Starting phenix.real_space_refine
on Sat Aug 23 22:29:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rlm_19341/08_2025/8rlm_19341.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rlm_19341/08_2025/8rlm_19341.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rlm_19341/08_2025/8rlm_19341.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rlm_19341/08_2025/8rlm_19341.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rlm_19341/08_2025/8rlm_19341.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rlm_19341/08_2025/8rlm_19341.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.028
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      42      5.16       5
     C    4662      2.51       5
     N    1374      2.21       5
     O    1356      1.98       5
     H    7236      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14670
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2445
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 2445
          Classifications: {'peptide': 157}
          Link IDs: {'PTRANS': 6, 'TRANS': 150}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 10
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
  Restraints were copied for chains:
    B, C, D, E, F
  Time building chain proxies: 1.80, per 1000 atoms: 0.12
  Number of scatterers: 14670
  At special positions: 0
  Unit cell: (67.158, 69.29, 132.184, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      42     16.00
     O    1356      8.00
     N    1374      7.00
     C    4662      6.00
     H    7236      1.00
    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: 1.12
  Conformation dependent library (CDL) restraints added in 388.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1836

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 6 sheets defined
      65.6% alpha, 9.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...
    Processing helix  chain 'A' and resid 402 through 404
      No H-bonds generated for 'chain 'A' and resid 402 through 404'
    Processing helix  chain 'A' and resid 405 through 419
    Processing helix  chain 'A' and resid 426 through 431
      removed outlier: 3.655A  pdb=" N   ASP A 430 " --> pdb=" O   THR A 426 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   PHE A 431 " --> pdb=" O   PHE A 427 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 426 through 431'
    Processing helix  chain 'A' and resid 442 through 448
      removed outlier: 3.600A  pdb=" N   HIS A 448 " --> pdb=" O   ASP A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 461
      removed outlier: 3.776A  pdb=" N   ASP A 461 " --> pdb=" O   SER A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 479
    Processing helix  chain 'A' and resid 495 through 499
      removed outlier: 3.859A  pdb=" N   LEU A 499 " --> pdb=" O   PRO A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 500 through 507
    Processing helix  chain 'A' and resid 519 through 528
    Processing helix  chain 'A' and resid 529 through 554
    Processing helix  chain 'B' and resid 402 through 404
      No H-bonds generated for 'chain 'B' and resid 402 through 404'
    Processing helix  chain 'B' and resid 405 through 419
    Processing helix  chain 'B' and resid 426 through 431
      removed outlier: 3.655A  pdb=" N   ASP B 430 " --> pdb=" O   THR B 426 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   PHE B 431 " --> pdb=" O   PHE B 427 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 426 through 431'
    Processing helix  chain 'B' and resid 442 through 448
      removed outlier: 3.599A  pdb=" N   HIS B 448 " --> pdb=" O   ASP B 444 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 457 through 461
      removed outlier: 3.775A  pdb=" N   ASP B 461 " --> pdb=" O   SER B 458 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 462 through 479
    Processing helix  chain 'B' and resid 495 through 499
      removed outlier: 3.859A  pdb=" N   LEU B 499 " --> pdb=" O   PRO B 496 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 500 through 507
    Processing helix  chain 'B' and resid 519 through 528
    Processing helix  chain 'B' and resid 529 through 554
    Processing helix  chain 'C' and resid 402 through 404
      No H-bonds generated for 'chain 'C' and resid 402 through 404'
    Processing helix  chain 'C' and resid 405 through 419
    Processing helix  chain 'C' and resid 426 through 431
      removed outlier: 3.655A  pdb=" N   ASP C 430 " --> pdb=" O   THR C 426 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   PHE C 431 " --> pdb=" O   PHE C 427 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 426 through 431'
    Processing helix  chain 'C' and resid 442 through 448
      removed outlier: 3.600A  pdb=" N   HIS C 448 " --> pdb=" O   ASP C 444 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 457 through 461
      removed outlier: 3.775A  pdb=" N   ASP C 461 " --> pdb=" O   SER C 458 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 462 through 479
    Processing helix  chain 'C' and resid 495 through 499
      removed outlier: 3.859A  pdb=" N   LEU C 499 " --> pdb=" O   PRO C 496 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 500 through 507
    Processing helix  chain 'C' and resid 519 through 528
    Processing helix  chain 'C' and resid 529 through 554
    Processing helix  chain 'D' and resid 402 through 404
      No H-bonds generated for 'chain 'D' and resid 402 through 404'
    Processing helix  chain 'D' and resid 405 through 419
    Processing helix  chain 'D' and resid 426 through 431
      removed outlier: 3.655A  pdb=" N   ASP D 430 " --> pdb=" O   THR D 426 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   PHE D 431 " --> pdb=" O   PHE D 427 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 426 through 431'
    Processing helix  chain 'D' and resid 442 through 448
      removed outlier: 3.599A  pdb=" N   HIS D 448 " --> pdb=" O   ASP D 444 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 457 through 461
      removed outlier: 3.775A  pdb=" N   ASP D 461 " --> pdb=" O   SER D 458 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 462 through 479
    Processing helix  chain 'D' and resid 495 through 499
      removed outlier: 3.859A  pdb=" N   LEU D 499 " --> pdb=" O   PRO D 496 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 500 through 507
    Processing helix  chain 'D' and resid 519 through 528
    Processing helix  chain 'D' and resid 529 through 554
    Processing helix  chain 'E' and resid 402 through 404
      No H-bonds generated for 'chain 'E' and resid 402 through 404'
    Processing helix  chain 'E' and resid 405 through 419
    Processing helix  chain 'E' and resid 426 through 431
      removed outlier: 3.656A  pdb=" N   ASP E 430 " --> pdb=" O   THR E 426 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   PHE E 431 " --> pdb=" O   PHE E 427 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 426 through 431'
    Processing helix  chain 'E' and resid 442 through 448
      removed outlier: 3.600A  pdb=" N   HIS E 448 " --> pdb=" O   ASP E 444 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 457 through 461
