helix  chain 'A' and resid 72 through 84
    Processing helix  chain 'A' and resid 86 through 91
      removed outlier: 3.516A  pdb=" N   ILE A  90 " --> pdb=" O   ASP A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 119
      removed outlier: 3.876A  pdb=" N   LEU A 112 " --> pdb=" O   ALA A 108 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ASP A 113 " --> pdb=" O   ALA A 109 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   SER A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ALA A 116 " --> pdb=" O   LEU A 112 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   THR A 117 " --> pdb=" O   ASP A 113 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLY A 119 " --> pdb=" O   ILE A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 220
      removed outlier: 3.511A  pdb=" N   LEU A 220 " --> pdb=" O   ILE A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 257
      removed outlier: 4.160A  pdb=" N   LEU A 236 " --> pdb=" O   GLN A 232 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   ARG A 237 " --> pdb=" O   GLY A 233 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ILE A 238 " --> pdb=" O   GLU A 234 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   VAL A 245 " --> pdb=" O   GLN A 241 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   LEU A 253 " --> pdb=" O   ALA A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 268
      removed outlier: 3.620A  pdb=" N   GLU A 265 " --> pdb=" O   SER A 262 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   LEU A 266 " --> pdb=" O   LEU A 263 " (cutoff:3.500A)
      removed outlier: 5.830A  pdb=" N   ASP A 267 " --> pdb=" O   GLU A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 292
    Processing helix  chain 'A' and resid 296 through 308
    Processing helix  chain 'A' and resid 316 through 320
    Processing helix  chain 'A' and resid 325 through 332
    Processing helix  chain 'A' and resid 335 through 350
      removed outlier: 3.733A  pdb=" N   LYS A 349 " --> pdb=" O   ARG A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 373
      removed outlier: 3.671A  pdb=" N   HIS A 372 " --> pdb=" O   ARG A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 391
      removed outlier: 3.776A  pdb=" N   GLU A 386 " --> pdb=" O   ALA A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 431
    Processing helix  chain 'A' and resid 434 through 438
      removed outlier: 4.271A  pdb=" N   ARG A 437 " --> pdb=" O   SER A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 450
      removed outlier: 3.748A  pdb=" N   LEU A 443 " --> pdb=" O   ALA A 440 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   GLU A 444 " --> pdb=" O   SER A 441 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   LEU A 447 " --> pdb=" O   GLU A 444 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ALA A 448 " --> pdb=" O   GLY A 445 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ILE A 450 " --> pdb=" O   LEU A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 478
      removed outlier: 3.516A  pdb=" N   GLN A 464 " --> pdb=" O   LEU A 460 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   GLN A 465 " --> pdb=" O   ASP A 461 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   LYS A 471 " --> pdb=" O   LYS A 467 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   GLU A 477 " --> pdb=" O   TYR A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 504 through 517
      removed outlier: 3.633A  pdb=" N   ILE A 508 " --> pdb=" O   ASN A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 537 through 554
      removed outlier: 3.594A  pdb=" N   LYS A 541 " --> pdb=" O   TYR A 537 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ILE A 544 " --> pdb=" O   ALA A 540 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   HIS A 545 " --> pdb=" O   LYS A 541 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   VAL A 546 " --> pdb=" O   ASP A 542 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 581
      removed outlier: 3.852A  pdb=" N   LYS A 579 " --> pdb=" O   THR A 575 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 582 through 584
      No H-bonds generated for 'chain 'A' and resid 582 through 584'
    Processing helix  chain 'A' and resid 601 through 608
      removed outlier: 3.930A  pdb=" N   PHE A 605 " --> pdb=" O   GLY A 601 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   MET A 606 " --> pdb=" O   ASN A 602 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ASN A 608 " --> pdb=" O   LLP A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 618 through 628
      removed outlier: 4.295A  pdb=" N   GLU A 622 " --> pdb=" O   GLY A 618 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   LEU A 626 " --> pdb=" O   GLU A 622 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   GLY A 628 " --> pdb=" O   HIS A 624 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 638 through 649
      removed outlier: 3.515A  pdb=" N   TYR A 646 " --> pdb=" O   VAL A 642 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 653 through 660
      removed outlier: 3.537A  pdb=" N   TYR A 657 " --> pdb=" O   ALA A 653 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ASN A 659 " --> pdb=" O   ASP A 655 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ASP A 660 " --> pdb=" O   TYR A 656 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 668
    Processing helix  chain 'A' and resid 682 through 693
      removed outlier: 3.777A  pdb=" N   HIS A 688 " --> pdb=" O   LEU A 684 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 702 through 715
      removed outlier: 3.703A  pdb=" N   ILE A 707 " --> pdb=" O   VAL A 703 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   GLN A 708 " --> pdb=" O   LYS A 704 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 719 through 733
      removed outlier: 3.830A  pdb=" N   LYS A 725 " --> pdb=" O   MET A 721 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   VAL A 729 " --> pdb=" O   LYS A 725 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ASN A 730 " --> pdb=" O   LYS A 726 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 738 through 750
    Processing helix  chain 'B' and resid 3 through 13
    Processing helix  chain 'B' and resid 20 through 40
      removed outlier: 3.946A  pdb=" N   GLY B  40 " --> pdb=" O   ALA B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 71
    Processing helix  chain 'B' and resid 72 through 84
    Processing helix  chain 'B' and resid 86 through 91
      removed outlier: 3.516A  pdb=" N   ILE B  90 " --> pdb=" O   ASP B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 119
      removed outlier: 3.876A  pdb=" N   LEU B 112 " --> pdb=" O   ALA B 108 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ASP B 113 " --> pdb=" O   ALA B 109 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   SER B 114 " --> pdb=" O   CYS B 110 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ALA B 116 " --> pdb=" O   LEU B 112 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   THR B 117 " --> pdb=" O   ASP B 113 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLY B 119 " --> pdb=" O   ILE B 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 215 through 220
      removed outlier: 3.511A  pdb=" N   LEU B 220 " --> pdb=" O   ILE B 216 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 257
      removed outlier: 4.160A  pdb=" N   LEU B 236 " --> pdb=" O   GLN B 232 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   ARG B 237 " --> pdb=" O   GLY B 233 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ILE B 238 " --> pdb=" O   GLU B 234 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   VAL B 245 " --> pdb=" O   GLN B 241 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   LEU B 253 " --> pdb=" O   ALA B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 262 through 268
      removed outlier: 3.620A  pdb=" N   GLU B 265 " --> pdb=" O   SER B 262 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   LEU B 266 " --> pdb=" O   LEU B 263 " (cutoff:3.500A)
      removed outlier: 5.830A  pdb=" N   ASP B 267 " --> pdb=" O   GLU B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 281 through 292
    Processing helix  chain 'B' and resid 296 through 308
    Processing helix  chain 'B' and resid 316 through 320
    Processing helix  chain 'B' and resid 325 through 332
    Processing helix  chain 'B' and resid 335 through 350
      removed outlier: 3.733A  pdb=" N   LYS B 349 " --> pdb=" O   ARG B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 373
