Starting phenix.real_space_refine
on Wed Mar  4 09:41:20 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wjm_32545/03_2026/7wjm_32545.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wjm_32545/03_2026/7wjm_32545.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wjm_32545/03_2026/7wjm_32545.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wjm_32545/03_2026/7wjm_32545.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wjm_32545/03_2026/7wjm_32545.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wjm_32545/03_2026/7wjm_32545.map"
  }
  resolution = 3.3
  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
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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      72      5.16       5
     C    8426      2.51       5
     N    2160      2.21       5
     O    2312      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12970
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 6485
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 807, 6485
          Classifications: {'peptide': 807}
          Link IDs: {'CIS': 1, 'PTRANS': 31, 'TRANS': 774}
          Chain breaks: 1
  Restraints were copied for chains:
    B
  Time building chain proxies: 4.91, per 1000 atoms: 0.38
  Number of scatterers: 12970
  At special positions: 0
  Unit cell: (120.91, 116.63, 131.61, 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      72     16.00
     O    2312      8.00
     N    2160      7.00
     C    8426      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: 1.02
  Conformation dependent library (CDL) restraints added in 549.4 milliseconds
  

  3212 Ramachandran restraints generated.
    1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3036

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 4 sheets defined
      65.6% alpha, 8.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 64 through 74
    Processing helix  chain 'A' and resid 77 through 91
      removed outlier: 3.703A  pdb=" N   ALA A  81 " --> pdb=" O   SER A  77 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   ILE A  91 " --> pdb=" O   THR A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 110
    Processing helix  chain 'A' and resid 112 through 131
      removed outlier: 3.830A  pdb=" N   ALA A 116 " --> pdb=" O   ARG A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 162
    Processing helix  chain 'A' and resid 194 through 199
    Processing helix  chain 'A' and resid 210 through 214
    Processing helix  chain 'A' and resid 221 through 227
    Processing helix  chain 'A' and resid 242 through 263
      removed outlier: 3.942A  pdb=" N   LEU A 246 " --> pdb=" O   GLY A 242 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLN A 263 " --> pdb=" O   TYR A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 282
    Processing helix  chain 'A' and resid 297 through 307
    Processing helix  chain 'A' and resid 311 through 319
    Processing helix  chain 'A' and resid 357 through 374
    Processing helix  chain 'A' and resid 390 through 403
      removed outlier: 3.615A  pdb=" N   HIS A 403 " --> pdb=" O   PHE A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 448
      removed outlier: 3.642A  pdb=" N   SER A 427 " --> pdb=" O   ASN A 423 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   PHE A 447 " --> pdb=" O   LEU A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 474
    Processing helix  chain 'A' and resid 474 through 479
    Processing helix  chain 'A' and resid 480 through 485
      removed outlier: 3.708A  pdb=" N   LEU A 484 " --> pdb=" O   GLU A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 485 through 492
      removed outlier: 3.658A  pdb=" N   MET A 491 " --> pdb=" O   PHE A 487 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   TYR A 492 " --> pdb=" O   ILE A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 505
      removed outlier: 3.802A  pdb=" N   LEU A 499 " --> pdb=" O   GLU A 495 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 528 through 554
      removed outlier: 3.856A  pdb=" N   LEU A 532 " --> pdb=" O   ASP A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 560
    Processing helix  chain 'A' and resid 564 through 587
      removed outlier: 3.748A  pdb=" N   PHE A 587 " --> pdb=" O   ALA A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 606
    Processing helix  chain 'A' and resid 619 through 647
      removed outlier: 3.992A  pdb=" N   ASP A 623 " --> pdb=" O   GLN A 619 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   VAL A 626 " --> pdb=" O   LEU A 622 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 652 through 681
    Processing helix  chain 'A' and resid 684 through 705
      removed outlier: 5.245A  pdb=" N   VAL A 697 " --> pdb=" O   LEU A 693 " (cutoff:3.500A)
      removed outlier: 5.754A  pdb=" N   TYR A 698 " --> pdb=" O   THR A 694 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   PHE A 699 " --> pdb=" O   VAL A 695 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 708 through 720
      removed outlier: 5.105A  pdb=" N   THR A 716 " --> pdb=" O   PHE A 712 " (cutoff:3.500A)
      removed outlier: 5.041A  pdb=" N   HIS A 717 " --> pdb=" O   MET A 713 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ALA A 720 " --> pdb=" O   THR A 716 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 721 through 736
    Processing helix  chain 'A' and resid 764 through 819
    Processing helix  chain 'A' and resid 824 through 857
      removed outlier: 4.855A  pdb=" N   GLY A 854 " --> pdb=" O   ILE A 850 " (cutoff:3.500A)
      removed outlier: 5.326A  pdb=" N   LEU A 855 " --> pdb=" O   HIS A 851 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 64 through 74
    Processing helix  chain 'B' and resid 77 through 91
      removed outlier: 3.701A  pdb=" N   ALA B  81 " --> pdb=" O   SER B  77 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   ILE B  91 " --> pdb=" O   THR B  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 110
    Processing helix  chain 'B' and resid 112 through 131
      removed outlier: 3.830A  pdb=" N   ALA B 116 " --> pdb=" O   ARG B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 136 through 162
    Processing helix  chain 'B' and resid 194 through 199
    Processing helix  chain 'B' and resid 210 through 214
    Processing helix  chain 'B' and resid 221 through 227
    Processing helix  chain 'B' and resid 242 through 263
      removed outlier: 3.942A  pdb=" N   LEU B 246 " --> pdb=" O   GLY B 242 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLN B 263 " --> pdb=" O   TYR B 259 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 279 through 282
    Processing helix  chain 'B' and resid 297 through 307
    Processing helix  chain 'B' and resid 311 through 319
    Processing helix  chain 'B' and resid 357 through 374
    Processing helix  chain 'B' and resid 390 through 403
      removed outlier: 3.616A  pdb=" N   HIS B 403 " --> pdb=" O   PHE B 399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 423 through 448
      removed outlier: 3.642A  pdb=" N   SER B 427 " --> pdb=" O   ASN B 423 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   PHE B 447 " --> pdb=" O   LEU B 443 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 467 through 474
    Processing helix  chain 'B' and resid 474 through 479
