Starting phenix.real_space_refine
on Wed Mar  4 01:47:44 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6wcz_21618/03_2026/6wcz_21618.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6wcz_21618/03_2026/6wcz_21618.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6wcz_21618/03_2026/6wcz_21618.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6wcz_21618/03_2026/6wcz_21618.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6wcz_21618/03_2026/6wcz_21618.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6wcz_21618/03_2026/6wcz_21618.map"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
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
     Zn      2      6.06       5
     S      56      5.16       5
     C    6251      2.51       5
     N    1776      2.21       5
     O    1809      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9894
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2829
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 350, 2829
          Classifications: {'peptide': 350}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 16, 'TRANS': 333}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 8
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 7063
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 881, 7063
          Classifications: {'peptide': 881}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 32, 'TRANS': 848}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   6330  SG  CYS B 448      58.566  50.765  29.088  1.00170.38           S
  ATOM   6352  SG  CYS B 451      56.478  53.324  30.558  1.00177.22           S
  ATOM   9587  SG  CYS B 849      21.281  71.420  51.638  1.00143.74           S

  Time building chain proxies: 2.33, per 1000 atoms: 0.24
  Number of scatterers: 9894
  At special positions: 0
  Unit cell: (82.39, 105.93, 157.29, 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)
     Zn      2     29.99
     S      56     16.00
     O    1809      8.00
     N    1776      7.00
     C    6251      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.77
  Conformation dependent library (CDL) restraints added in 528.9 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN B1001 "
        pdb="ZN    ZN B1001 " - pdb=" NE2 HIS B 443 "
        pdb="ZN    ZN B1001 " - pdb=" SG  CYS B 451 "
        pdb="ZN    ZN B1001 " - pdb=" SG  CYS B 448 "
      pdb="  ZN B1002 "
        pdb="ZN    ZN B1002 " - pdb=" NE2 HIS B 714 "
        pdb="ZN    ZN B1002 " - pdb=" SG  CYS B 849 "