      removed outlier: 3.671A  pdb=" N   HIS B 372 " --> pdb=" O   ARG B 368 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 391
      removed outlier: 3.776A  pdb=" N   GLU B 386 " --> pdb=" O   ALA B 382 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 423 through 431
    Processing helix  chain 'B' and resid 434 through 438
      removed outlier: 4.271A  pdb=" N   ARG B 437 " --> pdb=" O   SER B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 439 through 450
      removed outlier: 3.748A  pdb=" N   LEU B 443 " --> pdb=" O   ALA B 440 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   GLU B 444 " --> pdb=" O   SER B 441 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   LEU B 447 " --> pdb=" O   GLU B 444 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ALA B 448 " --> pdb=" O   GLY B 445 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ILE B 450 " --> pdb=" O   LEU B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 478
      removed outlier: 3.516A  pdb=" N   GLN B 464 " --> pdb=" O   LEU B 460 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   GLN B 465 " --> pdb=" O   ASP B 461 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   LYS B 471 " --> pdb=" O   LYS B 467 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   GLU B 477 " --> pdb=" O   TYR B 473 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 504 through 517
      removed outlier: 3.633A  pdb=" N   ILE B 508 " --> pdb=" O   ASN B 504 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 537 through 554
      removed outlier: 3.594A  pdb=" N   LYS B 541 " --> pdb=" O   TYR B 537 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ILE B 544 " --> pdb=" O   ALA B 540 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   HIS B 545 " --> pdb=" O   LYS B 541 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   VAL B 546 " --> pdb=" O   ASP B 542 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 573 through 581
      removed outlier: 3.852A  pdb=" N   LYS B 579 " --> pdb=" O   THR B 575 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 582 through 584
      No H-bonds generated for 'chain 'B' and resid 582 through 584'
    Processing helix  chain 'B' and resid 601 through 608
      removed outlier: 3.930A  pdb=" N   PHE B 605 " --> pdb=" O   GLY B 601 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   MET B 606 " --> pdb=" O   ASN B 602 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ASN B 608 " --> pdb=" O   LLP B 604 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 618 through 628
      removed outlier: 4.295A  pdb=" N   GLU B 622 " --> pdb=" O   GLY B 618 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   LEU B 626 " --> pdb=" O   GLU B 622 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   GLY B 628 " --> pdb=" O   HIS B 624 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 638 through 649
      removed outlier: 3.515A  pdb=" N   TYR B 646 " --> pdb=" O   VAL B 642 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 653 through 660
      removed outlier: 3.537A  pdb=" N   TYR B 657 " --> pdb=" O   ALA B 653 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ASN B 659 " --> pdb=" O   ASP B 655 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ASP B 660 " --> pdb=" O   TYR B 656 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 660 through 668
    Processing helix  chain 'B' and resid 682 through 693
      removed outlier: 3.777A  pdb=" N   HIS B 688 " --> pdb=" O   LEU B 684 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 702 through 715
      removed outlier: 3.703A  pdb=" N   ILE B 707 " --> pdb=" O   VAL B 703 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   GLN B 708 " --> pdb=" O   LYS B 704 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 719 through 733
      removed outlier: 3.830A  pdb=" N   LYS B 725 " --> pdb=" O   MET B 721 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   VAL B 729 " --> pdb=" O   LYS B 725 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ASN B 730 " --> pdb=" O   LYS B 726 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 738 through 750
    Processing sheet with id=1, first strand: chain 'A' and resid 158 through 159
    Processing sheet with id=2, first strand: chain 'A' and resid 158 through 159
      removed outlier: 6.952A  pdb=" N   GLY A 122 " --> pdb=" O   LYS A 191 " (cutoff:3.500A)
      removed outlier: 8.269A  pdb=" N   HIS A 193 " --> pdb=" O   GLY A 122 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   GLY A 124 " --> pdb=" O   HIS A 193 " (cutoff:3.500A)
      removed outlier: 7.775A  pdb=" N   PHE A 195 " --> pdb=" O   GLY A 124 " (cutoff:3.500A)
      removed outlier: 7.080A  pdb=" N   GLY A 126 " --> pdb=" O   PHE A 195 " (cutoff:3.500A)
      removed outlier: 9.241A  pdb=" N   ILE A 197 " --> pdb=" O   GLY A 126 " (cutoff:3.500A)
      removed outlier: 6.144A  pdb=" N   LYS A  49 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
      removed outlier: 7.358A  pdb=" N   GLN A 273 " --> pdb=" O   LYS A  49 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   TYR A  51 " --> pdb=" O   GLN A 273 " (cutoff:3.500A)
    Processing sheet with id=3, first strand: chain 'A' and resid 135 through 138
    Processing sheet with id=4, first strand: chain 'A' and resid 310 through 311
      removed outlier: 7.591A  pdb=" N   TYR A 310 " --> pdb=" O   ASN A 378 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=4
    Processing sheet with id=5, first strand: chain 'A' and resid 322 through 324
    Processing sheet with id=6, first strand: chain 'A' and resid 564 through 568
      removed outlier: 3.719A  pdb=" N   GLU A 588 " --> pdb=" O   ILE A 490 " (cutoff:3.500A)
      removed outlier: 5.324A  pdb=" N   ILE A 492 " --> pdb=" O   GLU A 588 " (cutoff:3.500A)
      removed outlier: 6.062A  pdb=" N   SER A 587 " --> pdb=" O   LEU A 613 " (cutoff:3.500A)
      removed outlier: 8.047A  pdb=" N   THR A 615 " --> pdb=" O   SER A 587 " (cutoff:3.500A)
      removed outlier: 7.355A  pdb=" N   GLN A 589 " --> pdb=" O   THR A 615 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   THR A 612 " --> pdb=" O   TYR A 633 " (cutoff:3.500A)
      removed outlier: 7.955A  pdb=" N   PHE A 635 " --> pdb=" O   THR A 612 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   GLY A 614 " --> pdb=" O   PHE A 635 " (cutoff:3.500A)
    Processing sheet with id=7, first strand: chain 'B' and resid 158 through 159
    Processing sheet with id=8, first strand: chain 'B' and resid 158 through 159
      removed outlier: 6.952A  pdb=" N   GLY B 122 " --> pdb=" O   LYS B 191 " (cutoff:3.500A)
      removed outlier: 8.269A  pdb=" N   HIS B 193 " --> pdb=" O   GLY B 122 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   GLY B 124 " --> pdb=" O   HIS B 193 " (cutoff:3.500A)
      removed outlier: 7.775A  pdb=" N   PHE B 195 " --> pdb=" O   GLY B 124 " (cutoff:3.500A)
      removed outlier: 7.080A  pdb=" N   GLY B 126 " --> pdb=" O   PHE B 195 " (cutoff:3.500A)
      removed outlier: 9.241A  pdb=" N   ILE B 197 " --> pdb=" O   GLY B 126 " (cutoff:3.500A)
      removed outlier: 6.144A  pdb=" N   LYS B  49 " --> pdb=" O   VAL B 271 " (cutoff:3.500A)
      removed outlier: 7.358A  pdb=" N   GLN B 273 " --> pdb=" O   LYS B  49 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   TYR B  51 " --> pdb=" O   GLN B 273 " (cutoff:3.500A)
    Processing sheet with id=9, first strand: chain 'B' and resid 135 through 138
    Processing sheet with id=10, first strand: chain 'B' and resid 310 through 311
      removed outlier: 7.591A  pdb=" N   TYR B 310 " --> pdb=" O   ASN B 378 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=10
    Processing sheet with id=11, first strand: chain 'B' and resid 322 through 324
    Processing sheet with id=12, first strand: chain 'B' and resid 564 through 568
      removed outlier: 3.719A  pdb=" N   GLU B 588 " --> pdb=" O   ILE B 490 " (cutoff:3.500A)
      removed outlier: 5.324A  pdb=" N   ILE B 492 " --> pdb=" O   GLU B 588 " (cutoff:3.500A)
      removed outlier: 6.062A  pdb=" N   SER B 587 " --> pdb=" O   LEU B 613 " (cutoff:3.500A)
      removed outlier: 8.047A  pdb=" N   THR B 615 " --> pdb=" O   SER B 587 " (cutoff:3.500A)
      removed outlier: 7.355A  pdb=" N   GLN B 589 " --> pdb=" O   THR B 615 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   THR B 612 " --> pdb=" O   TYR B 633 " (cutoff:3.500A)
      removed outlier: 7.955A  pdb=" N   PHE B 635 " --> pdb=" O   THR B 612 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   GLY B 614 " --> pdb=" O   PHE B 635 " (cutoff:3.500A)