    Processing helix  chain 'B' and resid 480 through 485
      removed outlier: 3.709A  pdb=" N   LEU B 484 " --> pdb=" O   GLU B 480 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 485 through 492
      removed outlier: 3.658A  pdb=" N   MET B 491 " --> pdb=" O   PHE B 487 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   TYR B 492 " --> pdb=" O   ILE B 488 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 495 through 505
      removed outlier: 3.803A  pdb=" N   LEU B 499 " --> pdb=" O   GLU B 495 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 528 through 554
      removed outlier: 3.856A  pdb=" N   LEU B 532 " --> pdb=" O   ASP B 528 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 555 through 560
    Processing helix  chain 'B' and resid 564 through 587
      removed outlier: 3.748A  pdb=" N   PHE B 587 " --> pdb=" O   ALA B 583 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 587 through 606
    Processing helix  chain 'B' and resid 619 through 647
      removed outlier: 3.992A  pdb=" N   ASP B 623 " --> pdb=" O   GLN B 619 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   VAL B 626 " --> pdb=" O   LEU B 622 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 652 through 681
    Processing helix  chain 'B' and resid 684 through 705
      removed outlier: 5.244A  pdb=" N   VAL B 697 " --> pdb=" O   LEU B 693 " (cutoff:3.500A)
      removed outlier: 5.753A  pdb=" N   TYR B 698 " --> pdb=" O   THR B 694 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   PHE B 699 " --> pdb=" O   VAL B 695 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 708 through 720
      removed outlier: 5.106A  pdb=" N   THR B 716 " --> pdb=" O   PHE B 712 " (cutoff:3.500A)
      removed outlier: 5.041A  pdb=" N   HIS B 717 " --> pdb=" O   MET B 713 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ALA B 720 " --> pdb=" O   THR B 716 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 721 through 736
    Processing helix  chain 'B' and resid 764 through 819
    Processing helix  chain 'B' and resid 824 through 857
      removed outlier: 4.855A  pdb=" N   GLY B 854 " --> pdb=" O   ILE B 850 " (cutoff:3.500A)
      removed outlier: 5.325A  pdb=" N   LEU B 855 " --> pdb=" O   HIS B 851 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 56
      removed outlier: 6.293A  pdb=" N   HIS B 175 " --> pdb=" O   PRO B 205 " (cutoff:3.500A)
      removed outlier: 7.960A  pdb=" N   ARG B 200 " --> pdb=" O   THR B 332 " (cutoff:3.500A)
      removed outlier: 5.808A  pdb=" N   THR B 332 " --> pdb=" O   ARG B 200 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   CYS B 326 " --> pdb=" O   VAL B 206 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   GLN B 346 " --> pdb=" O   VAL B 284 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   LEU B 232 " --> pdb=" O   LEU B 285 " (cutoff:3.500A)
      removed outlier: 8.018A  pdb=" N   CYS B 287 " --> pdb=" O   LEU B 232 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   ILE B 234 " --> pdb=" O   CYS B 287 " (cutoff:3.500A)
      removed outlier: 7.528A  pdb=" N   VAL B 289 " --> pdb=" O   ILE B 234 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   ILE B 236 " --> pdb=" O   VAL B 289 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   MET B 233 " --> pdb=" O   ALA B 379 " (cutoff:3.500A)
      removed outlier: 7.877A  pdb=" N   MET B 381 " --> pdb=" O   MET B 233 " (cutoff:3.500A)
      removed outlier: 5.869A  pdb=" N   CYS B 235 " --> pdb=" O   MET B 381 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   ARG B 461 " --> pdb=" O   GLY B 406 " (cutoff:3.500A)
      removed outlier: 7.280A  pdb=" N   GLY B 406 " --> pdb=" O   ARG B 461 " (cutoff:3.500A)
      removed outlier: 7.546A  pdb=" N   HIS B 514 " --> pdb=" O   GLY B 406 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   ALA B 408 " --> pdb=" O   HIS B 514 " (cutoff:3.500A)
      removed outlier: 7.119A  pdb=" N   VAL B 516 " --> pdb=" O   ALA B 408 " (cutoff:3.500A)
      removed outlier: 4.736A  pdb=" N   GLY B 410 " --> pdb=" O   VAL B 516 " (cutoff:3.500A)
      removed outlier: 7.915A  pdb=" N   ASP B 518 " --> pdb=" O   GLY B 410 " (cutoff:3.500A)
      removed outlier: 8.864A  pdb=" N   LEU B 412 " --> pdb=" O   ASP B 518 " (cutoff:3.500A)
      removed outlier: 8.077A  pdb=" N   VAL B 520 " --> pdb=" O   LEU B 412 " (cutoff:3.500A)
      removed outlier: 9.385A  pdb=" N   VAL B 414 " --> pdb=" O   VAL B 520 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   ARG B 522 " --> pdb=" O   VAL B 414 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 386 through 387
      removed outlier: 7.546A  pdb=" N   HIS A 514 " --> pdb=" O   GLY A 406 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   ALA A 408 " --> pdb=" O   HIS A 514 " (cutoff:3.500A)
      removed outlier: 7.119A  pdb=" N   VAL A 516 " --> pdb=" O   ALA A 408 " (cutoff:3.500A)
      removed outlier: 4.737A  pdb=" N   GLY A 410 " --> pdb=" O   VAL A 516 " (cutoff:3.500A)
      removed outlier: 7.914A  pdb=" N   ASP A 518 " --> pdb=" O   GLY A 410 " (cutoff:3.500A)
      removed outlier: 8.864A  pdb=" N   LEU A 412 " --> pdb=" O   ASP A 518 " (cutoff:3.500A)
      removed outlier: 8.076A  pdb=" N   VAL A 520 " --> pdb=" O   LEU A 412 " (cutoff:3.500A)
      removed outlier: 9.384A  pdb=" N   VAL A 414 " --> pdb=" O   VAL A 520 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   ARG A 522 " --> pdb=" O   VAL A 414 " (cutoff:3.500A)
      removed outlier: 7.279A  pdb=" N   GLY A 406 " --> pdb=" O   ARG A 461 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   ARG A 461 " --> pdb=" O   GLY A 406 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   MET A 233 " --> pdb=" O   ALA A 379 " (cutoff:3.500A)
      removed outlier: 7.877A  pdb=" N   MET A 381 " --> pdb=" O   MET A 233 " (cutoff:3.500A)
      removed outlier: 5.869A  pdb=" N   CYS A 235 " --> pdb=" O   MET A 381 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   LEU A 232 " --> pdb=" O   LEU A 285 " (cutoff:3.500A)
      removed outlier: 8.018A  pdb=" N   CYS A 287 " --> pdb=" O   LEU A 232 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   ILE A 234 " --> pdb=" O   CYS A 287 " (cutoff:3.500A)
      removed outlier: 7.528A  pdb=" N   VAL A 289 " --> pdb=" O   ILE A 234 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   ILE A 236 " --> pdb=" O   VAL A 289 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   GLN A 346 " --> pdb=" O   VAL A 284 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   CYS A 326 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      removed outlier: 5.808A  pdb=" N   THR A 332 " --> pdb=" O   ARG A 200 " (cutoff:3.500A)
      removed outlier: 7.960A  pdb=" N   ARG A 200 " --> pdb=" O   THR A 332 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   HIS A 175 " --> pdb=" O   PRO A 205 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   VAL A 174 " --> pdb=" O   VAL B  53 " (cutoff:3.500A)
      removed outlier: 7.857A  pdb=" N   SER B  55 " --> pdb=" O   VAL A 174 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   LYS A 176 " --> pdb=" O   SER B  55 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 336 through 337
    Processing sheet with id=AA4, first strand: chain 'B' and resid 336 through 337

    834 hydrogen bonds defined for protein.
    2460 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: 2.18