  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2278

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 9 sheets defined
      47.4% alpha, 7.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 140 through 182
      removed outlier: 3.669A  pdb=" N   GLU A 144 " --> pdb=" O   SER A 140 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   ASP A 168 " --> pdb=" O   SER A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 243
      removed outlier: 3.802A  pdb=" N   ARG A 223 " --> pdb=" O   ALA A 219 " (cutoff:3.500A)
      Proline residue:  A 233  - end of helix
    Processing helix  chain 'A' and resid 256 through 277
    Processing helix  chain 'A' and resid 294 through 314
    Processing helix  chain 'A' and resid 387 through 392
      removed outlier: 3.819A  pdb=" N   GLY A 391 " --> pdb=" O   THR A 387 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   GLN A 392 " --> pdb=" O   PRO A 388 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 387 through 392'
    Processing helix  chain 'A' and resid 423 through 427
      removed outlier: 3.771A  pdb=" N   GLU A 426 " --> pdb=" O   GLY A 423 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   GLU A 427 " --> pdb=" O   VAL A 424 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 423 through 427'
    Processing helix  chain 'A' and resid 460 through 474
      removed outlier: 4.109A  pdb=" N   ILE A 464 " --> pdb=" O   ASN A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 508
    Processing helix  chain 'B' and resid 8 through 10
      No H-bonds generated for 'chain 'B' and resid 8 through 10'
    Processing helix  chain 'B' and resid 11 through 19
      removed outlier: 4.316A  pdb=" N   ASN B  17 " --> pdb=" O   LYS B  13 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 20 through 29
      removed outlier: 3.792A  pdb=" N   PHE B  24 " --> pdb=" O   SER B  20 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   LYS B  29 " --> pdb=" O   TYR B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 39 through 47
      removed outlier: 4.536A  pdb=" N   LYS B  45 " --> pdb=" O   ARG B  41 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ASP B  46 " --> pdb=" O   ARG B  42 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   GLY B  47 " --> pdb=" O   ALA B  43 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 58 through 69
    Processing helix  chain 'B' and resid 85 through 93
      removed outlier: 3.931A  pdb=" N   THR B  93 " --> pdb=" O   TYR B  89 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 135
      removed outlier: 3.826A  pdb=" N   HIS B 134 " --> pdb=" O   ASP B 131 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   MET B 135 " --> pdb=" O   VAL B 132 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 131 through 135'
    Processing helix  chain 'B' and resid 153 through 172
      removed outlier: 4.123A  pdb=" N   GLU B 157 " --> pdb=" O   SER B 153 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ARG B 160 " --> pdb=" O   VAL B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 188 through 201
      removed outlier: 4.251A  pdb=" N   ARG B 197 " --> pdb=" O   GLU B 193 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   LEU B 198 " --> pdb=" O   THR B 194 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 228 through 237
    Processing helix  chain 'B' and resid 238 through 243
    Processing helix  chain 'B' and resid 274 through 277
    Processing helix  chain 'B' and resid 278 through 287
      removed outlier: 3.810A  pdb=" N   ILE B 282 " --> pdb=" O   ILE B 278 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 323 through 328
      removed outlier: 3.663A  pdb=" N   ARG B 327 " --> pdb=" O   ASN B 323 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 348 through 360
    Processing helix  chain 'B' and resid 368 through 390
      removed outlier: 3.957A  pdb=" N   ARG B 389 " --> pdb=" O   GLU B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 407
      removed outlier: 3.908A  pdb=" N   SER B 406 " --> pdb=" O   ASN B 402 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   ASN B 407 " --> pdb=" O   LYS B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 422 through 427
    Processing helix  chain 'B' and resid 430 through 446
    Processing helix  chain 'B' and resid 479 through 491
    Processing helix  chain 'B' and resid 491 through 496
    Processing helix  chain 'B' and resid 500 through 505
    Processing helix  chain 'B' and resid 515 through 522
      removed outlier: 3.564A  pdb=" N   ILE B 519 " --> pdb=" O   ARG B 515 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 539 through 543
      removed outlier: 3.870A  pdb=" N   ILE B 543 " --> pdb=" O   ASP B 540 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 544 through 549