    494 hydrogen bonds defined for protein.
    1410 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: 1.53

  Time building geometry restraints manager: 1.27 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3954
        1.34 -     1.46: 1810
        1.46 -     1.57: 6486
        1.57 -     1.69: 2
        1.69 -     1.81: 90
  Bond restraints: 12342
  Sorted by residual:
  bond pdb=" OP4 LLP B 604 "
       pdb=" P   LLP B 604 "
    ideal  model  delta    sigma   weight residual
    1.726  1.544  0.182 2.00e-02 2.50e+03 8.30e+01
  bond pdb=" OP4 LLP A 604 "
       pdb=" P   LLP A 604 "
    ideal  model  delta    sigma   weight residual
    1.726  1.544  0.182 2.00e-02 2.50e+03 8.30e+01
  bond pdb=" NZ  LLP A 604 "
       pdb=" C4' LLP A 604 "
    ideal  model  delta    sigma   weight residual
    1.273  1.431 -0.158 2.00e-02 2.50e+03 6.25e+01
  bond pdb=" NZ  LLP B 604 "
       pdb=" C4' LLP B 604 "
    ideal  model  delta    sigma   weight residual
    1.273  1.431 -0.158 2.00e-02 2.50e+03 6.25e+01
  bond pdb=" C4  LLP B 604 "
       pdb=" C4' LLP B 604 "
    ideal  model  delta    sigma   weight residual
    1.464  1.616 -0.152 2.00e-02 2.50e+03 5.78e+01
  ... (remaining 12337 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.01: 16416
        2.01 -     4.01: 238
        4.01 -     6.02: 32
        6.02 -     8.02: 6
        8.02 -    10.03: 6
  Bond angle restraints: 16698
  Sorted by residual:
  angle pdb=" CE  LLP B 604 "
        pdb=" NZ  LLP B 604 "
        pdb=" C4' LLP B 604 "
      ideal   model   delta    sigma   weight residual
     119.26  109.23   10.03 3.00e+00 1.11e-01 1.12e+01
  angle pdb=" CE  LLP A 604 "
        pdb=" NZ  LLP A 604 "
        pdb=" C4' LLP A 604 "
      ideal   model   delta    sigma   weight residual
     119.26  109.23   10.03 3.00e+00 1.11e-01 1.12e+01
  angle pdb=" C   ILE B 581 "
        pdb=" CA  ILE B 581 "
        pdb=" CB  ILE B 581 "
      ideal   model   delta    sigma   weight residual
     114.35  110.95    3.40 1.06e+00 8.90e-01 1.03e+01
  angle pdb=" C   ILE A 581 "
        pdb=" CA  ILE A 581 "
        pdb=" CB  ILE A 581 "
      ideal   model   delta    sigma   weight residual
     114.35  110.95    3.40 1.06e+00 8.90e-01 1.03e+01
  angle pdb=" OP1 LLP A 604 "
        pdb=" P   LLP A 604 "
        pdb=" OP4 LLP A 604 "
      ideal   model   delta    sigma   weight residual
     100.47  109.79   -9.32 3.00e+00 1.11e-01 9.66e+00
  ... (remaining 16693 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.98: 6512
       14.98 -    29.97: 666
       29.97 -    44.95: 168
       44.95 -    59.94: 60
       59.94 -    74.92: 28
  Dihedral angle restraints: 7434
    sinusoidal: 3030
      harmonic: 4404
  Sorted by residual:
  dihedral pdb=" CA  PHE A 697 "
           pdb=" C   PHE A 697 "
           pdb=" N   MET A 698 "
           pdb=" CA  MET A 698 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.58   16.42     0      5.00e+00 4.00e-02 1.08e+01
  dihedral pdb=" CA  PHE B 697 "
           pdb=" C   PHE B 697 "
           pdb=" N   MET B 698 "
           pdb=" CA  MET B 698 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.58   16.42     0      5.00e+00 4.00e-02 1.08e+01
  dihedral pdb=" CA  ASP B 421 "
           pdb=" CB  ASP B 421 "
           pdb=" CG  ASP B 421 "
           pdb=" OD1 ASP B 421 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -85.10   55.10     1      2.00e+01 2.50e-03 1.03e+01
  ... (remaining 7431 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 932
       0.026 -    0.053: 606
       0.053 -    0.079: 222
       0.079 -    0.105: 78
       0.105 -    0.131: 16
  Chirality restraints: 1854
  Sorted by residual:
  chirality pdb=" CA  VAL B 567 "
            pdb=" N   VAL B 567 "
            pdb=" C   VAL B 567 "
            pdb=" CB  VAL B 567 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.31e-01
  chirality pdb=" CA  VAL A 567 "
            pdb=" N   VAL A 567 "
            pdb=" C   VAL A 567 "
            pdb=" CB  VAL A 567 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.31e-01
  chirality pdb=" CA  ILE B 358 "
            pdb=" N   ILE B 358 "
            pdb=" C   ILE B 358 "
            pdb=" CB  ILE B 358 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.11 2.00e-01 2.50e+01 3.25e-01
  ... (remaining 1851 not shown)