  Time building geometry restraints manager: 1.39 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: 4100
        1.34 -     1.46: 2750
        1.46 -     1.57: 6362
        1.57 -     1.69: 0
        1.69 -     1.81: 112
  Bond restraints: 13324
  Sorted by residual:
  bond pdb=" C   SER B 534 "
       pdb=" O   SER B 534 "
    ideal  model  delta    sigma   weight residual
    1.237  1.248 -0.012 1.16e-02 7.43e+03 1.03e+00
  bond pdb=" C   SER A 534 "
       pdb=" O   SER A 534 "
    ideal  model  delta    sigma   weight residual
    1.237  1.248 -0.011 1.16e-02 7.43e+03 9.53e-01
  bond pdb=" C   ASN A 541 "
       pdb=" O   ASN A 541 "
    ideal  model  delta    sigma   weight residual
    1.236  1.247 -0.011 1.15e-02 7.56e+03 9.10e-01
  bond pdb=" C   ASN B 541 "
       pdb=" O   ASN B 541 "
    ideal  model  delta    sigma   weight residual
    1.236  1.247 -0.011 1.15e-02 7.56e+03 8.50e-01
  bond pdb=" C   PRO A 649 "
       pdb=" N   LYS A 650 "
    ideal  model  delta    sigma   weight residual
    1.332  1.320  0.013 1.40e-02 5.10e+03 8.06e-01
  ... (remaining 13319 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.13: 17572
        1.13 -     2.26: 387
        2.26 -     3.39: 95
        3.39 -     4.52: 28
        4.52 -     5.65: 12
  Bond angle restraints: 18094
  Sorted by residual:
  angle pdb=" C   GLY B 277 "
        pdb=" N   ASP B 278 "
        pdb=" CA  ASP B 278 "
      ideal   model   delta    sigma   weight residual
     121.54  127.19   -5.65 1.91e+00 2.74e-01 8.74e+00
  angle pdb=" C   GLY A 277 "
        pdb=" N   ASP A 278 "
        pdb=" CA  ASP A 278 "
      ideal   model   delta    sigma   weight residual
     121.54  127.12   -5.58 1.91e+00 2.74e-01 8.52e+00
  angle pdb=" C   PHE B 601 "
        pdb=" N   GLN B 602 "
        pdb=" CA  GLN B 602 "
      ideal   model   delta    sigma   weight residual
     121.14  116.81    4.33 1.75e+00 3.27e-01 6.13e+00
  angle pdb=" C   PHE A 601 "
        pdb=" N   GLN A 602 "
        pdb=" CA  GLN A 602 "
      ideal   model   delta    sigma   weight residual
     121.14  116.81    4.33 1.75e+00 3.27e-01 6.12e+00
  angle pdb=" N   GLN B 619 "
        pdb=" CA  GLN B 619 "
        pdb=" C   GLN B 619 "
      ideal   model   delta    sigma   weight residual
     113.72  110.18    3.54 1.52e+00 4.33e-01 5.43e+00
  ... (remaining 18089 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.19: 7290
       16.19 -    32.38: 410
       32.38 -    48.57: 64
       48.57 -    64.76: 16
       64.76 -    80.95: 6
  Dihedral angle restraints: 7786
    sinusoidal: 3058
      harmonic: 4728
  Sorted by residual:
  dihedral pdb=" CA  TYR A 617 "
           pdb=" C   TYR A 617 "
           pdb=" N   SER A 618 "
           pdb=" CA  SER A 618 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.37  -18.63     0      5.00e+00 4.00e-02 1.39e+01
  dihedral pdb=" CA  TYR B 617 "
           pdb=" C   TYR B 617 "
           pdb=" N   SER B 618 "
           pdb=" CA  SER B 618 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.40  -18.60     0      5.00e+00 4.00e-02 1.38e+01
  dihedral pdb=" CA  ALA A 494 "
           pdb=" C   ALA A 494 "
           pdb=" N   GLU A 495 "
           pdb=" CA  GLU A 495 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.96  -18.04     0      5.00e+00 4.00e-02 1.30e+01
  ... (remaining 7783 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 1137
       0.025 -    0.050: 505
       0.050 -    0.074: 226
       0.074 -    0.099: 64
       0.099 -    0.124: 52
  Chirality restraints: 1984
  Sorted by residual:
  chirality pdb=" CA  VAL B 348 "
            pdb=" N   VAL B 348 "
            pdb=" C   VAL B 348 "
            pdb=" CB  VAL B 348 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.83e-01
  chirality pdb=" CA  VAL A 348 "
            pdb=" N   VAL A 348 "
            pdb=" C   VAL A 348 "
            pdb=" CB  VAL A 348 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.72e-01
  chirality pdb=" CA  ILE A 345 "
            pdb=" N   ILE A 345 "
            pdb=" C   ILE A 345 "
            pdb=" CB  ILE A 345 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.62e-01
  ... (remaining 1981 not shown)

  Planarity restraints: 2290
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 598 "   -0.014 2.00e-02 2.50e+03   2.75e-02 7.54e+00
        pdb=" C   PHE A 598 "    0.047 2.00e-02 2.50e+03
        pdb=" O   PHE A 598 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   ILE A 599 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 598 "    0.014 2.00e-02 2.50e+03   2.73e-02 7.47e+00
        pdb=" C   PHE B 598 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   PHE B 598 "    0.018 2.00e-02 2.50e+03
        pdb=" N   ILE B 599 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 599 "    0.013 2.00e-02 2.50e+03   2.50e-02 6.26e+00
        pdb=" C   ILE B 599 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   ILE B 599 "    0.016 2.00e-02 2.50e+03
        pdb=" N   VAL B 600 "    0.015 2.00e-02 2.50e+03
  ... (remaining 2287 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 2970
        2.79 -     3.32: 11959
        3.32 -     3.85: 20135
        3.85 -     4.37: 21477
        4.37 -     4.90: 40906
  Nonbonded interactions: 97447
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 225 "
            pdb=" OH  TYR B  52 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" OH  TYR A  52 "
            pdb=" OE2 GLU B 225 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" O   VAL A 726 "
            pdb=" OG1 THR A 730 "
     model   vdw
     2.359 3.040
  nonbonded pdb=" O   VAL B 726 "
            pdb=" OG1 THR B 730 "
     model   vdw
     2.360 3.040
  nonbonded pdb=" OE1 GLU A 312 "
            pdb=" NH2 ARG B 773 "
     model   vdw
     2.367 3.120
  ... (remaining 97442 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.710
  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:          0.200
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     13.910
  Find NCS groups from input model:        0.090
  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:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13324  Z= 0.134
  Angle     :  0.477   5.648  18094  Z= 0.261
  Chirality :  0.038   0.124   1984
  Planarity :  0.004   0.032   2290
  Dihedral  : 10.785  80.950   4750
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  6.33 %
    Favored  : 93.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.13 %
    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:  1.87 (0.22), residues: 1606
  helix:  2.66 (0.17), residues: 984
  sheet: -0.16 (0.42), residues: 152
  loop : -1.49 (0.27), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 608 
 TYR   0.010   0.001   TYR B 460 
 PHE   0.013   0.001   PHE B 545 
 TRP   0.008   0.001   TRP A 804 
 HIS   0.003   0.001   HIS B 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (13324)
  covalent geometry    : angle       0.47745 (18094)
  hydrogen bonds       : bond        0.13260 (  834)
  hydrogen bonds       : angle       5.21558 ( 2460)