      removed outlier: 3.775A  pdb=" N   ASP E 461 " --> pdb=" O   SER E 458 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 462 through 479
    Processing helix  chain 'E' and resid 495 through 499
      removed outlier: 3.859A  pdb=" N   LEU E 499 " --> pdb=" O   PRO E 496 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 500 through 507
    Processing helix  chain 'E' and resid 519 through 528
    Processing helix  chain 'E' and resid 529 through 554
    Processing helix  chain 'F' and resid 402 through 404
      No H-bonds generated for 'chain 'F' and resid 402 through 404'
    Processing helix  chain 'F' and resid 405 through 419
    Processing helix  chain 'F' and resid 426 through 431
      removed outlier: 3.656A  pdb=" N   ASP F 430 " --> pdb=" O   THR F 426 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   PHE F 431 " --> pdb=" O   PHE F 427 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 426 through 431'
    Processing helix  chain 'F' and resid 442 through 448
      removed outlier: 3.600A  pdb=" N   HIS F 448 " --> pdb=" O   ASP F 444 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 457 through 461
      removed outlier: 3.775A  pdb=" N   ASP F 461 " --> pdb=" O   SER F 458 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 462 through 479
    Processing helix  chain 'F' and resid 495 through 499
      removed outlier: 3.860A  pdb=" N   LEU F 499 " --> pdb=" O   PRO F 496 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 500 through 507
    Processing helix  chain 'F' and resid 519 through 528
    Processing helix  chain 'F' and resid 529 through 554
    Processing sheet with id=AA1, first strand: chain 'A' and resid 395 through 400
      removed outlier: 6.896A  pdb=" N   ASN A 396 " --> pdb=" O   PHE A 451 " (cutoff:3.500A)
      removed outlier: 7.625A  pdb=" N   ILE A 453 " --> pdb=" O   ASN A 396 " (cutoff:3.500A)
      removed outlier: 5.972A  pdb=" N   VAL A 398 " --> pdb=" O   ILE A 453 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   LEU A 455 " --> pdb=" O   VAL A 398 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   LEU A 400 " --> pdb=" O   LEU A 455 " (cutoff:3.500A)
      removed outlier: 7.927A  pdb=" N   ILE A 487 " --> pdb=" O   ALA A 450 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   ILE A 452 " --> pdb=" O   ILE A 487 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   PHE A 489 " --> pdb=" O   ILE A 452 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   LEU A 454 " --> pdb=" O   PHE A 489 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 395 through 400
      removed outlier: 6.896A  pdb=" N   ASN B 396 " --> pdb=" O   PHE B 451 " (cutoff:3.500A)
      removed outlier: 7.625A  pdb=" N   ILE B 453 " --> pdb=" O   ASN B 396 " (cutoff:3.500A)
      removed outlier: 5.972A  pdb=" N   VAL B 398 " --> pdb=" O   ILE B 453 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   LEU B 455 " --> pdb=" O   VAL B 398 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   LEU B 400 " --> pdb=" O   LEU B 455 " (cutoff:3.500A)
      removed outlier: 7.928A  pdb=" N   ILE B 487 " --> pdb=" O   ALA B 450 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   ILE B 452 " --> pdb=" O   ILE B 487 " (cutoff:3.500A)
      removed outlier: 7.215A  pdb=" N   PHE B 489 " --> pdb=" O   ILE B 452 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   LEU B 454 " --> pdb=" O   PHE B 489 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 395 through 400
      removed outlier: 6.896A  pdb=" N   ASN C 396 " --> pdb=" O   PHE C 451 " (cutoff:3.500A)
      removed outlier: 7.625A  pdb=" N   ILE C 453 " --> pdb=" O   ASN C 396 " (cutoff:3.500A)
      removed outlier: 5.972A  pdb=" N   VAL C 398 " --> pdb=" O   ILE C 453 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   LEU C 455 " --> pdb=" O   VAL C 398 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   LEU C 400 " --> pdb=" O   LEU C 455 " (cutoff:3.500A)
      removed outlier: 7.927A  pdb=" N   ILE C 487 " --> pdb=" O   ALA C 450 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   ILE C 452 " --> pdb=" O   ILE C 487 " (cutoff:3.500A)
      removed outlier: 7.215A  pdb=" N   PHE C 489 " --> pdb=" O   ILE C 452 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   LEU C 454 " --> pdb=" O   PHE C 489 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 395 through 400
      removed outlier: 6.896A  pdb=" N   ASN D 396 " --> pdb=" O   PHE D 451 " (cutoff:3.500A)
      removed outlier: 7.625A  pdb=" N   ILE D 453 " --> pdb=" O   ASN D 396 " (cutoff:3.500A)
      removed outlier: 5.972A  pdb=" N   VAL D 398 " --> pdb=" O   ILE D 453 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   LEU D 455 " --> pdb=" O   VAL D 398 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   LEU D 400 " --> pdb=" O   LEU D 455 " (cutoff:3.500A)
      removed outlier: 7.928A  pdb=" N   ILE D 487 " --> pdb=" O   ALA D 450 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   ILE D 452 " --> pdb=" O   ILE D 487 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   PHE D 489 " --> pdb=" O   ILE D 452 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   LEU D 454 " --> pdb=" O   PHE D 489 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 395 through 400
      removed outlier: 6.896A  pdb=" N   ASN E 396 " --> pdb=" O   PHE E 451 " (cutoff:3.500A)
      removed outlier: 7.625A  pdb=" N   ILE E 453 " --> pdb=" O   ASN E 396 " (cutoff:3.500A)
      removed outlier: 5.971A  pdb=" N   VAL E 398 " --> pdb=" O   ILE E 453 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   LEU E 455 " --> pdb=" O   VAL E 398 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   LEU E 400 " --> pdb=" O   LEU E 455 " (cutoff:3.500A)
      removed outlier: 7.928A  pdb=" N   ILE E 487 " --> pdb=" O   ALA E 450 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   ILE E 452 " --> pdb=" O   ILE E 487 " (cutoff:3.500A)
      removed outlier: 7.215A  pdb=" N   PHE E 489 " --> pdb=" O   ILE E 452 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   LEU E 454 " --> pdb=" O   PHE E 489 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 395 through 400
      removed outlier: 6.895A  pdb=" N   ASN F 396 " --> pdb=" O   PHE F 451 " (cutoff:3.500A)
      removed outlier: 7.625A  pdb=" N   ILE F 453 " --> pdb=" O   ASN F 396 " (cutoff:3.500A)
      removed outlier: 5.971A  pdb=" N   VAL F 398 " --> pdb=" O   ILE F 453 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   LEU F 455 " --> pdb=" O   VAL F 398 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   LEU F 400 " --> pdb=" O   LEU F 455 " (cutoff:3.500A)
      removed outlier: 7.927A  pdb=" N   ILE F 487 " --> pdb=" O   ALA F 450 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   ILE F 452 " --> pdb=" O   ILE F 487 " (cutoff:3.500A)
      removed outlier: 7.215A  pdb=" N   PHE F 489 " --> pdb=" O   ILE F 452 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   LEU F 454 " --> pdb=" O   PHE F 489 " (cutoff:3.500A)

