Starting phenix.real_space_refine
on Wed Mar  4 11:38:24 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9m9p_63736/03_2026/9m9p_63736_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9m9p_63736/03_2026/9m9p_63736.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9m9p_63736/03_2026/9m9p_63736.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9m9p_63736/03_2026/9m9p_63736.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9m9p_63736/03_2026/9m9p_63736_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9m9p_63736/03_2026/9m9p_63736_neut.cif"
  }
  resolution = 2.93
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.017
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      46      5.16       5
     C    8204      2.51       5
     N    2244      2.21       5
     O    2434      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s

  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: 12930
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 6465
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 799, 6465
          Classifications: {'peptide': 799}
          Link IDs: {'PTRANS': 26, 'TRANS': 772}
          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: 5.95, per 1000 atoms: 0.46
  Number of scatterers: 12930
  At special positions: 0
  Unit cell: (115.37, 138.61, 78.85, 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      46     16.00
     P       2     15.00
     O    2434      8.00
     N    2244      7.00
     C    8204      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: 0.94
  Conformation dependent library (CDL) restraints added in 441.1 milliseconds
  

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3004

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 10 sheets defined
      56.2% alpha, 12.1% 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 15 through 28
      removed outlier: 3.907A  pdb=" N   MET A  26 " --> pdb=" O   ALA A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 67
      removed outlier: 3.533A  pdb=" N   ARG A  52 " --> pdb=" O   ALA A  48 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ARG A  56 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   ARG A  59 " --> pdb=" O   GLU A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 93
    Processing helix  chain 'A' and resid 94 through 104
    Processing helix  chain 'A' and resid 108 through 114
      removed outlier: 3.609A  pdb=" N   LEU A 112 " --> pdb=" O   ASN A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 141
      removed outlier: 3.894A  pdb=" N   GLY A 127 " --> pdb=" O   ASN A 123 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   ARG A 128 " --> pdb=" O   GLY A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 246
    Processing helix  chain 'A' and resid 251 through 255
    Processing helix  chain 'A' and resid 263 through 267
      removed outlier: 4.092A  pdb=" N   SER A 266 " --> pdb=" O   GLU A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 303
    Processing helix  chain 'A' and resid 310 through 314
      removed outlier: 3.536A  pdb=" N   LYS A 314 " --> pdb=" O   ASN A 310 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 310 through 314'
    Processing helix  chain 'A' and resid 323 through 325
      No H-bonds generated for 'chain 'A' and resid 323 through 325'
    Processing helix  chain 'A' and resid 326 through 340
      removed outlier: 3.590A  pdb=" N   MET A 332 " --> pdb=" O   ILE A 328 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   GLU A 338 " --> pdb=" O   LEU A 334 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   GLN A 340 " --> pdb=" O   ILE A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 353
    Processing helix  chain 'A' and resid 371 through 378
    Processing helix  chain 'A' and resid 378 through 400
    Processing helix  chain 'A' and resid 403 through 411
      removed outlier: 3.879A  pdb=" N   LEU A 407 " --> pdb=" O   ASP A 403 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   SER A 411 " --> pdb=" O   LEU A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 430
    Processing helix  chain 'A' and resid 438 through 448
    Processing helix  chain 'A' and resid 450 through 457
    Processing helix  chain 'A' and resid 478 through 490
    Processing helix  chain 'A' and resid 496 through 505
      removed outlier: 3.657A  pdb=" N   LEU A 499 " --> pdb=" O   ASP A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 536
      removed outlier: 3.705A  pdb=" N   VAL A 512 " --> pdb=" O   ASP A 508 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ALA A 515 " --> pdb=" O   MET A 511 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ASN A 536 " --> pdb=" O   ALA A 532 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 575
      removed outlier: 4.170A  pdb=" N   ASN A 561 " --> pdb=" O   ARG A 557 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 595 through 613
    Processing helix  chain 'A' and resid 631 through 639
      removed outlier: 3.563A  pdb=" N   LEU A 637 " --> pdb=" O   SER A 633 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 640 through 642
      No H-bonds generated for 'chain 'A' and resid 640 through 642'
    Processing helix  chain 'A' and resid 657 through 666
      removed outlier: 3.855A  pdb=" N   MET A 661 " --> pdb=" O   GLY A 657 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ASN A 666 " --> pdb=" O   LLP A 662 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 676 through 686
      removed outlier: 4.034A  pdb=" N   GLU A 680 " --> pdb=" O   GLY A 676 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   ASP A 683 " --> pdb=" O   VAL A 679 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 696 through 707
    Processing helix  chain 'A' and resid 709 through 717
      removed outlier: 4.234A  pdb=" N   TYR A 713 " --> pdb=" O   LYS A 709 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ASP A 717 " --> pdb=" O   TYR A 713 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 717 through 730
      removed outlier: 3.543A  pdb=" N   GLY A 730 " --> pdb=" O   GLN A 726 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 740 through 749
    Processing helix  chain 'A' and resid 759 through 775
      removed outlier: 3.721A  pdb=" N   GLU A 775 " --> pdb=" O   ASP A 771 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 776 through 790
      removed outlier: 3.783A  pdb=" N   THR A 781 " --> pdb=" O   GLN A 777 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   ALA A 782 " --> pdb=" O   GLU A 778 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LYS A 783 " --> pdb=" O   GLU A 779 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 795 through 807
    Processing helix  chain 'B' and resid 15 through 28
      removed outlier: 3.907A  pdb=" N   MET B  26 " --> pdb=" O   ALA B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 37 through 67
      removed outlier: 3.533A  pdb=" N   ARG B  52 " --> pdb=" O   ALA B  48 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ARG B  56 " --> pdb=" O   ARG B  52 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   ARG B  59 " --> pdb=" O   GLU B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 84 through 93
    Processing helix  chain 'B' and resid 94 through 104
    Processing helix  chain 'B' and resid 108 through 114
      removed outlier: 3.609A  pdb=" N   LEU B 112 " --> pdb=" O   ASN B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 141
      removed outlier: 3.894A  pdb=" N   GLY B 127 " --> pdb=" O   ASN B 123 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   ARG B 128 " --> pdb=" O   GLY B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 246
    Processing helix  chain 'B' and resid 251 through 255
    Processing helix  chain 'B' and resid 263 through 267
      removed outlier: 4.092A  pdb=" N   SER B 266 " --> pdb=" O   GLU B 263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 278 through 303
    Processing helix  chain 'B' and resid 310 through 314
      removed outlier: 3.536A  pdb=" N   LYS B 314 " --> pdb=" O   ASN B 310 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 310 through 314'
    Processing helix  chain 'B' and resid 323 through 325
      No H-bonds generated for 'chain 'B' and resid 323 through 325'
    Processing helix  chain 'B' and resid 326 through 340
      removed outlier: 3.590A  pdb=" N   MET B 332 " --> pdb=" O   ILE B 328 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   GLU B 338 " --> pdb=" O   LEU B 334 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   GLN B 340 " --> pdb=" O   ILE B 336 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 342 through 353
    Processing helix  chain 'B' and resid 371 through 378
    Processing helix  chain 'B' and resid 378 through 400
    Processing helix  chain 'B' and resid 403 through 411
      removed outlier: 3.879A  pdb=" N   LEU B 407 " --> pdb=" O   ASP B 403 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   SER B 411 " --> pdb=" O   LEU B 407 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 423 through 430
    Processing helix  chain 'B' and resid 438 through 448
    Processing helix  chain 'B' and resid 450 through 457
    Processing helix  chain 'B' and resid 478 through 490
    Processing helix  chain 'B' and resid 496 through 505
      removed outlier: 3.657A  pdb=" N   LEU B 499 " --> pdb=" O   ASP B 496 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 508 through 536
      removed outlier: 3.705A  pdb=" N   VAL B 512 " --> pdb=" O   ASP B 508 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ALA B 515 " --> pdb=" O   MET B 511 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ASN B 536 " --> pdb=" O   ALA B 532 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 557 through 575
      removed outlier: 4.170A  pdb=" N   ASN B 561 " --> pdb=" O   ARG B 557 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 595 through 613
    Processing helix  chain 'B' and resid 631 through 639
      removed outlier: 3.563A  pdb=" N   LEU B 637 " --> pdb=" O   SER B 633 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 640 through 642
      No H-bonds generated for 'chain 'B' and resid 640 through 642'
    Processing helix  chain 'B' and resid 657 through 666
      removed outlier: 3.855A  pdb=" N   MET B 661 " --> pdb=" O   GLY B 657 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ASN B 666 " --> pdb=" O   LLP B 662 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 676 through 686
      removed outlier: 4.034A  pdb=" N   GLU B 680 " --> pdb=" O   GLY B 676 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   ASP B 683 " --> pdb=" O   VAL B 679 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 696 through 707
    Processing helix  chain 'B' and resid 709 through 717
      removed outlier: 4.234A  pdb=" N   TYR B 713 " --> pdb=" O   LYS B 709 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ASP B 717 " --> pdb=" O   TYR B 713 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 717 through 730
      removed outlier: 3.543A  pdb=" N   GLY B 730 " --> pdb=" O   GLN B 726 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 740 through 749
    Processing helix  chain 'B' and resid 759 through 775
      removed outlier: 3.721A  pdb=" N   GLU B 775 " --> pdb=" O   ASP B 771 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 776 through 790
      removed outlier: 3.783A  pdb=" N   THR B 781 " --> pdb=" O   GLN B 777 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   ALA B 782 " --> pdb=" O   GLU B 778 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LYS B 783 " --> pdb=" O   GLU B 779 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 795 through 807
    Processing sheet with id=1, first strand: chain 'A' and resid 180 through 192
      removed outlier: 4.074A  pdb=" N   ALA A 215 " --> pdb=" O   ARG A 183 " (cutoff:3.500A)
      removed outlier: 8.363A  pdb=" N   ASN A 185 " --> pdb=" O   GLY A 213 " (cutoff:3.500A)
      removed outlier: 9.784A  pdb=" N   GLY A 213 " --> pdb=" O   ASN A 185 " (cutoff:3.500A)
      removed outlier: 9.519A  pdb=" N   ARG A 187 " --> pdb=" O   ILE A 211 " (cutoff:3.500A)
      removed outlier: 10.719A  pdb=" N   ILE A 211 " --> pdb=" O   ARG A 187 " (cutoff:3.500A)
      removed outlier: 9.417A  pdb=" N   LYS A 189 " --> pdb=" O   GLU A 209 " (cutoff:3.500A)
      removed outlier: 10.143A  pdb=" N   GLU A 209 " --> pdb=" O   LYS A 189 " (cutoff:3.500A)
      removed outlier: 7.402A  pdb=" N   GLY A 144 " --> pdb=" O   THR A 230 " (cutoff:3.500A)
      removed outlier: 8.553A  pdb=" N   ARG A 232 " --> pdb=" O   GLY A 144 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   GLY A 146 " --> pdb=" O   ARG A 232 " (cutoff:3.500A)
      removed outlier: 7.981A  pdb=" N   TRP A 234 " --> pdb=" O   GLY A 146 " (cutoff:3.500A)
      removed outlier: 7.182A  pdb=" N   GLY A 148 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
      removed outlier: 8.778A  pdb=" N   ALA A 236 " --> pdb=" O   GLY A 148 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   LYS A 433 " --> pdb=" O   PHE A 354 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   VAL A 434 " --> pdb=" O   THR A 462 " (cutoff:3.500A)
    Processing sheet with id=2, first strand: chain 'A' and resid 157 through 161
    Processing sheet with id=3, first strand: chain 'A' and resid 195 through 199
    Processing sheet with id=4, first strand: chain 'A' and resid 368 through 370
    Processing sheet with id=5, first strand: chain 'A' and resid 622 through 626
      removed outlier: 6.605A  pdb=" N   ARG A 583 " --> pdb=" O   LYS A 623 " (cutoff:3.500A)
      removed outlier: 7.754A  pdb=" N   VAL A 625 " --> pdb=" O   ARG A 583 " (cutoff:3.500A)
      removed outlier: 6.068A  pdb=" N   ASN A 585 " --> pdb=" O   VAL A 625 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   GLY A 588 " --> pdb=" O   GLN A 548 " (cutoff:3.500A)
      removed outlier: 5.944A  pdb=" N   ILE A 549 " --> pdb=" O   GLU A 646 " (cutoff:3.500A)
      removed outlier: 6.158A  pdb=" N   SER A 645 " --> pdb=" O   ILE A 671 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   THR A 670 " --> pdb=" O   PHE A 691 " (cutoff:3.500A)
    Processing sheet with id=6, first strand: chain 'B' and resid 180 through 192
      removed outlier: 4.074A  pdb=" N   ALA B 215 " --> pdb=" O   ARG B 183 " (cutoff:3.500A)
      removed outlier: 8.363A  pdb=" N   ASN B 185 " --> pdb=" O   GLY B 213 " (cutoff:3.500A)
      removed outlier: 9.784A  pdb=" N   GLY B 213 " --> pdb=" O   ASN B 185 " (cutoff:3.500A)
      removed outlier: 9.519A  pdb=" N   ARG B 187 " --> pdb=" O   ILE B 211 " (cutoff:3.500A)
      removed outlier: 10.719A  pdb=" N   ILE B 211 " --> pdb=" O   ARG B 187 " (cutoff:3.500A)
      removed outlier: 9.417A  pdb=" N   LYS B 189 " --> pdb=" O   GLU B 209 " (cutoff:3.500A)
      removed outlier: 10.143A  pdb=" N   GLU B 209 " --> pdb=" O   LYS B 189 " (cutoff:3.500A)
      removed outlier: 7.402A  pdb=" N   GLY B 144 " --> pdb=" O   THR B 230 " (cutoff:3.500A)
      removed outlier: 8.553A  pdb=" N   ARG B 232 " --> pdb=" O   GLY B 144 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   GLY B 146 " --> pdb=" O   ARG B 232 " (cutoff:3.500A)
      removed outlier: 7.981A  pdb=" N   TRP B 234 " --> pdb=" O   GLY B 146 " (cutoff:3.500A)
      removed outlier: 7.182A  pdb=" N   GLY B 148 " --> pdb=" O   TRP B 234 " (cutoff:3.500A)
      removed outlier: 8.778A  pdb=" N   ALA B 236 " --> pdb=" O   GLY B 148 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   LYS B 433 " --> pdb=" O   PHE B 354 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   VAL B 434 " --> pdb=" O   THR B 462 " (cutoff:3.500A)
    Processing sheet with id=7, first strand: chain 'B' and resid 157 through 161
    Processing sheet with id=8, first strand: chain 'B' and resid 195 through 199
    Processing sheet with id=9, first strand: chain 'B' and resid 368 through 370
    Processing sheet with id=10, first strand: chain 'B' and resid 622 through 626
      removed outlier: 6.605A  pdb=" N   ARG B 583 " --> pdb=" O   LYS B 623 " (cutoff:3.500A)
      removed outlier: 7.754A  pdb=" N   VAL B 625 " --> pdb=" O   ARG B 583 " (cutoff:3.500A)
      removed outlier: 6.068A  pdb=" N   ASN B 585 " --> pdb=" O   VAL B 625 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   GLY B 588 " --> pdb=" O   GLN B 548 " (cutoff:3.500A)
      removed outlier: 5.944A  pdb=" N   ILE B 549 " --> pdb=" O   GLU B 646 " (cutoff:3.500A)
      removed outlier: 6.158A  pdb=" N   SER B 645 " --> pdb=" O   ILE B 671 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   THR B 670 " --> pdb=" O   PHE B 691 " (cutoff:3.500A)