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

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

  3212 Ramachandran restraints generated.
    1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3212 Ramachandran restraints generated.
    1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 210
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
REVERT: A  652 MET cc_start: 0.7827 (mmm) cc_final: 0.7541 (mmm)
REVERT: A  790 LYS cc_start: 0.7904 (mttm) cc_final: 0.7541 (tttm)
REVERT: A  814 PHE cc_start: 0.8048 (m-10) cc_final: 0.7812 (t80)
REVERT: B  513 MET cc_start: 0.8443 (mtp) cc_final: 0.8187 (mtp)
REVERT: B  652 MET cc_start: 0.7959 (mmm) cc_final: 0.7683 (mmm)
REVERT: B  733 SER cc_start: 0.8132 (t) cc_final: 0.7792 (m)
REVERT: B  790 LYS cc_start: 0.7925 (mttm) cc_final: 0.7475 (tttm)
REVERT: B  814 PHE cc_start: 0.7920 (m-10) cc_final: 0.7686 (t80)
  outliers start: 4
  outliers final: 2
  residues processed: 212
  average time/residue: 0.1166
  time to fit residues: 35.5778
Evaluate side-chains
  117 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 115
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 HIS
Chi-restraints excluded: chain B residue  327 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 98 optimal weight:    0.0770
   chunk 107 optimal weight:    0.0050
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.6980
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:    0.6980
   overall best weight:    0.4752

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.119460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.092811 restraints weight = 19631.284|
|-----------------------------------------------------------------------------|
r_work (start): 0.3099 rms_B_bonded: 2.17
r_work: 0.2990 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2866 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.1196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  13324  Z= 0.126
  Angle     :  0.499   5.753  18094  Z= 0.268
  Chirality :  0.038   0.122   1984
  Planarity :  0.004   0.038   2290
  Dihedral  :  4.170  36.584   1774
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 11.22 %
    Favored  : 87.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.13 %
    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:  2.14 (0.22), residues: 1606
  helix:  2.73 (0.17), residues: 996
  sheet:  0.45 (0.42), residues: 164
  loop : -1.40 (0.28), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 785 
 TYR   0.009   0.001   TYR B 460 
 PHE   0.013   0.001   PHE A 545 
 TRP   0.006   0.001   TRP A 804 
 HIS   0.002   0.001   HIS A 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 (13324)
  covalent geometry    : angle       0.49886 (18094)
  hydrogen bonds       : bond        0.06120 (  834)
  hydrogen bonds       : angle       4.56912 ( 2460)

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

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

  3212 Ramachandran restraints generated.
    1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3212 Ramachandran restraints generated.
    1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 133
  time to evaluate  : 0.502 
Fit side-chains
REVERT: A  790 LYS cc_start: 0.8251 (mttm) cc_final: 0.7633 (tttm)
REVERT: A  814 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.7654 (t80)
REVERT: B  513 MET cc_start: 0.9069 (mtp) cc_final: 0.8816 (mtp)
REVERT: B  652 MET cc_start: 0.7938 (mmm) cc_final: 0.7583 (mmm)
REVERT: B  736 ASN cc_start: 0.8309 (m-40) cc_final: 0.8095 (m110)
REVERT: B  790 LYS cc_start: 0.8108 (mttm) cc_final: 0.7640 (tttm)
REVERT: B  814 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.7516 (t80)
  outliers start: 24
  outliers final: 15
  residues processed: 151
  average time/residue: 0.0982
  time to fit residues: 23.0364
Evaluate side-chains
  132 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  327 HIS
Chi-restraints excluded: chain A residue  496 ASP
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  671 SER
Chi-restraints excluded: chain A residue  688 ILE
Chi-restraints excluded: chain A residue  707 GLU
Chi-restraints excluded: chain A residue  814 PHE
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  327 HIS
Chi-restraints excluded: chain B residue  496 ASP
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  671 SER
Chi-restraints excluded: chain B residue  688 ILE
Chi-restraints excluded: chain B residue  707 GLU
Chi-restraints excluded: chain B residue  814 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 9 optimal weight:    6.9990
   chunk 143 optimal weight:    4.9990
   chunk 25 optimal weight:    4.9990
   chunk 104 optimal weight:    0.0970
   chunk 72 optimal weight:    0.9990
   chunk 157 optimal weight:    0.5980
   chunk 83 optimal weight:    7.9990
   chunk 26 optimal weight:    0.9980
   chunk 16 optimal weight:    5.9990
   chunk 101 optimal weight:    3.9990
   overall best weight:    1.3382

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

Flipped N/Q/H residues before XYZ refinement:
A 338 ASN
** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 736 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.116323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.089038 restraints weight = 20201.533|
|-----------------------------------------------------------------------------|
r_work (start): 0.3026 rms_B_bonded: 2.25
r_work: 0.2913 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2790 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8521
moved from start:          0.1464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026  13324  Z= 0.178
  Angle     :  0.536   6.875  18094  Z= 0.288
  Chirality :  0.040   0.131   1984
  Planarity :  0.004   0.033   2290
  Dihedral  :  4.234  36.002   1774
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 12.01 %
    Favored  : 85.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.13 %
    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:  2.01 (0.22), residues: 1606
  helix:  2.65 (0.17), residues: 998
  sheet:  0.21 (0.41), residues: 166
  loop : -1.44 (0.28), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 536 
 TYR   0.013   0.001   TYR A 207 
 PHE   0.016   0.001   PHE A 545 
 TRP   0.010   0.001   TRP A 804 
 HIS   0.003   0.001   HIS A 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 (13324)
  covalent geometry    : angle       0.53555 (18094)
  hydrogen bonds       : bond        0.07060 (  834)
  hydrogen bonds       : angle       4.59637 ( 2460)

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

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

  3212 Ramachandran restraints generated.
    1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3212 Ramachandran restraints generated.
    1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 124
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
REVERT: A  790 LYS cc_start: 0.8127 (mttm) cc_final: 0.7671 (tttm)
REVERT: A  814 PHE cc_start: 0.8566 (OUTLIER) cc_final: 0.7749 (t80)
REVERT: A  856 ARG cc_start: 0.6649 (ttt180) cc_final: 0.6300 (mmm160)
REVERT: B  513 MET cc_start: 0.9078 (mtp) cc_final: 0.8853 (mtp)
REVERT: B  790 LYS cc_start: 0.8148 (mttm) cc_final: 0.7701 (tttm)
REVERT: B  814 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.7618 (t80)
REVERT: B  856 ARG cc_start: 0.6677 (ttt180) cc_final: 0.6334 (mmm160)
  outliers start: 33
  outliers final: 24
  residues processed: 150
  average time/residue: 0.0950
  time to fit residues: 21.7464
Evaluate side-chains
  137 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 111
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  327 HIS
Chi-restraints excluded: chain A residue  334 GLN
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  671 SER
Chi-restraints excluded: chain A residue  684 THR
Chi-restraints excluded: chain A residue  688 ILE
Chi-restraints excluded: chain A residue  707 GLU
Chi-restraints excluded: chain A residue  733 SER
Chi-restraints excluded: chain A residue  814 PHE
Chi-restraints excluded: chain A residue  820 SER
Chi-restraints excluded: chain A residue  848 VAL
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  327 HIS
Chi-restraints excluded: chain B residue  524 ASP
Chi-restraints excluded: chain B residue  671 SER
Chi-restraints excluded: chain B residue  684 THR
Chi-restraints excluded: chain B residue  688 ILE
Chi-restraints excluded: chain B residue  707 GLU
Chi-restraints excluded: chain B residue  814 PHE
Chi-restraints excluded: chain B residue  848 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 113 optimal weight:    0.9990
   chunk 112 optimal weight:    0.7980
   chunk 107 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 83 optimal weight:    4.9990
   chunk 114 optimal weight:    0.9980
   chunk 121 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 152 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 736 ASN
B 109 ASN
** B 647 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 = 0.3438 r_free = 0.3438 target = 0.117441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.090111 restraints weight = 19971.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.3029 rms_B_bonded: 2.25
r_work: 0.2917 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2794 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
moved from start:          0.1582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  13324  Z= 0.146
  Angle     :  0.509   7.695  18094  Z= 0.273
  Chirality :  0.038   0.128   1984
  Planarity :  0.004   0.032   2290
  Dihedral  :  4.227  38.363   1774
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 12.59 %
    Favored  : 84.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.13 %
    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:  2.08 (0.22), residues: 1606
  helix:  2.73 (0.17), residues: 998
  sheet:  0.19 (0.41), residues: 166
  loop : -1.45 (0.28), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 772 
 TYR   0.012   0.001   TYR B 207 
 PHE   0.015   0.001   PHE A 545 
 TRP   0.009   0.001   TRP B 804 
 HIS   0.002   0.001   HIS A 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (13324)
  covalent geometry    : angle       0.50905 (18094)
  hydrogen bonds       : bond        0.06560 (  834)
  hydrogen bonds       : angle       4.51519 ( 2460)