  Planarity restraints: 2146
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CE  LLP A 604 "   -0.357 2.00e-02 2.50e+03   3.26e-01 1.06e+03
        pdb=" NZ  LLP A 604 "    0.386 2.00e-02 2.50e+03
        pdb=" C4  LLP A 604 "   -0.287 2.00e-02 2.50e+03
        pdb=" C4' LLP A 604 "    0.258 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CE  LLP B 604 "    0.357 2.00e-02 2.50e+03   3.26e-01 1.06e+03
        pdb=" NZ  LLP B 604 "   -0.386 2.00e-02 2.50e+03
        pdb=" C4  LLP B 604 "    0.287 2.00e-02 2.50e+03
        pdb=" C4' LLP B 604 "   -0.258 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 146 "   -0.041 5.00e-02 4.00e+02   6.20e-02 6.15e+00
        pdb=" N   PRO B 147 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO B 147 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO B 147 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 2143 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2740
        2.79 -     3.32: 10604
        3.32 -     3.84: 19268
        3.84 -     4.37: 24316
        4.37 -     4.90: 42259
  Nonbonded interactions: 99187
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B 439 "
            pdb=" OG  SER B 441 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" OD2 ASP A 439 "
            pdb=" OG  SER A 441 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" OE2 GLU B 585 "
            pdb=" OH  TYR B 717 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" OE2 GLU A 585 "
            pdb=" OH  TYR A 717 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" OH  TYR A 510 "
            pdb=" OE2 GLU A 711 "
     model   vdw
     2.293 3.040
  ... (remaining 99182 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:             2.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     12.120
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.010
  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: 0.8195
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      :  0.005   0.182  12342  Z= 0.262
  Angle     :  0.679  10.028  16698  Z= 0.411
  Chirality :  0.039   0.131   1854
  Planarity :  0.011   0.326   2146
  Dihedral  : 14.460  74.921   4598
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -2.31 (0.21), residues: 1492
  helix: -1.27 (0.19), residues: 768
  sheet: -1.60 (0.37), residues: 214
  loop : -1.58 (0.25), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 293 
 TYR   0.018   0.001   TYR A 350 
 PHE   0.011   0.001   PHE B 375 
 TRP   0.011   0.001   TRP B 361 
 HIS   0.005   0.001   HIS B 688 

Details of bonding type rmsd
  covalent geometry    : bond        0.00522 (12342)
  covalent geometry    : angle       0.67949 (16698)
  hydrogen bonds       : bond        0.24747 (  490)
  hydrogen bonds       : angle       7.62741 ( 1410)

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

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

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.486 
Fit side-chains
REVERT: A  450 ILE cc_start: 0.8596 (tt) cc_final: 0.8396 (tt)
REVERT: A  748 ARG cc_start: 0.7922 (ttp80) cc_final: 0.7607 (ttp80)
REVERT: A  749 ASP cc_start: 0.7825 (m-30) cc_final: 0.7450 (m-30)
REVERT: B  748 ARG cc_start: 0.7933 (ttp80) cc_final: 0.7589 (ttp80)
REVERT: B  749 ASP cc_start: 0.7827 (m-30) cc_final: 0.7457 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 150
  average time/residue: 0.1079
  time to fit residues: 23.7204
Evaluate side-chains
  130 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    8.9990
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    0.6980
   chunk 124 optimal weight:    0.0870
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:    1.9990
   overall best weight:    0.9362

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

Flipped N/Q/H residues before XYZ refinement:
A  83 ASN
A 219 ASN
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 747 ASN
** B  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 747 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.120770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.105699 restraints weight = 15105.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.3086 rms_B_bonded: 1.27
r_work: 0.2988 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.2870 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8547
moved from start:          0.1082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12342  Z= 0.141
  Angle     :  0.524   6.124  16698  Z= 0.277
  Chirality :  0.041   0.142   1854
  Planarity :  0.004   0.054   2146
  Dihedral  :  5.046  45.386   1630
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  5.43 %
    Favored  : 93.58 %
  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: -1.69 (0.22), residues: 1492
  helix: -0.70 (0.19), residues: 782
  sheet: -1.48 (0.37), residues: 216
  loop : -1.33 (0.27), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 293 
 TYR   0.014   0.002   TYR A 431 
 PHE   0.012   0.001   PHE A 605 
 TRP   0.013   0.001   TRP B 427 
 HIS   0.004   0.001   HIS A 688 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (12342)
  covalent geometry    : angle       0.52358 (16698)
  hydrogen bonds       : bond        0.04608 (  490)
  hydrogen bonds       : angle       4.46773 ( 1410)

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

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

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 119
  time to evaluate  : 0.403 
Fit side-chains
REVERT: A  476 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7642 (ttmm)
REVERT: A  581 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.7824 (mp)
REVERT: A  748 ARG cc_start: 0.8212 (ttp80) cc_final: 0.7959 (ttp80)
REVERT: A  749 ASP cc_start: 0.8056 (m-30) cc_final: 0.7744 (m-30)
REVERT: B  476 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7636 (ttmm)
REVERT: B  581 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.7829 (mp)
REVERT: B  748 ARG cc_start: 0.8216 (ttp80) cc_final: 0.7963 (ttp80)
REVERT: B  749 ASP cc_start: 0.8050 (m-30) cc_final: 0.7737 (m-30)
  outliers start: 13
  outliers final: 7
  residues processed: 124
  average time/residue: 0.1119
  time to fit residues: 20.1058
Evaluate side-chains
  125 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 114
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 ASN
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  369 MET
Chi-restraints excluded: chain A residue  476 LYS
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain A residue  581 ILE
Chi-restraints excluded: chain B residue  318 GLU
Chi-restraints excluded: chain B residue  369 MET
Chi-restraints excluded: chain B residue  476 LYS
Chi-restraints excluded: chain B residue  492 ILE
Chi-restraints excluded: chain B residue  581 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 143 optimal weight:    0.6980
   chunk 108 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 45 optimal weight:    0.5980
   chunk 113 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0770
   chunk 114 optimal weight:    0.6980
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
A  83 ASN
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  83 ASN
** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.112602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.095742 restraints weight = 15661.583|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 1.44
r_work: 0.3049 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2925 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
moved from start:          0.1300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  12342  Z= 0.100
  Angle     :  0.455   6.099  16698  Z= 0.241
  Chirality :  0.039   0.173   1854
  Planarity :  0.003   0.050   2146
  Dihedral  :  4.868  46.508   1630
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  6.73 %
    Favored  : 92.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.10 (0.23), residues: 1492
  helix: -0.17 (0.20), residues: 782
  sheet: -1.24 (0.38), residues: 216
  loop : -1.15 (0.28), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 293 
 TYR   0.013   0.001   TYR B 431 
 PHE   0.008   0.001   PHE B 375 
 TRP   0.011   0.001   TRP B 427 
 HIS   0.003   0.001   HIS B 688 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 (12342)
  covalent geometry    : angle       0.45534 (16698)
  hydrogen bonds       : bond        0.03529 (  490)
  hydrogen bonds       : angle       3.95478 ( 1410)