      removed outlier: 3.793A  pdb=" N   LEU B 548 " --> pdb=" O   SER B 544 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 550 through 558
      removed outlier: 3.660A  pdb=" N   LEU B 553 " --> pdb=" O   ASN B 550 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ILE B 554 " --> pdb=" O   GLU B 551 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   MET B 558 " --> pdb=" O   THR B 555 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 559 through 574
    Processing helix  chain 'B' and resid 585 through 589
    Processing helix  chain 'B' and resid 607 through 628
      removed outlier: 3.617A  pdb=" N   LEU B 611 " --> pdb=" O   VAL B 607 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 641 through 658
      removed outlier: 4.152A  pdb=" N   VAL B 645 " --> pdb=" O   LYS B 641 " (cutoff:3.500A)
      removed outlier: 7.594A  pdb=" N   TRP B 654 " --> pdb=" O   GLN B 650 " (cutoff:3.500A)
      removed outlier: 5.837A  pdb=" N   ASP B 655 " --> pdb=" O   SER B 651 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 674 through 679
      removed outlier: 3.748A  pdb=" N   ALA B 677 " --> pdb=" O   ASP B 674 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 680 through 687
    Processing helix  chain 'B' and resid 733 through 738
    Processing helix  chain 'B' and resid 750 through 767
    Processing helix  chain 'B' and resid 772 through 785
      removed outlier: 3.584A  pdb=" N   LEU B 776 " --> pdb=" O   ARG B 772 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 803 through 807
      removed outlier: 3.901A  pdb=" N   MET B 806 " --> pdb=" O   GLY B 803 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   THR B 807 " --> pdb=" O   GLU B 804 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 803 through 807'
    Processing helix  chain 'B' and resid 810 through 820
      removed outlier: 3.706A  pdb=" N   VAL B 814 " --> pdb=" O   ASP B 810 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 842 through 849
    Processing helix  chain 'B' and resid 855 through 862
    Processing helix  chain 'B' and resid 865 through 876
      removed outlier: 3.831A  pdb=" N   VAL B 872 " --> pdb=" O   THR B 868 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 320
      removed outlier: 5.874A  pdb=" N   VAL A 318 " --> pdb=" O   ARG A 345 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   ARG A 345 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ARG A 343 " --> pdb=" O   THR A 320 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 333 through 335
    Processing sheet with id=AA3, first strand: chain 'A' and resid 385 through 386
      removed outlier: 6.198A  pdb=" N   THR A 358 " --> pdb=" O   LYS A 436 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   LYS A 436 " --> pdb=" O   THR A 358 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 377 through 378
    Processing sheet with id=AA5, first strand: chain 'B' and resid 124 through 127
      removed outlier: 8.596A  pdb=" N   ARG B 125 " --> pdb=" O   GLN B  98 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   VAL B 100 " --> pdb=" O   ARG B 125 " (cutoff:3.500A)
      removed outlier: 7.087A  pdb=" N   LYS B 127 " --> pdb=" O   VAL B 100 " (cutoff:3.500A)
      removed outlier: 5.873A  pdb=" N   GLY B 102 " --> pdb=" O   LYS B 127 " (cutoff:3.500A)
      removed outlier: 7.098A  pdb=" N   GLY B  75 " --> pdb=" O   GLN B  98 " (cutoff:3.500A)
      removed outlier: 5.392A  pdb=" N   VAL B 100 " --> pdb=" O   GLY B  75 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   VAL B  77 " --> pdb=" O   VAL B 100 " (cutoff:3.500A)
      removed outlier: 5.467A  pdb=" N   GLY B 102 " --> pdb=" O   VAL B  77 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   ASP B  79 " --> pdb=" O   GLY B 102 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   LEU B 143 " --> pdb=" O   CYS B 180 " (cutoff:3.500A)
      removed outlier: 7.440A  pdb=" N   LYS B 182 " --> pdb=" O   LEU B 143 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   CYS B 145 " --> pdb=" O   LYS B 182 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   VAL B 207 " --> pdb=" O   TYR B 220 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 305 through 310
      removed outlier: 3.514A  pdb=" N   HIS B 307 " --> pdb=" O   ILE B 594 " (cutoff:3.500A)
      removed outlier: 6.056A  pdb=" N   ILE B 594 " --> pdb=" O   HIS B 307 " (cutoff:3.500A)
      removed outlier: 5.304A  pdb=" N   SER B 309 " --> pdb=" O   MET B 592 " (cutoff:3.500A)
      removed outlier: 7.372A  pdb=" N   MET B 592 " --> pdb=" O   SER B 309 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 453 through 457
    Processing sheet with id=AA8, first strand: chain 'B' and resid 660 through 661
    Processing sheet with id=AA9, first strand: chain 'B' and resid 714 through 718