    656 hydrogen bonds defined for protein.
    1860 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: 1.82

  Time building geometry restraints manager: 1.32 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: 4328
        1.34 -     1.46: 2158
        1.46 -     1.57: 6652
        1.57 -     1.69: 0
        1.69 -     1.81: 84
  Bond restraints: 13222
  Sorted by residual:
  bond pdb=" N   LEU A 102 "
       pdb=" CA  LEU A 102 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.036 1.26e-02 6.30e+03 7.98e+00
  bond pdb=" N   LEU B 102 "
       pdb=" CA  LEU B 102 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.036 1.26e-02 6.30e+03 7.98e+00
  bond pdb=" N   ILE B 297 "
       pdb=" CA  ILE B 297 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.032 1.17e-02 7.31e+03 7.69e+00
  bond pdb=" N   ILE A 297 "
       pdb=" CA  ILE A 297 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.032 1.17e-02 7.31e+03 7.69e+00
  bond pdb=" N   LEU B 107 "
       pdb=" CA  LEU B 107 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.26e-02 6.30e+03 6.24e+00
  ... (remaining 13217 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 17738
        2.10 -     4.19: 178
        4.19 -     6.29: 12
        6.29 -     8.38: 4
        8.38 -    10.48: 2
  Bond angle restraints: 17934
  Sorted by residual:
  angle pdb=" N   TYR A 153 "
        pdb=" CA  TYR A 153 "
        pdb=" CB  TYR A 153 "
      ideal   model   delta    sigma   weight residual
     111.43  104.25    7.18 1.48e+00 4.57e-01 2.36e+01
  angle pdb=" N   TYR B 153 "
        pdb=" CA  TYR B 153 "
        pdb=" CB  TYR B 153 "
      ideal   model   delta    sigma   weight residual
     111.43  104.25    7.18 1.48e+00 4.57e-01 2.36e+01
  angle pdb=" CB  GLN B 706 "
        pdb=" CG  GLN B 706 "
        pdb=" CD  GLN B 706 "
      ideal   model   delta    sigma   weight residual
     112.60  118.67   -6.07 1.70e+00 3.46e-01 1.28e+01
  angle pdb=" CB  GLN A 706 "
        pdb=" CG  GLN A 706 "
        pdb=" CD  GLN A 706 "
      ideal   model   delta    sigma   weight residual
     112.60  118.67   -6.07 1.70e+00 3.46e-01 1.28e+01
  angle pdb=" N   MET B 105 "
        pdb=" CA  MET B 105 "
        pdb=" C   MET B 105 "
      ideal   model   delta    sigma   weight residual
     112.92  108.60    4.32 1.23e+00 6.61e-01 1.24e+01
  ... (remaining 17929 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 6826
       17.85 -    35.70: 756
       35.70 -    53.55: 204
       53.55 -    71.40: 76
       71.40 -    89.25: 8
  Dihedral angle restraints: 7870
    sinusoidal: 3196
      harmonic: 4674
  Sorted by residual:
  dihedral pdb=" CG  ARG A  52 "
           pdb=" CD  ARG A  52 "
           pdb=" NE  ARG A  52 "
           pdb=" CZ  ARG A  52 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   41.03   48.97     2      1.50e+01 4.44e-03 1.21e+01
  dihedral pdb=" CG  ARG B  52 "
           pdb=" CD  ARG B  52 "
           pdb=" NE  ARG B  52 "
           pdb=" CZ  ARG B  52 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   41.03   48.97     2      1.50e+01 4.44e-03 1.21e+01
  dihedral pdb=" CA  ASP A 414 "
           pdb=" CB  ASP A 414 "
           pdb=" CG  ASP A 414 "
           pdb=" OD1 ASP A 414 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.48   57.48     1      2.00e+01 2.50e-03 1.11e+01
  ... (remaining 7867 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1432
       0.042 -    0.084: 404
       0.084 -    0.127: 94
       0.127 -    0.169: 10
       0.169 -    0.211: 4
  Chirality restraints: 1944
  Sorted by residual:
  chirality pdb=" CA  ILE B 297 "
            pdb=" N   ILE B 297 "
            pdb=" C   ILE B 297 "
            pdb=" CB  ILE B 297 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CA  ILE A 297 "
            pdb=" N   ILE A 297 "
            pdb=" C   ILE A 297 "
            pdb=" CB  ILE A 297 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CA  MET A 155 "
            pdb=" N   MET A 155 "
            pdb=" C   MET A 155 "
            pdb=" CB  MET A 155 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.03e+00
  ... (remaining 1941 not shown)