    378 hydrogen bonds defined for protein.
    1080 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: 2.74

  Time building geometry restraints manager: 1.54 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 7212
        1.03 -     1.23: 24
        1.23 -     1.42: 3168
        1.42 -     1.62: 4338
        1.62 -     1.81: 60
  Bond restraints: 14802
  Sorted by residual:
  bond pdb=" C   ILE B 487 "
       pdb=" O   ILE B 487 "
    ideal  model  delta    sigma   weight residual
    1.232  1.241 -0.009 1.01e-02 9.80e+03 8.08e-01
  bond pdb=" CG  ARG F 541 "
       pdb=" CD  ARG F 541 "
    ideal  model  delta    sigma   weight residual
    1.520  1.547 -0.027 3.00e-02 1.11e+03 7.91e-01
  bond pdb=" CG  ARG B 541 "
       pdb=" CD  ARG B 541 "
    ideal  model  delta    sigma   weight residual
    1.520  1.547 -0.027 3.00e-02 1.11e+03 7.90e-01
  bond pdb=" CG  ARG E 541 "
       pdb=" CD  ARG E 541 "
    ideal  model  delta    sigma   weight residual
    1.520  1.547 -0.027 3.00e-02 1.11e+03 7.87e-01
  bond pdb=" CG  ARG D 541 "
       pdb=" CD  ARG D 541 "
    ideal  model  delta    sigma   weight residual
    1.520  1.547 -0.027 3.00e-02 1.11e+03 7.86e-01
  ... (remaining 14797 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.78: 26396
        1.78 -     3.56: 232
        3.56 -     5.35: 24
        5.35 -     7.13: 6
        7.13 -     8.91: 6
  Bond angle restraints: 26664
  Sorted by residual:
  angle pdb=" CA  LEU D 410 "
        pdb=" CB  LEU D 410 "
        pdb=" CG  LEU D 410 "
      ideal   model   delta    sigma   weight residual
     116.30  125.21   -8.91 3.50e+00 8.16e-02 6.48e+00
  angle pdb=" CA  LEU B 410 "
        pdb=" CB  LEU B 410 "
        pdb=" CG  LEU B 410 "
      ideal   model   delta    sigma   weight residual
     116.30  125.21   -8.91 3.50e+00 8.16e-02 6.48e+00
  angle pdb=" CA  LEU F 410 "
        pdb=" CB  LEU F 410 "
        pdb=" CG  LEU F 410 "
      ideal   model   delta    sigma   weight residual
     116.30  125.20   -8.90 3.50e+00 8.16e-02 6.46e+00
  angle pdb=" CA  LEU E 410 "
        pdb=" CB  LEU E 410 "
        pdb=" CG  LEU E 410 "
      ideal   model   delta    sigma   weight residual
     116.30  125.20   -8.90 3.50e+00 8.16e-02 6.46e+00
  angle pdb=" CA  LEU A 410 "
        pdb=" CB  LEU A 410 "
        pdb=" CG  LEU A 410 "
      ideal   model   delta    sigma   weight residual
     116.30  125.19   -8.89 3.50e+00 8.16e-02 6.46e+00
  ... (remaining 26659 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.38: 6026
       17.38 -    34.76: 694
       34.76 -    52.14: 162
       52.14 -    69.51: 42
       69.51 -    86.89: 18
  Dihedral angle restraints: 6942
    sinusoidal: 3768
      harmonic: 3174
  Sorted by residual:
  dihedral pdb=" CB  GLU A 429 "
           pdb=" CG  GLU A 429 "
           pdb=" CD  GLU A 429 "
           pdb=" OE1 GLU A 429 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.89  -86.89     1      3.00e+01 1.11e-03 1.01e+01
  dihedral pdb=" CB  GLU E 429 "
           pdb=" CG  GLU E 429 "
           pdb=" CD  GLU E 429 "
           pdb=" OE1 GLU E 429 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.87  -86.87     1      3.00e+01 1.11e-03 1.01e+01
  dihedral pdb=" CB  GLU B 429 "
           pdb=" CG  GLU B 429 "
           pdb=" CD  GLU B 429 "
           pdb=" OE1 GLU B 429 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.87  -86.87     1      3.00e+01 1.11e-03 1.01e+01
  ... (remaining 6939 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 700
       0.025 -    0.049: 294
       0.049 -    0.074: 74
       0.074 -    0.099: 32
       0.099 -    0.123: 46
  Chirality restraints: 1146
  Sorted by residual:
  chirality pdb=" CA  ILE A 487 "
            pdb=" N   ILE A 487 "
            pdb=" C   ILE A 487 "
            pdb=" CB  ILE A 487 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.80e-01
  chirality pdb=" CA  ILE B 453 "
            pdb=" N   ILE B 453 "
            pdb=" C   ILE B 453 "
            pdb=" CB  ILE B 453 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.73e-01
  chirality pdb=" CA  ILE D 453 "
            pdb=" N   ILE D 453 "
            pdb=" C   ILE D 453 "
            pdb=" CB  ILE D 453 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.73e-01
  ... (remaining 1143 not shown)