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

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

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 136
  time to evaluate  : 0.453 
Fit side-chains
REVERT: A  165 ASP cc_start: 0.7861 (p0) cc_final: 0.7620 (t70)
REVERT: A  399 ILE cc_start: 0.8150 (mt) cc_final: 0.7912 (mt)
REVERT: A  581 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.7733 (mp)
REVERT: A  748 ARG cc_start: 0.8272 (ttp80) cc_final: 0.7983 (ttp80)
REVERT: A  749 ASP cc_start: 0.8068 (m-30) cc_final: 0.7745 (m-30)
REVERT: B  165 ASP cc_start: 0.7868 (p0) cc_final: 0.7624 (t70)
REVERT: B  399 ILE cc_start: 0.8140 (mt) cc_final: 0.7898 (mt)
REVERT: B  581 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.7749 (mp)
REVERT: B  748 ARG cc_start: 0.8281 (ttp80) cc_final: 0.7997 (ttp80)
REVERT: B  749 ASP cc_start: 0.8064 (m-30) cc_final: 0.7746 (m-30)
  outliers start: 16
  outliers final: 8
  residues processed: 142
  average time/residue: 0.1143
  time to fit residues: 23.6884
Evaluate side-chains
  133 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 123
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 ASN
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  454 GLU
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain A residue  581 ILE
Chi-restraints excluded: chain B residue   83 ASN
Chi-restraints excluded: chain B residue  318 GLU
Chi-restraints excluded: chain B residue  454 GLU
Chi-restraints excluded: chain B residue  492 ILE
Chi-restraints excluded: chain B residue  581 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 104 optimal weight:    4.9990
   chunk 148 optimal weight:    3.9990
   chunk 129 optimal weight:    0.5980
   chunk 136 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 85 optimal weight:    3.9990
   chunk 111 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9990
   chunk 75 optimal weight:    7.9990
   chunk 86 optimal weight:    3.9990
   overall best weight:    2.7188

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

Flipped N/Q/H residues before XYZ refinement:
A  83 ASN
A 140 ASN
A 219 ASN
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 313 HIS
B  83 ASN
B 140 ASN
B 219 ASN
** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 313 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.113677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.098654 restraints weight = 15517.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.2898 rms_B_bonded: 1.22
r_work: 0.2806 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.2692 rms_B_bonded: 2.89 restraints_weight: 0.2500
r_work (final): 0.2692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8626
moved from start:          0.1644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.064  12342  Z= 0.327
  Angle     :  0.679   7.702  16698  Z= 0.352
  Chirality :  0.047   0.205   1854
  Planarity :  0.004   0.049   2146
  Dihedral  :  5.309  47.911   1630
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  :  8.41 %
    Favored  : 89.14 %
  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: -1.56 (0.22), residues: 1492
  helix: -0.48 (0.19), residues: 784
  sheet: -1.55 (0.36), residues: 220
  loop : -1.42 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 106 
 TYR   0.016   0.002   TYR B 746 
 PHE   0.016   0.002   PHE B 605 
 TRP   0.010   0.002   TRP B 416 
 HIS   0.006   0.002   HIS A 688 

Details of bonding type rmsd
  covalent geometry    : bond        0.00823 (12342)
  covalent geometry    : angle       0.67927 (16698)
  hydrogen bonds       : bond        0.05114 (  490)
  hydrogen bonds       : angle       4.46686 ( 1410)

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

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

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 118
  time to evaluate  : 0.453 
Fit side-chains
REVERT: A   90 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8569 (mt)
REVERT: A  581 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.7810 (mp)
REVERT: A  603 MET cc_start: 0.8984 (mtt) cc_final: 0.8779 (mtt)
REVERT: A  748 ARG cc_start: 0.8225 (ttp80) cc_final: 0.7970 (ttp80)
REVERT: A  749 ASP cc_start: 0.8074 (m-30) cc_final: 0.7814 (m-30)
REVERT: B   86 ASP cc_start: 0.7163 (t0) cc_final: 0.6932 (t0)
REVERT: B   90 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8563 (mt)
REVERT: B  581 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.7830 (mp)
REVERT: B  603 MET cc_start: 0.8988 (mtt) cc_final: 0.8786 (mtt)
REVERT: B  748 ARG cc_start: 0.8225 (ttp80) cc_final: 0.7969 (ttp80)
REVERT: B  749 ASP cc_start: 0.8089 (m-30) cc_final: 0.7829 (m-30)
  outliers start: 32
  outliers final: 18
  residues processed: 142
  average time/residue: 0.1033
  time to fit residues: 21.8355
Evaluate side-chains
  132 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 110
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   83 ASN
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  171 PHE
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  454 GLU
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain A residue  581 ILE
Chi-restraints excluded: chain A residue  644 GLU
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   83 ASN
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain B residue  158 THR
Chi-restraints excluded: chain B residue  171 PHE
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  318 GLU
Chi-restraints excluded: chain B residue  454 GLU
Chi-restraints excluded: chain B residue  492 ILE
Chi-restraints excluded: chain B residue  581 ILE
Chi-restraints excluded: chain B residue  644 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 142 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 121 optimal weight:    0.6980
   chunk 93 optimal weight:    3.9990
   chunk 83 optimal weight:    1.9990
   chunk 135 optimal weight:    0.5980
   chunk 91 optimal weight:    0.7980
   chunk 145 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 81 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  83 ASN
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  83 ASN
** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.109187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.092141 restraints weight = 15741.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3131 rms_B_bonded: 1.44
r_work: 0.3021 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.2894 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.2894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8572
moved from start:          0.1617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12342  Z= 0.116
  Angle     :  0.486   6.469  16698  Z= 0.256
  Chirality :  0.041   0.175   1854
  Planarity :  0.003   0.049   2146
  Dihedral  :  4.965  51.413   1630
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  :  8.87 %
    Favored  : 88.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.08 (0.22), residues: 1492
  helix: -0.06 (0.19), residues: 790
  sheet: -1.24 (0.37), residues: 216
  loop : -1.33 (0.27), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 106 
 TYR   0.013   0.001   TYR B 498 
 PHE   0.009   0.001   PHE B 605 
 TRP   0.009   0.001   TRP A 416 
 HIS   0.004   0.001   HIS A 688 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (12342)
  covalent geometry    : angle       0.48634 (16698)
  hydrogen bonds       : bond        0.03583 (  490)
  hydrogen bonds       : angle       3.94250 ( 1410)