  Planarity restraints: 2336
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 152 "    0.010 2.00e-02 2.50e+03   1.99e-02 3.95e+00
        pdb=" C   ASP A 152 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   ASP A 152 "    0.013 2.00e-02 2.50e+03
        pdb=" N   TYR A 153 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 152 "   -0.010 2.00e-02 2.50e+03   1.99e-02 3.95e+00
        pdb=" C   ASP B 152 "    0.034 2.00e-02 2.50e+03
        pdb=" O   ASP B 152 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   TYR B 153 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  52 "   -0.096 9.50e-02 1.11e+02   4.32e-02 1.52e+00
        pdb=" NE  ARG A  52 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  52 "   -0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  52 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  52 "    0.000 2.00e-02 2.50e+03
  ... (remaining 2333 not shown)

  Histogram of nonbonded interaction distances:
        2.58 -     3.05: 7736
        3.05 -     3.51: 12842
        3.51 -     3.97: 21171
        3.97 -     4.44: 26120
        4.44 -     4.90: 40872
  Nonbonded interactions: 108741
  Sorted by model distance:
  nonbonded pdb=" N   ASN A  37 "
            pdb=" OD1 ASN A  37 "
     model   vdw
     2.583 3.120
  nonbonded pdb=" N   ASN B  37 "
            pdb=" OD1 ASN B  37 "
     model   vdw
     2.583 3.120
  nonbonded pdb=" O   GLN A 295 "
            pdb=" OG  SER A 299 "
     model   vdw
     2.614 3.040
  nonbonded pdb=" O   GLN B 295 "
            pdb=" OG  SER B 299 "
     model   vdw
     2.614 3.040
  nonbonded pdb=" N   PHE B 156 "
            pdb=" O   PHE B 156 "
     model   vdw
     2.617 2.496
  ... (remaining 108736 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:             3.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     14.880
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:6.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
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      :  0.003   0.046  13222  Z= 0.173
  Angle     :  0.563  10.476  17934  Z= 0.357
  Chirality :  0.041   0.211   1944
  Planarity :  0.004   0.043   2336
  Dihedral  : 16.977  89.247   4866
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 20.63 %
    Favored  : 76.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.09 (0.22), residues: 1588
  helix:  0.65 (0.19), residues: 838
  sheet: -0.04 (0.35), residues: 218
  loop : -1.08 (0.27), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A  52 
 TYR   0.017   0.001   TYR B  23 
 PHE   0.016   0.001   PHE A 247 
 TRP   0.011   0.001   TRP A  57 
 HIS   0.002   0.000   HIS A 318 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (13222)
  covalent geometry    : angle       0.56288 (17934)
  hydrogen bonds       : bond        0.16135 (  656)
  hydrogen bonds       : angle       6.65826 ( 1860)

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

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

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 168
  time to evaluate  : 0.486 
Fit side-chains
REVERT: A   15 GLU cc_start: 0.6416 (tp30) cc_final: 0.5943 (tm-30)
REVERT: A   31 LYS cc_start: 0.8474 (mmtt) cc_final: 0.8144 (mmtp)
REVERT: A  180 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7416 (pt0)
REVERT: A  202 LYS cc_start: 0.7543 (mtpm) cc_final: 0.6251 (mtmt)
REVERT: A  204 ARG cc_start: 0.8112 (tpp-160) cc_final: 0.7441 (mmm-85)
REVERT: A  241 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7904 (mm-30)
REVERT: A  391 TYR cc_start: 0.8105 (t80) cc_final: 0.7358 (t80)
REVERT: A  414 ASP cc_start: 0.8347 (t70) cc_final: 0.8052 (t0)
REVERT: A  455 LYS cc_start: 0.7850 (mttp) cc_final: 0.7009 (ttpt)
REVERT: A  511 MET cc_start: 0.7528 (tpt) cc_final: 0.7131 (mpm)
REVERT: A  597 MET cc_start: 0.7347 (tpp) cc_final: 0.6818 (tpp)
REVERT: A  649 SER cc_start: 0.8915 (OUTLIER) cc_final: 0.8553 (t)
REVERT: A  654 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7356 (tt0)
REVERT: A  698 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7515 (mp0)
REVERT: A  771 ASP cc_start: 0.7827 (m-30) cc_final: 0.7482 (m-30)
REVERT: B   15 GLU cc_start: 0.6424 (tp30) cc_final: 0.5947 (tm-30)
REVERT: B   31 LYS cc_start: 0.8477 (mmtt) cc_final: 0.8152 (mmtp)
REVERT: B  180 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7417 (pt0)
REVERT: B  202 LYS cc_start: 0.7540 (mtpm) cc_final: 0.6250 (mtmt)
REVERT: B  204 ARG cc_start: 0.8114 (tpp-160) cc_final: 0.7442 (mmm-85)
REVERT: B  241 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7903 (mm-30)
REVERT: B  391 TYR cc_start: 0.8104 (t80) cc_final: 0.7356 (t80)
REVERT: B  414 ASP cc_start: 0.8346 (t70) cc_final: 0.8051 (t0)
REVERT: B  455 LYS cc_start: 0.7849 (mttp) cc_final: 0.7009 (ttpt)
REVERT: B  511 MET cc_start: 0.7526 (tpt) cc_final: 0.7131 (mpm)
REVERT: B  597 MET cc_start: 0.7346 (tpp) cc_final: 0.6816 (tpp)
REVERT: B  649 SER cc_start: 0.8912 (OUTLIER) cc_final: 0.8552 (t)
REVERT: B  654 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7351 (tt0)
REVERT: B  698 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7515 (mp0)
REVERT: B  771 ASP cc_start: 0.7828 (m-30) cc_final: 0.7485 (m-30)
  outliers start: 38
  outliers final: 24
  residues processed: 188
  average time/residue: 0.5604
  time to fit residues: 115.3220
Evaluate side-chains
  182 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 154
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  171 TYR
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  432 HIS
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  620 ASP
Chi-restraints excluded: chain A residue  643 ASP
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  654 GLU
Chi-restraints excluded: chain A residue  776 LEU
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  171 TYR
Chi-restraints excluded: chain B residue  196 ILE
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  430 VAL
Chi-restraints excluded: chain B residue  432 HIS
Chi-restraints excluded: chain B residue  440 LEU
Chi-restraints excluded: chain B residue  620 ASP
Chi-restraints excluded: chain B residue  643 ASP
Chi-restraints excluded: chain B residue  649 SER
Chi-restraints excluded: chain B residue  654 GLU
Chi-restraints excluded: chain B residue  776 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    0.7980
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    6.9990
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:    0.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
A 158 GLN
A 198 GLN
A 435 ASN
B 158 GLN
B 198 GLN
B 435 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.127341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.107170 restraints weight = 15959.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.3202 rms_B_bonded: 1.91
r_work: 0.3068 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2928 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.0868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  13222  Z= 0.192
  Angle     :  0.505   6.085  17934  Z= 0.272
  Chirality :  0.042   0.136   1944
  Planarity :  0.004   0.033   2336
  Dihedral  :  6.732  76.520   1824
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 18.04 %
    Favored  : 77.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.00 (0.22), residues: 1588
  helix:  0.71 (0.19), residues: 848
  sheet:  0.09 (0.36), residues: 204
  loop : -1.07 (0.27), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  52 
 TYR   0.015   0.002   TYR B 400 
 PHE   0.016   0.002   PHE B 156 
 TRP   0.010   0.001   TRP A 473 
 HIS   0.006   0.001   HIS B 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 (13222)
  covalent geometry    : angle       0.50470 (17934)
  hydrogen bonds       : bond        0.05019 (  656)
  hydrogen bonds       : angle       4.77918 ( 1860)