  Planarity restraints: 2244
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG E 541 "   -0.167 9.50e-02 1.11e+02   5.59e-02 4.14e+00
        pdb=" NE  ARG E 541 "    0.015 2.00e-02 2.50e+03
        pdb=" CZ  ARG E 541 "   -0.014 2.00e-02 2.50e+03
        pdb=" NH1 ARG E 541 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG E 541 "   -0.001 2.00e-02 2.50e+03
        pdb="HH11 ARG E 541 "    0.004 2.00e-02 2.50e+03
        pdb="HH12 ARG E 541 "   -0.001 2.00e-02 2.50e+03
        pdb="HH21 ARG E 541 "   -0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG E 541 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 541 "    0.166 9.50e-02 1.11e+02   5.59e-02 4.14e+00
        pdb=" NE  ARG C 541 "   -0.015 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 541 "    0.014 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 541 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 541 "    0.001 2.00e-02 2.50e+03
        pdb="HH11 ARG C 541 "   -0.003 2.00e-02 2.50e+03
        pdb="HH12 ARG C 541 "    0.001 2.00e-02 2.50e+03
        pdb="HH21 ARG C 541 "    0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG C 541 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 541 "    0.166 9.50e-02 1.11e+02   5.58e-02 4.12e+00
        pdb=" NE  ARG A 541 "   -0.015 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 541 "    0.014 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 541 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 541 "    0.001 2.00e-02 2.50e+03
        pdb="HH11 ARG A 541 "   -0.003 2.00e-02 2.50e+03
        pdb="HH12 ARG A 541 "    0.001 2.00e-02 2.50e+03
        pdb="HH21 ARG A 541 "    0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG A 541 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 2241 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.19: 1011
        2.19 -     2.79: 29840
        2.79 -     3.40: 41618
        3.40 -     4.00: 51205
        4.00 -     4.60: 77510
  Nonbonded interactions: 201184
  Sorted by model distance:
  nonbonded pdb=" HZ3 LYS E 523 "
            pdb=" O   GLN F 432 "
     model   vdw
     1.589 2.450
  nonbonded pdb=" O   ALA E 450 "
            pdb="HH12 ARG E 536 "
     model   vdw
     1.624 2.450
  nonbonded pdb=" O   ALA D 450 "
            pdb="HH12 ARG D 536 "
     model   vdw
     1.625 2.450
  nonbonded pdb=" O   ALA C 450 "
            pdb="HH12 ARG C 536 "
     model   vdw
     1.625 2.450
  nonbonded pdb=" O   ALA A 450 "
            pdb="HH12 ARG A 536 "
     model   vdw
     1.625 2.450
  ... (remaining 201179 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.700
  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:             0.050
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     12.670
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6860
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7566  Z= 0.114
  Angle     :  0.583   8.910  10212  Z= 0.288
  Chirality :  0.037   0.123   1146
  Planarity :  0.006   0.074   1350
  Dihedral  : 17.958  86.894   2814
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  : 25.70 %
    Favored  : 74.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.26 (0.28), residues: 918
  helix:  1.18 (0.24), residues: 498
  sheet: -1.84 (0.64), residues: 78
  loop : -0.73 (0.30), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG C 541 
 TYR   0.006   0.002   TYR E 395 
 PHE   0.008   0.001   PHE F 427 
 TRP   0.007   0.002   TRP B 540 
 HIS   0.002   0.000   HIS D 448 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 7566)
  covalent geometry    : angle       0.58319 (10212)
  hydrogen bonds       : bond        0.15905 (  378)
  hydrogen bonds       : angle       5.66805 ( 1080)

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Evaluate side-chains
  185 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 183
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 2
  residues processed: 183
  average time/residue: 0.2204
  time to fit residues: 51.4807
Evaluate side-chains
  160 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 158
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain C residue  419 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    5.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    2.5188

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

Flipped N/Q/H residues before XYZ refinement:
A 476 ASN
C 396 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4453 r_free = 0.4453 target = 0.175439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.143484 restraints weight = 33426.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.150912 restraints weight = 16458.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.155753 restraints weight = 10207.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.158882 restraints weight = 7243.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.161112 restraints weight = 5635.116|
|-----------------------------------------------------------------------------|
r_work (final): 0.4271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6906
moved from start:          0.1794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7566  Z= 0.193
  Angle     :  0.621   8.346  10212  Z= 0.315
  Chirality :  0.042   0.129   1146
  Planarity :  0.005   0.037   1350
  Dihedral  :  4.408  33.819   1012
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 13.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 24.30 %
    Favored  : 74.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.42 (0.28), residues: 918
  helix:  1.49 (0.23), residues: 492
  sheet: -2.43 (0.64), residues: 78
  loop : -0.77 (0.30), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 536 
 TYR   0.004   0.001   TYR E 395 
 PHE   0.014   0.002   PHE E 489 
 TRP   0.002   0.001   TRP F 540 
 HIS   0.006   0.001   HIS C 448 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 ( 7566)
  covalent geometry    : angle       0.62125 (10212)
  hydrogen bonds       : bond        0.03434 (  378)
  hydrogen bonds       : angle       4.81745 ( 1080)

