Starting phenix.real_space_refine
on Tue Nov 18 02:31:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wla_32579/11_2025/7wla_32579.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wla_32579/11_2025/7wla_32579.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wla_32579/11_2025/7wla_32579.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wla_32579/11_2025/7wla_32579.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wla_32579/11_2025/7wla_32579.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wla_32579/11_2025/7wla_32579.cif"
  }
  resolution = 3.76
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.021
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      42      5.16       5
     C    6653      2.51       5
     N    1687      2.21       5
     O    1811      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10193
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5099
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 665, 5099
          Classifications: {'peptide': 665}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 26, 'TRANS': 638}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 46
          Unresolved non-hydrogen dihedrals: 32
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 30
    Chain: "B"
      Number of atoms: 5094
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 662, 5094
          Classifications: {'peptide': 662}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 26, 'TRANS': 635}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 15
  Time building chain proxies: 2.58, per 1000 atoms: 0.25
  Number of scatterers: 10193
  At special positions: 0
  Unit cell: (85.772, 127.612, 123.428, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      42     16.00
     O    1811      8.00
     N    1687      7.00
     C    6653      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: 0.95
  Conformation dependent library (CDL) restraints added in 413.2 milliseconds
  

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2466

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 6 sheets defined
      64.3% alpha, 2.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 34
      removed outlier: 3.765A  pdb=" N   GLN A  33 " --> pdb=" O   GLU A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 57 through 69
    Processing helix  chain 'A' and resid 70 through 75
      removed outlier: 3.851A  pdb=" N   TRP A  74 " --> pdb=" O   PRO A  70 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LEU A  75 " --> pdb=" O   ILE A  71 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 70 through 75'
    Processing helix  chain 'A' and resid 79 through 106
      removed outlier: 5.125A  pdb=" N   LEU A  85 " --> pdb=" O   LYS A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 120
      removed outlier: 3.967A  pdb=" N   GLY A 116 " --> pdb=" O   PRO A 112 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   LEU A 117 " --> pdb=" O   VAL A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 129
      removed outlier: 3.958A  pdb=" N   VAL A 129 " --> pdb=" O   LEU A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 156
    Processing helix  chain 'A' and resid 157 through 161
      removed outlier: 3.699A  pdb=" N   HIS A 160 " --> pdb=" O   PRO A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 206
      removed outlier: 3.909A  pdb=" N   ALA A 183 " --> pdb=" O   GLY A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 215
      removed outlier: 3.598A  pdb=" N   VAL A 212 " --> pdb=" O   GLY A 209 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   TYR A 214 " --> pdb=" O   ILE A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 241
    Processing helix  chain 'A' and resid 251 through 263
    Processing helix  chain 'A' and resid 268 through 292
    Processing helix  chain 'A' and resid 301 through 317
      removed outlier: 3.673A  pdb=" N   ALA A 317 " --> pdb=" O   ILE A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 374
    Processing helix  chain 'A' and resid 380 through 397
      removed outlier: 3.582A  pdb=" N   PHE A 397 " --> pdb=" O   VAL A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 417
      removed outlier: 3.560A  pdb=" N   GLN A 413 " --> pdb=" O   ARG A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 437
      removed outlier: 3.608A  pdb=" N   VAL A 431 " --> pdb=" O   SER A 427 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   ALA A 437 " --> pdb=" O   VAL A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 443
    Processing helix  chain 'A' and resid 446 through 457
      removed outlier: 3.844A  pdb=" N   LEU A 450 " --> pdb=" O   GLN A 446 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   VAL A 453 " --> pdb=" O   VAL A 449 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   VAL A 454 " --> pdb=" O   LEU A 450 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   ILE A 455 " --> pdb=" O   ALA A 451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 463
    Processing helix  chain 'A' and resid 464 through 466
      No H-bonds generated for 'chain 'A' and resid 464 through 466'
    Processing helix  chain 'A' and resid 467 through 474
      removed outlier: 3.728A  pdb=" N   LYS A 473 " --> pdb=" O   PRO A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 492
      removed outlier: 3.653A  pdb=" N   ALA A 479 " --> pdb=" O   ASN A 475 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ILE A 490 " --> pdb=" O   CYS A 486 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU A 492 " --> pdb=" O   MET A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 515
      removed outlier: 3.642A  pdb=" N   LEU A 498 " --> pdb=" O   LEU A 494 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   LEU A 499 " --> pdb=" O   ASP A 495 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 558 through 571
    Processing helix  chain 'A' and resid 573 through 595
      removed outlier: 3.738A  pdb=" N   TYR A 578 " --> pdb=" O   ALA A 574 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ARG A 587 " --> pdb=" O   LYS A 583 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   LYS A 593 " --> pdb=" O   GLN A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 669 through 686
      removed outlier: 3.547A  pdb=" N   VAL A 673 " --> pdb=" O   ASP A 669 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   SER A 675 " --> pdb=" O   VAL A 671 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ILE A 686 " --> pdb=" O   GLU A 682 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 696 through 706
      removed outlier: 3.770A  pdb=" N   GLN A 705 " --> pdb=" O   GLU A 701 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 714 through 718
      removed outlier: 3.908A  pdb=" N   ARG A 717 " --> pdb=" O   ARG A 714 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 721 through 736
      removed outlier: 3.752A  pdb=" N   ALA A 725 " --> pdb=" O   THR A 721 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ILE A 726 " --> pdb=" O   VAL A 722 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 34
      removed outlier: 3.622A  pdb=" N   GLN B  34 " --> pdb=" O   LEU B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 57 through 69
      removed outlier: 3.878A  pdb=" N   ALA B  61 " --> pdb=" O   SER B  57 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 109
      removed outlier: 3.540A  pdb=" N   SER B  93 " --> pdb=" O   ILE B  89 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ALA B 106 " --> pdb=" O   GLY B 102 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   LEU B 107 " --> pdb=" O   MET B 103 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   LEU B 108 " --> pdb=" O   ALA B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 120
    Processing helix  chain 'B' and resid 121 through 130
      removed outlier: 3.546A  pdb=" N   LEU B 125 " --> pdb=" O   PHE B 121 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   THR B 126 " --> pdb=" O   PHE B 122 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   VAL B 129 " --> pdb=" O   LEU B 125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 141 through 156
      removed outlier: 3.716A  pdb=" N   LEU B 146 " --> pdb=" O   PRO B 142 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   MET B 147 " --> pdb=" O   VAL B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 204
      removed outlier: 3.839A  pdb=" N   GLY B 204 " --> pdb=" O   GLN B 200 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 215
    Processing helix  chain 'B' and resid 216 through 224
    Processing helix  chain 'B' and resid 225 through 240
      removed outlier: 4.136A  pdb=" N   ILE B 238 " --> pdb=" O   SER B 234 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 263
    Processing helix  chain 'B' and resid 268 through 292
      removed outlier: 3.651A  pdb=" N   ILE B 280 " --> pdb=" O   LEU B 276 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   VAL B 281 " --> pdb=" O   LEU B 277 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   MET B 283 " --> pdb=" O   ILE B 279 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 316
    Processing helix  chain 'B' and resid 342 through 344
      No H-bonds generated for 'chain 'B' and resid 342 through 344'
    Processing helix  chain 'B' and resid 345 through 370
      removed outlier: 4.130A  pdb=" N   ALA B 351 " --> pdb=" O   SER B 347 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   ALA B 352 " --> pdb=" O   ASP B 348 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   PHE B 354 " --> pdb=" O   LEU B 350 " (cutoff:3.500A)
      removed outlier: 5.327A  pdb=" N   SER B 355 " --> pdb=" O   ALA B 351 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ILE B 356 " --> pdb=" O   ALA B 352 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   VAL B 359 " --> pdb=" O   SER B 355 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   GLY B 368 " --> pdb=" O   ALA B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 380 through 396
      removed outlier: 3.525A  pdb=" N   GLU B 384 " --> pdb=" O   ASP B 380 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ILE B 386 " --> pdb=" O   ASN B 382 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 408 through 416
      removed outlier: 3.578A  pdb=" N   GLU B 414 " --> pdb=" O   THR B 410 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   THR B 416 " --> pdb=" O   VAL B 412 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 421 through 437
      removed outlier: 3.525A  pdb=" N   LEU B 425 " --> pdb=" O   GLN B 421 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   VAL B 436 " --> pdb=" O   MET B 432 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 458
      removed outlier: 3.651A  pdb=" N   ALA B 456 " --> pdb=" O   ALA B 452 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ASN B 457 " --> pdb=" O   VAL B 453 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 458 through 463
    Processing helix  chain 'B' and resid 466 through 475
      removed outlier: 3.885A  pdb=" N   ARG B 470 " --> pdb=" O   CYS B 466 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   LYS B 473 " --> pdb=" O   PRO B 469 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 475 through 492
      removed outlier: 3.552A  pdb=" N   ALA B 479 " --> pdb=" O   ASN B 475 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ILE B 491 " --> pdb=" O   ILE B 487 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 492 through 513
      removed outlier: 3.690A  pdb=" N   LEU B 496 " --> pdb=" O   LEU B 492 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   LEU B 498 " --> pdb=" O   LEU B 494 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   LEU B 499 " --> pdb=" O   ASP B 495 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 558 through 570
    Processing helix  chain 'B' and resid 575 through 595
      removed outlier: 3.590A  pdb=" N   ASN B 579 " --> pdb=" O   ILE B 575 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LEU B 591 " --> pdb=" O   ARG B 587 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LYS B 593 " --> pdb=" O   GLN B 589 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 669 through 685
      removed outlier: 3.602A  pdb=" N   ARG B 685 " --> pdb=" O   LYS B 681 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 697 through 706
      removed outlier: 4.177A  pdb=" N   GLU B 701 " --> pdb=" O   ASP B 697 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   MET B 703 " --> pdb=" O   VAL B 699 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLU B 704 " --> pdb=" O   LEU B 700 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 714 through 718
      removed outlier: 3.575A  pdb=" N   ARG B 717 " --> pdb=" O   ARG B 714 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 721 through 733
      removed outlier: 3.724A  pdb=" N   ALA B 725 " --> pdb=" O   THR B 721 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ILE B 726 " --> pdb=" O   VAL B 722 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   VAL B 733 " --> pdb=" O   LEU B 729 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 138 through 139
    Processing sheet with id=AA2, first strand: chain 'A' and resid 522 through 523
    Processing sheet with id=AA3, first strand: chain 'A' and resid 545 through 549
      removed outlier: 6.743A  pdb=" N   LYS A 546 " --> pdb=" O   VAL A 659 " (cutoff:3.500A)
      removed outlier: 7.553A  pdb=" N   ASP A 661 " --> pdb=" O   LYS A 546 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   LEU A 548 " --> pdb=" O   ASP A 661 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   LEU A 658 " --> pdb=" O   TYR A 691 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 138 through 139
    Processing sheet with id=AA5, first strand: chain 'B' and resid 521 through 523
    Processing sheet with id=AA6, first strand: chain 'B' and resid 545 through 548
      removed outlier: 6.375A  pdb=" N   LYS B 546 " --> pdb=" O   VAL B 659 " (cutoff:3.500A)

    544 hydrogen bonds defined for protein.
    1593 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: 1.54

  Time building geometry restraints manager: 1.26 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3212
        1.34 -     1.46: 2247
        1.46 -     1.58: 4872
        1.58 -     1.69: 0
        1.69 -     1.81: 64
  Bond restraints: 10395
  Sorted by residual:
  bond pdb=" C   VAL A 653 "
       pdb=" N   PRO A 654 "
    ideal  model  delta    sigma   weight residual
    1.334  1.356 -0.022 2.34e-02 1.83e+03 8.64e-01
  bond pdb=" CB  PRO B 164 "
       pdb=" CG  PRO B 164 "
    ideal  model  delta    sigma   weight residual
    1.492  1.535 -0.043 5.00e-02 4.00e+02 7.45e-01
  bond pdb=" C   GLU B 443 "
       pdb=" N   PRO B 444 "
    ideal  model  delta    sigma   weight residual
    1.334  1.354 -0.020 2.34e-02 1.83e+03 7.08e-01
  bond pdb=" CA  PHE A 122 "
       pdb=" C   PHE A 122 "
    ideal  model  delta    sigma   weight residual
    1.521  1.530 -0.009 1.14e-02 7.69e+03 6.08e-01
  bond pdb=" N   PRO B 337 "
       pdb=" CA  PRO B 337 "
    ideal  model  delta    sigma   weight residual
    1.457  1.467 -0.010 1.31e-02 5.83e+03 5.47e-01
  ... (remaining 10390 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.09: 13736
        1.09 -     2.19: 298
        2.19 -     3.28: 64
        3.28 -     4.38: 19
        4.38 -     5.47: 11
  Bond angle restraints: 14128
  Sorted by residual:
  angle pdb=" N   ARG A 134 "
        pdb=" CA  ARG A 134 "
        pdb=" C   ARG A 134 "
      ideal   model   delta    sigma   weight residual
     114.56  111.18    3.38 1.27e+00 6.20e-01 7.09e+00
  angle pdb=" C   PHE A 121 "
        pdb=" N   PHE A 122 "
        pdb=" CA  PHE A 122 "
      ideal   model   delta    sigma   weight residual
     119.78  122.74   -2.96 1.24e+00 6.50e-01 5.72e+00
  angle pdb=" N   VAL A  80 "
        pdb=" CA  VAL A  80 "
        pdb=" C   VAL A  80 "
      ideal   model   delta    sigma   weight residual
     109.34  113.74   -4.40 2.08e+00 2.31e-01 4.47e+00
  angle pdb=" C   ASP A 669 "
        pdb=" N   VAL A 670 "
        pdb=" CA  VAL A 670 "
      ideal   model   delta    sigma   weight residual
     121.97  125.76   -3.79 1.80e+00 3.09e-01 4.43e+00
  angle pdb=" C   VAL A 328 "
        pdb=" N   LYS A 329 "
        pdb=" CA  LYS A 329 "
      ideal   model   delta    sigma   weight residual
     121.54  125.51   -3.97 1.91e+00 2.74e-01 4.32e+00
  ... (remaining 14123 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.76: 5965
       17.76 -    35.51: 179
       35.51 -    53.27: 32
       53.27 -    71.03: 0
       71.03 -    88.79: 4
  Dihedral angle restraints: 6180
    sinusoidal: 2353
      harmonic: 3827
  Sorted by residual:
  dihedral pdb=" CB  GLU B 259 "
           pdb=" CG  GLU B 259 "
           pdb=" CD  GLU B 259 "
           pdb=" OE1 GLU B 259 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.02  -86.02     1      3.00e+01 1.11e-03 9.93e+00
  dihedral pdb=" N   ARG B  43 "
           pdb=" CA  ARG B  43 "
           pdb=" CB  ARG B  43 "
           pdb=" CG  ARG B  43 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -128.09  -51.91     3      1.50e+01 4.44e-03 9.06e+00
  dihedral pdb=" N   ARG A  36 "
           pdb=" CA  ARG A  36 "
           pdb=" CB  ARG A  36 "
           pdb=" CG  ARG A  36 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -128.25  -51.75     3      1.50e+01 4.44e-03 9.05e+00
  ... (remaining 6177 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 957
       0.026 -    0.052: 503
       0.052 -    0.078: 177
       0.078 -    0.104: 62
       0.104 -    0.130: 17
  Chirality restraints: 1716
  Sorted by residual:
  chirality pdb=" CA  VAL A 524 "
            pdb=" N   VAL A 524 "
            pdb=" C   VAL A 524 "
            pdb=" CB  VAL A 524 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.21e-01
  chirality pdb=" CA  PRO A 553 "
            pdb=" N   PRO A 553 "
            pdb=" C   PRO A 553 "
            pdb=" CB  PRO A 553 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.19e-01
  chirality pdb=" CA  ILE B 296 "
            pdb=" N   ILE B 296 "
            pdb=" C   ILE B 296 "
            pdb=" CB  ILE B 296 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.88e-01
  ... (remaining 1713 not shown)