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

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

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 162
  time to evaluate  : 0.442 
Fit side-chains
REVERT: A  204 ARG cc_start: 0.8234 (tpp-160) cc_final: 0.7726 (mmm-85)
REVERT: A  241 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7939 (mm-30)
REVERT: A  391 TYR cc_start: 0.8196 (t80) cc_final: 0.7433 (t80)
REVERT: A  414 ASP cc_start: 0.8390 (t70) cc_final: 0.8125 (t0)
REVERT: A  447 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.6809 (mt0)
REVERT: A  455 LYS cc_start: 0.7959 (mttp) cc_final: 0.7074 (ttpt)
REVERT: A  511 MET cc_start: 0.7582 (tpt) cc_final: 0.7207 (mpm)
REVERT: A  597 MET cc_start: 0.7463 (tpp) cc_final: 0.6980 (tpp)
REVERT: A  600 HIS cc_start: 0.8329 (OUTLIER) cc_final: 0.7470 (t70)
REVERT: A  698 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7472 (mp0)
REVERT: A  759 ASP cc_start: 0.8453 (m-30) cc_final: 0.8233 (m-30)
REVERT: A  771 ASP cc_start: 0.7897 (m-30) cc_final: 0.7560 (m-30)
REVERT: B  204 ARG cc_start: 0.8228 (tpp-160) cc_final: 0.7720 (mmm-85)
REVERT: B  241 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7937 (mm-30)
REVERT: B  391 TYR cc_start: 0.8193 (t80) cc_final: 0.7427 (t80)
REVERT: B  414 ASP cc_start: 0.8385 (t70) cc_final: 0.8123 (t0)
REVERT: B  447 GLN cc_start: 0.7496 (OUTLIER) cc_final: 0.6788 (mt0)
REVERT: B  455 LYS cc_start: 0.7956 (mttp) cc_final: 0.7068 (ttpt)
REVERT: B  511 MET cc_start: 0.7570 (tpt) cc_final: 0.7206 (mpm)
REVERT: B  597 MET cc_start: 0.7449 (tpp) cc_final: 0.6962 (tpp)
REVERT: B  600 HIS cc_start: 0.8325 (OUTLIER) cc_final: 0.7463 (t70)
REVERT: B  698 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7471 (mp0)
REVERT: B  759 ASP cc_start: 0.8443 (m-30) cc_final: 0.8233 (m-30)
REVERT: B  771 ASP cc_start: 0.7894 (m-30) cc_final: 0.7557 (m-30)
  outliers start: 60
  outliers final: 24
  residues processed: 202
  average time/residue: 0.5904
  time to fit residues: 129.9555
Evaluate side-chains
  172 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 144
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  171 TYR
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  447 GLN
Chi-restraints excluded: chain A residue  496 ASP
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  529 GLU
Chi-restraints excluded: chain A residue  600 HIS
Chi-restraints excluded: chain A residue  675 ASP
Chi-restraints excluded: chain A residue  766 CYS
Chi-restraints excluded: chain A residue  796 SER
Chi-restraints excluded: chain B residue   34 VAL
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  171 TYR
Chi-restraints excluded: chain B residue  439 GLU
Chi-restraints excluded: chain B residue  447 GLN
Chi-restraints excluded: chain B residue  496 ASP
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  529 GLU
Chi-restraints excluded: chain B residue  600 HIS
Chi-restraints excluded: chain B residue  675 ASP
Chi-restraints excluded: chain B residue  766 CYS
Chi-restraints excluded: chain B residue  796 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 66 optimal weight:    6.9990
   chunk 2 optimal weight:    0.7980
   chunk 56 optimal weight:    7.9990
   chunk 121 optimal weight:    7.9990
   chunk 105 optimal weight:    4.9990
   chunk 111 optimal weight:    0.9980
   chunk 86 optimal weight:    0.9980
   chunk 133 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 126 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   overall best weight:    1.3582

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

Flipped N/Q/H residues before XYZ refinement:
A 198 GLN
A 435 ASN
B 158 GLN
B 198 GLN
B 435 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.127574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.107082 restraints weight = 16164.690|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 1.94
r_work: 0.3073 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2930 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
moved from start:          0.1048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13222  Z= 0.155
  Angle     :  0.472   5.205  17934  Z= 0.254
  Chirality :  0.041   0.137   1944
  Planarity :  0.004   0.041   2336
  Dihedral  :  5.566  76.877   1784
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 17.39 %
    Favored  : 77.27 %
  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: 1588
  helix:  0.96 (0.19), residues: 828
  sheet:  0.18 (0.37), residues: 204
  loop : -0.83 (0.27), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  52 
 TYR   0.018   0.002   TYR B  23 
 PHE   0.013   0.002   PHE B 156 
 TRP   0.009   0.001   TRP B  57 
 HIS   0.005   0.001   HIS B 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 (13222)
  covalent geometry    : angle       0.47206 (17934)
  hydrogen bonds       : bond        0.04421 (  656)
  hydrogen bonds       : angle       4.49789 ( 1860)

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

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

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 150
  time to evaluate  : 0.453 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  202 LYS cc_start: 0.7629 (mtpm) cc_final: 0.6323 (mtmt)
REVERT: A  204 ARG cc_start: 0.8236 (tpp-160) cc_final: 0.7520 (mmm-85)
REVERT: A  241 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7999 (mm-30)
REVERT: A  259 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8429 (mptt)
REVERT: A  362 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7550 (mmt)
REVERT: A  391 TYR cc_start: 0.8190 (t80) cc_final: 0.7327 (t80)
REVERT: A  447 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.6800 (mt0)
REVERT: A  455 LYS cc_start: 0.7921 (mttp) cc_final: 0.7044 (ttpt)
REVERT: A  505 GLN cc_start: 0.4609 (OUTLIER) cc_final: 0.4186 (pm20)
REVERT: A  511 MET cc_start: 0.7585 (tpt) cc_final: 0.7208 (mpm)
REVERT: A  597 MET cc_start: 0.7479 (tpp) cc_final: 0.6833 (tpp)
REVERT: A  600 HIS cc_start: 0.8278 (OUTLIER) cc_final: 0.7651 (t70)
REVERT: A  698 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7498 (mp0)
REVERT: A  771 ASP cc_start: 0.7897 (m-30) cc_final: 0.7561 (m-30)
REVERT: B  202 LYS cc_start: 0.7611 (mtpm) cc_final: 0.6303 (mtmt)
REVERT: B  204 ARG cc_start: 0.8232 (tpp-160) cc_final: 0.7501 (mmm-85)
REVERT: B  241 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8007 (mm-30)
REVERT: B  259 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8437 (mptt)
REVERT: B  362 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7554 (mmt)
REVERT: B  391 TYR cc_start: 0.8169 (t80) cc_final: 0.7306 (t80)
REVERT: B  447 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.6783 (mt0)
REVERT: B  455 LYS cc_start: 0.7916 (mttp) cc_final: 0.7043 (ttpt)
REVERT: B  505 GLN cc_start: 0.4590 (OUTLIER) cc_final: 0.4166 (pm20)
REVERT: B  511 MET cc_start: 0.7554 (tpt) cc_final: 0.7195 (mpm)
REVERT: B  597 MET cc_start: 0.7484 (tpp) cc_final: 0.6835 (tpp)
REVERT: B  600 HIS cc_start: 0.8279 (OUTLIER) cc_final: 0.7647 (t70)
REVERT: B  698 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7509 (mp0)
REVERT: B  771 ASP cc_start: 0.7898 (m-30) cc_final: 0.7565 (m-30)
  outliers start: 74
  outliers final: 40
  residues processed: 192
  average time/residue: 0.5753
  time to fit residues: 120.6529
Evaluate side-chains
  198 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 148
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  171 TYR
Chi-restraints excluded: chain A residue  185 ASN
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  259 LYS
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  362 MET
Chi-restraints excluded: chain A residue  432 HIS
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  447 GLN
Chi-restraints excluded: chain A residue  496 ASP
Chi-restraints excluded: chain A residue  505 GLN
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  529 GLU
Chi-restraints excluded: chain A residue  600 HIS
Chi-restraints excluded: chain A residue  620 ASP
Chi-restraints excluded: chain A residue  643 ASP
Chi-restraints excluded: chain A residue  658 THR
Chi-restraints excluded: chain A residue  675 ASP
Chi-restraints excluded: chain A residue  766 CYS
Chi-restraints excluded: chain A residue  796 SER
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  171 TYR
Chi-restraints excluded: chain B residue  185 ASN
Chi-restraints excluded: chain B residue  196 ILE
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  259 LYS
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  362 MET
Chi-restraints excluded: chain B residue  432 HIS
Chi-restraints excluded: chain B residue  439 GLU
Chi-restraints excluded: chain B residue  447 GLN
Chi-restraints excluded: chain B residue  496 ASP
Chi-restraints excluded: chain B residue  505 GLN
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  529 GLU
Chi-restraints excluded: chain B residue  600 HIS
Chi-restraints excluded: chain B residue  620 ASP
Chi-restraints excluded: chain B residue  643 ASP
Chi-restraints excluded: chain B residue  658 THR
Chi-restraints excluded: chain B residue  675 ASP
Chi-restraints excluded: chain B residue  766 CYS
Chi-restraints excluded: chain B residue  796 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 151 optimal weight:    0.6980
   chunk 21 optimal weight:    4.9990
   chunk 112 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 48 optimal weight:    2.9990
   chunk 139 optimal weight:    4.9990
   chunk 71 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 146 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 198 GLN
A 435 ASN
B 158 GLN
B 198 GLN
B 435 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.127919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.107562 restraints weight = 15967.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.3219 rms_B_bonded: 1.93
r_work: 0.3082 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2939 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8450
moved from start:          0.1120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13222  Z= 0.136
  Angle     :  0.453   5.901  17934  Z= 0.244
  Chirality :  0.040   0.134   1944
  Planarity :  0.003   0.043   2336
  Dihedral  :  5.474  76.746   1780
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 18.90 %
    Favored  : 76.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.22 (0.22), residues: 1588
  helix:  0.88 (0.19), residues: 848
  sheet:  0.28 (0.37), residues: 204
  loop : -1.00 (0.27), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  52 
 TYR   0.016   0.002   TYR A 400 
 PHE   0.013   0.001   PHE B 156 
 TRP   0.008   0.001   TRP B  57 
 HIS   0.005   0.001   HIS B 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (13222)
  covalent geometry    : angle       0.45322 (17934)
  hydrogen bonds       : bond        0.04115 (  656)
  hydrogen bonds       : angle       4.35799 ( 1860)