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Evaluate side-chains
  183 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 173
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.7549 (OUTLIER) cc_final: 0.7328 (t0)
REVERT: C  414 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7846 (mm-30)
REVERT: E  542 LYS cc_start: 0.9252 (ptmt) cc_final: 0.9009 (ptpp)
REVERT: F  395 TYR cc_start: 0.7389 (m-80) cc_final: 0.7160 (m-80)
  outliers start: 10
  outliers final: 4
  residues processed: 174
  average time/residue: 0.1896
  time to fit residues: 43.8851
Evaluate side-chains
  171 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 166
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  405 ASP
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain D residue  405 ASP
Chi-restraints excluded: chain E residue  405 ASP
Chi-restraints excluded: chain E residue  419 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 55 optimal weight:    5.9990
   chunk 42 optimal weight:    5.9990
   chunk 87 optimal weight:    0.0470
   chunk 88 optimal weight:    0.8980
   chunk 82 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 83 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 1 optimal weight:    6.9990
   chunk 70 optimal weight:    8.9990
   overall best weight:    1.3882

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

Flipped N/Q/H residues before XYZ refinement:
D 476 ASN
** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 476 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4464 r_free = 0.4464 target = 0.176175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.144216 restraints weight = 33705.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.151688 restraints weight = 16355.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.156510 restraints weight = 10066.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.159808 restraints weight = 7136.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.162016 restraints weight = 5508.276|
|-----------------------------------------------------------------------------|
r_work (final): 0.4287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6881
moved from start:          0.2216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7566  Z= 0.129
  Angle     :  0.562   8.601  10212  Z= 0.279
  Chirality :  0.040   0.131   1146
  Planarity :  0.004   0.035   1350
  Dihedral  :  4.022  15.237   1008
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 24.94 %
    Favored  : 73.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.24 (0.28), residues: 918
  helix:  1.46 (0.23), residues: 504
  sheet: -2.95 (0.59), residues: 78
  loop : -1.02 (0.29), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 411 
 TYR   0.005   0.001   TYR B 395 
 PHE   0.007   0.001   PHE B 431 
 TRP   0.001   0.000   TRP C 540 
 HIS   0.004   0.001   HIS C 448 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 7566)
  covalent geometry    : angle       0.56203 (10212)
  hydrogen bonds       : bond        0.03084 (  378)
  hydrogen bonds       : angle       4.56071 ( 1080)

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Evaluate side-chains
  181 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 169
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.7361 (OUTLIER) cc_final: 0.7114 (t0)
REVERT: C  414 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7859 (mm-30)
REVERT: E  542 LYS cc_start: 0.9262 (ptmt) cc_final: 0.9039 (ptpp)
  outliers start: 12
  outliers final: 7
  residues processed: 175
  average time/residue: 0.1905
  time to fit residues: 45.5601
Evaluate side-chains
  170 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 162
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  405 ASP
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  421 VAL
Chi-restraints excluded: chain D residue  405 ASP
Chi-restraints excluded: chain D residue  433 VAL
Chi-restraints excluded: chain E residue  419 LEU
Chi-restraints excluded: chain E residue  421 VAL
Chi-restraints excluded: chain F residue  421 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 11 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 80 optimal weight:    4.9990
   chunk 13 optimal weight:    5.9990
   chunk 29 optimal weight:    9.9990
   chunk 26 optimal weight:    3.9990
   chunk 40 optimal weight:    9.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 471 GLN
** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 544 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.166991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.134705 restraints weight = 33788.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.141759 restraints weight = 16640.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.146473 restraints weight = 10542.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.149463 restraints weight = 7583.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.151576 restraints weight = 5989.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.4163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7046
moved from start:          0.3273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.068   7566  Z= 0.287
  Angle     :  0.677   8.462  10212  Z= 0.357
  Chirality :  0.046   0.144   1146
  Planarity :  0.006   0.041   1350
  Dihedral  :  4.484  16.657   1008
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 17.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.52 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 24.30 %
    Favored  : 72.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.52 (0.27), residues: 918
  helix:  0.90 (0.23), residues: 504
  sheet: -3.42 (0.60), residues: 72
  loop : -1.47 (0.29), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 512 
 TYR   0.006   0.001   TYR E 395 
 PHE   0.020   0.003   PHE E 489 
 TRP   0.003   0.001   TRP C 540 
 HIS   0.006   0.001   HIS C 448 

Details of bonding type rmsd
  covalent geometry    : bond        0.00662 ( 7566)
  covalent geometry    : angle       0.67663 (10212)
  hydrogen bonds       : bond        0.03490 (  378)
  hydrogen bonds       : angle       5.00202 ( 1080)