  Planarity restraints: 1757
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B  75 "    0.028 5.00e-02 4.00e+02   4.27e-02 2.91e+00
        pdb=" N   PRO B  76 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO B  76 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B  76 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 552 "    0.023 5.00e-02 4.00e+02   3.54e-02 2.00e+00
        pdb=" N   PRO A 553 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO A 553 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 553 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 653 "   -0.021 5.00e-02 4.00e+02   3.21e-02 1.65e+00
        pdb=" N   PRO B 654 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO B 654 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 654 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 1754 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 705
        2.74 -     3.28: 11232
        3.28 -     3.82: 16750
        3.82 -     4.36: 19648
        4.36 -     4.90: 33038
  Nonbonded interactions: 81373
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  78 "
            pdb=" OD2 ASP A  87 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" OG  SER A  90 "
            pdb=" O   GLY A 417 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" OD1 ASN A 475 "
            pdb=" OG1 THR A 477 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" OH  TYR A 118 "
            pdb=" O   GLY A 334 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" O   ASP A 669 "
            pdb=" N   GLY A 672 "
     model   vdw
     2.242 3.120
  ... (remaining 81368 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: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 18 through 733)
  selection = (chain 'B' and (resid 18 through 42 or (resid 43 through 44 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 45 through 46 or (resid 47 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 48 through 51 or (res \ 
id 52 and (name N or name CA or name C or name O or name CB )) or resid 53 throu \ 
gh 590 or (resid 591 and (name N or name CA or name C or name O or name CB )) or \ 
 resid 592 through 595 or resid 651 through 733))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.590
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6852
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      :  0.002   0.043  10395  Z= 0.091
  Angle     :  0.445   5.469  14128  Z= 0.251
  Chirality :  0.037   0.130   1716
  Planarity :  0.003   0.043   1757
  Dihedral  :  8.816  88.787   3714
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  :  5.52 %
    Favored  : 90.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.06 (0.19), residues: 1319
  helix: -2.14 (0.15), residues: 815
  sheet: -3.23 (0.68), residues: 30
  loop : -3.49 (0.24), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 512 
 TYR   0.005   0.001   TYR A 377 
 PHE   0.008   0.001   PHE A 555 
 TRP   0.005   0.000   TRP B  83 
 HIS   0.001   0.000   HIS A 723 

Details of bonding type rmsd
  covalent geometry    : bond        0.00169 (10395)
  covalent geometry    : angle       0.44482 (14128)
  hydrogen bonds       : bond        0.23262 (  544)
  hydrogen bonds       : angle       6.79140 ( 1593)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  423 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 378
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 ARG cc_start: 0.7321 (tpp-160) cc_final: 0.7066 (mmt90)
REVERT: A   93 SER cc_start: 0.8253 (t) cc_final: 0.7920 (p)
REVERT: A  122 PHE cc_start: 0.7110 (m-80) cc_final: 0.6612 (m-10)
REVERT: A  195 LEU cc_start: 0.8547 (tp) cc_final: 0.7962 (tp)
REVERT: A  199 ILE cc_start: 0.8218 (mt) cc_final: 0.7783 (mt)
REVERT: A  206 LEU cc_start: 0.7834 (mt) cc_final: 0.7563 (mt)
REVERT: A  213 ARG cc_start: 0.7481 (mtt180) cc_final: 0.7195 (mtm-85)
REVERT: A  231 VAL cc_start: 0.8650 (t) cc_final: 0.7990 (p)
REVERT: A  235 GLN cc_start: 0.7974 (mm-40) cc_final: 0.7666 (mm-40)
REVERT: A  237 LYS cc_start: 0.8348 (ttpp) cc_final: 0.7839 (ttpp)
REVERT: A  238 ILE cc_start: 0.8539 (mt) cc_final: 0.8339 (tp)
REVERT: A  260 ILE cc_start: 0.8844 (mt) cc_final: 0.8503 (tp)
REVERT: A  272 PHE cc_start: 0.7779 (t80) cc_final: 0.7542 (t80)
REVERT: A  280 ILE cc_start: 0.8880 (mt) cc_final: 0.8622 (tp)
REVERT: A  286 LYS cc_start: 0.9159 (tppt) cc_final: 0.8796 (mmmm)
REVERT: A  355 SER cc_start: 0.7752 (m) cc_final: 0.7495 (p)
REVERT: A  384 GLU cc_start: 0.6190 (mm-30) cc_final: 0.5550 (mm-30)
REVERT: A  398 PHE cc_start: 0.7104 (m-80) cc_final: 0.6473 (m-10)
REVERT: A  432 MET cc_start: 0.7370 (tpt) cc_final: 0.6650 (tpt)
REVERT: A  473 LYS cc_start: 0.7991 (mtpt) cc_final: 0.7502 (mtpt)
REVERT: A  484 PHE cc_start: 0.8200 (t80) cc_final: 0.7761 (t80)
REVERT: A  488 MET cc_start: 0.7136 (tpp) cc_final: 0.6686 (tpp)
REVERT: A  512 ARG cc_start: 0.8525 (mtm-85) cc_final: 0.8309 (mtm-85)
REVERT: A  546 LYS cc_start: 0.8240 (tptm) cc_final: 0.7857 (tptm)
REVERT: A  564 LYS cc_start: 0.8491 (ttmm) cc_final: 0.8221 (ttmm)
REVERT: A  676 LEU cc_start: 0.8143 (mt) cc_final: 0.7890 (tp)
REVERT: A  681 LYS cc_start: 0.7819 (tptt) cc_final: 0.6864 (tptt)
REVERT: A  686 ILE cc_start: 0.8389 (pt) cc_final: 0.7896 (mm)
REVERT: A  687 ASP cc_start: 0.6664 (t0) cc_final: 0.6180 (t0)
REVERT: A  723 HIS cc_start: 0.7182 (t-170) cc_final: 0.6781 (t-90)
REVERT: B   48 ASP cc_start: 0.6066 (p0) cc_final: 0.5755 (m-30)
REVERT: B  118 TYR cc_start: 0.6964 (m-10) cc_final: 0.6603 (m-80)
REVERT: B  137 SER cc_start: 0.8017 (t) cc_final: 0.7779 (p)
REVERT: B  151 VAL cc_start: 0.7229 (m) cc_final: 0.6544 (p)
REVERT: B  195 LEU cc_start: 0.6325 (OUTLIER) cc_final: 0.5859 (tp)
REVERT: B  199 ILE cc_start: 0.7579 (mp) cc_final: 0.7350 (mp)
REVERT: B  231 VAL cc_start: 0.8453 (p) cc_final: 0.7928 (p)
REVERT: B  232 LEU cc_start: 0.8370 (tp) cc_final: 0.8116 (tt)
REVERT: B  235 GLN cc_start: 0.7536 (mm-40) cc_final: 0.7169 (mm-40)
REVERT: B  238 ILE cc_start: 0.8276 (tp) cc_final: 0.8035 (mt)
REVERT: B  244 THR cc_start: 0.6562 (t) cc_final: 0.6358 (p)
REVERT: B  251 LEU cc_start: 0.8599 (mm) cc_final: 0.6964 (mm)
REVERT: B  255 TYR cc_start: 0.8066 (m-10) cc_final: 0.7567 (m-80)
REVERT: B  260 ILE cc_start: 0.9166 (mt) cc_final: 0.8938 (tp)
REVERT: B  262 GLN cc_start: 0.7759 (tp-100) cc_final: 0.7242 (tp-100)
REVERT: B  286 LYS cc_start: 0.7972 (ttmm) cc_final: 0.7316 (ttmm)
REVERT: B  293 LYS cc_start: 0.8550 (pptt) cc_final: 0.8230 (pptt)
REVERT: B  309 ILE cc_start: 0.8849 (pt) cc_final: 0.8511 (mm)
REVERT: B  320 GLU cc_start: 0.7648 (tp30) cc_final: 0.7428 (tp30)
REVERT: B  371 TYR cc_start: 0.7105 (m-80) cc_final: 0.6726 (m-80)
REVERT: B  375 HIS cc_start: 0.6369 (t-90) cc_final: 0.6065 (t-90)
REVERT: B  426 ILE cc_start: 0.8357 (tp) cc_final: 0.8116 (pt)
REVERT: B  473 LYS cc_start: 0.7903 (mttp) cc_final: 0.6765 (mttp)
REVERT: B  475 ASN cc_start: 0.7784 (t0) cc_final: 0.7357 (t0)
REVERT: B  483 VAL cc_start: 0.8716 (p) cc_final: 0.8459 (t)
REVERT: B  487 ILE cc_start: 0.8462 (pt) cc_final: 0.8142 (mp)
REVERT: B  488 MET cc_start: 0.6912 (tpp) cc_final: 0.5808 (tpp)
REVERT: B  492 LEU cc_start: 0.8447 (mt) cc_final: 0.7570 (mt)
REVERT: B  515 PHE cc_start: 0.8051 (m-80) cc_final: 0.7396 (m-80)
REVERT: B  580 LYS cc_start: 0.8176 (mmmt) cc_final: 0.7920 (mmmt)
REVERT: B  583 LYS cc_start: 0.8768 (tmmt) cc_final: 0.8374 (tttm)
REVERT: B  677 ARG cc_start: 0.7336 (ttt180) cc_final: 0.7098 (ttp80)
REVERT: B  682 GLU cc_start: 0.7805 (tp30) cc_final: 0.7533 (tp30)
REVERT: B  695 LEU cc_start: 0.5728 (OUTLIER) cc_final: 0.4754 (mp)
REVERT: B  701 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7096 (mm-30)
REVERT: B  705 GLN cc_start: 0.8165 (tt0) cc_final: 0.7898 (tt0)
REVERT: B  706 CYS cc_start: 0.7461 (m) cc_final: 0.6640 (m)
  outliers start: 45
  outliers final: 19
  residues processed: 413
  average time/residue: 0.1180
  time to fit residues: 65.4434
Evaluate side-chains
  332 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 311
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   59 LYS
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  303 GLU
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain B residue   43 ARG
Chi-restraints excluded: chain B residue   79 ARG
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  405 THR
Chi-restraints excluded: chain B residue  688 VAL
Chi-restraints excluded: chain B residue  694 LEU
Chi-restraints excluded: chain B residue  695 LEU
Chi-restraints excluded: chain B residue  713 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 98 optimal weight:    0.0070
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 66 optimal weight:    0.0370
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.5278

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

Flipped N/Q/H residues before XYZ refinement:
A 114 GLN
A 135 HIS
A 246 ASN
A 289 ASN
A 413 GLN
A 514 GLN
A 519 ASN
A 567 ASN
A 730 GLN
A 732 GLN
** B  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 262 GLN
B 289 ASN
B 322 ASN
B 324 ASN
B 383 GLN
B 446 GLN
B 457 ASN
B 474 GLN
** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 514 GLN
B 689 ASN