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

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

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 150
  time to evaluate  : 0.501 
Fit side-chains
REVERT: A  204 ARG cc_start: 0.8235 (tpp-160) cc_final: 0.7720 (mmm-85)
REVERT: A  241 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7962 (mm-30)
REVERT: A  259 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8426 (mptt)
REVERT: A  391 TYR cc_start: 0.8189 (t80) cc_final: 0.7306 (t80)
REVERT: A  414 ASP cc_start: 0.8437 (t70) cc_final: 0.8161 (t0)
REVERT: A  447 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.6781 (mt0)
REVERT: A  455 LYS cc_start: 0.7893 (mttp) cc_final: 0.7040 (ttpt)
REVERT: A  505 GLN cc_start: 0.4626 (OUTLIER) cc_final: 0.4184 (pm20)
REVERT: A  511 MET cc_start: 0.7575 (tpt) cc_final: 0.7192 (mpm)
REVERT: A  597 MET cc_start: 0.7457 (tpp) cc_final: 0.6974 (tpp)
REVERT: A  600 HIS cc_start: 0.8263 (OUTLIER) cc_final: 0.7639 (t70)
REVERT: A  698 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7478 (mp0)
REVERT: A  771 ASP cc_start: 0.7879 (m-30) cc_final: 0.7545 (m-30)
REVERT: A  785 MET cc_start: 0.7990 (mtp) cc_final: 0.7699 (mtm)
REVERT: B  204 ARG cc_start: 0.8234 (tpp-160) cc_final: 0.7707 (mmm-85)
REVERT: B  241 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7963 (mm-30)
REVERT: B  259 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8441 (mptt)
REVERT: B  391 TYR cc_start: 0.8180 (t80) cc_final: 0.7293 (t80)
REVERT: B  414 ASP cc_start: 0.8436 (t70) cc_final: 0.8159 (t0)
REVERT: B  447 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.6768 (mt0)
REVERT: B  455 LYS cc_start: 0.7891 (mttp) cc_final: 0.7042 (ttpt)
REVERT: B  505 GLN cc_start: 0.4611 (OUTLIER) cc_final: 0.4165 (pm20)
REVERT: B  511 MET cc_start: 0.7543 (tpt) cc_final: 0.7183 (mpm)
REVERT: B  597 MET cc_start: 0.7465 (tpp) cc_final: 0.6981 (tpp)
REVERT: B  600 HIS cc_start: 0.8268 (OUTLIER) cc_final: 0.7642 (t70)
REVERT: B  698 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7488 (mp0)
REVERT: B  771 ASP cc_start: 0.7880 (m-30) cc_final: 0.7548 (m-30)
REVERT: B  785 MET cc_start: 0.8001 (mtp) cc_final: 0.7713 (mtm)
  outliers start: 62
  outliers final: 36
  residues processed: 184
  average time/residue: 0.5505
  time to fit residues: 110.7074
Evaluate side-chains
  186 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 142
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  185 ASN
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  259 LYS
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  432 HIS
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  447 GLN
Chi-restraints excluded: chain A residue  496 ASP
Chi-restraints excluded: chain A residue  505 GLN
Chi-restraints excluded: chain A residue  529 GLU
Chi-restraints excluded: chain A residue  600 HIS
Chi-restraints excluded: chain A residue  620 ASP
Chi-restraints excluded: chain A residue  643 ASP
Chi-restraints excluded: chain A residue  658 THR
Chi-restraints excluded: chain A residue  675 ASP
Chi-restraints excluded: chain A residue  766 CYS
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  185 ASN
Chi-restraints excluded: chain B residue  196 ILE
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  259 LYS
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  432 HIS
Chi-restraints excluded: chain B residue  439 GLU
Chi-restraints excluded: chain B residue  447 GLN
Chi-restraints excluded: chain B residue  496 ASP
Chi-restraints excluded: chain B residue  505 GLN
Chi-restraints excluded: chain B residue  529 GLU
Chi-restraints excluded: chain B residue  600 HIS
Chi-restraints excluded: chain B residue  620 ASP
Chi-restraints excluded: chain B residue  643 ASP
Chi-restraints excluded: chain B residue  658 THR
Chi-restraints excluded: chain B residue  675 ASP
Chi-restraints excluded: chain B residue  766 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 71 optimal weight:    5.9990
   chunk 125 optimal weight:    0.7980
   chunk 26 optimal weight:    6.9990
   chunk 24 optimal weight:    0.5980
   chunk 39 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 117 optimal weight:    0.0770
   chunk 36 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   overall best weight:    0.6938

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

Flipped N/Q/H residues before XYZ refinement:
A 198 GLN
A 435 ASN
B 158 GLN
B 198 GLN
B 435 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.129460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.109164 restraints weight = 16030.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.3221 rms_B_bonded: 1.93
r_work: 0.3091 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2951 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.1144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  13222  Z= 0.104
  Angle     :  0.430   6.136  17934  Z= 0.231
  Chirality :  0.039   0.133   1944
  Planarity :  0.003   0.042   2336
  Dihedral  :  5.060  76.816   1776
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 19.41 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.62 (0.22), residues: 1588
  helix:  1.19 (0.19), residues: 828
  sheet:  0.24 (0.36), residues: 224
  loop : -0.64 (0.27), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  52 
 TYR   0.016   0.001   TYR B 400 
 PHE   0.011   0.001   PHE A 156 
 TRP   0.008   0.001   TRP B  57 
 HIS   0.004   0.001   HIS B 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 (13222)
  covalent geometry    : angle       0.42977 (17934)
  hydrogen bonds       : bond        0.03623 (  656)
  hydrogen bonds       : angle       4.18949 ( 1860)