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

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

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 117
  time to evaluate  : 0.443 
Fit side-chains
REVERT: A   90 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8476 (mp)
REVERT: A  165 ASP cc_start: 0.7940 (p0) cc_final: 0.7538 (p0)
REVERT: A  371 MET cc_start: 0.8746 (mtm) cc_final: 0.8531 (mtm)
REVERT: A  399 ILE cc_start: 0.8108 (mt) cc_final: 0.7902 (mt)
REVERT: A  450 ILE cc_start: 0.8855 (tt) cc_final: 0.8644 (tt)
REVERT: A  581 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.7788 (mp)
REVERT: A  748 ARG cc_start: 0.8274 (ttp80) cc_final: 0.8006 (ttp80)
REVERT: A  749 ASP cc_start: 0.8011 (m-30) cc_final: 0.7688 (m-30)
REVERT: B   90 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8479 (mt)
REVERT: B  165 ASP cc_start: 0.7961 (p0) cc_final: 0.7560 (p0)
REVERT: B  371 MET cc_start: 0.8753 (mtm) cc_final: 0.8537 (mtm)
REVERT: B  399 ILE cc_start: 0.8106 (mt) cc_final: 0.7893 (mt)
REVERT: B  581 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.7801 (mp)
REVERT: B  748 ARG cc_start: 0.8264 (ttp80) cc_final: 0.7999 (ttp80)
REVERT: B  749 ASP cc_start: 0.8010 (m-30) cc_final: 0.7687 (m-30)
  outliers start: 28
  outliers final: 16
  residues processed: 137
  average time/residue: 0.1007
  time to fit residues: 20.5779
Evaluate side-chains
  137 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 117
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 ASN
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  171 PHE
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  454 GLU
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain A residue  581 ILE
Chi-restraints excluded: chain A residue  644 GLU
Chi-restraints excluded: chain A residue  652 VAL
Chi-restraints excluded: chain B residue   83 ASN
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain B residue  171 PHE
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  318 GLU
Chi-restraints excluded: chain B residue  454 GLU
Chi-restraints excluded: chain B residue  492 ILE
Chi-restraints excluded: chain B residue  581 ILE
Chi-restraints excluded: chain B residue  644 GLU
Chi-restraints excluded: chain B residue  652 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 106 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 136 optimal weight:    1.9990
   chunk 114 optimal weight:    0.9990
   chunk 102 optimal weight:    2.9990
   chunk 93 optimal weight:    0.0020
   chunk 36 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   chunk 120 optimal weight:    1.9990
   chunk 18 optimal weight:    0.4980
   overall best weight:    0.8392

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

Flipped N/Q/H residues before XYZ refinement:
A  30 ASN
A  83 ASN
A 140 ASN
A 219 ASN
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  83 ASN
B 140 ASN
** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.119274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.105449 restraints weight = 15096.697|
|-----------------------------------------------------------------------------|
r_work (start): 0.3005 rms_B_bonded: 1.12
r_work: 0.2914 rms_B_bonded: 1.51 restraints_weight: 0.5000
r_work: 0.2803 rms_B_bonded: 2.63 restraints_weight: 0.2500
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
moved from start:          0.1673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12342  Z= 0.124
  Angle     :  0.476   6.257  16698  Z= 0.250
  Chirality :  0.041   0.176   1854
  Planarity :  0.003   0.047   2146
  Dihedral  :  4.883  52.628   1630
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  :  8.41 %
    Favored  : 89.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.63 (0.22), residues: 1492
  helix:  0.34 (0.20), residues: 764
  sheet: -1.08 (0.37), residues: 216
  loop : -1.10 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 106 
 TYR   0.013   0.001   TYR B 498 
 PHE   0.009   0.001   PHE A 134 
 TRP   0.009   0.001   TRP B 427 
 HIS   0.004   0.001   HIS B 688 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (12342)
  covalent geometry    : angle       0.47650 (16698)
  hydrogen bonds       : bond        0.03445 (  490)
  hydrogen bonds       : angle       3.82056 ( 1410)

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

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

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 114
  time to evaluate  : 0.438 
Fit side-chains
REVERT: A   90 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8498 (mt)
REVERT: A  165 ASP cc_start: 0.7734 (p0) cc_final: 0.7497 (t70)
REVERT: A  581 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.7773 (mp)
REVERT: A  748 ARG cc_start: 0.8199 (ttp80) cc_final: 0.7968 (ttp80)
REVERT: A  749 ASP cc_start: 0.7961 (m-30) cc_final: 0.7677 (m-30)
REVERT: B   83 ASN cc_start: 0.8075 (OUTLIER) cc_final: 0.7765 (m-40)
REVERT: B   90 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8513 (mt)
REVERT: B  165 ASP cc_start: 0.7742 (p0) cc_final: 0.7499 (t70)
REVERT: B  581 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.7783 (mp)
REVERT: B  748 ARG cc_start: 0.8194 (ttp80) cc_final: 0.7964 (ttp80)
REVERT: B  749 ASP cc_start: 0.7965 (m-30) cc_final: 0.7682 (m-30)
  outliers start: 33
  outliers final: 21
  residues processed: 139
  average time/residue: 0.1010
  time to fit residues: 21.0379
Evaluate side-chains
  135 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 109
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   83 ASN
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  171 PHE
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  275 ASN
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  454 GLU
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain A residue  581 ILE
Chi-restraints excluded: chain A residue  644 GLU
Chi-restraints excluded: chain A residue  652 VAL
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   83 ASN
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  171 PHE
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  275 ASN
Chi-restraints excluded: chain B residue  318 GLU
Chi-restraints excluded: chain B residue  454 GLU
Chi-restraints excluded: chain B residue  492 ILE
Chi-restraints excluded: chain B residue  581 ILE
Chi-restraints excluded: chain B residue  644 GLU
Chi-restraints excluded: chain B residue  652 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 143 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 15 optimal weight:    0.3980
   chunk 142 optimal weight:    0.8980
   chunk 60 optimal weight:    3.9990
   chunk 122 optimal weight:    3.9990
   chunk 27 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   chunk 106 optimal weight:    3.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A  83 ASN
A 140 ASN
A 273 GLN
B  83 ASN
B 140 ASN
** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.110555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.093388 restraints weight = 15444.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.3137 rms_B_bonded: 1.44
r_work: 0.3026 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.2900 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8562
moved from start:          0.1726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12342  Z= 0.116
  Angle     :  0.470   7.541  16698  Z= 0.246
  Chirality :  0.041   0.212   1854
  Planarity :  0.003   0.047   2146
  Dihedral  :  4.819  53.001   1630
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  :  9.17 %
    Favored  : 88.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.43 (0.22), residues: 1492
  helix:  0.49 (0.20), residues: 764
  sheet: -0.95 (0.38), residues: 216
  loop : -1.01 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 106 
 TYR   0.013   0.001   TYR A 498 
 PHE   0.009   0.001   PHE B 134 
 TRP   0.009   0.001   TRP A 427 
 HIS   0.004   0.001   HIS B 688 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (12342)
  covalent geometry    : angle       0.47029 (16698)
  hydrogen bonds       : bond        0.03351 (  490)
  hydrogen bonds       : angle       3.78108 ( 1410)