Total number of N/Q/H flips: 20

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.140622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.121294 restraints weight = 20479.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.125274 restraints weight = 11420.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.127924 restraints weight = 7227.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.129736 restraints weight = 4998.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.130980 restraints weight = 3740.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6942
moved from start:          0.2481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10395  Z= 0.153
  Angle     :  0.614   7.664  14128  Z= 0.319
  Chirality :  0.042   0.213   1716
  Planarity :  0.005   0.043   1757
  Dihedral  :  5.803  79.769   1458
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 13.71 %
    Favored  : 81.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.27 (0.21), residues: 1319
  helix: -0.61 (0.17), residues: 813
  sheet: -2.94 (0.77), residues: 32
  loop : -2.96 (0.26), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  24 
 TYR   0.022   0.001   TYR A 556 
 PHE   0.017   0.001   PHE B 229 
 TRP   0.013   0.001   TRP B  83 
 HIS   0.004   0.001   HIS A 723 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (10395)
  covalent geometry    : angle       0.61373 (14128)
  hydrogen bonds       : bond        0.04614 (  544)
  hydrogen bonds       : angle       4.20509 ( 1593)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  381 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 325
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLN cc_start: 0.7669 (mm-40) cc_final: 0.7233 (mm110)
REVERT: A   36 ARG cc_start: 0.7609 (tpp-160) cc_final: 0.7211 (mmt90)
REVERT: A   93 SER cc_start: 0.8454 (t) cc_final: 0.8066 (p)
REVERT: A  122 PHE cc_start: 0.7274 (m-80) cc_final: 0.6808 (m-10)
REVERT: A  123 PRO cc_start: 0.8350 (Cg_exo) cc_final: 0.8123 (Cg_endo)
REVERT: A  195 LEU cc_start: 0.8475 (tp) cc_final: 0.7888 (tp)
REVERT: A  199 ILE cc_start: 0.8166 (mt) cc_final: 0.7840 (mt)
REVERT: A  231 VAL cc_start: 0.8730 (t) cc_final: 0.8005 (p)
REVERT: A  235 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7650 (mm-40)
REVERT: A  237 LYS cc_start: 0.8457 (ttpp) cc_final: 0.7989 (ttpp)
REVERT: A  247 TYR cc_start: 0.7304 (m-10) cc_final: 0.6221 (m-10)
REVERT: A  272 PHE cc_start: 0.7887 (t80) cc_final: 0.7334 (t80)
REVERT: A  280 ILE cc_start: 0.8931 (mt) cc_final: 0.8702 (tp)
REVERT: A  286 LYS cc_start: 0.9163 (tppt) cc_final: 0.8770 (mmmm)
REVERT: A  355 SER cc_start: 0.7863 (m) cc_final: 0.7558 (p)
REVERT: A  384 GLU cc_start: 0.6707 (mm-30) cc_final: 0.5949 (mm-30)
REVERT: A  395 SER cc_start: 0.8566 (m) cc_final: 0.8236 (p)
REVERT: A  398 PHE cc_start: 0.7090 (m-80) cc_final: 0.6416 (m-10)
REVERT: A  432 MET cc_start: 0.7302 (tpt) cc_final: 0.6662 (tpt)
REVERT: A  473 LYS cc_start: 0.8345 (mtpt) cc_final: 0.7884 (mtpt)
REVERT: A  484 PHE cc_start: 0.8278 (t80) cc_final: 0.7888 (t80)
REVERT: A  488 MET cc_start: 0.7427 (tpp) cc_final: 0.6992 (tpp)
REVERT: A  512 ARG cc_start: 0.8580 (mtm-85) cc_final: 0.8334 (mtm-85)
REVERT: A  530 TYR cc_start: 0.7162 (m-80) cc_final: 0.6926 (m-80)
REVERT: A  546 LYS cc_start: 0.8281 (tptm) cc_final: 0.7775 (tptm)
REVERT: A  549 ARG cc_start: 0.6972 (ttt90) cc_final: 0.6736 (ttm-80)
REVERT: A  556 TYR cc_start: 0.8124 (p90) cc_final: 0.7692 (p90)
REVERT: A  560 ASP cc_start: 0.8177 (m-30) cc_final: 0.7845 (t0)
REVERT: A  563 LYS cc_start: 0.8217 (mmmt) cc_final: 0.7945 (ttmm)
REVERT: A  662 CYS cc_start: 0.7958 (m) cc_final: 0.7522 (m)
REVERT: A  686 ILE cc_start: 0.8595 (pt) cc_final: 0.8357 (mm)
REVERT: A  687 ASP cc_start: 0.6696 (t0) cc_final: 0.6254 (t0)
REVERT: A  723 HIS cc_start: 0.7134 (t-170) cc_final: 0.6886 (t-90)
REVERT: B  118 TYR cc_start: 0.7142 (m-10) cc_final: 0.6778 (m-80)
REVERT: B  199 ILE cc_start: 0.7807 (OUTLIER) cc_final: 0.7492 (mp)
REVERT: B  207 GLN cc_start: 0.7624 (tm-30) cc_final: 0.7171 (tm-30)
REVERT: B  230 GLN cc_start: 0.7957 (tp40) cc_final: 0.7386 (tm-30)
REVERT: B  231 VAL cc_start: 0.8665 (p) cc_final: 0.7895 (p)
REVERT: B  235 GLN cc_start: 0.7634 (mm-40) cc_final: 0.7256 (mm-40)
REVERT: B  236 LEU cc_start: 0.8097 (tp) cc_final: 0.7727 (tp)
REVERT: B  237 LYS cc_start: 0.8201 (pttt) cc_final: 0.7689 (pmtt)
REVERT: B  251 LEU cc_start: 0.8318 (mm) cc_final: 0.6441 (mm)
REVERT: B  255 TYR cc_start: 0.8241 (m-10) cc_final: 0.7680 (m-80)
REVERT: B  259 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7687 (tm-30)
REVERT: B  263 ASN cc_start: 0.7331 (t0) cc_final: 0.7003 (t0)
REVERT: B  271 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7535 (p0)
REVERT: B  286 LYS cc_start: 0.8144 (ttmm) cc_final: 0.7909 (ttmm)
REVERT: B  293 LYS cc_start: 0.8563 (pptt) cc_final: 0.8265 (tppt)
REVERT: B  309 ILE cc_start: 0.8846 (pt) cc_final: 0.8630 (mm)
REVERT: B  320 GLU cc_start: 0.7600 (tp30) cc_final: 0.7253 (tp30)
REVERT: B  359 VAL cc_start: 0.7805 (p) cc_final: 0.7528 (m)
REVERT: B  395 SER cc_start: 0.7525 (m) cc_final: 0.6991 (p)
REVERT: B  473 LYS cc_start: 0.7856 (mttp) cc_final: 0.7542 (mttp)
REVERT: B  487 ILE cc_start: 0.8593 (pt) cc_final: 0.8168 (mp)
REVERT: B  488 MET cc_start: 0.7152 (tpp) cc_final: 0.5960 (tpp)
REVERT: B  492 LEU cc_start: 0.8528 (mt) cc_final: 0.7724 (mt)
REVERT: B  499 LEU cc_start: 0.8253 (tp) cc_final: 0.7995 (tp)
REVERT: B  560 ASP cc_start: 0.7972 (p0) cc_final: 0.7683 (p0)
REVERT: B  583 LYS cc_start: 0.8768 (tmmt) cc_final: 0.8441 (tttm)
REVERT: B  669 ASP cc_start: 0.7284 (p0) cc_final: 0.7046 (p0)
REVERT: B  677 ARG cc_start: 0.7571 (ttt180) cc_final: 0.7078 (ttp80)
REVERT: B  686 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8115 (mt)
REVERT: B  701 GLU cc_start: 0.7173 (mm-30) cc_final: 0.6941 (mm-30)
REVERT: B  702 LYS cc_start: 0.7134 (tttm) cc_final: 0.6582 (tptm)
REVERT: B  705 GLN cc_start: 0.8316 (tt0) cc_final: 0.8072 (tt0)
REVERT: B  706 CYS cc_start: 0.7370 (m) cc_final: 0.6380 (m)
  outliers start: 56
  outliers final: 32
  residues processed: 359
  average time/residue: 0.1092
  time to fit residues: 53.7790
Evaluate side-chains
  324 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 289
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   59 LYS
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  182 ASP
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  303 GLU
Chi-restraints excluded: chain A residue  349 MET
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain A residue  461 MET
Chi-restraints excluded: chain A residue  463 MET
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  701 GLU
Chi-restraints excluded: chain B residue   79 ARG
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  199 ILE
Chi-restraints excluded: chain B residue  271 ASP
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  405 THR
Chi-restraints excluded: chain B residue  590 LYS
Chi-restraints excluded: chain B residue  686 ILE
Chi-restraints excluded: chain B residue  688 VAL
Chi-restraints excluded: chain B residue  694 LEU
Chi-restraints excluded: chain B residue  713 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 34 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 81 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 128 optimal weight:    0.9980
   chunk 96 optimal weight:    0.0670
   chunk 42 optimal weight:    0.5980
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
A 114 GLN
A 289 ASN
A 514 GLN
A 519 ASN
A 567 ASN
A 728 HIS
A 732 GLN
B 324 ASN
B 475 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.137394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.118482 restraints weight = 20675.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.122311 restraints weight = 11614.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.124937 restraints weight = 7339.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.126675 restraints weight = 5063.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.127878 restraints weight = 3781.745|
|-----------------------------------------------------------------------------|
r_work (final): 0.3908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6991
moved from start:          0.3223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10395  Z= 0.150
  Angle     :  0.619   8.562  14128  Z= 0.320
  Chirality :  0.043   0.162   1716
  Planarity :  0.004   0.052   1757
  Dihedral  :  5.633  79.900   1448
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 16.83 %
    Favored  : 78.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.64 (0.23), residues: 1319
  helix: -0.08 (0.18), residues: 801
  sheet: -2.49 (0.86), residues: 32
  loop : -2.69 (0.27), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  24 
 TYR   0.018   0.001   TYR A 556 
 PHE   0.016   0.001   PHE B 555 
 TRP   0.011   0.001   TRP B  83 
 HIS   0.005   0.001   HIS A 728 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (10395)
  covalent geometry    : angle       0.61888 (14128)
  hydrogen bonds       : bond        0.04198 (  544)
  hydrogen bonds       : angle       4.09528 ( 1593)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  365 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 311
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 ARG cc_start: 0.7692 (tpp-160) cc_final: 0.7381 (mmt90)
REVERT: A   37 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6499 (pm20)
REVERT: A   39 ARG cc_start: 0.7540 (ttm-80) cc_final: 0.7322 (ttm-80)
REVERT: A   93 SER cc_start: 0.8465 (t) cc_final: 0.8116 (p)
REVERT: A  122 PHE cc_start: 0.7260 (m-80) cc_final: 0.6782 (m-10)
REVERT: A  123 PRO cc_start: 0.8297 (Cg_exo) cc_final: 0.8052 (Cg_endo)
REVERT: A  195 LEU cc_start: 0.8443 (tp) cc_final: 0.7857 (tp)
REVERT: A  199 ILE cc_start: 0.8169 (mt) cc_final: 0.7838 (mt)
REVERT: A  213 ARG cc_start: 0.7606 (mtm180) cc_final: 0.7319 (mtm-85)
REVERT: A  231 VAL cc_start: 0.8744 (t) cc_final: 0.8134 (p)
REVERT: A  235 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7748 (mm-40)
REVERT: A  237 LYS cc_start: 0.8383 (ttpp) cc_final: 0.7976 (ttpp)
REVERT: A  280 ILE cc_start: 0.8946 (mt) cc_final: 0.8697 (tp)
REVERT: A  286 LYS cc_start: 0.9191 (tppt) cc_final: 0.8832 (mmmm)
REVERT: A  355 SER cc_start: 0.7871 (m) cc_final: 0.7566 (p)
REVERT: A  384 GLU cc_start: 0.6635 (mm-30) cc_final: 0.5814 (mm-30)
REVERT: A  395 SER cc_start: 0.8594 (m) cc_final: 0.8035 (p)
REVERT: A  398 PHE cc_start: 0.7120 (m-80) cc_final: 0.6443 (m-10)
REVERT: A  409 ARG cc_start: 0.7776 (ttp-170) cc_final: 0.7435 (ttp-110)
REVERT: A  432 MET cc_start: 0.7352 (tpt) cc_final: 0.6962 (tpt)
REVERT: A  447 LYS cc_start: 0.8501 (mtpt) cc_final: 0.7991 (mttp)
REVERT: A  473 LYS cc_start: 0.8380 (mtpt) cc_final: 0.7964 (mtpt)
REVERT: A  476 LYS cc_start: 0.8717 (mtpt) cc_final: 0.8450 (mtpp)
REVERT: A  478 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7705 (t0)
REVERT: A  484 PHE cc_start: 0.8285 (t80) cc_final: 0.7917 (t80)
REVERT: A  488 MET cc_start: 0.7542 (tpp) cc_final: 0.7086 (tpp)
REVERT: A  498 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7814 (tp)
REVERT: A  511 LEU cc_start: 0.8761 (mt) cc_final: 0.8550 (mt)
REVERT: A  530 TYR cc_start: 0.7302 (m-80) cc_final: 0.7078 (m-80)
REVERT: A  546 LYS cc_start: 0.8251 (tptm) cc_final: 0.7727 (tptm)
REVERT: A  556 TYR cc_start: 0.8157 (p90) cc_final: 0.7829 (p90)
REVERT: A  560 ASP cc_start: 0.8137 (m-30) cc_final: 0.7809 (t0)
REVERT: A  563 LYS cc_start: 0.8380 (mmmt) cc_final: 0.8061 (ttmm)
REVERT: A  662 CYS cc_start: 0.7987 (m) cc_final: 0.7617 (m)
REVERT: A  686 ILE cc_start: 0.8638 (pt) cc_final: 0.8392 (mm)
REVERT: A  687 ASP cc_start: 0.6769 (t0) cc_final: 0.6319 (t0)
REVERT: A  715 LYS cc_start: 0.7597 (mtpp) cc_final: 0.7120 (mmmm)
REVERT: B   29 GLU cc_start: 0.6794 (mp0) cc_final: 0.6259 (mp0)