    404 hydrogen bonds defined for protein.
    1155 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.56

  Time building geometry restraints manager: 1.05 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2401
        1.33 -     1.45: 2089
        1.45 -     1.57: 5527
        1.57 -     1.69: 1
        1.69 -     1.81: 91
  Bond restraints: 10109
  Sorted by residual:
  bond pdb=" N   ARG B  42 "
       pdb=" CA  ARG B  42 "
    ideal  model  delta    sigma   weight residual
    1.454  1.487 -0.033 1.31e-02 5.83e+03 6.36e+00
  bond pdb=" N   GLY B 107 "
       pdb=" CA  GLY B 107 "
    ideal  model  delta    sigma   weight residual
    1.443  1.477 -0.034 1.37e-02 5.33e+03 6.21e+00
  bond pdb=" N   GLN A 141 "
       pdb=" CA  GLN A 141 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.23e-02 6.61e+03 5.55e+00
  bond pdb=" CB  TRP B 498 "
       pdb=" CG  TRP B 498 "
    ideal  model  delta    sigma   weight residual
    1.498  1.426  0.072 3.10e-02 1.04e+03 5.47e+00
  bond pdb=" CB  THR B 263 "
       pdb=" CG2 THR B 263 "
    ideal  model  delta    sigma   weight residual
    1.521  1.453  0.068 3.30e-02 9.18e+02 4.31e+00
  ... (remaining 10104 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 12370
        1.90 -     3.79: 1071
        3.79 -     5.69: 160
        5.69 -     7.59: 37
        7.59 -     9.48: 24
  Bond angle restraints: 13662
  Sorted by residual:
  angle pdb=" N   VAL B 132 "
        pdb=" CA  VAL B 132 "
        pdb=" CB  VAL B 132 "
      ideal   model   delta    sigma   weight residual
     112.39  105.29    7.10 1.17e+00 7.31e-01 3.68e+01
  angle pdb=" C   LEU A 307 "
        pdb=" N   LEU A 308 "
        pdb=" CA  LEU A 308 "
      ideal   model   delta    sigma   weight residual
     121.14  113.38    7.76 1.75e+00 3.27e-01 1.97e+01
  angle pdb=" CG  ARG A 300 "
        pdb=" CD  ARG A 300 "
        pdb=" NE  ARG A 300 "
      ideal   model   delta    sigma   weight residual
     112.00  121.48   -9.48 2.20e+00 2.07e-01 1.86e+01
  angle pdb=" C   ARG B 681 "
        pdb=" N   PHE B 682 "
        pdb=" CA  PHE B 682 "
      ideal   model   delta    sigma   weight residual
     121.54  129.66   -8.12 1.91e+00 2.74e-01 1.81e+01
  angle pdb=" N   LEU A 232 "
        pdb=" CA  LEU A 232 "
        pdb=" C   LEU A 232 "
      ideal   model   delta    sigma   weight residual
     109.81  118.81   -9.00 2.21e+00 2.05e-01 1.66e+01
  ... (remaining 13657 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.81: 5545
       16.81 -    33.63: 432
       33.63 -    50.44: 87
       50.44 -    67.26: 8
       67.26 -    84.07: 4
  Dihedral angle restraints: 6076
    sinusoidal: 2539
      harmonic: 3537
  Sorted by residual:
  dihedral pdb=" CA  ASN B 407 "
           pdb=" C   ASN B 407 "
           pdb=" N   ALA B 408 "
           pdb=" CA  ALA B 408 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -135.58  -44.42     0      5.00e+00 4.00e-02 7.89e+01
  dihedral pdb=" CA  LYS A 375 "
           pdb=" C   LYS A 375 "
           pdb=" N   PHE A 376 "
           pdb=" CA  PHE A 376 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  144.33   35.67     0      5.00e+00 4.00e-02 5.09e+01
  dihedral pdb=" CA  ILE B 278 "
           pdb=" C   ILE B 278 "
           pdb=" N   GLY B 279 "
           pdb=" CA  GLY B 279 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -145.72  -34.28     0      5.00e+00 4.00e-02 4.70e+01
  ... (remaining 6073 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 875
       0.050 -    0.100: 427
       0.100 -    0.150: 135
       0.150 -    0.199: 30
       0.199 -    0.249: 7
  Chirality restraints: 1474
  Sorted by residual:
  chirality pdb=" CG  LEU B 435 "
            pdb=" CB  LEU B 435 "
            pdb=" CD1 LEU B 435 "
            pdb=" CD2 LEU B 435 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.34   -0.25 2.00e-01 2.50e+01 1.55e+00
  chirality pdb=" CB  ILE A 431 "
            pdb=" CA  ILE A 431 "
            pdb=" CG1 ILE A 431 "
            pdb=" CG2 ILE A 431 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.24 2.00e-01 2.50e+01 1.40e+00
  chirality pdb=" CB  ILE A 363 "
            pdb=" CA  ILE A 363 "
            pdb=" CG1 ILE A 363 "
            pdb=" CG2 ILE A 363 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.23 2.00e-01 2.50e+01 1.36e+00
  ... (remaining 1471 not shown)