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

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

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 154
  time to evaluate  : 0.496 
Fit side-chains
REVERT: A  180 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7466 (pt0)
REVERT: A  202 LYS cc_start: 0.7534 (mtpm) cc_final: 0.6252 (mtmt)
REVERT: A  204 ARG cc_start: 0.8137 (tpp-160) cc_final: 0.7504 (mmm-85)
REVERT: A  241 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7957 (mm-30)
REVERT: A  259 LYS cc_start: 0.8647 (mttt) cc_final: 0.8434 (mptt)
REVERT: A  361 LEU cc_start: 0.8825 (tp) cc_final: 0.8576 (tt)
REVERT: A  391 TYR cc_start: 0.8178 (t80) cc_final: 0.7295 (t80)
REVERT: A  447 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.6788 (mt0)
REVERT: A  455 LYS cc_start: 0.7889 (mttp) cc_final: 0.7042 (ttpt)
REVERT: A  511 MET cc_start: 0.7537 (tpt) cc_final: 0.7177 (mpm)
REVERT: A  597 MET cc_start: 0.7398 (tpp) cc_final: 0.6664 (tpp)
REVERT: A  600 HIS cc_start: 0.8253 (OUTLIER) cc_final: 0.7719 (t70)
REVERT: A  698 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7509 (mp0)
REVERT: B  180 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7475 (pt0)
REVERT: B  202 LYS cc_start: 0.7517 (mtpm) cc_final: 0.6228 (mtmt)
REVERT: B  204 ARG cc_start: 0.8140 (tpp-160) cc_final: 0.7494 (mmm-85)
REVERT: B  241 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7959 (mm-30)
REVERT: B  259 LYS cc_start: 0.8661 (mttt) cc_final: 0.8451 (mptt)
REVERT: B  361 LEU cc_start: 0.8820 (tp) cc_final: 0.8571 (tt)
REVERT: B  391 TYR cc_start: 0.8171 (t80) cc_final: 0.7280 (t80)
REVERT: B  447 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.6775 (mt0)
REVERT: B  455 LYS cc_start: 0.7879 (mttp) cc_final: 0.7035 (ttpt)
REVERT: B  511 MET cc_start: 0.7510 (tpt) cc_final: 0.7165 (mpm)
REVERT: B  597 MET cc_start: 0.7407 (tpp) cc_final: 0.6672 (tpp)
REVERT: B  600 HIS cc_start: 0.8254 (OUTLIER) cc_final: 0.7722 (t70)
REVERT: B  698 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7517 (mp0)
  outliers start: 64
  outliers final: 36
  residues processed: 192
  average time/residue: 0.5737
  time to fit residues: 120.4720
Evaluate side-chains
  192 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 152
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  432 HIS
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  447 GLN
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  529 GLU
Chi-restraints excluded: chain A residue  600 HIS
Chi-restraints excluded: chain A residue  620 ASP
Chi-restraints excluded: chain A residue  643 ASP
Chi-restraints excluded: chain A residue  675 ASP
Chi-restraints excluded: chain A residue  762 SER
Chi-restraints excluded: chain A residue  766 CYS
Chi-restraints excluded: chain A residue  796 SER
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  196 ILE
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  432 HIS
Chi-restraints excluded: chain B residue  439 GLU
Chi-restraints excluded: chain B residue  440 LEU
Chi-restraints excluded: chain B residue  447 GLN
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  529 GLU
Chi-restraints excluded: chain B residue  600 HIS
Chi-restraints excluded: chain B residue  620 ASP
Chi-restraints excluded: chain B residue  643 ASP
Chi-restraints excluded: chain B residue  675 ASP
Chi-restraints excluded: chain B residue  762 SER
Chi-restraints excluded: chain B residue  766 CYS
Chi-restraints excluded: chain B residue  796 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 37 optimal weight:    0.7980
   chunk 157 optimal weight:    0.9990
   chunk 140 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0980
   chunk 59 optimal weight:    1.9990
   chunk 70 optimal weight:    7.9990
   chunk 3 optimal weight:    0.6980
   chunk 79 optimal weight:    5.9990
   chunk 31 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   chunk 136 optimal weight:    1.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
A 198 GLN
A 435 ASN
B 158 GLN
B 198 GLN
B 435 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.129765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.109468 restraints weight = 15911.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 1.93
r_work: 0.3106 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2967 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.1229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  13222  Z= 0.103
  Angle     :  0.424   4.497  17934  Z= 0.229
  Chirality :  0.039   0.133   1944
  Planarity :  0.003   0.043   2336
  Dihedral  :  5.001  75.423   1776
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 19.62 %
    Favored  : 75.90 %
  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:  0.50 (0.22), residues: 1588
  helix:  1.09 (0.19), residues: 848
  sheet:  0.40 (0.37), residues: 216
  loop : -0.86 (0.27), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  52 
 TYR   0.016   0.001   TYR A 400 
 PHE   0.011   0.001   PHE B 156 
 TRP   0.007   0.001   TRP B  57 
 HIS   0.004   0.001   HIS B 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 (13222)
  covalent geometry    : angle       0.42390 (17934)
  hydrogen bonds       : bond        0.03510 (  656)
  hydrogen bonds       : angle       4.09094 ( 1860)

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

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

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 156
  time to evaluate  : 0.396 
Fit side-chains
REVERT: A   17 LEU cc_start: 0.7866 (mt) cc_final: 0.7635 (mp)
REVERT: A  180 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7500 (pt0)
REVERT: A  202 LYS cc_start: 0.7545 (mtpm) cc_final: 0.6271 (mtmt)
REVERT: A  204 ARG cc_start: 0.8152 (tpp-160) cc_final: 0.7504 (mmm-85)
REVERT: A  241 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7947 (mm-30)
REVERT: A  391 TYR cc_start: 0.8161 (t80) cc_final: 0.7522 (t80)
REVERT: A  455 LYS cc_start: 0.7862 (mttp) cc_final: 0.7027 (ttpt)
REVERT: A  511 MET cc_start: 0.7510 (tpt) cc_final: 0.7182 (mpm)
REVERT: A  551 ARG cc_start: 0.8627 (ttm170) cc_final: 0.8255 (ttt180)
REVERT: A  597 MET cc_start: 0.7404 (tpp) cc_final: 0.6650 (tpp)
REVERT: A  600 HIS cc_start: 0.8244 (OUTLIER) cc_final: 0.7701 (t70)
REVERT: A  698 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7519 (mp0)
REVERT: A  785 MET cc_start: 0.8057 (mtp) cc_final: 0.7834 (mtm)
REVERT: B   17 LEU cc_start: 0.7847 (mt) cc_final: 0.7617 (mp)
REVERT: B  180 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7504 (pt0)
REVERT: B  202 LYS cc_start: 0.7533 (mtpm) cc_final: 0.6257 (mtmt)
REVERT: B  204 ARG cc_start: 0.8155 (tpp-160) cc_final: 0.7499 (mmm-85)
REVERT: B  241 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7945 (mm-30)
REVERT: B  391 TYR cc_start: 0.8158 (t80) cc_final: 0.7518 (t80)
REVERT: B  455 LYS cc_start: 0.7861 (mttp) cc_final: 0.7029 (ttpt)
REVERT: B  511 MET cc_start: 0.7478 (tpt) cc_final: 0.7167 (mpm)
REVERT: B  551 ARG cc_start: 0.8613 (ttm170) cc_final: 0.8237 (ttt180)
REVERT: B  597 MET cc_start: 0.7402 (tpp) cc_final: 0.6642 (tpp)
REVERT: B  600 HIS cc_start: 0.8244 (OUTLIER) cc_final: 0.7698 (t70)
REVERT: B  698 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7524 (mp0)
REVERT: B  785 MET cc_start: 0.8078 (mtp) cc_final: 0.7859 (mtm)
  outliers start: 62
  outliers final: 36
  residues processed: 194
  average time/residue: 0.5287
  time to fit residues: 112.4747
Evaluate side-chains
  184 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 146
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  432 HIS
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  529 GLU
Chi-restraints excluded: chain A residue  600 HIS
Chi-restraints excluded: chain A residue  620 ASP
Chi-restraints excluded: chain A residue  643 ASP
Chi-restraints excluded: chain A residue  658 THR
Chi-restraints excluded: chain A residue  762 SER
Chi-restraints excluded: chain A residue  766 CYS
Chi-restraints excluded: chain A residue  796 SER
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  432 HIS
Chi-restraints excluded: chain B residue  439 GLU
Chi-restraints excluded: chain B residue  440 LEU
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  529 GLU
Chi-restraints excluded: chain B residue  600 HIS
Chi-restraints excluded: chain B residue  620 ASP
Chi-restraints excluded: chain B residue  643 ASP
Chi-restraints excluded: chain B residue  658 THR
Chi-restraints excluded: chain B residue  762 SER
Chi-restraints excluded: chain B residue  766 CYS
Chi-restraints excluded: chain B residue  796 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 85 optimal weight:    0.0980
   chunk 57 optimal weight:    5.9990
   chunk 69 optimal weight:    0.8980
   chunk 126 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 37 optimal weight:    0.5980
   chunk 66 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 78 optimal weight:    0.0980
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 198 GLN
A 435 ASN
B 198 GLN
B 435 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.130788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.110376 restraints weight = 15947.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 1.96
r_work: 0.3121 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2979 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.1340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  13222  Z= 0.093
  Angle     :  0.417   5.025  17934  Z= 0.225
  Chirality :  0.038   0.132   1944
  Planarity :  0.003   0.042   2336
  Dihedral  :  4.956  74.683   1776
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 19.62 %
    Favored  : 76.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.22), residues: 1588
  helix:  1.34 (0.19), residues: 830
  sheet:  0.41 (0.38), residues: 216
  loop : -0.59 (0.27), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  52 
 TYR   0.016   0.001   TYR A 400 
 PHE   0.011   0.001   PHE B 156 
 TRP   0.007   0.001   TRP B 780 
 HIS   0.004   0.001   HIS A 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00207 (13222)
  covalent geometry    : angle       0.41736 (17934)
  hydrogen bonds       : bond        0.03290 (  656)
  hydrogen bonds       : angle       3.98290 ( 1860)