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Evaluate side-chains
  185 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 158
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  405 ASP cc_start: 0.8116 (m-30) cc_final: 0.7878 (m-30)
REVERT: B  484 ASP cc_start: 0.4696 (OUTLIER) cc_final: 0.4111 (t70)
REVERT: C  484 ASP cc_start: 0.5364 (OUTLIER) cc_final: 0.4164 (t70)
REVERT: C  527 THR cc_start: 0.7291 (OUTLIER) cc_final: 0.7045 (t)
REVERT: D  484 ASP cc_start: 0.5497 (OUTLIER) cc_final: 0.4557 (t70)
REVERT: E  484 ASP cc_start: 0.5767 (OUTLIER) cc_final: 0.4468 (t70)
REVERT: E  541 ARG cc_start: 0.8337 (tpm170) cc_final: 0.7930 (tpm170)
REVERT: F  484 ASP cc_start: 0.5927 (OUTLIER) cc_final: 0.5356 (t70)
  outliers start: 27
  outliers final: 12
  residues processed: 176
  average time/residue: 0.1707
  time to fit residues: 41.3535
Evaluate side-chains
  168 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 150
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  408 ILE
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  461 ASP
Chi-restraints excluded: chain B residue  405 ASP
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  421 VAL
Chi-restraints excluded: chain B residue  484 ASP
Chi-restraints excluded: chain C residue  419 LEU
Chi-restraints excluded: chain C residue  484 ASP
Chi-restraints excluded: chain C residue  527 THR
Chi-restraints excluded: chain D residue  405 ASP
Chi-restraints excluded: chain D residue  408 ILE
Chi-restraints excluded: chain D residue  433 VAL
Chi-restraints excluded: chain D residue  484 ASP
Chi-restraints excluded: chain E residue  419 LEU
Chi-restraints excluded: chain E residue  484 ASP
Chi-restraints excluded: chain F residue  421 VAL
Chi-restraints excluded: chain F residue  484 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 84 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 88 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 55 optimal weight:    5.9990
   chunk 79 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
B 544 GLN
** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.167993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.136766 restraints weight = 33076.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.143858 restraints weight = 15873.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.148538 restraints weight = 9749.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.151646 restraints weight = 6899.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.153744 restraints weight = 5348.017|
|-----------------------------------------------------------------------------|
r_work (final): 0.4205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6916
moved from start:          0.3280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7566  Z= 0.122
  Angle     :  0.573   9.722  10212  Z= 0.283
  Chirality :  0.040   0.131   1146
  Planarity :  0.005   0.042   1350
  Dihedral  :  4.231  15.270   1008
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 24.94 %
    Favored  : 72.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.39 (0.28), residues: 918
  helix:  1.53 (0.23), residues: 492
  sheet: -3.23 (0.59), residues: 72
  loop : -0.73 (0.30), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 536 
 TYR   0.008   0.002   TYR D 395 
 PHE   0.009   0.001   PHE E 431 
 TRP   0.004   0.001   TRP C 540 
 HIS   0.003   0.001   HIS C 448 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 7566)
  covalent geometry    : angle       0.57350 (10212)
  hydrogen bonds       : bond        0.02683 (  378)
  hydrogen bonds       : angle       4.58589 ( 1080)

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Evaluate side-chains
  184 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 165
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  414 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7858 (mm-30)
REVERT: E  542 LYS cc_start: 0.8979 (ptpp) cc_final: 0.8751 (ptpp)
  outliers start: 19
  outliers final: 10
  residues processed: 173
  average time/residue: 0.1531
  time to fit residues: 36.5866
Evaluate side-chains
  170 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 160
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  453 ILE
Chi-restraints excluded: chain C residue  419 LEU
Chi-restraints excluded: chain C residue  442 LEU
Chi-restraints excluded: chain D residue  405 ASP
Chi-restraints excluded: chain D residue  433 VAL
Chi-restraints excluded: chain E residue  419 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 69 optimal weight:    0.7980
   chunk 55 optimal weight:    9.9990
   chunk 1 optimal weight:    6.9990
   chunk 24 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9980
   chunk 84 optimal weight:    0.5980
   chunk 35 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
C 468 GLN
C 544 GLN
** D 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 476 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 = 0.4416 r_free = 0.4416 target = 0.170870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.139472 restraints weight = 33929.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.147024 restraints weight = 16263.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.151949 restraints weight = 10006.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.155205 restraints weight = 7062.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.157410 restraints weight = 5442.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.4261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6922
moved from start:          0.3402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7566  Z= 0.119
  Angle     :  0.564   9.785  10212  Z= 0.276
  Chirality :  0.040   0.151   1146
  Planarity :  0.005   0.038   1350
  Dihedral  :  4.080  15.406   1008
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 25.70 %
    Favored  : 72.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.61 (0.28), residues: 918
  helix:  1.71 (0.23), residues: 492
  sheet: -3.10 (0.60), residues: 72
  loop : -0.63 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F 411 
 TYR   0.006   0.001   TYR F 395 
 PHE   0.007   0.001   PHE E 431 
 TRP   0.003   0.001   TRP C 540 
 HIS   0.002   0.000   HIS C 448 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 7566)
  covalent geometry    : angle       0.56369 (10212)
  hydrogen bonds       : bond        0.02616 (  378)
  hydrogen bonds       : angle       4.45546 ( 1080)

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Evaluate side-chains
  181 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 164
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  414 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7807 (mm-30)
REVERT: E  541 ARG cc_start: 0.8382 (tpm170) cc_final: 0.7936 (tpm170)
  outliers start: 17
  outliers final: 14
  residues processed: 173
  average time/residue: 0.1372
  time to fit residues: 33.4095
Evaluate side-chains
  173 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 159
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  453 ILE
Chi-restraints excluded: chain C residue  442 LEU
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain D residue  405 ASP
Chi-restraints excluded: chain D residue  433 VAL
Chi-restraints excluded: chain E residue  396 ASN
Chi-restraints excluded: chain E residue  419 LEU
Chi-restraints excluded: chain E residue  442 LEU
Chi-restraints excluded: chain E residue  453 ILE
Chi-restraints excluded: chain F residue  419 LEU
Chi-restraints excluded: chain F residue  421 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 54 optimal weight:    0.7980
   chunk 85 optimal weight:    6.9990
   chunk 60 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 76 optimal weight:    4.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 476 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 = 0.4351 r_free = 0.4351 target = 0.166302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.136471 restraints weight = 33549.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.143358 restraints weight = 16053.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.147857 restraints weight = 9816.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.150889 restraints weight = 6901.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.152700 restraints weight = 5312.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.4187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6924
moved from start:          0.3567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7566  Z= 0.136
  Angle     :  0.573   9.809  10212  Z= 0.282
  Chirality :  0.040   0.130   1146
  Planarity :  0.005   0.036   1350
  Dihedral  :  4.093  14.934   1008
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 25.32 %
    Favored  : 71.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.28), residues: 918
  helix:  1.74 (0.23), residues: 492
  sheet: -3.04 (0.59), residues: 72
  loop : -0.64 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 536 
 TYR   0.005   0.001   TYR F 395 
 PHE   0.009   0.001   PHE E 489 
 TRP   0.003   0.001   TRP C 540 
 HIS   0.002   0.000   HIS C 448 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 7566)
  covalent geometry    : angle       0.57264 (10212)
  hydrogen bonds       : bond        0.02611 (  378)
  hydrogen bonds       : angle       4.43544 ( 1080)