  Planarity restraints: 1749
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 107 "    0.065 5.00e-02 4.00e+02   9.85e-02 1.55e+01
        pdb=" N   PRO B 108 "   -0.170 5.00e-02 4.00e+02
        pdb=" CA  PRO B 108 "    0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO B 108 "    0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  42 "   -0.239 9.50e-02 1.11e+02   1.07e-01 7.01e+00
        pdb=" NE  ARG B  42 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  42 "    0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  42 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  42 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 497 "    0.042 5.00e-02 4.00e+02   6.34e-02 6.42e+00
        pdb=" N   PRO A 498 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO A 498 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 498 "    0.035 5.00e-02 4.00e+02
  ... (remaining 1746 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 255
        2.65 -     3.21: 9063
        3.21 -     3.77: 16102
        3.77 -     4.34: 20515
        4.34 -     4.90: 31925
  Nonbonded interactions: 77860
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 439 "
            pdb="ZN    ZN B1001 "
     model   vdw
     2.085 2.230
  nonbonded pdb=" O   ARG B  41 "
            pdb=" NE  ARG B  42 "
     model   vdw
     2.115 3.120
  nonbonded pdb=" O   LEU B 611 "
            pdb=" OG1 THR B 615 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" O   MET B 375 "
            pdb=" OG  SER B 379 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" O   GLU A 259 "
            pdb=" OG1 THR A 263 "
     model   vdw
     2.236 3.040
  ... (remaining 77855 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.87 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:             1.570
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.720
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
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      :  0.012   0.608  10114  Z= 0.484
  Angle     :  1.216   9.485  13662  Z= 0.659
  Chirality :  0.064   0.249   1474
  Planarity :  0.009   0.107   1749
  Dihedral  : 12.526  84.069   3798
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 14.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.94 %
    Favored  : 87.06 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  :  8.40 %
    Favored  : 89.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.51 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.79 (0.18), residues: 1221
  helix: -3.20 (0.15), residues: 510
  sheet: -2.21 (0.47), residues: 93
  loop : -3.34 (0.21), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.002   ARG B 459 
 TYR   0.031   0.004   TYR B 882 
 PHE   0.025   0.005   PHE B 432 
 TRP   0.039   0.005   TRP A 238 
 HIS   0.011   0.003   HIS A 271 

Details of bonding type rmsd
  covalent geometry    : bond        0.00917 (10109)
  covalent geometry    : angle       1.21645 (13662)
  hydrogen bonds       : bond        0.17164 (  404)
  hydrogen bonds       : angle      11.71766 ( 1155)
  metal coordination   : bond        0.32845 (    5)

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

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

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 171
  time to evaluate  : 0.276 
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
TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  389 GLU cc_start: 0.8598 (pt0) cc_final: 0.8300 (pm20)
REVERT: A  459 MET cc_start: 0.8583 (mmm) cc_final: 0.8344 (mmp)
REVERT: A  502 TRP cc_start: 0.6829 (m-10) cc_final: 0.6444 (m-10)
REVERT: B   17 ASN cc_start: 0.8891 (t160) cc_final: 0.8652 (m-40)
REVERT: B   45 LYS cc_start: 0.6963 (OUTLIER) cc_final: 0.6685 (tptt)
REVERT: B  101 ARG cc_start: 0.8076 (mtt180) cc_final: 0.7603 (mtm180)
REVERT: B  127 LYS cc_start: 0.8884 (tttt) cc_final: 0.8608 (ttmm)
REVERT: B  167 MET cc_start: 0.8698 (tpp) cc_final: 0.8265 (tpp)
REVERT: B  219 MET cc_start: 0.7572 (mtp) cc_final: 0.7096 (ttm)
REVERT: B  403 LYS cc_start: 0.9098 (tttt) cc_final: 0.8763 (tptp)
REVERT: B  531 MET cc_start: 0.8435 (mmp) cc_final: 0.7851 (mmm)
REVERT: B  581 VAL cc_start: 0.9169 (m) cc_final: 0.8967 (m)
REVERT: B  643 GLU cc_start: 0.9301 (tt0) cc_final: 0.9033 (tp30)
REVERT: B  647 ARG cc_start: 0.9145 (ttm110) cc_final: 0.8658 (tpt90)
REVERT: B  735 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8422 (mp0)
  outliers start: 27
  outliers final: 12
  residues processed: 194
  average time/residue: 0.1336
  time to fit residues: 33.4946
Evaluate side-chains
  116 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  290 ASP
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   45 LYS
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  609 TYR
Chi-restraints excluded: chain B residue  739 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 108 optimal weight:    0.0870
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:    6.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:   40.0000
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    3.9990
   chunk 117 optimal weight:   10.0000
   overall best weight:    1.9964