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

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

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 160
  time to evaluate  : 0.505 
Fit side-chains
REVERT: A  180 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7518 (pt0)
REVERT: A  204 ARG cc_start: 0.8152 (tpp-160) cc_final: 0.7684 (mmm-85)
REVERT: A  241 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7922 (mm-30)
REVERT: A  340 GLN cc_start: 0.8428 (mm-40) cc_final: 0.7357 (mp10)
REVERT: A  391 TYR cc_start: 0.8148 (t80) cc_final: 0.7312 (t80)
REVERT: A  447 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.6651 (mt0)
REVERT: A  455 LYS cc_start: 0.7820 (mttp) cc_final: 0.6990 (ttpt)
REVERT: A  511 MET cc_start: 0.7484 (tpt) cc_final: 0.7216 (mmt)
REVERT: A  597 MET cc_start: 0.7331 (tpp) cc_final: 0.6750 (tpp)
REVERT: A  600 HIS cc_start: 0.8274 (OUTLIER) cc_final: 0.7836 (t70)
REVERT: A  698 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7494 (mp0)
REVERT: B  180 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7515 (pt0)
REVERT: B  204 ARG cc_start: 0.8144 (tpp-160) cc_final: 0.7669 (mmm-85)
REVERT: B  241 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7918 (mm-30)
REVERT: B  340 GLN cc_start: 0.8425 (mm-40) cc_final: 0.7348 (mp10)
REVERT: B  391 TYR cc_start: 0.8153 (t80) cc_final: 0.7312 (t80)
REVERT: B  447 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.6625 (mt0)
REVERT: B  455 LYS cc_start: 0.7821 (mttp) cc_final: 0.6997 (ttpt)
REVERT: B  511 MET cc_start: 0.7459 (tpt) cc_final: 0.7204 (mmt)
REVERT: B  597 MET cc_start: 0.7329 (tpp) cc_final: 0.6744 (tpp)
REVERT: B  600 HIS cc_start: 0.8275 (OUTLIER) cc_final: 0.7837 (t70)
REVERT: B  698 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7486 (mp0)
  outliers start: 58
  outliers final: 36
  residues processed: 198
  average time/residue: 0.5509
  time to fit residues: 119.5172
Evaluate side-chains
  184 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 144
  time to evaluate  : 0.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  432 HIS
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  447 GLN
Chi-restraints excluded: chain A residue  496 ASP
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  529 GLU
Chi-restraints excluded: chain A residue  600 HIS
Chi-restraints excluded: chain A residue  620 ASP
Chi-restraints excluded: chain A residue  643 ASP
Chi-restraints excluded: chain A residue  658 THR
Chi-restraints excluded: chain A residue  762 SER
Chi-restraints excluded: chain A residue  766 CYS
Chi-restraints excluded: chain A residue  796 SER
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  196 ILE
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  432 HIS
Chi-restraints excluded: chain B residue  439 GLU
Chi-restraints excluded: chain B residue  447 GLN
Chi-restraints excluded: chain B residue  496 ASP
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  529 GLU
Chi-restraints excluded: chain B residue  600 HIS
Chi-restraints excluded: chain B residue  620 ASP
Chi-restraints excluded: chain B residue  643 ASP
Chi-restraints excluded: chain B residue  658 THR
Chi-restraints excluded: chain B residue  762 SER
Chi-restraints excluded: chain B residue  766 CYS
Chi-restraints excluded: chain B residue  796 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 125 optimal weight:    0.7980
   chunk 124 optimal weight:    0.7980
   chunk 102 optimal weight:    0.9990
   chunk 156 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 133 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 101 optimal weight:    0.7980
   chunk 67 optimal weight:    0.8980
   chunk 98 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 198 GLN
A 435 ASN
B 198 GLN
B 435 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.129774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.109349 restraints weight = 15928.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 1.94
r_work: 0.3105 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2965 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8419
moved from start:          0.1357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13222  Z= 0.117
  Angle     :  0.453   7.254  17934  Z= 0.242
  Chirality :  0.040   0.132   1944
  Planarity :  0.003   0.046   2336
  Dihedral  :  4.968  73.244   1776
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 20.35 %
    Favored  : 76.05 %
  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:  0.78 (0.22), residues: 1588
  helix:  1.31 (0.19), residues: 830
  sheet:  0.45 (0.38), residues: 216
  loop : -0.62 (0.27), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  52 
 TYR   0.016   0.001   TYR B 400 
 PHE   0.013   0.001   PHE A 156 
 TRP   0.007   0.001   TRP B 780 
 HIS   0.004   0.001   HIS A 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (13222)
  covalent geometry    : angle       0.45314 (17934)
  hydrogen bonds       : bond        0.03566 (  656)
  hydrogen bonds       : angle       4.02475 ( 1860)

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

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

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 150
  time to evaluate  : 0.567 
Fit side-chains
REVERT: A  111 GLU cc_start: 0.7316 (mp0) cc_final: 0.6118 (tp30)
REVERT: A  180 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7519 (pt0)
REVERT: A  202 LYS cc_start: 0.7500 (mtpm) cc_final: 0.6178 (mtmt)
REVERT: A  204 ARG cc_start: 0.8133 (tpp-160) cc_final: 0.7536 (mmm-85)
REVERT: A  241 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7954 (mm-30)
REVERT: A  340 GLN cc_start: 0.8436 (mm-40) cc_final: 0.7376 (mp10)
REVERT: A  391 TYR cc_start: 0.8170 (t80) cc_final: 0.7517 (t80)
REVERT: A  455 LYS cc_start: 0.7814 (mttp) cc_final: 0.6994 (ttpt)
REVERT: A  511 MET cc_start: 0.7470 (tpt) cc_final: 0.7224 (mmt)
REVERT: A  597 MET cc_start: 0.7381 (tpp) cc_final: 0.6642 (tpp)
REVERT: A  600 HIS cc_start: 0.8332 (OUTLIER) cc_final: 0.7906 (t70)
REVERT: A  698 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7521 (mp0)
REVERT: A  759 ASP cc_start: 0.8313 (m-30) cc_final: 0.7921 (m-30)
REVERT: B  111 GLU cc_start: 0.7321 (mp0) cc_final: 0.6116 (tp30)
REVERT: B  180 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7527 (pt0)
REVERT: B  202 LYS cc_start: 0.7495 (mtpm) cc_final: 0.6175 (mtmt)
REVERT: B  204 ARG cc_start: 0.8121 (tpp-160) cc_final: 0.7520 (mmm-85)
REVERT: B  241 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7965 (mm-30)
REVERT: B  340 GLN cc_start: 0.8438 (mm-40) cc_final: 0.7372 (mp10)
REVERT: B  391 TYR cc_start: 0.8167 (t80) cc_final: 0.7509 (t80)
REVERT: B  455 LYS cc_start: 0.7819 (mttp) cc_final: 0.7000 (ttpt)
REVERT: B  511 MET cc_start: 0.7446 (tpt) cc_final: 0.7205 (mmt)
REVERT: B  597 MET cc_start: 0.7366 (tpp) cc_final: 0.6624 (tpp)
REVERT: B  600 HIS cc_start: 0.8326 (OUTLIER) cc_final: 0.7901 (t70)
REVERT: B  698 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7520 (mp0)
REVERT: B  759 ASP cc_start: 0.8323 (m-30) cc_final: 0.7933 (m-30)
  outliers start: 50
  outliers final: 40
  residues processed: 182
  average time/residue: 0.5759
  time to fit residues: 114.4552
Evaluate side-chains
  189 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 147
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  432 HIS
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  496 ASP
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  529 GLU
Chi-restraints excluded: chain A residue  600 HIS
Chi-restraints excluded: chain A residue  620 ASP
Chi-restraints excluded: chain A residue  643 ASP
Chi-restraints excluded: chain A residue  658 THR
Chi-restraints excluded: chain A residue  762 SER
Chi-restraints excluded: chain A residue  766 CYS
Chi-restraints excluded: chain A residue  796 SER
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  196 ILE
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  432 HIS
Chi-restraints excluded: chain B residue  439 GLU
Chi-restraints excluded: chain B residue  440 LEU
Chi-restraints excluded: chain B residue  496 ASP
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  529 GLU
Chi-restraints excluded: chain B residue  600 HIS
Chi-restraints excluded: chain B residue  620 ASP
Chi-restraints excluded: chain B residue  643 ASP
Chi-restraints excluded: chain B residue  658 THR
Chi-restraints excluded: chain B residue  762 SER
Chi-restraints excluded: chain B residue  766 CYS
Chi-restraints excluded: chain B residue  796 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 42 optimal weight:    0.3980
   chunk 90 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 108 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   chunk 70 optimal weight:    4.9990
   chunk 63 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 115 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
A 159 ASN
A 198 GLN
A 435 ASN
B 198 GLN
B 435 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.128008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.107588 restraints weight = 16072.239|
|-----------------------------------------------------------------------------|
r_work (start): 0.3210 rms_B_bonded: 1.94
r_work: 0.3079 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2939 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.1384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13222  Z= 0.151
  Angle     :  0.484   8.850  17934  Z= 0.258
  Chirality :  0.041   0.135   1944
  Planarity :  0.004   0.051   2336
  Dihedral  :  5.047  72.017   1776
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 20.13 %
    Favored  : 76.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.63 (0.22), residues: 1588
  helix:  1.20 (0.19), residues: 834
  sheet:  0.51 (0.39), residues: 204
  loop : -0.77 (0.26), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A  52 
 TYR   0.017   0.002   TYR B 400 
 PHE   0.017   0.002   PHE A 156 
 TRP   0.007   0.001   TRP A  57 
 HIS   0.004   0.001   HIS A 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (13222)
  covalent geometry    : angle       0.48429 (17934)
  hydrogen bonds       : bond        0.04058 (  656)
  hydrogen bonds       : angle       4.14356 ( 1860)