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Evaluate side-chains
  184 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 161
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  541 ARG cc_start: 0.8381 (tpm170) cc_final: 0.7875 (tpm170)
  outliers start: 23
  outliers final: 19
  residues processed: 175
  average time/residue: 0.1526
  time to fit residues: 37.0038
Evaluate side-chains
  181 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 162
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  461 ASP
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  421 VAL
Chi-restraints excluded: chain B residue  453 ILE
Chi-restraints excluded: chain C residue  419 LEU
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  442 LEU
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain D residue  405 ASP
Chi-restraints excluded: chain D residue  433 VAL
Chi-restraints excluded: chain E residue  396 ASN
Chi-restraints excluded: chain E residue  419 LEU
Chi-restraints excluded: chain E residue  421 VAL
Chi-restraints excluded: chain E residue  453 ILE
Chi-restraints excluded: chain F residue  419 LEU
Chi-restraints excluded: chain F residue  421 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9980
   chunk 52 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 71 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 44 optimal weight:    9.9990
   chunk 26 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 76 optimal weight:    0.6980
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 476 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 = 0.4333 r_free = 0.4333 target = 0.164343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.134098 restraints weight = 34357.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.140898 restraints weight = 16466.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.145409 restraints weight = 10180.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.148414 restraints weight = 7204.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.150512 restraints weight = 5587.536|
|-----------------------------------------------------------------------------|
r_work (final): 0.4164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6969
moved from start:          0.3888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7566  Z= 0.166
  Angle     :  0.587   9.711  10212  Z= 0.295
  Chirality :  0.041   0.154   1146
  Planarity :  0.005   0.041   1350
  Dihedral  :  4.185  15.176   1008
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.63 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 25.70 %
    Favored  : 71.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.28), residues: 918
  helix:  1.65 (0.23), residues: 492
  sheet: -3.05 (0.60), residues: 72
  loop : -0.72 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F 411 
 TYR   0.004   0.001   TYR D 395 
 PHE   0.012   0.002   PHE E 489 
 TRP   0.002   0.001   TRP C 540 
 HIS   0.003   0.001   HIS C 448 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 7566)
  covalent geometry    : angle       0.58669 (10212)
  hydrogen bonds       : bond        0.02695 (  378)
  hydrogen bonds       : angle       4.55125 ( 1080)

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Evaluate side-chains
  178 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 158
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  461 ASP cc_start: 0.8236 (t70) cc_final: 0.7974 (t70)
REVERT: E  541 ARG cc_start: 0.8390 (tpm170) cc_final: 0.7911 (tpm170)
REVERT: F  527 THR cc_start: 0.7805 (OUTLIER) cc_final: 0.7599 (t)
  outliers start: 20
  outliers final: 18
  residues processed: 170
  average time/residue: 0.1301
  time to fit residues: 31.3452
Evaluate side-chains
  176 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 157
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  461 ASP
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  453 ILE
Chi-restraints excluded: chain C residue  419 LEU
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  442 LEU
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain D residue  405 ASP
Chi-restraints excluded: chain D residue  433 VAL
Chi-restraints excluded: chain E residue  396 ASN
Chi-restraints excluded: chain E residue  419 LEU
Chi-restraints excluded: chain E residue  421 VAL
Chi-restraints excluded: chain E residue  453 ILE
Chi-restraints excluded: chain F residue  419 LEU
Chi-restraints excluded: chain F residue  421 VAL
Chi-restraints excluded: chain F residue  527 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 67 optimal weight:    4.9990
   chunk 47 optimal weight:    6.9990
   chunk 89 optimal weight:    9.9990
   chunk 2 optimal weight:    4.9990
   chunk 13 optimal weight:    0.6980
   chunk 62 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 74 optimal weight:   10.0000
   chunk 59 optimal weight:    9.9990
   chunk 79 optimal weight:    2.9990
   overall best weight:    2.7388

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

Flipped N/Q/H residues before XYZ refinement:
** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 476 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 = 0.4307 r_free = 0.4307 target = 0.161926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.131747 restraints weight = 34007.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.138507 restraints weight = 16423.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.142931 restraints weight = 10156.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.145917 restraints weight = 7221.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.147960 restraints weight = 5607.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.4142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6999
moved from start:          0.4187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   7566  Z= 0.200
  Angle     :  0.617  10.137  10212  Z= 0.314
  Chirality :  0.043   0.151   1146
  Planarity :  0.005   0.048   1350
  Dihedral  :  4.388  15.355   1008
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 14.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.08 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 25.45 %
    Favored  : 71.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.31 (0.27), residues: 918
  helix:  1.08 (0.22), residues: 528
  sheet: -3.08 (0.61), residues: 72
  loop : -0.31 (0.33), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 512 
 TYR   0.005   0.001   TYR D 395 
 PHE   0.013   0.002   PHE E 489 
 TRP   0.003   0.001   TRP C 540 
 HIS   0.004   0.001   HIS C 448 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 ( 7566)
  covalent geometry    : angle       0.61695 (10212)
  hydrogen bonds       : bond        0.02780 (  378)
  hydrogen bonds       : angle       4.69586 ( 1080)