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

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

  3212 Ramachandran restraints generated.
    1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3212 Ramachandran restraints generated.
    1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 121
  time to evaluate  : 0.576 
Fit side-chains
   revert: symmetry clash
REVERT: A  737 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7278 (tt)
REVERT: A  790 LYS cc_start: 0.8137 (mttm) cc_final: 0.7736 (tttm)
REVERT: A  814 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.7733 (t80)
REVERT: A  856 ARG cc_start: 0.6682 (ttt180) cc_final: 0.6443 (mmm160)
REVERT: B  513 MET cc_start: 0.9088 (mtp) cc_final: 0.8863 (mtp)
REVERT: B  737 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7177 (tt)
REVERT: B  790 LYS cc_start: 0.8107 (mttm) cc_final: 0.7675 (tttm)
REVERT: B  814 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.7613 (t80)
REVERT: B  856 ARG cc_start: 0.6650 (ttt180) cc_final: 0.6339 (mmm160)
  outliers start: 43
  outliers final: 30
  residues processed: 159
  average time/residue: 0.1069
  time to fit residues: 25.6273
Evaluate side-chains
  147 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 113
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  327 HIS
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  671 SER
Chi-restraints excluded: chain A residue  684 THR
Chi-restraints excluded: chain A residue  688 ILE
Chi-restraints excluded: chain A residue  707 GLU
Chi-restraints excluded: chain A residue  733 SER
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  814 PHE
Chi-restraints excluded: chain A residue  820 SER
Chi-restraints excluded: chain A residue  848 VAL
Chi-restraints excluded: chain B residue   70 ASP
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  327 HIS
Chi-restraints excluded: chain B residue  452 VAL
Chi-restraints excluded: chain B residue  524 ASP
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  671 SER
Chi-restraints excluded: chain B residue  684 THR
Chi-restraints excluded: chain B residue  688 ILE
Chi-restraints excluded: chain B residue  707 GLU
Chi-restraints excluded: chain B residue  737 LEU
Chi-restraints excluded: chain B residue  814 PHE
Chi-restraints excluded: chain B residue  848 VAL
Chi-restraints excluded: chain B residue  851 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 117 optimal weight:    4.9990
   chunk 29 optimal weight:    4.9990
   chunk 18 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 70 optimal weight:   10.0000
   chunk 62 optimal weight:    0.8980
   chunk 87 optimal weight:    5.9990
   chunk 140 optimal weight:    2.9990
   chunk 95 optimal weight:    0.0870
   chunk 159 optimal weight:    2.9990
   chunk 97 optimal weight:    0.5980
   overall best weight:    1.5162

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

Flipped N/Q/H residues before XYZ refinement:
** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 736 ASN
** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 736 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.114458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.087344 restraints weight = 20208.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.3007 rms_B_bonded: 2.20
r_work: 0.2892 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2768 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.1759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030  13324  Z= 0.196
  Angle     :  0.544   7.810  18094  Z= 0.293
  Chirality :  0.040   0.134   1984
  Planarity :  0.004   0.083   2290
  Dihedral  :  4.318  38.169   1774
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 13.24 %
    Favored  : 83.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.13 %
    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:  1.94 (0.22), residues: 1606
  helix:  2.66 (0.17), residues: 998
  sheet:  0.02 (0.40), residues: 166
  loop : -1.59 (0.28), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 839 
 TYR   0.014   0.001   TYR B 207 
 PHE   0.017   0.001   PHE A 545 
 TRP   0.011   0.001   TRP A 804 
 HIS   0.003   0.001   HIS B 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 (13324)
  covalent geometry    : angle       0.54427 (18094)
  hydrogen bonds       : bond        0.07307 (  834)
  hydrogen bonds       : angle       4.60301 ( 2460)