REVERT: B  103 MET cc_start: 0.6149 (mmt) cc_final: 0.5892 (mmt)
REVERT: B  118 TYR cc_start: 0.7154 (m-10) cc_final: 0.6895 (m-80)
REVERT: B  199 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7576 (mp)
REVERT: B  207 GLN cc_start: 0.7930 (tm-30) cc_final: 0.7339 (tm-30)
REVERT: B  230 GLN cc_start: 0.7960 (tp40) cc_final: 0.7351 (tm-30)
REVERT: B  231 VAL cc_start: 0.8644 (p) cc_final: 0.7859 (p)
REVERT: B  235 GLN cc_start: 0.7657 (mm-40) cc_final: 0.7248 (mm-40)
REVERT: B  236 LEU cc_start: 0.8106 (tp) cc_final: 0.7734 (tp)
REVERT: B  251 LEU cc_start: 0.8402 (mm) cc_final: 0.6555 (mm)
REVERT: B  255 TYR cc_start: 0.8259 (m-10) cc_final: 0.7684 (m-80)
REVERT: B  259 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7969 (tm-30)
REVERT: B  263 ASN cc_start: 0.7376 (t0) cc_final: 0.7023 (t0)
REVERT: B  286 LYS cc_start: 0.8231 (ttmm) cc_final: 0.8007 (ttmm)
REVERT: B  293 LYS cc_start: 0.8574 (pptt) cc_final: 0.8273 (pptt)
REVERT: B  309 ILE cc_start: 0.8862 (pt) cc_final: 0.8653 (mm)
REVERT: B  320 GLU cc_start: 0.7654 (tp30) cc_final: 0.7327 (tp30)
REVERT: B  395 SER cc_start: 0.7596 (m) cc_final: 0.7055 (p)
REVERT: B  475 ASN cc_start: 0.7901 (t0) cc_final: 0.7522 (t0)
REVERT: B  476 LYS cc_start: 0.8727 (mmmm) cc_final: 0.8516 (mmmm)
REVERT: B  487 ILE cc_start: 0.8573 (pt) cc_final: 0.8351 (mt)
REVERT: B  488 MET cc_start: 0.7175 (tpp) cc_final: 0.5880 (tpp)
REVERT: B  492 LEU cc_start: 0.8596 (mt) cc_final: 0.7718 (mt)
REVERT: B  499 LEU cc_start: 0.8263 (tp) cc_final: 0.8023 (tp)
REVERT: B  502 LEU cc_start: 0.7894 (tp) cc_final: 0.7560 (mt)
REVERT: B  503 LEU cc_start: 0.8132 (mm) cc_final: 0.7796 (mp)
REVERT: B  537 LYS cc_start: 0.6573 (mmmt) cc_final: 0.6368 (mmmt)
REVERT: B  677 ARG cc_start: 0.7560 (ttt180) cc_final: 0.7113 (ttp80)
REVERT: B  686 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8182 (mt)
REVERT: B  702 LYS cc_start: 0.7129 (tttm) cc_final: 0.6475 (tptp)
REVERT: B  705 GLN cc_start: 0.8367 (tt0) cc_final: 0.8126 (tt0)
REVERT: B  706 CYS cc_start: 0.7251 (m) cc_final: 0.6065 (m)
  outliers start: 54
  outliers final: 33
  residues processed: 341
  average time/residue: 0.1100
  time to fit residues: 50.9797
Evaluate side-chains
  336 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 298
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   59 LYS
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  182 ASP
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  303 GLU
Chi-restraints excluded: chain A residue  349 MET
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  461 MET
Chi-restraints excluded: chain A residue  463 MET
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  478 ASP
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  498 LEU
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  704 GLU
Chi-restraints excluded: chain A residue  728 HIS
Chi-restraints excluded: chain B residue   79 ARG
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  199 ILE
Chi-restraints excluded: chain B residue  271 ASP
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  405 THR
Chi-restraints excluded: chain B residue  590 LYS
Chi-restraints excluded: chain B residue  681 LYS
Chi-restraints excluded: chain B residue  686 ILE
Chi-restraints excluded: chain B residue  688 VAL
Chi-restraints excluded: chain B residue  694 LEU
Chi-restraints excluded: chain B residue  713 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   chunk 115 optimal weight:    0.7980
   chunk 61 optimal weight:    0.5980
   chunk 70 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 85 optimal weight:    1.9990
   chunk 91 optimal weight:    0.3980
   chunk 77 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 84 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 246 ASN
A 519 ASN
A 728 HIS
B 324 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.135575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.116556 restraints weight = 20621.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.120469 restraints weight = 11544.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.123011 restraints weight = 7260.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.124770 restraints weight = 5026.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.125861 restraints weight = 3758.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.3875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7043
moved from start:          0.3713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10395  Z= 0.168
  Angle     :  0.619   8.647  14128  Z= 0.325
  Chirality :  0.043   0.215   1716
  Planarity :  0.004   0.055   1757
  Dihedral  :  5.711  82.799   1447
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 13.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 19.06 %
    Favored  : 75.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.43 (0.23), residues: 1319
  helix:  0.06 (0.18), residues: 822
  sheet: -2.30 (0.91), residues: 32
  loop : -2.70 (0.28), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  24 
 TYR   0.024   0.002   TYR A 105 
 PHE   0.014   0.001   PHE A 385 
 TRP   0.012   0.001   TRP B  83 
 HIS   0.013   0.001   HIS A 728 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (10395)
  covalent geometry    : angle       0.61892 (14128)
  hydrogen bonds       : bond        0.03936 (  544)
  hydrogen bonds       : angle       4.06889 ( 1593)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  364 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 307
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 ARG cc_start: 0.7812 (tpp-160) cc_final: 0.7526 (mmt90)
REVERT: A   37 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6420 (pm20)
REVERT: A   93 SER cc_start: 0.8463 (t) cc_final: 0.8093 (p)
REVERT: A  122 PHE cc_start: 0.7252 (m-80) cc_final: 0.6795 (m-10)
REVERT: A  123 PRO cc_start: 0.8297 (Cg_exo) cc_final: 0.8035 (Cg_endo)
REVERT: A  195 LEU cc_start: 0.8475 (tp) cc_final: 0.7917 (tp)
REVERT: A  199 ILE cc_start: 0.8183 (mt) cc_final: 0.7868 (mt)
REVERT: A  231 VAL cc_start: 0.8773 (t) cc_final: 0.8149 (p)
REVERT: A  235 GLN cc_start: 0.8157 (mm-40) cc_final: 0.7767 (mm-40)
REVERT: A  237 LYS cc_start: 0.8388 (ttpp) cc_final: 0.8013 (ttpp)
REVERT: A  279 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8728 (mm)
REVERT: A  280 ILE cc_start: 0.8972 (mt) cc_final: 0.8745 (tp)
REVERT: A  283 MET cc_start: 0.8052 (tpp) cc_final: 0.7814 (mpp)
REVERT: A  286 LYS cc_start: 0.9188 (tppt) cc_final: 0.8835 (mmmm)
REVERT: A  384 GLU cc_start: 0.6774 (mm-30) cc_final: 0.5925 (mm-30)
REVERT: A  395 SER cc_start: 0.8407 (m) cc_final: 0.8054 (p)
REVERT: A  398 PHE cc_start: 0.7073 (m-80) cc_final: 0.6490 (m-80)
REVERT: A  409 ARG cc_start: 0.7834 (ttp-170) cc_final: 0.7582 (ttp-170)
REVERT: A  432 MET cc_start: 0.7389 (tpt) cc_final: 0.7050 (tpt)
REVERT: A  447 LYS cc_start: 0.8477 (mtpt) cc_final: 0.7951 (mttp)
REVERT: A  457 ASN cc_start: 0.8108 (m110) cc_final: 0.7589 (m110)
REVERT: A  473 LYS cc_start: 0.8414 (mtpt) cc_final: 0.7986 (mtpt)
REVERT: A  476 LYS cc_start: 0.8690 (mtpt) cc_final: 0.8358 (mtpp)
REVERT: A  478 ASP cc_start: 0.8255 (t0) cc_final: 0.7846 (t0)
REVERT: A  484 PHE cc_start: 0.8278 (t80) cc_final: 0.7944 (t80)
REVERT: A  488 MET cc_start: 0.7601 (tpp) cc_final: 0.7136 (tpp)
REVERT: A  512 ARG cc_start: 0.8482 (mtm180) cc_final: 0.7441 (mtm180)
REVERT: A  546 LYS cc_start: 0.8268 (tptm) cc_final: 0.7740 (tptm)
REVERT: A  556 TYR cc_start: 0.8262 (p90) cc_final: 0.8035 (p90)
REVERT: A  563 LYS cc_start: 0.8568 (mmmt) cc_final: 0.8314 (ttmm)
REVERT: A  662 CYS cc_start: 0.8026 (m) cc_final: 0.7670 (m)
REVERT: A  679 ILE cc_start: 0.8614 (mt) cc_final: 0.8348 (mt)
REVERT: A  686 ILE cc_start: 0.8680 (pt) cc_final: 0.7838 (mm)
REVERT: A  710 ASP cc_start: 0.7264 (p0) cc_final: 0.6969 (p0)
REVERT: A  715 LYS cc_start: 0.7771 (mtpp) cc_final: 0.7188 (mmmm)
REVERT: B  103 MET cc_start: 0.5775 (mmt) cc_final: 0.5530 (mmp)
REVERT: B  118 TYR cc_start: 0.7209 (m-10) cc_final: 0.6968 (m-80)
REVERT: B  134 ARG cc_start: 0.6380 (mtt90) cc_final: 0.6100 (mtt90)
REVERT: B  158 ASP cc_start: 0.5270 (m-30) cc_final: 0.5036 (m-30)
REVERT: B  199 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7623 (mp)
REVERT: B  207 GLN cc_start: 0.8092 (tm-30) cc_final: 0.7463 (tm-30)
REVERT: B  230 GLN cc_start: 0.7891 (tp40) cc_final: 0.7295 (tm-30)
REVERT: B  231 VAL cc_start: 0.8651 (p) cc_final: 0.7880 (p)
REVERT: B  235 GLN cc_start: 0.7731 (mm-40) cc_final: 0.7331 (mm-40)
REVERT: B  236 LEU cc_start: 0.8067 (tp) cc_final: 0.7684 (tp)
REVERT: B  237 LYS cc_start: 0.8237 (pttt) cc_final: 0.7805 (pttt)
REVERT: B  251 LEU cc_start: 0.8464 (mm) cc_final: 0.6698 (mm)
REVERT: B  255 TYR cc_start: 0.8251 (m-10) cc_final: 0.7668 (m-80)
REVERT: B  259 GLU cc_start: 0.8349 (tm-30) cc_final: 0.7928 (tm-30)
REVERT: B  263 ASN cc_start: 0.7440 (t0) cc_final: 0.6960 (t0)
REVERT: B  286 LYS cc_start: 0.8227 (ttmm) cc_final: 0.8001 (ttmm)
REVERT: B  293 LYS cc_start: 0.8599 (pptt) cc_final: 0.8328 (pptt)
REVERT: B  320 GLU cc_start: 0.7693 (tp30) cc_final: 0.7356 (tp30)
REVERT: B  324 ASN cc_start: 0.7758 (t0) cc_final: 0.7425 (t0)
REVERT: B  395 SER cc_start: 0.7762 (m) cc_final: 0.7241 (p)
REVERT: B  487 ILE cc_start: 0.8547 (pt) cc_final: 0.8338 (mt)
REVERT: B  488 MET cc_start: 0.7171 (tpp) cc_final: 0.5854 (tpp)
REVERT: B  492 LEU cc_start: 0.8653 (mt) cc_final: 0.7758 (mt)
REVERT: B  499 LEU cc_start: 0.8281 (tp) cc_final: 0.7967 (tp)
REVERT: B  502 LEU cc_start: 0.7945 (tp) cc_final: 0.7500 (tp)
REVERT: B  537 LYS cc_start: 0.7033 (mmmt) cc_final: 0.6393 (tptp)
REVERT: B  677 ARG cc_start: 0.7567 (ttt180) cc_final: 0.7112 (ttp80)
REVERT: B  686 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8243 (mt)
REVERT: B  687 ASP cc_start: 0.6798 (t0) cc_final: 0.6428 (t0)
REVERT: B  705 GLN cc_start: 0.8363 (tt0) cc_final: 0.8068 (tt0)
REVERT: B  706 CYS cc_start: 0.7356 (m) cc_final: 0.6525 (m)
  outliers start: 57
  outliers final: 41
  residues processed: 336
  average time/residue: 0.1167
  time to fit residues: 53.2585
Evaluate side-chains
  343 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 298
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   59 LYS
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  182 ASP
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  230 GLN
Chi-restraints excluded: chain A residue  246 ASN
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  303 GLU
Chi-restraints excluded: chain A residue  349 MET
Chi-restraints excluded: chain A residue  400 CYS
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  461 MET
Chi-restraints excluded: chain A residue  463 MET
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  678 MET
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  704 GLU
Chi-restraints excluded: chain A residue  728 HIS
Chi-restraints excluded: chain B residue   79 ARG
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  199 ILE
Chi-restraints excluded: chain B residue  271 ASP
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  405 THR
Chi-restraints excluded: chain B residue  590 LYS
Chi-restraints excluded: chain B residue  666 SER
Chi-restraints excluded: chain B residue  681 LYS
Chi-restraints excluded: chain B residue  686 ILE
Chi-restraints excluded: chain B residue  688 VAL
Chi-restraints excluded: chain B residue  694 LEU
Chi-restraints excluded: chain B residue  713 ILE
Chi-restraints excluded: chain B residue  721 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 126 optimal weight:    0.5980
   chunk 44 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 100 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9980
   chunk 102 optimal weight:    0.0270
   chunk 128 optimal weight:    0.8980
   chunk 56 optimal weight:    9.9990
   chunk 55 optimal weight:    0.9980
   chunk 76 optimal weight:    1.9990
   overall best weight:    0.7038