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

Flipped N/Q/H residues before XYZ refinement:
A 271 HIS
A 313 HIS
A 461 GLN
A 480 GLN
B  17 ASN
B 228 ASN
B 402 ASN
** B 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 550 ASN
B 576 ASN
B 762 GLN
** B 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.079898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.064688 restraints weight = 42408.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.066958 restraints weight = 24409.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.068485 restraints weight = 16264.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.069563 restraints weight = 12019.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.070316 restraints weight = 9596.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3619
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3619 r_free = 0.3619    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3619 r_free = 0.3619    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3619
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.2519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10114  Z= 0.170
  Angle     :  0.733   7.396  13662  Z= 0.388
  Chirality :  0.044   0.165   1474
  Planarity :  0.006   0.063   1749
  Dihedral  :  7.882  55.649   1379
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 14.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 12.37 %
    Favored  : 84.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.13 (0.22), residues: 1221
  helix: -1.32 (0.21), residues: 499
  sheet: -1.80 (0.49), residues: 91
  loop : -2.81 (0.23), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 314 
 TYR   0.025   0.002   TYR A 288 
 PHE   0.026   0.002   PHE A 504 
 TRP   0.022   0.002   TRP B 476 
 HIS   0.013   0.001   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (10109)
  covalent geometry    : angle       0.73254 (13662)
  hydrogen bonds       : bond        0.04893 (  404)
  hydrogen bonds       : angle       6.89834 ( 1155)
  metal coordination   : bond        0.00441 (    5)

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

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

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 122
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  365 ARG cc_start: 0.7694 (ptt-90) cc_final: 0.7471 (pmt-80)
REVERT: A  389 GLU cc_start: 0.8723 (pt0) cc_final: 0.8457 (pm20)
REVERT: A  507 TYR cc_start: 0.7645 (m-10) cc_final: 0.7425 (m-10)
REVERT: B   80 LEU cc_start: 0.8964 (tp) cc_final: 0.8750 (tt)
REVERT: B  499 MET cc_start: 0.8745 (mtt) cc_final: 0.8475 (mmm)
REVERT: B  531 MET cc_start: 0.8291 (mmp) cc_final: 0.7874 (mmt)
REVERT: B  623 ARG cc_start: 0.9027 (ttt180) cc_final: 0.8499 (ttt180)
REVERT: B  643 GLU cc_start: 0.9229 (tt0) cc_final: 0.8893 (tp30)
REVERT: B  762 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8417 (mm-40)
REVERT: B  777 MET cc_start: 0.8069 (tpt) cc_final: 0.7806 (tpt)
REVERT: B  805 TRP cc_start: 0.8161 (p-90) cc_final: 0.7793 (p90)
  outliers start: 36
  outliers final: 20
  residues processed: 151
  average time/residue: 0.1012
  time to fit residues: 21.1514
Evaluate side-chains
  119 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  313 HIS
Chi-restraints excluded: chain A residue  366 ASN
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  478 ASN
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  456 MET
Chi-restraints excluded: chain B residue  490 LEU
Chi-restraints excluded: chain B residue  495 GLU
Chi-restraints excluded: chain B residue  550 ASN
Chi-restraints excluded: chain B residue  609 TYR
Chi-restraints excluded: chain B residue  808 THR
Chi-restraints excluded: chain B residue  852 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 41 optimal weight:    7.9990
   chunk 17 optimal weight:   10.0000
   chunk 74 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 101 optimal weight:    5.9990
   chunk 77 optimal weight:    0.9980
   chunk 56 optimal weight:    3.9990
   chunk 67 optimal weight:    0.0470
   chunk 13 optimal weight:    8.9990
   overall best weight:    0.9882

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

Flipped N/Q/H residues before XYZ refinement:
A 313 HIS
B 449 HIS
B 598 GLN
** B 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.081195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.066097 restraints weight = 41224.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.068367 restraints weight = 23685.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.069909 restraints weight = 15768.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.071009 restraints weight = 11583.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.071832 restraints weight = 9188.751|
|-----------------------------------------------------------------------------|
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.3316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10114  Z= 0.135
  Angle     :  0.672   7.862  13662  Z= 0.345
  Chirality :  0.042   0.160   1474
  Planarity :  0.005   0.065   1749
  Dihedral  :  6.776  58.426   1363
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 13.31 %
    Favored  : 82.25 %
  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 are not related in a simple way.
  whole: -2.53 (0.23), residues: 1221
  helix: -0.60 (0.22), residues: 507
  sheet: -1.72 (0.50), residues: 99
  loop : -2.69 (0.23), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 724 
 TYR   0.020   0.001   TYR A 288 
 PHE   0.025   0.002   PHE A 504 
 TRP   0.014   0.001   TRP B 848 
 HIS   0.012   0.001   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (10109)
  covalent geometry    : angle       0.67195 (13662)
  hydrogen bonds       : bond        0.04181 (  404)
  hydrogen bonds       : angle       6.10775 ( 1155)
  metal coordination   : bond        0.00082 (    5)