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

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

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 112
  time to evaluate  : 0.475 
Fit side-chains
REVERT: A   90 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8510 (mt)
REVERT: A  165 ASP cc_start: 0.7872 (p0) cc_final: 0.7619 (t70)
REVERT: A  371 MET cc_start: 0.8699 (mtm) cc_final: 0.8494 (mtm)
REVERT: A  581 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.7778 (mp)
REVERT: A  748 ARG cc_start: 0.8272 (ttp80) cc_final: 0.8047 (ttp80)
REVERT: A  749 ASP cc_start: 0.8017 (m-30) cc_final: 0.7645 (m-30)
REVERT: B   90 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8523 (mt)
REVERT: B  165 ASP cc_start: 0.7877 (p0) cc_final: 0.7615 (t70)
REVERT: B  371 MET cc_start: 0.8706 (mtm) cc_final: 0.8498 (mtm)
REVERT: B  581 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.7787 (mp)
REVERT: B  748 ARG cc_start: 0.8261 (ttp80) cc_final: 0.8032 (ttp80)
REVERT: B  749 ASP cc_start: 0.8026 (m-30) cc_final: 0.7658 (m-30)
  outliers start: 33
  outliers final: 22
  residues processed: 137
  average time/residue: 0.1048
  time to fit residues: 21.4960
Evaluate side-chains
  134 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 108
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   83 ASN
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  171 PHE
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  275 ASN
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  454 GLU
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain A residue  581 ILE
Chi-restraints excluded: chain A residue  644 GLU
Chi-restraints excluded: chain A residue  652 VAL
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  171 PHE
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  275 ASN
Chi-restraints excluded: chain B residue  318 GLU
Chi-restraints excluded: chain B residue  454 GLU
Chi-restraints excluded: chain B residue  492 ILE
Chi-restraints excluded: chain B residue  581 ILE
Chi-restraints excluded: chain B residue  644 GLU
Chi-restraints excluded: chain B residue  652 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 71 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 38 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9980
   chunk 64 optimal weight:    3.9990
   chunk 117 optimal weight:    2.9990
   chunk 128 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 96 optimal weight:    2.9990
   chunk 142 optimal weight:    0.6980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  83 ASN
A 140 ASN
B  83 ASN
B 140 ASN
** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.119677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.104723 restraints weight = 15056.835|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 1.19
r_work: 0.3048 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.2928 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8565
moved from start:          0.1778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12342  Z= 0.120
  Angle     :  0.474   7.662  16698  Z= 0.247
  Chirality :  0.041   0.210   1854
  Planarity :  0.003   0.046   2146
  Dihedral  :  4.786  53.187   1630
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  :  9.17 %
    Favored  : 88.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.29 (0.22), residues: 1492
  helix:  0.62 (0.20), residues: 762
  sheet: -0.90 (0.38), residues: 216
  loop : -0.96 (0.27), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 106 
 TYR   0.013   0.001   TYR B 498 
 PHE   0.009   0.001   PHE B 134 
 TRP   0.008   0.001   TRP A 427 
 HIS   0.004   0.001   HIS B 688 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (12342)
  covalent geometry    : angle       0.47435 (16698)
  hydrogen bonds       : bond        0.03326 (  490)
  hydrogen bonds       : angle       3.75597 ( 1410)

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

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

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 114
  time to evaluate  : 0.503 
Fit side-chains
REVERT: A   90 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8602 (mt)
REVERT: A  165 ASP cc_start: 0.7850 (p0) cc_final: 0.7648 (t70)
REVERT: A  581 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.7809 (mp)
REVERT: A  603 MET cc_start: 0.8808 (mtt) cc_final: 0.8595 (mtt)
REVERT: A  749 ASP cc_start: 0.7967 (m-30) cc_final: 0.7613 (m-30)
REVERT: B   90 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8630 (mt)
REVERT: B  165 ASP cc_start: 0.7855 (p0) cc_final: 0.7645 (t70)
REVERT: B  581 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.7815 (mp)
REVERT: B  603 MET cc_start: 0.8821 (mtt) cc_final: 0.8613 (mtt)
REVERT: B  749 ASP cc_start: 0.7967 (m-30) cc_final: 0.7619 (m-30)
  outliers start: 35
  outliers final: 24
  residues processed: 141
  average time/residue: 0.1019
  time to fit residues: 21.6642
Evaluate side-chains
  137 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 109
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   83 ASN
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  171 PHE
Chi-restraints excluded: chain A residue  198 GLU
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  275 ASN
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  454 GLU
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain A residue  581 ILE
Chi-restraints excluded: chain A residue  644 GLU
Chi-restraints excluded: chain A residue  652 VAL
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   83 ASN
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  171 PHE
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  275 ASN
Chi-restraints excluded: chain B residue  318 GLU
Chi-restraints excluded: chain B residue  454 GLU
Chi-restraints excluded: chain B residue  492 ILE
Chi-restraints excluded: chain B residue  581 ILE
Chi-restraints excluded: chain B residue  644 GLU
Chi-restraints excluded: chain B residue  652 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 13 optimal weight:    0.2980
   chunk 140 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 83 optimal weight:    0.8980
   chunk 137 optimal weight:    1.9990
   chunk 136 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 142 optimal weight:    0.0000
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.5784