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

Flipped N/Q/H residues before XYZ refinement:
A 207 GLN
A 289 ASN
** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 475 ASN
** B 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.133672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.114556 restraints weight = 20646.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.118257 restraints weight = 11665.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.120856 restraints weight = 7454.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.122651 restraints weight = 5167.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.123866 restraints weight = 3855.110|
|-----------------------------------------------------------------------------|
r_work (final): 0.3860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7063
moved from start:          0.4062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10395  Z= 0.172
  Angle     :  0.635   8.383  14128  Z= 0.333
  Chirality :  0.044   0.194   1716
  Planarity :  0.004   0.050   1757
  Dihedral  :  5.829  84.194   1447
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 14.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 20.30 %
    Favored  : 74.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.38 (0.23), residues: 1319
  helix:  0.07 (0.18), residues: 827
  sheet: -2.17 (0.93), residues: 32
  loop : -2.65 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  24 
 TYR   0.023   0.002   TYR A 105 
 PHE   0.024   0.001   PHE A 130 
 TRP   0.012   0.001   TRP B  83 
 HIS   0.005   0.001   HIS A 728 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 (10395)
  covalent geometry    : angle       0.63516 (14128)
  hydrogen bonds       : bond        0.03947 (  544)
  hydrogen bonds       : angle       4.09773 ( 1593)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  354 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 296
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 ARG cc_start: 0.7884 (tpp-160) cc_final: 0.7603 (mmt90)
REVERT: A   37 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6501 (pm20)
REVERT: A   93 SER cc_start: 0.8461 (t) cc_final: 0.8097 (p)
REVERT: A  122 PHE cc_start: 0.7210 (m-80) cc_final: 0.6760 (m-10)
REVERT: A  123 PRO cc_start: 0.8330 (Cg_exo) cc_final: 0.8052 (Cg_endo)
REVERT: A  195 LEU cc_start: 0.8516 (tp) cc_final: 0.8015 (tp)
REVERT: A  199 ILE cc_start: 0.8203 (mt) cc_final: 0.7874 (mt)
REVERT: A  229 PHE cc_start: 0.8380 (t80) cc_final: 0.8160 (m-80)
REVERT: A  231 VAL cc_start: 0.8794 (t) cc_final: 0.8165 (p)
REVERT: A  234 SER cc_start: 0.8801 (m) cc_final: 0.8359 (t)
REVERT: A  235 GLN cc_start: 0.8105 (mm-40) cc_final: 0.7720 (mm-40)
REVERT: A  237 LYS cc_start: 0.8404 (ttpp) cc_final: 0.8101 (ttpp)
REVERT: A  279 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8701 (mm)
REVERT: A  280 ILE cc_start: 0.8938 (mt) cc_final: 0.8734 (tp)
REVERT: A  283 MET cc_start: 0.7837 (tpp) cc_final: 0.7632 (mpp)
REVERT: A  286 LYS cc_start: 0.9191 (tppt) cc_final: 0.8819 (mmmm)
REVERT: A  307 THR cc_start: 0.8442 (m) cc_final: 0.8142 (p)
REVERT: A  395 SER cc_start: 0.8433 (m) cc_final: 0.8087 (p)
REVERT: A  398 PHE cc_start: 0.7044 (m-80) cc_final: 0.6507 (m-80)
REVERT: A  409 ARG cc_start: 0.7847 (ttp-170) cc_final: 0.7573 (ttp-170)
REVERT: A  447 LYS cc_start: 0.8421 (mtpt) cc_final: 0.7940 (mttp)
REVERT: A  473 LYS cc_start: 0.8427 (mtpt) cc_final: 0.8007 (mtpt)
REVERT: A  484 PHE cc_start: 0.8239 (t80) cc_final: 0.7913 (t80)
REVERT: A  488 MET cc_start: 0.7556 (tpp) cc_final: 0.7108 (tpp)
REVERT: A  511 LEU cc_start: 0.8870 (mt) cc_final: 0.8660 (mt)
REVERT: A  512 ARG cc_start: 0.8494 (mtm180) cc_final: 0.7340 (mtm180)
REVERT: A  546 LYS cc_start: 0.8249 (tptm) cc_final: 0.7729 (tptm)
REVERT: A  563 LYS cc_start: 0.8563 (mmmt) cc_final: 0.8305 (ttmm)
REVERT: A  662 CYS cc_start: 0.7885 (m) cc_final: 0.7543 (m)
REVERT: A  679 ILE cc_start: 0.8606 (mt) cc_final: 0.8227 (mt)
REVERT: A  686 ILE cc_start: 0.8248 (pt) cc_final: 0.8005 (mm)
REVERT: A  715 LYS cc_start: 0.7887 (mtpp) cc_final: 0.7255 (mmmm)
REVERT: A  716 ASP cc_start: 0.7178 (t0) cc_final: 0.6828 (t0)
REVERT: B  103 MET cc_start: 0.5753 (mmt) cc_final: 0.5528 (mmp)
REVERT: B  118 TYR cc_start: 0.7203 (m-10) cc_final: 0.6969 (m-80)
REVERT: B  134 ARG cc_start: 0.6369 (mtt90) cc_final: 0.6101 (mtt90)
REVERT: B  158 ASP cc_start: 0.5285 (m-30) cc_final: 0.3720 (m-30)
REVERT: B  185 ARG cc_start: 0.6945 (mmt180) cc_final: 0.5732 (mmt180)
REVERT: B  199 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7652 (mp)
REVERT: B  207 GLN cc_start: 0.8138 (tm-30) cc_final: 0.7524 (tm-30)
REVERT: B  230 GLN cc_start: 0.7865 (tp40) cc_final: 0.7260 (tm-30)
REVERT: B  231 VAL cc_start: 0.8650 (p) cc_final: 0.7859 (p)
REVERT: B  235 GLN cc_start: 0.7692 (mm-40) cc_final: 0.7300 (mm-40)
REVERT: B  236 LEU cc_start: 0.8103 (tp) cc_final: 0.7714 (tp)
REVERT: B  237 LYS cc_start: 0.8233 (pttt) cc_final: 0.7722 (pttp)
REVERT: B  251 LEU cc_start: 0.8459 (mm) cc_final: 0.6618 (mm)
REVERT: B  255 TYR cc_start: 0.8212 (m-10) cc_final: 0.7685 (m-80)
REVERT: B  259 GLU cc_start: 0.8324 (tm-30) cc_final: 0.8063 (tm-30)
REVERT: B  263 ASN cc_start: 0.7385 (t0) cc_final: 0.6927 (t0)
REVERT: B  271 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7373 (p0)
REVERT: B  320 GLU cc_start: 0.7678 (tp30) cc_final: 0.7390 (tp30)
REVERT: B  395 SER cc_start: 0.7842 (m) cc_final: 0.7320 (p)
REVERT: B  473 LYS cc_start: 0.8069 (mttt) cc_final: 0.7370 (mtpp)
REVERT: B  475 ASN cc_start: 0.7902 (t0) cc_final: 0.7514 (t0)
REVERT: B  487 ILE cc_start: 0.8630 (pt) cc_final: 0.8402 (mt)
REVERT: B  488 MET cc_start: 0.7125 (tpp) cc_final: 0.5799 (tpp)
REVERT: B  492 LEU cc_start: 0.8657 (mt) cc_final: 0.7734 (mt)
REVERT: B  499 LEU cc_start: 0.8286 (tp) cc_final: 0.7976 (tp)
REVERT: B  526 SER cc_start: 0.8442 (m) cc_final: 0.8193 (p)
REVERT: B  677 ARG cc_start: 0.7509 (ttt180) cc_final: 0.7091 (ttp80)
REVERT: B  682 GLU cc_start: 0.7949 (tp30) cc_final: 0.7365 (tp30)
REVERT: B  685 ARG cc_start: 0.7990 (ptm160) cc_final: 0.7667 (ptp90)
REVERT: B  687 ASP cc_start: 0.6735 (t0) cc_final: 0.6327 (t0)
REVERT: B  705 GLN cc_start: 0.8419 (tt0) cc_final: 0.8115 (tt0)
REVERT: B  720 LEU cc_start: 0.8522 (mp) cc_final: 0.8269 (mp)
REVERT: B  724 ASP cc_start: 0.7084 (m-30) cc_final: 0.6722 (m-30)
  outliers start: 58
  outliers final: 38
  residues processed: 325
  average time/residue: 0.1095
  time to fit residues: 49.0458
Evaluate side-chains
  328 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 286
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   59 LYS
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  182 ASP
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  207 GLN
Chi-restraints excluded: chain A residue  230 GLN
Chi-restraints excluded: chain A residue  245 LYS
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  303 GLU
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  461 MET
Chi-restraints excluded: chain A residue  463 MET
Chi-restraints excluded: chain A residue  478 ASP
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  704 GLU
Chi-restraints excluded: chain A residue  728 HIS
Chi-restraints excluded: chain B residue   79 ARG
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  199 ILE
Chi-restraints excluded: chain B residue  244 THR
Chi-restraints excluded: chain B residue  271 ASP
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  405 THR
Chi-restraints excluded: chain B residue  688 VAL
Chi-restraints excluded: chain B residue  694 LEU
Chi-restraints excluded: chain B residue  703 MET
Chi-restraints excluded: chain B residue  713 ILE
Chi-restraints excluded: chain B residue  721 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 19 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   chunk 57 optimal weight:    0.0020
   chunk 44 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9990
   chunk 95 optimal weight:    0.7980
   chunk 17 optimal weight:    0.6980
   chunk 110 optimal weight:    0.8980
   chunk 131 optimal weight:    0.7980
   overall best weight:    0.6188

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

Flipped N/Q/H residues before XYZ refinement:
A 207 GLN
** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 728 HIS
B 324 ASN
** B 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.133224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.114269 restraints weight = 20746.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.117988 restraints weight = 11672.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.120572 restraints weight = 7448.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.122387 restraints weight = 5149.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.123504 restraints weight = 3824.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.3846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7076
moved from start:          0.4336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10395  Z= 0.160
  Angle     :  0.656  16.624  14128  Z= 0.335
  Chirality :  0.044   0.280   1716
  Planarity :  0.004   0.062   1757
  Dihedral  :  5.887  85.663   1447
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 14.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.75 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 20.84 %
    Favored  : 73.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.20 (0.23), residues: 1319
  helix:  0.22 (0.18), residues: 823
  sheet: -2.58 (0.98), residues: 28
  loop : -2.52 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  39 
 TYR   0.031   0.002   TYR A 556 
 PHE   0.025   0.001   PHE A 130 
 TRP   0.012   0.001   TRP B  83 
 HIS   0.005   0.001   HIS A 728 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (10395)
  covalent geometry    : angle       0.65590 (14128)
  hydrogen bonds       : bond        0.03837 (  544)
  hydrogen bonds       : angle       4.06308 ( 1593)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  355 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 295
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 ARG cc_start: 0.7904 (tpp-160) cc_final: 0.7610 (mmt90)
REVERT: A   37 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6488 (pm20)
REVERT: A  122 PHE cc_start: 0.7167 (m-80) cc_final: 0.6681 (m-10)
REVERT: A  123 PRO cc_start: 0.8260 (Cg_exo) cc_final: 0.8010 (Cg_endo)
REVERT: A  195 LEU cc_start: 0.8521 (tp) cc_final: 0.8019 (tp)
REVERT: A  199 ILE cc_start: 0.8198 (mt) cc_final: 0.7845 (mt)
REVERT: A  213 ARG cc_start: 0.7682 (mtm180) cc_final: 0.7385 (mtm-85)
REVERT: A  231 VAL cc_start: 0.8811 (t) cc_final: 0.8138 (p)
REVERT: A  234 SER cc_start: 0.8777 (m) cc_final: 0.8293 (t)
REVERT: A  235 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7738 (mm-40)
REVERT: A  237 LYS cc_start: 0.8449 (ttpp) cc_final: 0.8148 (ttpp)
REVERT: A  279 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8696 (mm)
REVERT: A  283 MET cc_start: 0.7865 (tpp) cc_final: 0.7620 (mpp)
REVERT: A  286 LYS cc_start: 0.9199 (tppt) cc_final: 0.8842 (mmmm)
REVERT: A  335 PHE cc_start: 0.7151 (OUTLIER) cc_final: 0.6877 (t80)
REVERT: A  395 SER cc_start: 0.8417 (m) cc_final: 0.8054 (p)
REVERT: A  398 PHE cc_start: 0.7013 (m-80) cc_final: 0.6463 (m-80)
REVERT: A  409 ARG cc_start: 0.7827 (ttp-170) cc_final: 0.7536 (ttp-170)
REVERT: A  447 LYS cc_start: 0.8431 (mtpt) cc_final: 0.7925 (mttp)
REVERT: A  457 ASN cc_start: 0.8159 (m110) cc_final: 0.7722 (m-40)
REVERT: A  473 LYS cc_start: 0.8457 (mtpt) cc_final: 0.8051 (mtpt)
REVERT: A  476 LYS cc_start: 0.8621 (mtpp) cc_final: 0.8415 (mmmt)
REVERT: A  478 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7759 (t0)
REVERT: A  484 PHE cc_start: 0.8242 (t80) cc_final: 0.7919 (t80)
REVERT: A  488 MET cc_start: 0.7551 (tpp) cc_final: 0.7080 (tpp)
REVERT: A  512 ARG cc_start: 0.8508 (mtm180) cc_final: 0.7297 (mtm180)
REVERT: A  537 LYS cc_start: 0.8201 (mtpp) cc_final: 0.7971 (mmtt)
REVERT: A  546 LYS cc_start: 0.8251 (tptm) cc_final: 0.7713 (tptm)
REVERT: A  563 LYS cc_start: 0.8560 (mmmt) cc_final: 0.8318 (ttmm)
REVERT: A  662 CYS cc_start: 0.7830 (m) cc_final: 0.7504 (m)
REVERT: A  679 ILE cc_start: 0.8571 (mt) cc_final: 0.8237 (mt)
REVERT: A  715 LYS cc_start: 0.7840 (mtpp) cc_final: 0.7129 (mmmm)
REVERT: A  716 ASP cc_start: 0.7232 (t0) cc_final: 0.6902 (t0)
REVERT: B   39 ARG cc_start: 0.6303 (ttm170) cc_final: 0.5737 (mtp180)
REVERT: B  118 TYR cc_start: 0.7207 (m-10) cc_final: 0.7007 (m-80)
REVERT: B  134 ARG cc_start: 0.6338 (mtt90) cc_final: 0.6038 (mtt90)
REVERT: B  158 ASP cc_start: 0.5491 (m-30) cc_final: 0.5257 (m-30)
REVERT: B  192 LEU cc_start: 0.8624 (tp) cc_final: 0.8146 (pp)
REVERT: B  207 GLN cc_start: 0.8307 (tm-30) cc_final: 0.7677 (tm-30)
REVERT: B  230 GLN cc_start: 0.7889 (tp40) cc_final: 0.7313 (tm-30)
REVERT: B  231 VAL cc_start: 0.8648 (p) cc_final: 0.8181 (p)
REVERT: B  236 LEU cc_start: 0.8028 (tp) cc_final: 0.7635 (tp)
REVERT: B  237 LYS cc_start: 0.8268 (pttt) cc_final: 0.7723 (pttp)
REVERT: B  251 LEU cc_start: 0.8477 (mm) cc_final: 0.6580 (mm)
REVERT: B  255 TYR cc_start: 0.8215 (m-10) cc_final: 0.7697 (m-80)
REVERT: B  259 GLU cc_start: 0.8323 (tm-30) cc_final: 0.8045 (tm-30)
REVERT: B  263 ASN cc_start: 0.7418 (t0) cc_final: 0.6913 (t0)
REVERT: B  271 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7405 (p0)
REVERT: B  293 LYS cc_start: 0.8430 (mmmm) cc_final: 0.7995 (mmtm)
REVERT: B  320 GLU cc_start: 0.7620 (tp30) cc_final: 0.7370 (tp30)
REVERT: B  324 ASN cc_start: 0.7698 (t0) cc_final: 0.7391 (t0)
REVERT: B  340 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6811 (pp)
REVERT: B  395 SER cc_start: 0.7823 (m) cc_final: 0.7292 (p)
REVERT: B  457 ASN cc_start: 0.7322 (m110) cc_final: 0.7101 (m-40)
REVERT: B  473 LYS cc_start: 0.8084 (mttt) cc_final: 0.7277 (mtpp)
REVERT: B  487 ILE cc_start: 0.8626 (pt) cc_final: 0.8369 (mm)
REVERT: B  488 MET cc_start: 0.7158 (tpp) cc_final: 0.5822 (tpp)
REVERT: B  492 LEU cc_start: 0.8699 (mt) cc_final: 0.7745 (mt)
REVERT: B  499 LEU cc_start: 0.8216 (tp) cc_final: 0.7923 (tp)
REVERT: B  526 SER cc_start: 0.8514 (m) cc_final: 0.8280 (p)
REVERT: B  556 TYR cc_start: 0.8315 (p90) cc_final: 0.8092 (p90)
REVERT: B  677 ARG cc_start: 0.7459 (ttt180) cc_final: 0.7131 (ttp80)
REVERT: B  681 LYS cc_start: 0.8435 (ptmm) cc_final: 0.8048 (ttpp)
REVERT: B  682 GLU cc_start: 0.8039 (tp30) cc_final: 0.7553 (tp30)
REVERT: B  685 ARG cc_start: 0.8000 (ptm160) cc_final: 0.7762 (ptp90)
REVERT: B  687 ASP cc_start: 0.6827 (t0) cc_final: 0.6432 (t0)
REVERT: B  705 GLN cc_start: 0.8366 (tt0) cc_final: 0.8055 (tt0)
REVERT: B  720 LEU cc_start: 0.8511 (mp) cc_final: 0.8220 (mp)
REVERT: B  724 ASP cc_start: 0.7193 (m-30) cc_final: 0.6895 (m-30)
  outliers start: 60
  outliers final: 40
  residues processed: 331
  average time/residue: 0.1049
  time to fit residues: 47.7749
Evaluate side-chains
  334 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 288
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   59 LYS
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  182 ASP
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  230 GLN
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  461 MET
Chi-restraints excluded: chain A residue  463 MET
Chi-restraints excluded: chain A residue  478 ASP
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  728 HIS
Chi-restraints excluded: chain B residue   79 ARG
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  244 THR
Chi-restraints excluded: chain B residue  271 ASP
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain B residue  340 LEU
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  405 THR
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  582 LEU
Chi-restraints excluded: chain B residue  666 SER
Chi-restraints excluded: chain B residue  688 VAL
Chi-restraints excluded: chain B residue  694 LEU
Chi-restraints excluded: chain B residue  703 MET
Chi-restraints excluded: chain B residue  713 ILE
Chi-restraints excluded: chain B residue  721 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 123 optimal weight:    0.8980
   chunk 127 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 10 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 74 optimal weight:    2.9990
   chunk 120 optimal weight:    0.0370
   chunk 88 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 21 optimal weight:    0.6980
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.6058