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Evaluate side-chains
  178 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 155
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  396 ASN cc_start: 0.8043 (t0) cc_final: 0.7797 (t0)
REVERT: F  527 THR cc_start: 0.7829 (OUTLIER) cc_final: 0.7621 (t)
  outliers start: 23
  outliers final: 22
  residues processed: 170
  average time/residue: 0.1401
  time to fit residues: 33.2497
Evaluate side-chains
  173 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 150
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  461 ASP
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  421 VAL
Chi-restraints excluded: chain B residue  426 THR
Chi-restraints excluded: chain B residue  453 ILE
Chi-restraints excluded: chain C residue  419 LEU
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  442 LEU
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain C residue  519 ILE
Chi-restraints excluded: chain D residue  405 ASP
Chi-restraints excluded: chain D residue  433 VAL
Chi-restraints excluded: chain E residue  396 ASN
Chi-restraints excluded: chain E residue  419 LEU
Chi-restraints excluded: chain E residue  421 VAL
Chi-restraints excluded: chain E residue  453 ILE
Chi-restraints excluded: chain F residue  419 LEU
Chi-restraints excluded: chain F residue  421 VAL
Chi-restraints excluded: chain F residue  426 THR
Chi-restraints excluded: chain F residue  453 ILE
Chi-restraints excluded: chain F residue  527 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 56 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9990
   chunk 76 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 75 optimal weight:    0.6980
   chunk 73 optimal weight:    1.9990
   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 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 544 GLN ** 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 = 0.4347 r_free = 0.4347 target = 0.165309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.135371 restraints weight = 33611.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.142221 restraints weight = 16155.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.146756 restraints weight = 9893.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.149752 restraints weight = 6964.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.151835 restraints weight = 5369.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.4189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6927
moved from start:          0.4145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7566  Z= 0.113
  Angle     :  0.578  10.083  10212  Z= 0.282
  Chirality :  0.040   0.137   1146
  Planarity :  0.005   0.065   1350
  Dihedral  :  4.187  14.607   1008
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 26.59 %
    Favored  : 71.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.28), residues: 918
  helix:  1.78 (0.23), residues: 492
  sheet: -2.92 (0.60), residues: 72
  loop : -0.58 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 411 
 TYR   0.007   0.001   TYR F 395 
 PHE   0.008   0.001   PHE E 427 
 TRP   0.004   0.001   TRP F 540 
 HIS   0.003   0.000   HIS C 448 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 7566)
  covalent geometry    : angle       0.57781 (10212)
  hydrogen bonds       : bond        0.02537 (  378)
  hydrogen bonds       : angle       4.40825 ( 1080)

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  500 is missing expected H atoms. Skipping.
Residue SER  501 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue SER  505 is missing expected H atoms. Skipping.
Residue LEU  506 is missing expected H atoms. Skipping.
Evaluate side-chains
  178 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 161
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  396 ASN cc_start: 0.7939 (t0) cc_final: 0.7729 (t0)
REVERT: B  405 ASP cc_start: 0.7750 (m-30) cc_final: 0.7522 (m-30)
REVERT: C  491 PRO cc_start: 0.7303 (Cg_exo) cc_final: 0.6922 (Cg_endo)
REVERT: D  429 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7500 (tp30)
  outliers start: 17
  outliers final: 16
  residues processed: 172
  average time/residue: 0.1209
  time to fit residues: 29.9127
Evaluate side-chains
  175 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 159
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  461 ASP
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  421 VAL
Chi-restraints excluded: chain B residue  426 THR
Chi-restraints excluded: chain C residue  442 LEU
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain D residue  405 ASP
Chi-restraints excluded: chain D residue  433 VAL
Chi-restraints excluded: chain E residue  396 ASN
Chi-restraints excluded: chain E residue  419 LEU
Chi-restraints excluded: chain E residue  421 VAL
Chi-restraints excluded: chain E residue  453 ILE
Chi-restraints excluded: chain F residue  419 LEU
Chi-restraints excluded: chain F residue  426 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 85 optimal weight:    9.9990
   chunk 76 optimal weight:    6.9990
   chunk 7 optimal weight:    0.6980
   chunk 84 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 544 GLN ** 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 = 0.4337 r_free = 0.4337 target = 0.164704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.135019 restraints weight = 33597.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.141855 restraints weight = 16046.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.146314 restraints weight = 9812.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.149268 restraints weight = 6923.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.151289 restraints weight = 5340.728|
|-----------------------------------------------------------------------------|
r_work (final): 0.4181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6938
moved from start:          0.4205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7566  Z= 0.125
  Angle     :  0.577  10.089  10212  Z= 0.284
  Chirality :  0.040   0.134   1146
  Planarity :  0.005   0.050   1350
  Dihedral  :  4.151  14.463   1008
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 11.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 25.95 %
    Favored  : 71.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.79 (0.28), residues: 918
  helix:  1.83 (0.23), residues: 492
  sheet: -2.89 (0.61), residues: 72
  loop : -0.53 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 411 
 TYR   0.006   0.001   TYR F 395 
 PHE   0.009   0.001   PHE B 451 
 TRP   0.003   0.001   TRP C 540 
 HIS   0.002   0.000   HIS C 448 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 7566)
  covalent geometry    : angle       0.57683 (10212)
  hydrogen bonds       : bond        0.02524 (  378)
  hydrogen bonds       : angle       4.36829 ( 1080)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2298.65 seconds
wall clock time: 40 minutes 5.23 seconds (2405.23 seconds total)