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

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

  3212 Ramachandran restraints generated.
    1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3212 Ramachandran restraints generated.
    1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 118
  time to evaluate  : 0.491 
Fit side-chains
REVERT: A   39 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7187 (pp)
REVERT: A  510 ASN cc_start: 0.9157 (OUTLIER) cc_final: 0.8721 (p0)
REVERT: A  737 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7386 (tt)
REVERT: A  790 LYS cc_start: 0.8182 (mttm) cc_final: 0.7725 (tttm)
REVERT: A  814 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.7814 (t80)
REVERT: A  852 THR cc_start: 0.8425 (t) cc_final: 0.8220 (t)
REVERT: A  856 ARG cc_start: 0.6768 (ttt180) cc_final: 0.6356 (mmm160)
REVERT: B   39 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7217 (pp)
REVERT: B  510 ASN cc_start: 0.9152 (OUTLIER) cc_final: 0.8742 (p0)
REVERT: B  737 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7429 (tt)
REVERT: B  790 LYS cc_start: 0.8150 (mttm) cc_final: 0.7626 (tttm)
REVERT: B  814 PHE cc_start: 0.8599 (OUTLIER) cc_final: 0.7756 (t80)
REVERT: B  856 ARG cc_start: 0.6619 (ttt180) cc_final: 0.6249 (mmm160)
  outliers start: 51
  outliers final: 36
  residues processed: 164
  average time/residue: 0.1112
  time to fit residues: 26.4829
Evaluate side-chains
  153 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 109
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  327 HIS
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  510 ASN
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  671 SER
Chi-restraints excluded: chain A residue  684 THR
Chi-restraints excluded: chain A residue  688 ILE
Chi-restraints excluded: chain A residue  693 LEU
Chi-restraints excluded: chain A residue  697 VAL
Chi-restraints excluded: chain A residue  707 GLU
Chi-restraints excluded: chain A residue  733 SER
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  814 PHE
Chi-restraints excluded: chain A residue  820 SER
Chi-restraints excluded: chain A residue  848 VAL
Chi-restraints excluded: chain A residue  851 HIS
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain B residue   70 ASP
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  327 HIS
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  452 VAL
Chi-restraints excluded: chain B residue  510 ASN
Chi-restraints excluded: chain B residue  524 ASP
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  671 SER
Chi-restraints excluded: chain B residue  684 THR
Chi-restraints excluded: chain B residue  688 ILE
Chi-restraints excluded: chain B residue  693 LEU
Chi-restraints excluded: chain B residue  707 GLU
Chi-restraints excluded: chain B residue  737 LEU
Chi-restraints excluded: chain B residue  814 PHE
Chi-restraints excluded: chain B residue  848 VAL
Chi-restraints excluded: chain B residue  851 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 79 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 110 optimal weight:    0.2980
   chunk 38 optimal weight:    2.9990
   chunk 116 optimal weight:    2.9990
   chunk 47 optimal weight:    0.3980
   chunk 49 optimal weight:    0.8980
   chunk 111 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 130 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 736 ASN
** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 736 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.118345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.092389 restraints weight = 19531.803|
|-----------------------------------------------------------------------------|
r_work (start): 0.3058 rms_B_bonded: 2.11
r_work: 0.2947 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2824 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.1788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13324  Z= 0.130
  Angle     :  0.492   8.545  18094  Z= 0.263
  Chirality :  0.038   0.125   1984
  Planarity :  0.004   0.065   2290
  Dihedral  :  4.219  40.448   1774
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 14.46 %
    Favored  : 82.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.13 %
    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:  2.14 (0.22), residues: 1606
  helix:  2.85 (0.17), residues: 988
  sheet:  0.24 (0.41), residues: 166
  loop : -1.54 (0.27), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 772 
 TYR   0.015   0.001   TYR B  52 
 PHE   0.015   0.001   PHE A 487 
 TRP   0.009   0.001   TRP B 804 
 HIS   0.002   0.001   HIS A 175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (13324)
  covalent geometry    : angle       0.49173 (18094)
  hydrogen bonds       : bond        0.06271 (  834)
  hydrogen bonds       : angle       4.46745 ( 2460)

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

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

  3212 Ramachandran restraints generated.
    1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3212 Ramachandran restraints generated.
    1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 118
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 ARG cc_start: 0.7852 (ptm160) cc_final: 0.7345 (mtm110)
REVERT: A  134 GLN cc_start: 0.9203 (mm-40) cc_final: 0.8951 (mm-40)
REVERT: A  510 ASN cc_start: 0.9135 (OUTLIER) cc_final: 0.8679 (p0)
REVERT: A  736 ASN cc_start: 0.8390 (m-40) cc_final: 0.8164 (m110)
REVERT: A  737 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7288 (tt)
REVERT: A  790 LYS cc_start: 0.8129 (mttm) cc_final: 0.7726 (tttm)
REVERT: A  814 PHE cc_start: 0.8553 (OUTLIER) cc_final: 0.7744 (t80)
REVERT: B   39 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7117 (pp)
REVERT: B  510 ASN cc_start: 0.9142 (OUTLIER) cc_final: 0.8718 (p0)
REVERT: B  737 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7338 (tt)
REVERT: B  790 LYS cc_start: 0.8080 (mttm) cc_final: 0.7653 (tttm)
REVERT: B  814 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.7688 (t80)
REVERT: B  856 ARG cc_start: 0.6589 (ttt180) cc_final: 0.6211 (mmm160)
  outliers start: 45
  outliers final: 31
  residues processed: 158
  average time/residue: 0.1010
  time to fit residues: 24.2886
Evaluate side-chains
  151 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 113
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  327 HIS
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  510 ASN
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  671 SER
Chi-restraints excluded: chain A residue  684 THR
Chi-restraints excluded: chain A residue  733 SER
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  814 PHE
Chi-restraints excluded: chain A residue  820 SER
Chi-restraints excluded: chain A residue  851 HIS
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain B residue   70 ASP
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  327 HIS
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  452 VAL
Chi-restraints excluded: chain B residue  499 LEU
Chi-restraints excluded: chain B residue  510 ASN
Chi-restraints excluded: chain B residue  524 ASP
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  671 SER
Chi-restraints excluded: chain B residue  684 THR
Chi-restraints excluded: chain B residue  707 GLU
Chi-restraints excluded: chain B residue  737 LEU
Chi-restraints excluded: chain B residue  814 PHE
Chi-restraints excluded: chain B residue  851 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 149 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 134 optimal weight:    2.9990
   chunk 88 optimal weight:    4.9990
   chunk 115 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9980
   chunk 13 optimal weight:    4.9990
   chunk 43 optimal weight:    0.8980
   chunk 129 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 736 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.117848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.091882 restraints weight = 19588.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.3051 rms_B_bonded: 2.11
r_work: 0.2940 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2817 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8489
moved from start:          0.1848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  13324  Z= 0.141
  Angle     :  0.509   8.955  18094  Z= 0.271
  Chirality :  0.038   0.127   1984
  Planarity :  0.004   0.056   2290
  Dihedral  :  4.181  40.031   1774
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 14.75 %
    Favored  : 81.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.13 %
    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:  2.12 (0.22), residues: 1606
  helix:  2.84 (0.17), residues: 988
  sheet:  0.22 (0.40), residues: 166
  loop : -1.56 (0.27), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 772 
 TYR   0.012   0.001   TYR A 207 
 PHE   0.015   0.001   PHE A 545 
 TRP   0.010   0.001   TRP B 804 
 HIS   0.002   0.001   HIS A 430 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (13324)
  covalent geometry    : angle       0.50858 (18094)
  hydrogen bonds       : bond        0.06365 (  834)
  hydrogen bonds       : angle       4.47477 ( 2460)

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

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

  3212 Ramachandran restraints generated.
    1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3212 Ramachandran restraints generated.
    1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 119
  time to evaluate  : 0.460 
Fit side-chains
REVERT: A   39 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7265 (pp)
REVERT: A   86 ARG cc_start: 0.7888 (ptm160) cc_final: 0.7348 (mtm110)
REVERT: A  134 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8942 (mm-40)
REVERT: A  510 ASN cc_start: 0.9137 (OUTLIER) cc_final: 0.8673 (p0)
REVERT: A  737 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7331 (tt)
REVERT: A  790 LYS cc_start: 0.8172 (mttm) cc_final: 0.7752 (tttm)
REVERT: A  814 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.7745 (t80)
REVERT: A  856 ARG cc_start: 0.6711 (ttt180) cc_final: 0.6326 (mmm160)
REVERT: B   39 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7185 (pp)
REVERT: B  510 ASN cc_start: 0.9156 (OUTLIER) cc_final: 0.8706 (p0)
REVERT: B  737 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7351 (tt)
REVERT: B  790 LYS cc_start: 0.8108 (mttm) cc_final: 0.7659 (tttm)
REVERT: B  814 PHE cc_start: 0.8507 (OUTLIER) cc_final: 0.7685 (t80)
REVERT: B  856 ARG cc_start: 0.6621 (ttt180) cc_final: 0.6231 (mmm160)
  outliers start: 50
  outliers final: 32
  residues processed: 164
  average time/residue: 0.0984
  time to fit residues: 24.6639
Evaluate side-chains
  152 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 112
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  327 HIS
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  510 ASN
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  671 SER
Chi-restraints excluded: chain A residue  684 THR
Chi-restraints excluded: chain A residue  693 LEU
Chi-restraints excluded: chain A residue  707 GLU
Chi-restraints excluded: chain A residue  733 SER
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  814 PHE
Chi-restraints excluded: chain A residue  820 SER
Chi-restraints excluded: chain A residue  851 HIS
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain B residue   70 ASP
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  327 HIS
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  452 VAL
Chi-restraints excluded: chain B residue  510 ASN
Chi-restraints excluded: chain B residue  524 ASP
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  671 SER
Chi-restraints excluded: chain B residue  684 THR
Chi-restraints excluded: chain B residue  693 LEU
Chi-restraints excluded: chain B residue  737 LEU
Chi-restraints excluded: chain B residue  814 PHE
Chi-restraints excluded: chain B residue  851 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 66 optimal weight:    0.8980
   chunk 5 optimal weight:    5.9990
   chunk 84 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 146 optimal weight:    0.5980
   chunk 110 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 128 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0040
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.5992