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

Flipped N/Q/H residues before XYZ refinement:
** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 446 GLN
A 728 HIS
B 475 ASN
** B 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.132792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.113955 restraints weight = 20516.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.117629 restraints weight = 11590.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.120157 restraints weight = 7425.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.121956 restraints weight = 5149.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.123175 restraints weight = 3851.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7070
moved from start:          0.4526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  10395  Z= 0.161
  Angle     :  0.676  17.354  14128  Z= 0.342
  Chirality :  0.045   0.390   1716
  Planarity :  0.004   0.058   1757
  Dihedral  :  5.448  52.733   1444
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 14.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 22.08 %
    Favored  : 73.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.18 (0.23), residues: 1319
  helix:  0.19 (0.18), residues: 826
  sheet: -2.52 (0.99), residues: 28
  loop : -2.45 (0.28), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 213 
 TYR   0.027   0.002   TYR A 556 
 PHE   0.023   0.001   PHE A 130 
 TRP   0.014   0.001   TRP A  83 
 HIS   0.009   0.001   HIS A 728 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (10395)
  covalent geometry    : angle       0.67594 (14128)
  hydrogen bonds       : bond        0.03890 (  544)
  hydrogen bonds       : angle       4.09499 ( 1593)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  347 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 293
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 ARG cc_start: 0.7821 (tpp-160) cc_final: 0.7591 (mmt90)
REVERT: A   37 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6460 (pm20)
REVERT: A   79 ARG cc_start: 0.7791 (mmm-85) cc_final: 0.7368 (mmt90)
REVERT: A   93 SER cc_start: 0.8445 (t) cc_final: 0.8124 (p)
REVERT: A   97 VAL cc_start: 0.8561 (OUTLIER) cc_final: 0.8348 (p)
REVERT: A  122 PHE cc_start: 0.7095 (m-80) cc_final: 0.6643 (m-10)
REVERT: A  123 PRO cc_start: 0.8311 (Cg_exo) cc_final: 0.8031 (Cg_endo)
REVERT: A  195 LEU cc_start: 0.8537 (tp) cc_final: 0.8070 (tp)
REVERT: A  199 ILE cc_start: 0.8170 (mt) cc_final: 0.7834 (mt)
REVERT: A  231 VAL cc_start: 0.8772 (t) cc_final: 0.8088 (p)
REVERT: A  234 SER cc_start: 0.8786 (m) cc_final: 0.8227 (t)
REVERT: A  235 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7664 (mm-40)
REVERT: A  237 LYS cc_start: 0.8431 (ttpp) cc_final: 0.8158 (ttpp)
REVERT: A  276 LEU cc_start: 0.8534 (mm) cc_final: 0.8149 (mm)
REVERT: A  279 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8712 (mm)
REVERT: A  283 MET cc_start: 0.7700 (tpp) cc_final: 0.7482 (mpp)
REVERT: A  286 LYS cc_start: 0.9203 (tppt) cc_final: 0.8865 (mmmm)
REVERT: A  303 GLU cc_start: 0.8217 (mp0) cc_final: 0.7996 (mp0)
REVERT: A  335 PHE cc_start: 0.7054 (OUTLIER) cc_final: 0.6795 (t80)
REVERT: A  395 SER cc_start: 0.8418 (m) cc_final: 0.8085 (p)
REVERT: A  398 PHE cc_start: 0.6971 (m-80) cc_final: 0.6466 (m-80)
REVERT: A  409 ARG cc_start: 0.7830 (ttp-170) cc_final: 0.7509 (ttp-170)
REVERT: A  457 ASN cc_start: 0.8113 (m110) cc_final: 0.7699 (m-40)
REVERT: A  473 LYS cc_start: 0.8399 (mtpt) cc_final: 0.8043 (mtpt)
REVERT: A  478 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7606 (t0)
REVERT: A  484 PHE cc_start: 0.8181 (t80) cc_final: 0.7885 (t80)
REVERT: A  488 MET cc_start: 0.7444 (tpp) cc_final: 0.7007 (tpp)
REVERT: A  511 LEU cc_start: 0.8845 (mp) cc_final: 0.8594 (mm)
REVERT: A  512 ARG cc_start: 0.8490 (mtm180) cc_final: 0.8244 (mtm-85)
REVERT: A  546 LYS cc_start: 0.8241 (tptm) cc_final: 0.7715 (tptm)
REVERT: A  563 LYS cc_start: 0.8413 (mmmt) cc_final: 0.8086 (ttmm)
REVERT: A  662 CYS cc_start: 0.7843 (m) cc_final: 0.7554 (m)
REVERT: A  679 ILE cc_start: 0.8524 (mt) cc_final: 0.8260 (mt)
REVERT: A  681 LYS cc_start: 0.8094 (tptt) cc_final: 0.7692 (tptt)
REVERT: A  682 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7628 (mt-10)
REVERT: A  715 LYS cc_start: 0.7924 (mtpp) cc_final: 0.7593 (mtpt)
REVERT: A  716 ASP cc_start: 0.7184 (t0) cc_final: 0.6875 (t0)
REVERT: B  134 ARG cc_start: 0.6310 (mtt90) cc_final: 0.6063 (mtt90)
REVERT: B  158 ASP cc_start: 0.5410 (m-30) cc_final: 0.5176 (m-30)
REVERT: B  192 LEU cc_start: 0.8598 (tp) cc_final: 0.8161 (pp)
REVERT: B  207 GLN cc_start: 0.8339 (tm-30) cc_final: 0.7738 (tm-30)
REVERT: B  230 GLN cc_start: 0.7868 (tp40) cc_final: 0.7355 (tm-30)
REVERT: B  231 VAL cc_start: 0.8686 (p) cc_final: 0.7954 (p)
REVERT: B  235 GLN cc_start: 0.7692 (mm-40) cc_final: 0.7227 (mm-40)
REVERT: B  236 LEU cc_start: 0.8055 (tp) cc_final: 0.7647 (tp)
REVERT: B  237 LYS cc_start: 0.8203 (pttt) cc_final: 0.7792 (pttt)
REVERT: B  251 LEU cc_start: 0.8450 (mm) cc_final: 0.6581 (mm)
REVERT: B  255 TYR cc_start: 0.8138 (m-10) cc_final: 0.7671 (m-80)
REVERT: B  259 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7998 (tm-30)
REVERT: B  263 ASN cc_start: 0.7302 (t0) cc_final: 0.6736 (t0)
REVERT: B  271 ASP cc_start: 0.7977 (OUTLIER) cc_final: 0.7369 (p0)
REVERT: B  293 LYS cc_start: 0.8497 (mmmm) cc_final: 0.8091 (mmtm)
REVERT: B  320 GLU cc_start: 0.7504 (tp30) cc_final: 0.7262 (tp30)
REVERT: B  340 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6853 (pp)
REVERT: B  395 SER cc_start: 0.7888 (m) cc_final: 0.7338 (p)
REVERT: B  457 ASN cc_start: 0.7282 (m110) cc_final: 0.7030 (m-40)
REVERT: B  473 LYS cc_start: 0.8022 (mttt) cc_final: 0.7335 (mtpp)
REVERT: B  475 ASN cc_start: 0.7919 (t0) cc_final: 0.7580 (t0)
REVERT: B  487 ILE cc_start: 0.8642 (pt) cc_final: 0.8359 (mm)
REVERT: B  488 MET cc_start: 0.7059 (tpp) cc_final: 0.5780 (tpp)
REVERT: B  492 LEU cc_start: 0.8683 (mt) cc_final: 0.7725 (mt)
REVERT: B  499 LEU cc_start: 0.8227 (tp) cc_final: 0.7938 (tp)
REVERT: B  526 SER cc_start: 0.8517 (m) cc_final: 0.8276 (p)
REVERT: B  537 LYS cc_start: 0.6814 (mmmt) cc_final: 0.6191 (tppt)
REVERT: B  580 LYS cc_start: 0.8238 (mmmt) cc_final: 0.7985 (mmmm)
REVERT: B  677 ARG cc_start: 0.7376 (ttt180) cc_final: 0.7112 (ttp80)
REVERT: B  681 LYS cc_start: 0.8436 (ptmm) cc_final: 0.8022 (ttpp)
REVERT: B  682 GLU cc_start: 0.8035 (tp30) cc_final: 0.7539 (tp30)
REVERT: B  685 ARG cc_start: 0.7970 (ptm160) cc_final: 0.7765 (ptp90)
REVERT: B  687 ASP cc_start: 0.6750 (t0) cc_final: 0.6383 (t0)
REVERT: B  705 GLN cc_start: 0.8305 (tt0) cc_final: 0.7997 (tt0)
REVERT: B  720 LEU cc_start: 0.8466 (mp) cc_final: 0.8173 (mp)
REVERT: B  724 ASP cc_start: 0.7229 (m-30) cc_final: 0.6893 (m-30)
  outliers start: 54
  outliers final: 44
  residues processed: 325
  average time/residue: 0.1094
  time to fit residues: 48.8165
Evaluate side-chains
  339 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 288
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   59 LYS
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  182 ASP
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  230 GLN
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  400 CYS
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  461 MET
Chi-restraints excluded: chain A residue  463 MET
Chi-restraints excluded: chain A residue  478 ASP
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  704 GLU
Chi-restraints excluded: chain A residue  722 VAL
Chi-restraints excluded: chain A residue  728 HIS
Chi-restraints excluded: chain B residue   79 ARG
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  244 THR
Chi-restraints excluded: chain B residue  271 ASP
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain B residue  340 LEU
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  405 THR
Chi-restraints excluded: chain B residue  462 PHE
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  582 LEU
Chi-restraints excluded: chain B residue  666 SER
Chi-restraints excluded: chain B residue  688 VAL
Chi-restraints excluded: chain B residue  694 LEU
Chi-restraints excluded: chain B residue  703 MET
Chi-restraints excluded: chain B residue  713 ILE
Chi-restraints excluded: chain B residue  721 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 10 optimal weight:    0.0070
   chunk 6 optimal weight:    0.9990
   chunk 31 optimal weight:    0.0870
   chunk 103 optimal weight:    4.9990
   chunk 78 optimal weight:    0.9980
   chunk 117 optimal weight:    1.9990
   chunk 90 optimal weight:    0.4980
   chunk 7 optimal weight:    0.6980
   chunk 63 optimal weight:    0.7980
   chunk 93 optimal weight:    0.5980
   chunk 23 optimal weight:    0.3980
   overall best weight:    0.3176