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

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

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 152
  time to evaluate  : 0.382 
Fit side-chains
REVERT: A  111 GLU cc_start: 0.7460 (mp0) cc_final: 0.6214 (tp30)
REVERT: A  202 LYS cc_start: 0.7545 (mtpm) cc_final: 0.6206 (mtmt)
REVERT: A  204 ARG cc_start: 0.8144 (tpp-160) cc_final: 0.7554 (mmm-85)
REVERT: A  241 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7955 (mm-30)
REVERT: A  391 TYR cc_start: 0.8194 (t80) cc_final: 0.7361 (t80)
REVERT: A  455 LYS cc_start: 0.7838 (mttp) cc_final: 0.7015 (ttpt)
REVERT: A  511 MET cc_start: 0.7552 (tpt) cc_final: 0.7300 (mmt)
REVERT: A  551 ARG cc_start: 0.8640 (ttm170) cc_final: 0.8268 (ttt180)
REVERT: A  597 MET cc_start: 0.7407 (tpp) cc_final: 0.6673 (tpp)
REVERT: A  600 HIS cc_start: 0.8292 (OUTLIER) cc_final: 0.7794 (t70)
REVERT: A  698 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7535 (mp0)
REVERT: B  111 GLU cc_start: 0.7447 (mp0) cc_final: 0.6207 (tp30)
REVERT: B  202 LYS cc_start: 0.7520 (mtpm) cc_final: 0.6184 (mtmt)
REVERT: B  204 ARG cc_start: 0.8134 (tpp-160) cc_final: 0.7544 (mmm-85)
REVERT: B  241 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7953 (mm-30)
REVERT: B  391 TYR cc_start: 0.8194 (t80) cc_final: 0.7355 (t80)
REVERT: B  455 LYS cc_start: 0.7836 (mttp) cc_final: 0.7013 (ttpt)
REVERT: B  511 MET cc_start: 0.7515 (tpt) cc_final: 0.7284 (mmt)
REVERT: B  551 ARG cc_start: 0.8642 (ttm170) cc_final: 0.8270 (ttt180)
REVERT: B  597 MET cc_start: 0.7400 (tpp) cc_final: 0.6663 (tpp)
REVERT: B  600 HIS cc_start: 0.8296 (OUTLIER) cc_final: 0.7796 (t70)
REVERT: B  698 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7541 (mp0)
  outliers start: 51
  outliers final: 40
  residues processed: 185
  average time/residue: 0.5587
  time to fit residues: 113.2004
Evaluate side-chains
  188 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 146
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 MET
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  432 HIS
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  496 ASP
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  529 GLU
Chi-restraints excluded: chain A residue  600 HIS
Chi-restraints excluded: chain A residue  620 ASP
Chi-restraints excluded: chain A residue  643 ASP
Chi-restraints excluded: chain A residue  658 THR
Chi-restraints excluded: chain A residue  762 SER
Chi-restraints excluded: chain A residue  766 CYS
Chi-restraints excluded: chain A residue  796 SER
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  196 ILE
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  432 HIS
Chi-restraints excluded: chain B residue  439 GLU
Chi-restraints excluded: chain B residue  496 ASP
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  529 GLU
Chi-restraints excluded: chain B residue  600 HIS
Chi-restraints excluded: chain B residue  620 ASP
Chi-restraints excluded: chain B residue  643 ASP
Chi-restraints excluded: chain B residue  658 THR
Chi-restraints excluded: chain B residue  762 SER
Chi-restraints excluded: chain B residue  766 CYS
Chi-restraints excluded: chain B residue  796 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 68 optimal weight:    6.9990
   chunk 71 optimal weight:    4.9990
   chunk 107 optimal weight:    0.9990
   chunk 96 optimal weight:    0.9980
   chunk 103 optimal weight:    0.0970
   chunk 137 optimal weight:    0.8980
   chunk 97 optimal weight:    1.9990
   chunk 29 optimal weight:    5.9990
   chunk 7 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 159 ASN
A 198 GLN
A 435 ASN
B 159 ASN
B 198 GLN
B 435 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.128731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.108335 restraints weight = 16037.458|
|-----------------------------------------------------------------------------|
r_work (start): 0.3217 rms_B_bonded: 1.94
r_work: 0.3086 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2948 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.1393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13222  Z= 0.128
  Angle     :  0.468   8.695  17934  Z= 0.250
  Chirality :  0.040   0.133   1944
  Planarity :  0.003   0.048   2336
  Dihedral  :  5.053  72.288   1776
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 20.63 %
    Favored  : 76.05 %
  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:  0.66 (0.22), residues: 1588
  helix:  1.22 (0.19), residues: 836
  sheet:  0.42 (0.38), residues: 216
  loop : -0.71 (0.26), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A  52 
 TYR   0.017   0.001   TYR A 400 
 PHE   0.014   0.001   PHE A 156 
 TRP   0.007   0.001   TRP B  57 
 HIS   0.004   0.001   HIS B 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (13222)
  covalent geometry    : angle       0.46786 (17934)
  hydrogen bonds       : bond        0.03826 (  656)
  hydrogen bonds       : angle       4.11081 ( 1860)

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

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

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 156
  time to evaluate  : 0.562 
Fit side-chains
REVERT: A  111 GLU cc_start: 0.7422 (mp0) cc_final: 0.6172 (tp30)
REVERT: A  202 LYS cc_start: 0.7541 (mtpm) cc_final: 0.6256 (mtmt)
REVERT: A  204 ARG cc_start: 0.8143 (tpp-160) cc_final: 0.7555 (mmm-85)
REVERT: A  241 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7944 (mm-30)
REVERT: A  391 TYR cc_start: 0.8183 (t80) cc_final: 0.7342 (t80)
REVERT: A  455 LYS cc_start: 0.7819 (mttp) cc_final: 0.6998 (ttpt)
REVERT: A  511 MET cc_start: 0.7538 (tpt) cc_final: 0.7295 (mmt)
REVERT: A  597 MET cc_start: 0.7389 (tpp) cc_final: 0.6649 (tpp)
REVERT: A  600 HIS cc_start: 0.8271 (OUTLIER) cc_final: 0.7769 (t70)
REVERT: A  698 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7528 (mp0)
REVERT: A  759 ASP cc_start: 0.8380 (m-30) cc_final: 0.8000 (m-30)
REVERT: B  111 GLU cc_start: 0.7421 (mp0) cc_final: 0.6171 (tp30)
REVERT: B  202 LYS cc_start: 0.7517 (mtpm) cc_final: 0.6232 (mtmt)
REVERT: B  204 ARG cc_start: 0.8133 (tpp-160) cc_final: 0.7542 (mmm-85)
REVERT: B  241 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7938 (mm-30)
REVERT: B  391 TYR cc_start: 0.8186 (t80) cc_final: 0.7337 (t80)
REVERT: B  455 LYS cc_start: 0.7814 (mttp) cc_final: 0.6996 (ttpt)
REVERT: B  511 MET cc_start: 0.7500 (tpt) cc_final: 0.7284 (mmt)
REVERT: B  597 MET cc_start: 0.7394 (tpp) cc_final: 0.6652 (tpp)
REVERT: B  600 HIS cc_start: 0.8270 (OUTLIER) cc_final: 0.7769 (t70)
REVERT: B  698 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7535 (mp0)
REVERT: B  759 ASP cc_start: 0.8378 (m-30) cc_final: 0.7998 (m-30)
  outliers start: 46
  outliers final: 40
  residues processed: 184
  average time/residue: 0.5887
  time to fit residues: 118.2554
Evaluate side-chains
  190 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 148
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 MET
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  432 HIS
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  496 ASP
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  529 GLU
Chi-restraints excluded: chain A residue  600 HIS
Chi-restraints excluded: chain A residue  620 ASP
Chi-restraints excluded: chain A residue  643 ASP
Chi-restraints excluded: chain A residue  658 THR
Chi-restraints excluded: chain A residue  762 SER
Chi-restraints excluded: chain A residue  766 CYS
Chi-restraints excluded: chain A residue  796 SER
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  196 ILE
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  432 HIS
Chi-restraints excluded: chain B residue  439 GLU
Chi-restraints excluded: chain B residue  496 ASP
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  529 GLU
Chi-restraints excluded: chain B residue  600 HIS
Chi-restraints excluded: chain B residue  620 ASP
Chi-restraints excluded: chain B residue  643 ASP
Chi-restraints excluded: chain B residue  658 THR
Chi-restraints excluded: chain B residue  762 SER
Chi-restraints excluded: chain B residue  766 CYS
Chi-restraints excluded: chain B residue  796 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 101 optimal weight:    2.9990
   chunk 157 optimal weight:    0.8980
   chunk 141 optimal weight:    2.9990
   chunk 68 optimal weight:    4.9990
   chunk 134 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 138 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 159 ASN
A 198 GLN
B 198 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.125750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.105310 restraints weight = 16093.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 1.93
r_work: 0.3044 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2903 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.1503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  13222  Z= 0.210
  Angle     :  0.535   9.400  17934  Z= 0.284
  Chirality :  0.044   0.138   1944
  Planarity :  0.004   0.052   2336
  Dihedral  :  5.217  71.864   1776
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 20.56 %
    Favored  : 75.90 %
  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:  0.22 (0.22), residues: 1588
  helix:  0.87 (0.19), residues: 854
  sheet:  0.42 (0.38), residues: 204
  loop : -1.05 (0.26), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  52 
 TYR   0.018   0.002   TYR B 400 
 PHE   0.021   0.002   PHE A 156 
 TRP   0.008   0.001   TRP B  57 
 HIS   0.005   0.001   HIS A 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00509 (13222)
  covalent geometry    : angle       0.53516 (17934)
  hydrogen bonds       : bond        0.04724 (  656)
  hydrogen bonds       : angle       4.34364 ( 1860)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3907.88 seconds
wall clock time: 67 minutes 20.12 seconds (4040.12 seconds total)