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

Flipped N/Q/H residues before XYZ refinement:
** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 736 ASN
** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 736 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.119388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.093553 restraints weight = 19512.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.3082 rms_B_bonded: 2.11
r_work: 0.2973 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2850 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8459
moved from start:          0.1926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13324  Z= 0.122
  Angle     :  0.498   8.800  18094  Z= 0.265
  Chirality :  0.038   0.123   1984
  Planarity :  0.004   0.051   2290
  Dihedral  :  4.125  40.882   1774
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 15.18 %
    Favored  : 81.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.13 %
    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:  2.18 (0.22), residues: 1606
  helix:  2.87 (0.17), residues: 990
  sheet:  0.30 (0.41), residues: 166
  loop : -1.54 (0.27), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 772 
 TYR   0.010   0.001   TYR B  52 
 PHE   0.013   0.001   PHE A 545 
 TRP   0.008   0.001   TRP B 804 
 HIS   0.002   0.001   HIS A 514 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 (13324)
  covalent geometry    : angle       0.49786 (18094)
  hydrogen bonds       : bond        0.05836 (  834)
  hydrogen bonds       : angle       4.41989 ( 2460)

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

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

  3212 Ramachandran restraints generated.
    1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3212 Ramachandran restraints generated.
    1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 122
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7343 (pp)
REVERT: A   86 ARG cc_start: 0.7907 (ptm160) cc_final: 0.7377 (mtm110)
REVERT: A  134 GLN cc_start: 0.9178 (mm-40) cc_final: 0.8935 (mm-40)
REVERT: A  314 LEU cc_start: 0.8709 (tp) cc_final: 0.8504 (tp)
REVERT: A  510 ASN cc_start: 0.9123 (OUTLIER) cc_final: 0.8719 (p0)
REVERT: A  737 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7250 (tt)
REVERT: A  790 LYS cc_start: 0.8187 (mttm) cc_final: 0.7810 (tttm)
REVERT: A  814 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.7679 (t80)
REVERT: A  856 ARG cc_start: 0.6599 (ttt180) cc_final: 0.6190 (mmm160)
REVERT: B   39 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7100 (pp)
REVERT: B  510 ASN cc_start: 0.9145 (OUTLIER) cc_final: 0.8714 (p0)
REVERT: B  737 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7223 (tt)
REVERT: B  790 LYS cc_start: 0.8083 (mttm) cc_final: 0.7679 (tttm)
REVERT: B  814 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.7673 (t80)
REVERT: B  856 ARG cc_start: 0.6608 (ttt180) cc_final: 0.6209 (mmm160)
  outliers start: 49
  outliers final: 30
  residues processed: 166
  average time/residue: 0.1086
  time to fit residues: 26.8111
Evaluate side-chains
  154 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 116
  time to evaluate  : 0.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  327 HIS
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  510 ASN
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  671 SER
Chi-restraints excluded: chain A residue  693 LEU
Chi-restraints excluded: chain A residue  733 SER
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  814 PHE
Chi-restraints excluded: chain A residue  820 SER
Chi-restraints excluded: chain A residue  851 HIS
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain B residue   70 ASP
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  327 HIS
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  452 VAL
Chi-restraints excluded: chain B residue  499 LEU
Chi-restraints excluded: chain B residue  510 ASN
Chi-restraints excluded: chain B residue  524 ASP
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  671 SER
Chi-restraints excluded: chain B residue  693 LEU
Chi-restraints excluded: chain B residue  737 LEU
Chi-restraints excluded: chain B residue  814 PHE
Chi-restraints excluded: chain B residue  851 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   chunk 36 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 83 optimal weight:    3.9990
   chunk 85 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9980
   chunk 52 optimal weight:    0.1980
   chunk 88 optimal weight:    4.9990
   chunk 125 optimal weight:    0.8980
   chunk 156 optimal weight:    2.9990
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 736 ASN
B 420 ASN
** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 736 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.116011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.089235 restraints weight = 19964.807|
|-----------------------------------------------------------------------------|
r_work (start): 0.3040 rms_B_bonded: 2.16
r_work: 0.2928 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2806 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.1970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13324  Z= 0.165
  Angle     :  0.534   9.183  18094  Z= 0.285
  Chirality :  0.039   0.137   1984
  Planarity :  0.004   0.083   2290
  Dihedral  :  4.166  39.667   1774
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 15.25 %
    Favored  : 81.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.13 %
    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:  2.08 (0.22), residues: 1606
  helix:  2.81 (0.17), residues: 988
  sheet:  0.13 (0.40), residues: 166
  loop : -1.54 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 785 
 TYR   0.014   0.001   TYR A 207 
 PHE   0.015   0.001   PHE A 545 
 TRP   0.009   0.001   TRP A 804 
 HIS   0.003   0.001   HIS B 430 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 (13324)
  covalent geometry    : angle       0.53438 (18094)
  hydrogen bonds       : bond        0.06614 (  834)
  hydrogen bonds       : angle       4.48836 ( 2460)