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

Flipped N/Q/H residues before XYZ refinement:
A 207 GLN
** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 446 GLN
A 567 ASN
B 324 ASN
** B 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.134121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.115323 restraints weight = 20384.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.119121 restraints weight = 11504.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.121674 restraints weight = 7272.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.123410 restraints weight = 5033.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.124630 restraints weight = 3757.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7041
moved from start:          0.4631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10395  Z= 0.135
  Angle     :  0.678  17.024  14128  Z= 0.341
  Chirality :  0.044   0.376   1716
  Planarity :  0.004   0.057   1757
  Dihedral  :  5.327  52.438   1442
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 14.24
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.37 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 21.99 %
    Favored  : 73.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.12 (0.23), residues: 1319
  helix:  0.23 (0.18), residues: 819
  sheet: -2.40 (1.00), residues: 28
  loop : -2.37 (0.28), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 213 
 TYR   0.025   0.002   TYR A 556 
 PHE   0.015   0.001   PHE A 719 
 TRP   0.014   0.002   TRP A  83 
 HIS   0.006   0.001   HIS A 728 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 (10395)
  covalent geometry    : angle       0.67814 (14128)
  hydrogen bonds       : bond        0.03828 (  544)
  hydrogen bonds       : angle       4.06788 ( 1593)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  355 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 301
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 ARG cc_start: 0.7820 (tpp-160) cc_final: 0.7564 (mmt90)
REVERT: A   37 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6416 (pm20)
REVERT: A   79 ARG cc_start: 0.7753 (mmm-85) cc_final: 0.7401 (mmt90)
REVERT: A   93 SER cc_start: 0.8441 (t) cc_final: 0.8112 (p)
REVERT: A  122 PHE cc_start: 0.7117 (m-80) cc_final: 0.6671 (m-10)
REVERT: A  123 PRO cc_start: 0.8287 (Cg_exo) cc_final: 0.7978 (Cg_endo)
REVERT: A  145 SER cc_start: 0.8084 (m) cc_final: 0.7691 (p)
REVERT: A  195 LEU cc_start: 0.8514 (tp) cc_final: 0.8005 (tp)
REVERT: A  199 ILE cc_start: 0.8120 (mt) cc_final: 0.7782 (mt)
REVERT: A  231 VAL cc_start: 0.8779 (t) cc_final: 0.8065 (p)
REVERT: A  235 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7747 (mm-40)
REVERT: A  237 LYS cc_start: 0.8424 (ttpp) cc_final: 0.8123 (ttpp)
REVERT: A  276 LEU cc_start: 0.8532 (mm) cc_final: 0.8140 (mm)
REVERT: A  279 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8691 (mm)
REVERT: A  283 MET cc_start: 0.7711 (tpp) cc_final: 0.7511 (mpp)
REVERT: A  286 LYS cc_start: 0.9184 (tppt) cc_final: 0.8865 (mmmm)
REVERT: A  303 GLU cc_start: 0.8212 (mp0) cc_final: 0.7984 (mp0)
REVERT: A  335 PHE cc_start: 0.6960 (OUTLIER) cc_final: 0.6745 (t80)
REVERT: A  385 PHE cc_start: 0.8260 (t80) cc_final: 0.8016 (t80)
REVERT: A  395 SER cc_start: 0.8411 (m) cc_final: 0.8070 (p)
REVERT: A  398 PHE cc_start: 0.6932 (m-80) cc_final: 0.6422 (m-80)
REVERT: A  457 ASN cc_start: 0.8117 (m110) cc_final: 0.7701 (m-40)
REVERT: A  473 LYS cc_start: 0.8431 (mtpt) cc_final: 0.8050 (mtpt)
REVERT: A  476 LYS cc_start: 0.8642 (mtpt) cc_final: 0.8332 (mmmm)
REVERT: A  478 ASP cc_start: 0.7977 (OUTLIER) cc_final: 0.7525 (t0)
REVERT: A  484 PHE cc_start: 0.8177 (t80) cc_final: 0.7831 (t80)
REVERT: A  488 MET cc_start: 0.7418 (tpp) cc_final: 0.6986 (tpp)
REVERT: A  511 LEU cc_start: 0.8824 (mp) cc_final: 0.8558 (mm)
REVERT: A  546 LYS cc_start: 0.8244 (tptm) cc_final: 0.7730 (tptm)
REVERT: A  563 LYS cc_start: 0.8248 (mmmt) cc_final: 0.7942 (ttmm)
REVERT: A  662 CYS cc_start: 0.7807 (m) cc_final: 0.7526 (m)
REVERT: A  681 LYS cc_start: 0.8039 (tptt) cc_final: 0.7649 (tptt)
REVERT: A  715 LYS cc_start: 0.7905 (mtpp) cc_final: 0.7492 (mtpt)
REVERT: A  716 ASP cc_start: 0.7178 (t0) cc_final: 0.6880 (t0)
REVERT: A  722 VAL cc_start: 0.8383 (OUTLIER) cc_final: 0.8165 (t)
REVERT: B  134 ARG cc_start: 0.6310 (mtt90) cc_final: 0.6050 (mtt90)
REVERT: B  192 LEU cc_start: 0.8597 (tp) cc_final: 0.8144 (pp)
REVERT: B  207 GLN cc_start: 0.8340 (tm-30) cc_final: 0.7755 (tm-30)
REVERT: B  230 GLN cc_start: 0.7867 (tp40) cc_final: 0.7436 (tm-30)
REVERT: B  231 VAL cc_start: 0.8681 (p) cc_final: 0.8021 (p)
REVERT: B  235 GLN cc_start: 0.7588 (mm-40) cc_final: 0.7222 (mm-40)
REVERT: B  236 LEU cc_start: 0.8043 (tp) cc_final: 0.7635 (tp)
REVERT: B  237 LYS cc_start: 0.8161 (pttt) cc_final: 0.7737 (pttt)
REVERT: B  251 LEU cc_start: 0.8428 (mm) cc_final: 0.6597 (mm)
REVERT: B  255 TYR cc_start: 0.8116 (m-10) cc_final: 0.7679 (m-80)
REVERT: B  259 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7970 (tm-30)
REVERT: B  263 ASN cc_start: 0.7265 (t0) cc_final: 0.6780 (t0)
REVERT: B  271 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7311 (p0)
REVERT: B  320 GLU cc_start: 0.7516 (tp30) cc_final: 0.7224 (tp30)
REVERT: B  324 ASN cc_start: 0.7659 (t0) cc_final: 0.7388 (t0)
REVERT: B  340 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7226 (pp)
REVERT: B  395 SER cc_start: 0.7817 (m) cc_final: 0.7305 (p)
REVERT: B  457 ASN cc_start: 0.7364 (m110) cc_final: 0.7082 (m-40)
REVERT: B  459 LYS cc_start: 0.7896 (mmtt) cc_final: 0.7612 (mmtt)
REVERT: B  475 ASN cc_start: 0.7893 (t0) cc_final: 0.7552 (t0)
REVERT: B  487 ILE cc_start: 0.8609 (pt) cc_final: 0.8397 (mt)
REVERT: B  488 MET cc_start: 0.6991 (tpp) cc_final: 0.5624 (tpp)
REVERT: B  492 LEU cc_start: 0.8591 (mt) cc_final: 0.7339 (mt)
REVERT: B  499 LEU cc_start: 0.8218 (tp) cc_final: 0.7920 (tp)
REVERT: B  526 SER cc_start: 0.8475 (m) cc_final: 0.8241 (p)
REVERT: B  537 LYS cc_start: 0.6979 (mmmt) cc_final: 0.6549 (tptp)
REVERT: B  677 ARG cc_start: 0.7383 (ttt180) cc_final: 0.7066 (ttp80)
REVERT: B  687 ASP cc_start: 0.6738 (t0) cc_final: 0.6362 (t0)
REVERT: B  705 GLN cc_start: 0.8254 (tt0) cc_final: 0.7922 (tt0)
REVERT: B  720 LEU cc_start: 0.8383 (mp) cc_final: 0.8177 (tp)
REVERT: B  724 ASP cc_start: 0.7211 (m-30) cc_final: 0.6920 (m-30)
  outliers start: 54
  outliers final: 43
  residues processed: 337
  average time/residue: 0.1112
  time to fit residues: 51.1388
Evaluate side-chains
  349 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 299
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   59 LYS
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  207 GLN
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  400 CYS
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  461 MET
Chi-restraints excluded: chain A residue  463 MET
Chi-restraints excluded: chain A residue  478 ASP
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  704 GLU
Chi-restraints excluded: chain A residue  722 VAL
Chi-restraints excluded: chain A residue  728 HIS
Chi-restraints excluded: chain B residue   79 ARG
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  264 ILE
Chi-restraints excluded: chain B residue  271 ASP
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain B residue  340 LEU
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  405 THR
Chi-restraints excluded: chain B residue  462 PHE
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  582 LEU
Chi-restraints excluded: chain B residue  666 SER
Chi-restraints excluded: chain B residue  688 VAL
Chi-restraints excluded: chain B residue  694 LEU
Chi-restraints excluded: chain B residue  699 VAL
Chi-restraints excluded: chain B residue  703 MET
Chi-restraints excluded: chain B residue  713 ILE
Chi-restraints excluded: chain B residue  721 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 82 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 112 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 130 optimal weight:    1.9990
   chunk 98 optimal weight:    0.0060
   chunk 99 optimal weight:    0.9980
   chunk 127 optimal weight:    0.1980
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.4796

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

Flipped N/Q/H residues before XYZ refinement:
** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 728 HIS
** B 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.132846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.113889 restraints weight = 20562.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.117675 restraints weight = 11660.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.120202 restraints weight = 7408.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.121947 restraints weight = 5144.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.123059 restraints weight = 3855.693|
|-----------------------------------------------------------------------------|
r_work (final): 0.3846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7065
moved from start:          0.4777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10395  Z= 0.150
  Angle     :  0.715  16.814  14128  Z= 0.359
  Chirality :  0.046   0.432   1716
  Planarity :  0.004   0.056   1757
  Dihedral  :  5.387  53.042   1442
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 14.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.75 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 23.33 %
    Favored  : 72.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.11 (0.23), residues: 1319
  helix:  0.27 (0.18), residues: 799
  sheet: -2.40 (1.00), residues: 28
  loop : -2.32 (0.28), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 213 
 TYR   0.024   0.002   TYR A 556 
 PHE   0.023   0.001   PHE B 484 
 TRP   0.014   0.001   TRP B  83 
 HIS   0.006   0.001   HIS A 723 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (10395)
  covalent geometry    : angle       0.71529 (14128)
  hydrogen bonds       : bond        0.03850 (  544)
  hydrogen bonds       : angle       4.13764 ( 1593)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  343 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 296
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 ARG cc_start: 0.7818 (tpp-160) cc_final: 0.7606 (mmt90)
REVERT: A   37 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6440 (pm20)
REVERT: A   93 SER cc_start: 0.8467 (t) cc_final: 0.8139 (p)
REVERT: A  122 PHE cc_start: 0.7143 (m-80) cc_final: 0.6653 (m-10)
REVERT: A  123 PRO cc_start: 0.8219 (Cg_exo) cc_final: 0.7946 (Cg_endo)
REVERT: A  145 SER cc_start: 0.8132 (m) cc_final: 0.7747 (p)
REVERT: A  195 LEU cc_start: 0.8534 (tp) cc_final: 0.8036 (tp)
REVERT: A  199 ILE cc_start: 0.8154 (mt) cc_final: 0.7825 (mt)
REVERT: A  231 VAL cc_start: 0.8762 (t) cc_final: 0.8072 (p)
REVERT: A  234 SER cc_start: 0.8770 (m) cc_final: 0.8226 (t)
REVERT: A  235 GLN cc_start: 0.8081 (mm-40) cc_final: 0.7664 (mm-40)
REVERT: A  237 LYS cc_start: 0.8443 (ttpp) cc_final: 0.8148 (ttpp)
REVERT: A  276 LEU cc_start: 0.8541 (mm) cc_final: 0.8141 (mm)
REVERT: A  279 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8677 (mm)
REVERT: A  283 MET cc_start: 0.7729 (tpp) cc_final: 0.7525 (mpp)
REVERT: A  286 LYS cc_start: 0.9182 (tppt) cc_final: 0.8873 (mmmm)
REVERT: A  303 GLU cc_start: 0.8217 (mp0) cc_final: 0.7992 (mp0)
REVERT: A  320 GLU cc_start: 0.6608 (tp30) cc_final: 0.6261 (tp30)
REVERT: A  335 PHE cc_start: 0.6957 (OUTLIER) cc_final: 0.6737 (t80)
REVERT: A  377 TYR cc_start: 0.7081 (p90) cc_final: 0.6869 (p90)
REVERT: A  384 GLU cc_start: 0.6598 (mm-30) cc_final: 0.5765 (mm-30)
REVERT: A  395 SER cc_start: 0.8431 (m) cc_final: 0.8092 (p)
REVERT: A  398 PHE cc_start: 0.6929 (m-80) cc_final: 0.6427 (m-80)
REVERT: A  457 ASN cc_start: 0.8133 (m110) cc_final: 0.7724 (m-40)
REVERT: A  473 LYS cc_start: 0.8424 (mtpt) cc_final: 0.8065 (mtpt)
REVERT: A  478 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7518 (t0)
REVERT: A  484 PHE cc_start: 0.8171 (t80) cc_final: 0.7832 (t80)
REVERT: A  488 MET cc_start: 0.7425 (tpp) cc_final: 0.6980 (tpp)
REVERT: A  546 LYS cc_start: 0.8264 (tptm) cc_final: 0.7738 (tptm)
REVERT: A  563 LYS cc_start: 0.8429 (mmmt) cc_final: 0.8190 (ttmm)
REVERT: A  662 CYS cc_start: 0.7861 (m) cc_final: 0.7586 (m)
REVERT: A  667 PHE cc_start: 0.7812 (p90) cc_final: 0.7492 (p90)
REVERT: A  681 LYS cc_start: 0.8156 (tptt) cc_final: 0.7749 (tptt)
REVERT: A  682 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7879 (mp0)
REVERT: A  715 LYS cc_start: 0.7910 (mtpp) cc_final: 0.7508 (mtpt)
REVERT: A  716 ASP cc_start: 0.7183 (t0) cc_final: 0.6877 (t0)
REVERT: B  134 ARG cc_start: 0.6368 (mtt90) cc_final: 0.6104 (mtt90)
REVERT: B  192 LEU cc_start: 0.8616 (tp) cc_final: 0.8142 (pp)
REVERT: B  207 GLN cc_start: 0.8392 (tm-30) cc_final: 0.7833 (tm-30)
REVERT: B  230 GLN cc_start: 0.7866 (tp40) cc_final: 0.7347 (tm-30)
REVERT: B  231 VAL cc_start: 0.8682 (p) cc_final: 0.8018 (p)
REVERT: B  235 GLN cc_start: 0.7610 (mm-40) cc_final: 0.7212 (mm-40)
REVERT: B  236 LEU cc_start: 0.8067 (tp) cc_final: 0.7660 (tp)
REVERT: B  237 LYS cc_start: 0.8196 (pttt) cc_final: 0.7788 (pttt)
REVERT: B  251 LEU cc_start: 0.8431 (mm) cc_final: 0.6579 (mm)
REVERT: B  255 TYR cc_start: 0.8134 (m-10) cc_final: 0.7689 (m-80)
REVERT: B  259 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7949 (tm-30)
REVERT: B  263 ASN cc_start: 0.7307 (t0) cc_final: 0.6798 (t0)
REVERT: B  293 LYS cc_start: 0.8537 (mmmm) cc_final: 0.8188 (mptt)
REVERT: B  320 GLU cc_start: 0.7551 (tp30) cc_final: 0.7294 (tp30)
REVERT: B  324 ASN cc_start: 0.7778 (t0) cc_final: 0.7531 (t0)
REVERT: B  340 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7231 (pp)
REVERT: B  395 SER cc_start: 0.7995 (m) cc_final: 0.7500 (p)
REVERT: B  457 ASN cc_start: 0.7299 (m110) cc_final: 0.7028 (m-40)
REVERT: B  459 LYS cc_start: 0.7908 (mmtt) cc_final: 0.7668 (tmmt)
REVERT: B  473 LYS cc_start: 0.8002 (mttp) cc_final: 0.7222 (ttpp)
REVERT: B  475 ASN cc_start: 0.7955 (t0) cc_final: 0.7711 (t0)
REVERT: B  487 ILE cc_start: 0.8641 (pt) cc_final: 0.8417 (mt)
REVERT: B  488 MET cc_start: 0.7021 (tpp) cc_final: 0.5805 (tpp)
REVERT: B  492 LEU cc_start: 0.8619 (mt) cc_final: 0.7289 (mt)
REVERT: B  499 LEU cc_start: 0.8223 (tp) cc_final: 0.7931 (tp)
REVERT: B  526 SER cc_start: 0.8520 (m) cc_final: 0.8276 (p)
REVERT: B  537 LYS cc_start: 0.7124 (mmmt) cc_final: 0.6182 (tptp)
REVERT: B  580 LYS cc_start: 0.8229 (mmmt) cc_final: 0.7996 (mmmm)
REVERT: B  677 ARG cc_start: 0.7392 (ttt180) cc_final: 0.7072 (ttp80)
REVERT: B  681 LYS cc_start: 0.8432 (ptmm) cc_final: 0.8047 (ttpp)
REVERT: B  687 ASP cc_start: 0.6763 (t0) cc_final: 0.6382 (t0)
REVERT: B  705 GLN cc_start: 0.8229 (tt0) cc_final: 0.7927 (tt0)
REVERT: B  720 LEU cc_start: 0.8385 (mp) cc_final: 0.8149 (mp)
REVERT: B  724 ASP cc_start: 0.7218 (m-30) cc_final: 0.6953 (m-30)
  outliers start: 47
  outliers final: 36
  residues processed: 328
  average time/residue: 0.1020
  time to fit residues: 46.5335
Evaluate side-chains
  333 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 292
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   59 LYS
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  461 MET
Chi-restraints excluded: chain A residue  478 ASP
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  704 GLU
Chi-restraints excluded: chain A residue  728 HIS
Chi-restraints excluded: chain B residue   79 ARG
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain B residue  340 LEU
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  405 THR
Chi-restraints excluded: chain B residue  449 VAL
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  582 LEU
Chi-restraints excluded: chain B residue  688 VAL
Chi-restraints excluded: chain B residue  694 LEU
Chi-restraints excluded: chain B residue  699 VAL
Chi-restraints excluded: chain B residue  703 MET
Chi-restraints excluded: chain B residue  713 ILE
Chi-restraints excluded: chain B residue  721 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 131 optimal weight:    0.0570
   chunk 38 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9990
   chunk 83 optimal weight:    0.5980
   chunk 82 optimal weight:    0.0980
   chunk 91 optimal weight:    0.0980
   chunk 74 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 114 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 96 optimal weight:    0.4980
   overall best weight:    0.2698