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

Flipped N/Q/H residues before XYZ refinement:
A  83 ASN
A 140 ASN
A 219 ASN
** B  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 140 ASN
** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.120733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.106918 restraints weight = 14963.881|
|-----------------------------------------------------------------------------|
r_work (start): 0.3034 rms_B_bonded: 1.14
r_work: 0.2945 rms_B_bonded: 1.51 restraints_weight: 0.5000
r_work: 0.2833 rms_B_bonded: 2.63 restraints_weight: 0.2500
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
moved from start:          0.1818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  12342  Z= 0.103
  Angle     :  0.472   7.464  16698  Z= 0.246
  Chirality :  0.041   0.213   1854
  Planarity :  0.003   0.051   2146
  Dihedral  :  4.750  53.569   1630
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  :  9.56 %
    Favored  : 88.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.13 (0.22), residues: 1492
  helix:  0.74 (0.20), residues: 762
  sheet: -0.81 (0.38), residues: 216
  loop : -0.88 (0.27), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 748 
 TYR   0.014   0.001   TYR B 498 
 PHE   0.008   0.001   PHE A 134 
 TRP   0.009   0.001   TRP A 427 
 HIS   0.004   0.001   HIS B 688 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 (12342)
  covalent geometry    : angle       0.47191 (16698)
  hydrogen bonds       : bond        0.03150 (  490)
  hydrogen bonds       : angle       3.76643 ( 1410)

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

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

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 105
  time to evaluate  : 0.542 
Fit side-chains
REVERT: A   90 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8533 (mt)
REVERT: A  581 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.7760 (mp)
REVERT: B   90 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8531 (mt)
REVERT: B  581 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.7761 (mp)
  outliers start: 31
  outliers final: 22
  residues processed: 129
  average time/residue: 0.1008
  time to fit residues: 19.9465
Evaluate side-chains
  129 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 103
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  171 PHE
Chi-restraints excluded: chain A residue  198 GLU
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  275 ASN
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  454 GLU
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain A residue  581 ILE
Chi-restraints excluded: chain A residue  644 GLU
Chi-restraints excluded: chain A residue  652 VAL
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  171 PHE
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  275 ASN
Chi-restraints excluded: chain B residue  318 GLU
Chi-restraints excluded: chain B residue  454 GLU
Chi-restraints excluded: chain B residue  492 ILE
Chi-restraints excluded: chain B residue  581 ILE
Chi-restraints excluded: chain B residue  644 GLU
Chi-restraints excluded: chain B residue  652 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 136 optimal weight:    0.8980
   chunk 61 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 103 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 82 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 87 optimal weight:    4.9990
   chunk 71 optimal weight:    1.9990
   chunk 105 optimal weight:    0.8980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 140 ASN
B  30 ASN
B  83 ASN
B 140 ASN
** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.109783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.092601 restraints weight = 15647.384|
|-----------------------------------------------------------------------------|
r_work (start): 0.3103 rms_B_bonded: 1.45
r_work: 0.2991 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2865 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.2865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8591
moved from start:          0.1875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12342  Z= 0.173
  Angle     :  0.529   7.332  16698  Z= 0.275
  Chirality :  0.043   0.252   1854
  Planarity :  0.004   0.066   2146
  Dihedral  :  4.881  51.930   1630
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  :  9.94 %
    Favored  : 87.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.32 (0.22), residues: 1492
  helix:  0.61 (0.20), residues: 766
  sheet: -0.93 (0.37), residues: 216
  loop : -1.00 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 748 
 TYR   0.012   0.001   TYR A 498 
 PHE   0.010   0.001   PHE B 375 
 TRP   0.008   0.001   TRP A 427 
 HIS   0.005   0.001   HIS B 688 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 (12342)
  covalent geometry    : angle       0.52901 (16698)
  hydrogen bonds       : bond        0.03755 (  490)
  hydrogen bonds       : angle       3.94027 ( 1410)

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

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

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 101
  time to evaluate  : 0.487 
Fit side-chains
REVERT: A   90 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8474 (mt)
REVERT: A  581 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.7817 (mp)
REVERT: A  603 MET cc_start: 0.8951 (mtt) cc_final: 0.8746 (mtt)
REVERT: B   90 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8471 (mt)
REVERT: B  581 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.7830 (mp)
REVERT: B  603 MET cc_start: 0.8948 (mtt) cc_final: 0.8743 (mtt)
  outliers start: 28
  outliers final: 24
  residues processed: 124
  average time/residue: 0.0971
  time to fit residues: 18.3921
Evaluate side-chains
  126 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 98
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  171 PHE
Chi-restraints excluded: chain A residue  198 GLU
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  275 ASN
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  454 GLU
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain A residue  581 ILE
Chi-restraints excluded: chain A residue  644 GLU
Chi-restraints excluded: chain A residue  652 VAL
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   83 ASN
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  171 PHE
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  275 ASN
Chi-restraints excluded: chain B residue  318 GLU
Chi-restraints excluded: chain B residue  454 GLU
Chi-restraints excluded: chain B residue  492 ILE
Chi-restraints excluded: chain B residue  581 ILE
Chi-restraints excluded: chain B residue  644 GLU
Chi-restraints excluded: chain B residue  652 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 96 optimal weight:    0.6980
   chunk 112 optimal weight:    1.9990
   chunk 102 optimal weight:    0.4980
   chunk 8 optimal weight:    0.5980
   chunk 24 optimal weight:    2.9990
   chunk 69 optimal weight:    0.0470
   chunk 41 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 149 optimal weight:    0.9980
   chunk 82 optimal weight:    4.9990
   overall best weight:    0.5078

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

Flipped N/Q/H residues before XYZ refinement:
A  83 ASN
B 219 ASN
** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 275 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.117704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.104056 restraints weight = 15112.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3019 rms_B_bonded: 1.13
r_work: 0.2922 rms_B_bonded: 1.55 restraints_weight: 0.5000
r_work: 0.2810 rms_B_bonded: 2.69 restraints_weight: 0.2500
r_work (final): 0.2810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8556
moved from start:          0.1868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.155  12342  Z= 0.194
  Angle     :  0.825  59.197  16698  Z= 0.478
  Chirality :  0.046   0.863   1854
  Planarity :  0.004   0.087   2146
  Dihedral  :  4.901  51.899   1630
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 10.02 %
    Favored  : 87.69 %
  Cbeta Deviations :  0.07 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.32 (0.22), residues: 1492
  helix:  0.62 (0.20), residues: 766
  sheet: -0.94 (0.37), residues: 216
  loop : -1.00 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 748 
 TYR   0.012   0.001   TYR A 498 
 PHE   0.009   0.001   PHE B 375 
 TRP   0.009   0.001   TRP A 427 
 HIS   0.004   0.001   HIS B 688 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 (12342)
  covalent geometry    : angle       0.82480 (16698)
  hydrogen bonds       : bond        0.03809 (  490)
  hydrogen bonds       : angle       3.98014 ( 1410)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2633.84 seconds
wall clock time: 45 minutes 58.43 seconds (2758.43 seconds total)