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

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

  3212 Ramachandran restraints generated.
    1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3212 Ramachandran restraints generated.
    1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 115
  time to evaluate  : 0.504 
Fit side-chains
REVERT: A   39 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7246 (pp)
REVERT: A   86 ARG cc_start: 0.7884 (ptm160) cc_final: 0.7331 (mtm110)
REVERT: A  134 GLN cc_start: 0.9206 (mm-40) cc_final: 0.8951 (mm-40)
REVERT: A  510 ASN cc_start: 0.9124 (OUTLIER) cc_final: 0.8643 (p0)
REVERT: A  737 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7365 (tt)
REVERT: A  790 LYS cc_start: 0.8272 (mttm) cc_final: 0.7835 (tttm)
REVERT: A  814 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.7767 (t80)
REVERT: A  856 ARG cc_start: 0.6759 (ttt180) cc_final: 0.6354 (mmm160)
REVERT: B   39 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7164 (pp)
REVERT: B  510 ASN cc_start: 0.9157 (OUTLIER) cc_final: 0.8689 (p0)
REVERT: B  737 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7356 (tt)
REVERT: B  790 LYS cc_start: 0.8155 (mttm) cc_final: 0.7753 (tttm)
REVERT: B  814 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.7722 (t80)
REVERT: B  856 ARG cc_start: 0.6620 (ttt180) cc_final: 0.6192 (mmm160)
  outliers start: 45
  outliers final: 32
  residues processed: 155
  average time/residue: 0.1010
  time to fit residues: 23.4744
Evaluate side-chains
  153 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 113
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  327 HIS
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  510 ASN
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  671 SER
Chi-restraints excluded: chain A residue  693 LEU
Chi-restraints excluded: chain A residue  707 GLU
Chi-restraints excluded: chain A residue  733 SER
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  814 PHE
Chi-restraints excluded: chain A residue  820 SER
Chi-restraints excluded: chain A residue  851 HIS
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain B residue   70 ASP
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  327 HIS
Chi-restraints excluded: chain B residue  420 ASN
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  452 VAL
Chi-restraints excluded: chain B residue  499 LEU
Chi-restraints excluded: chain B residue  510 ASN
Chi-restraints excluded: chain B residue  524 ASP
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  671 SER
Chi-restraints excluded: chain B residue  693 LEU
Chi-restraints excluded: chain B residue  707 GLU
Chi-restraints excluded: chain B residue  737 LEU
Chi-restraints excluded: chain B residue  814 PHE
Chi-restraints excluded: chain B residue  851 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 152 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   chunk 144 optimal weight:    0.3980
   chunk 11 optimal weight:    2.9990
   chunk 128 optimal weight:    0.8980
   chunk 92 optimal weight:    0.9980
   chunk 30 optimal weight:    4.9990
   chunk 39 optimal weight:    0.8980
   chunk 103 optimal weight:    0.0470
   chunk 36 optimal weight:    0.0670
   chunk 97 optimal weight:    0.5980
   overall best weight:    0.4016

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

Flipped N/Q/H residues before XYZ refinement:
** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 736 ASN
B 420 ASN
** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 736 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.116260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.089485 restraints weight = 19903.477|
|-----------------------------------------------------------------------------|
r_work (start): 0.3044 rms_B_bonded: 2.16
r_work: 0.2932 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2809 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.1978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.088  13324  Z= 0.165
  Angle     :  0.762  59.200  18094  Z= 0.450
  Chirality :  0.040   0.513   1984
  Planarity :  0.005   0.079   2290
  Dihedral  :  4.197  39.840   1774
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 15.90 %
    Favored  : 81.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.13 %
    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:  2.07 (0.22), residues: 1606
  helix:  2.81 (0.17), residues: 988
  sheet:  0.14 (0.40), residues: 166
  loop : -1.58 (0.27), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 785 
 TYR   0.014   0.001   TYR A 207 
 PHE   0.015   0.001   PHE A 545 
 TRP   0.008   0.001   TRP A 804 
 HIS   0.002   0.001   HIS B 430 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (13324)
  covalent geometry    : angle       0.76205 (18094)
  hydrogen bonds       : bond        0.06502 (  834)
  hydrogen bonds       : angle       4.48691 ( 2460)

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

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

  3212 Ramachandran restraints generated.
    1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3212 Ramachandran restraints generated.
    1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 113
  time to evaluate  : 0.415 
Fit side-chains
REVERT: A   39 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7277 (pp)
REVERT: A   86 ARG cc_start: 0.7875 (ptm160) cc_final: 0.7323 (mtm110)
REVERT: A  134 GLN cc_start: 0.9203 (mm-40) cc_final: 0.8948 (mm-40)
REVERT: A  737 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7330 (tt)
REVERT: A  790 LYS cc_start: 0.8278 (mttm) cc_final: 0.7845 (tttm)
REVERT: A  814 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.7763 (t80)
REVERT: A  856 ARG cc_start: 0.6745 (ttt180) cc_final: 0.6339 (mmm160)
REVERT: B   39 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7159 (pp)
REVERT: B  510 ASN cc_start: 0.9152 (OUTLIER) cc_final: 0.8688 (p0)
REVERT: B  737 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7354 (tt)
REVERT: B  790 LYS cc_start: 0.8146 (mttm) cc_final: 0.7745 (tttm)
REVERT: B  814 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.7719 (t80)
REVERT: B  856 ARG cc_start: 0.6611 (ttt180) cc_final: 0.6183 (mmm160)
  outliers start: 41
  outliers final: 33
  residues processed: 149
  average time/residue: 0.1010
  time to fit residues: 22.8277
Evaluate side-chains
  153 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 113
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  327 HIS
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  671 SER
Chi-restraints excluded: chain A residue  693 LEU
Chi-restraints excluded: chain A residue  707 GLU
Chi-restraints excluded: chain A residue  733 SER
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  814 PHE
Chi-restraints excluded: chain A residue  820 SER
Chi-restraints excluded: chain A residue  830 ILE
Chi-restraints excluded: chain A residue  851 HIS
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain B residue   70 ASP
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  327 HIS
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  452 VAL
Chi-restraints excluded: chain B residue  499 LEU
Chi-restraints excluded: chain B residue  510 ASN
Chi-restraints excluded: chain B residue  524 ASP
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  671 SER
Chi-restraints excluded: chain B residue  693 LEU
Chi-restraints excluded: chain B residue  707 GLU
Chi-restraints excluded: chain B residue  737 LEU
Chi-restraints excluded: chain B residue  814 PHE
Chi-restraints excluded: chain B residue  830 ILE
Chi-restraints excluded: chain B residue  851 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 126 optimal weight:    0.9990
   chunk 70 optimal weight:    9.9990
   chunk 155 optimal weight:    2.9990
   chunk 131 optimal weight:    0.3980
   chunk 3 optimal weight:    6.9990
   chunk 143 optimal weight:    3.9990
   chunk 107 optimal weight:    0.5980
   chunk 20 optimal weight:    0.5980
   chunk 52 optimal weight:    0.7980
   chunk 6 optimal weight:    4.9990
   chunk 153 optimal weight:    4.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.116297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.089514 restraints weight = 19809.116|
|-----------------------------------------------------------------------------|
r_work (start): 0.3044 rms_B_bonded: 2.16
r_work: 0.2932 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2809 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.088  13324  Z= 0.165
  Angle     :  0.762  59.200  18094  Z= 0.450
  Chirality :  0.040   0.513   1984
  Planarity :  0.005   0.079   2290
  Dihedral  :  4.197  39.840   1774
  Min Nonbonded Distance : 1.678

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 15.90 %
    Favored  : 81.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.13 %
    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:  2.07 (0.22), residues: 1606
  helix:  2.81 (0.17), residues: 988
  sheet:  0.14 (0.40), residues: 166
  loop : -1.58 (0.27), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 785 
 TYR   0.014   0.001   TYR A 207 
 PHE   0.015   0.001   PHE A 545 
 TRP   0.008   0.001   TRP A 804 
 HIS   0.002   0.001   HIS B 430 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (13324)
  covalent geometry    : angle       0.76205 (18094)
  hydrogen bonds       : bond        0.06502 (  834)
  hydrogen bonds       : angle       4.48691 ( 2460)

===============================================================================
Job complete
usr+sys time: 3036.89 seconds
wall clock time: 52 minutes 33.56 seconds (3153.56 seconds total)