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

Flipped N/Q/H residues before XYZ refinement:
** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 446 GLN
** A 728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 241 ASN
** B 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.133834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.114883 restraints weight = 20292.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.118667 restraints weight = 11514.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.121240 restraints weight = 7337.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.122984 restraints weight = 5087.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.124076 restraints weight = 3807.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.3870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7044
moved from start:          0.4829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10395  Z= 0.137
  Angle     :  0.729  17.096  14128  Z= 0.360
  Chirality :  0.046   0.391   1716
  Planarity :  0.005   0.062   1757
  Dihedral  :  5.396  53.009   1442
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 14.87
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.67 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 23.78 %
    Favored  : 72.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.07 (0.23), residues: 1319
  helix:  0.28 (0.18), residues: 800
  sheet: -2.32 (1.02), residues: 28
  loop : -2.26 (0.28), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 213 
 TYR   0.031   0.002   TYR A 691 
 PHE   0.031   0.001   PHE A 210 
 TRP   0.014   0.002   TRP A  83 
 HIS   0.007   0.001   HIS A 723 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (10395)
  covalent geometry    : angle       0.72909 (14128)
  hydrogen bonds       : bond        0.03855 (  544)
  hydrogen bonds       : angle       4.13442 ( 1593)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  334 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 294
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 ARG cc_start: 0.7818 (tpp-160) cc_final: 0.7610 (mmt90)
REVERT: A   37 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6404 (pm20)
REVERT: A   93 SER cc_start: 0.8439 (t) cc_final: 0.8099 (p)
REVERT: A  122 PHE cc_start: 0.7139 (m-80) cc_final: 0.6720 (m-10)
REVERT: A  123 PRO cc_start: 0.8198 (Cg_exo) cc_final: 0.7957 (Cg_endo)
REVERT: A  145 SER cc_start: 0.8106 (m) cc_final: 0.7821 (m)
REVERT: A  195 LEU cc_start: 0.8547 (tp) cc_final: 0.8006 (tp)
REVERT: A  199 ILE cc_start: 0.8062 (mt) cc_final: 0.7729 (mt)
REVERT: A  206 LEU cc_start: 0.7994 (mt) cc_final: 0.7661 (mt)
REVERT: A  231 VAL cc_start: 0.8764 (t) cc_final: 0.8045 (p)
REVERT: A  235 GLN cc_start: 0.8080 (mm-40) cc_final: 0.7742 (mm-40)
REVERT: A  237 LYS cc_start: 0.8432 (ttpp) cc_final: 0.8127 (ttpp)
REVERT: A  276 LEU cc_start: 0.8548 (mm) cc_final: 0.8142 (mm)
REVERT: A  279 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8689 (mm)
REVERT: A  283 MET cc_start: 0.7751 (tpp) cc_final: 0.7540 (mpp)
REVERT: A  286 LYS cc_start: 0.9187 (tppt) cc_final: 0.8888 (mmmm)
REVERT: A  303 GLU cc_start: 0.8209 (mp0) cc_final: 0.7978 (mp0)
REVERT: A  355 SER cc_start: 0.7881 (m) cc_final: 0.7598 (p)
REVERT: A  377 TYR cc_start: 0.7053 (p90) cc_final: 0.6835 (p90)
REVERT: A  383 GLN cc_start: 0.7143 (mm-40) cc_final: 0.6647 (tp40)
REVERT: A  385 PHE cc_start: 0.8276 (t80) cc_final: 0.8057 (t80)
REVERT: A  395 SER cc_start: 0.8418 (m) cc_final: 0.8059 (p)
REVERT: A  457 ASN cc_start: 0.8112 (m110) cc_final: 0.7680 (m-40)
REVERT: A  473 LYS cc_start: 0.8429 (mtpt) cc_final: 0.8037 (mtpt)
REVERT: A  476 LYS cc_start: 0.8556 (mmmt) cc_final: 0.8049 (mmmm)
REVERT: A  488 MET cc_start: 0.7434 (tpp) cc_final: 0.6983 (tpp)
REVERT: A  530 TYR cc_start: 0.7183 (m-80) cc_final: 0.6968 (m-80)
REVERT: A  546 LYS cc_start: 0.8272 (tptm) cc_final: 0.7752 (tptm)
REVERT: A  563 LYS cc_start: 0.8422 (mmmt) cc_final: 0.8157 (ttmm)
REVERT: A  662 CYS cc_start: 0.7770 (m) cc_final: 0.7507 (m)
REVERT: A  667 PHE cc_start: 0.7753 (p90) cc_final: 0.7480 (p90)
REVERT: A  681 LYS cc_start: 0.8153 (tptt) cc_final: 0.7751 (tptt)
REVERT: A  682 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7857 (mp0)
REVERT: A  715 LYS cc_start: 0.7884 (mtpp) cc_final: 0.7601 (mtpt)
REVERT: A  716 ASP cc_start: 0.7152 (t0) cc_final: 0.6850 (t0)
REVERT: A  724 ASP cc_start: 0.6675 (m-30) cc_final: 0.6332 (m-30)
REVERT: B  134 ARG cc_start: 0.6398 (mtt90) cc_final: 0.6100 (mtt90)
REVERT: B  207 GLN cc_start: 0.8387 (tm-30) cc_final: 0.7833 (tm-30)
REVERT: B  230 GLN cc_start: 0.7855 (tp40) cc_final: 0.7319 (tm-30)
REVERT: B  231 VAL cc_start: 0.8686 (p) cc_final: 0.8005 (p)
REVERT: B  232 LEU cc_start: 0.8309 (tt) cc_final: 0.8106 (tp)
REVERT: B  235 GLN cc_start: 0.7570 (mm-40) cc_final: 0.7164 (mm-40)
REVERT: B  236 LEU cc_start: 0.8039 (tp) cc_final: 0.7636 (tp)
REVERT: B  237 LYS cc_start: 0.8181 (pttt) cc_final: 0.7781 (pttt)
REVERT: B  251 LEU cc_start: 0.8407 (mm) cc_final: 0.6558 (mm)
REVERT: B  255 TYR cc_start: 0.8161 (m-10) cc_final: 0.7711 (m-80)
REVERT: B  259 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7963 (tm-30)
REVERT: B  266 ASP cc_start: 0.7620 (p0) cc_final: 0.7333 (p0)
REVERT: B  293 LYS cc_start: 0.8481 (mmmm) cc_final: 0.8105 (mptt)
REVERT: B  320 GLU cc_start: 0.7495 (tp30) cc_final: 0.7252 (tp30)
REVERT: B  324 ASN cc_start: 0.7705 (t0) cc_final: 0.7448 (t0)
REVERT: B  340 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7224 (pp)
REVERT: B  395 SER cc_start: 0.7761 (m) cc_final: 0.7207 (p)
REVERT: B  457 ASN cc_start: 0.7358 (m110) cc_final: 0.7081 (m-40)
REVERT: B  459 LYS cc_start: 0.7900 (mmtt) cc_final: 0.7659 (tmmt)
REVERT: B  473 LYS cc_start: 0.8018 (mttp) cc_final: 0.7411 (ttpp)
REVERT: B  475 ASN cc_start: 0.7973 (t0) cc_final: 0.7756 (t0)
REVERT: B  487 ILE cc_start: 0.8618 (pt) cc_final: 0.8405 (mt)
REVERT: B  488 MET cc_start: 0.6987 (tpp) cc_final: 0.5758 (tpp)
REVERT: B  492 LEU cc_start: 0.8595 (mt) cc_final: 0.7207 (mt)
REVERT: B  499 LEU cc_start: 0.8175 (tp) cc_final: 0.7893 (tp)
REVERT: B  526 SER cc_start: 0.8465 (m) cc_final: 0.8253 (p)
REVERT: B  537 LYS cc_start: 0.7114 (mmmt) cc_final: 0.6145 (tptp)
REVERT: B  580 LYS cc_start: 0.8235 (mmmt) cc_final: 0.8002 (mmmm)
REVERT: B  677 ARG cc_start: 0.7442 (ttt180) cc_final: 0.7193 (ttp80)
REVERT: B  681 LYS cc_start: 0.8423 (ptmm) cc_final: 0.8084 (ttpp)
REVERT: B  687 ASP cc_start: 0.6752 (t0) cc_final: 0.6356 (t0)
REVERT: B  705 GLN cc_start: 0.8233 (tt0) cc_final: 0.7917 (tt0)
REVERT: B  720 LEU cc_start: 0.8487 (mp) cc_final: 0.8202 (mp)
REVERT: B  724 ASP cc_start: 0.7183 (m-30) cc_final: 0.6924 (m-30)
  outliers start: 40
  outliers final: 35
  residues processed: 322
  average time/residue: 0.1070
  time to fit residues: 47.8659
Evaluate side-chains
  333 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 295
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   59 LYS
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  461 MET
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  704 GLU
Chi-restraints excluded: chain B residue   79 ARG
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain B residue  340 LEU
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  405 THR
Chi-restraints excluded: chain B residue  449 VAL
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  582 LEU
Chi-restraints excluded: chain B residue  688 VAL
Chi-restraints excluded: chain B residue  694 LEU
Chi-restraints excluded: chain B residue  699 VAL
Chi-restraints excluded: chain B residue  703 MET
Chi-restraints excluded: chain B residue  713 ILE
Chi-restraints excluded: chain B residue  721 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 62 optimal weight:    0.7980
   chunk 109 optimal weight:    0.9980
   chunk 35 optimal weight:    0.0470
   chunk 117 optimal weight:    0.4980
   chunk 73 optimal weight:    0.5980
   chunk 82 optimal weight:    0.2980
   chunk 84 optimal weight:    0.6980
   chunk 65 optimal weight:    0.8980
   chunk 101 optimal weight:    0.6980
   chunk 39 optimal weight:    0.7980
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.4278

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

Flipped N/Q/H residues before XYZ refinement:
** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 446 GLN
** B 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.133702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.114261 restraints weight = 20521.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.118168 restraints weight = 11631.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.120784 restraints weight = 7383.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.122570 restraints weight = 5134.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.123704 restraints weight = 3840.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.3850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7069
moved from start:          0.4940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10395  Z= 0.148
  Angle     :  0.738  16.407  14128  Z= 0.369
  Chirality :  0.046   0.356   1716
  Planarity :  0.004   0.054   1757
  Dihedral  :  5.421  53.037   1442
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 15.40
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.05 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 24.04 %
    Favored  : 71.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.01 (0.23), residues: 1319
  helix:  0.34 (0.18), residues: 788
  sheet: -2.31 (1.02), residues: 28
  loop : -2.21 (0.28), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 213 
 TYR   0.036   0.002   TYR A 530 
 PHE   0.032   0.001   PHE B 484 
 TRP   0.017   0.002   TRP A  83 
 HIS   0.017   0.001   HIS A 728 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (10395)
  covalent geometry    : angle       0.73817 (14128)
  hydrogen bonds       : bond        0.03870 (  544)
  hydrogen bonds       : angle       4.16438 ( 1593)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1999.02 seconds
wall clock time: 35 minutes 17.35 seconds (2117.35 seconds total)