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

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

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 127
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A  150 LEU cc_start: 0.9226 (mt) cc_final: 0.8955 (pp)
REVERT: A  365 ARG cc_start: 0.7808 (ptt-90) cc_final: 0.7581 (pmt-80)
REVERT: A  389 GLU cc_start: 0.8854 (pt0) cc_final: 0.8570 (pm20)
REVERT: B   19 MET cc_start: 0.6032 (mmt) cc_final: 0.5794 (ptp)
REVERT: B  218 GLU cc_start: 0.8872 (pt0) cc_final: 0.8301 (pm20)
REVERT: B  344 MET cc_start: 0.5926 (mtt) cc_final: 0.5437 (ppp)
REVERT: B  519 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8709 (tp)
REVERT: B  531 MET cc_start: 0.8280 (mmp) cc_final: 0.7796 (mmm)
REVERT: B  558 MET cc_start: 0.7041 (ptt) cc_final: 0.6777 (ptt)
REVERT: B  623 ARG cc_start: 0.8984 (ttt180) cc_final: 0.8489 (ttt180)
REVERT: B  643 GLU cc_start: 0.9219 (tt0) cc_final: 0.8955 (tp30)
  outliers start: 47
  outliers final: 21
  residues processed: 168
  average time/residue: 0.0850
  time to fit residues: 20.7687
Evaluate side-chains
  128 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 106
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  313 HIS
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  478 ASN
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  456 MET
Chi-restraints excluded: chain B residue  490 LEU
Chi-restraints excluded: chain B residue  519 ILE
Chi-restraints excluded: chain B residue  609 TYR
Chi-restraints excluded: chain B residue  619 VAL
Chi-restraints excluded: chain B residue  708 VAL
Chi-restraints excluded: chain B residue  808 THR
Chi-restraints excluded: chain B residue  852 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 72 optimal weight:    0.8980
   chunk 20 optimal weight:    6.9990
   chunk 112 optimal weight:    8.9990
   chunk 102 optimal weight:    4.9990
   chunk 43 optimal weight:    3.9990
   chunk 115 optimal weight:    7.9990
   chunk 76 optimal weight:    5.9990
   chunk 111 optimal weight:    1.9990
   chunk 88 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 313 HIS
** B 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 870 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.079661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.064492 restraints weight = 42171.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.066777 restraints weight = 24966.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.068287 restraints weight = 16474.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.069326 restraints weight = 12148.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.070147 restraints weight = 9692.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.3649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10114  Z= 0.169
  Angle     :  0.700   9.056  13662  Z= 0.359
  Chirality :  0.044   0.176   1474
  Planarity :  0.005   0.064   1749
  Dihedral  :  6.675  59.173   1363
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 15.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.27 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 16.43 %
    Favored  : 79.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.32 (0.23), residues: 1221
  helix: -0.35 (0.22), residues: 520
  sheet: -1.63 (0.52), residues: 97
  loop : -2.68 (0.23), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 775 
 TYR   0.020   0.002   TYR A 507 
 PHE   0.025   0.002   PHE A 504 
 TRP   0.037   0.002   TRP B 539 
 HIS   0.015   0.002   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 (10109)
  covalent geometry    : angle       0.69957 (13662)
  hydrogen bonds       : bond        0.04055 (  404)
  hydrogen bonds       : angle       5.88902 ( 1155)
  metal coordination   : bond        0.00245 (    5)

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

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

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 106
  time to evaluate  : 0.367 
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
TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A  288 TYR cc_start: 0.7787 (t80) cc_final: 0.7512 (t80)
REVERT: A  365 ARG cc_start: 0.7758 (ptt-90) cc_final: 0.7537 (pmt-80)
REVERT: A  389 GLU cc_start: 0.8835 (pt0) cc_final: 0.8544 (pm20)
REVERT: B  344 MET cc_start: 0.5864 (mtt) cc_final: 0.5370 (ppp)
REVERT: B  465 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.6448 (mt-10)
REVERT: B  499 MET cc_start: 0.8863 (mtt) cc_final: 0.8662 (mmm)
REVERT: B  519 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8733 (tp)
REVERT: B  531 MET cc_start: 0.8362 (mmp) cc_final: 0.7928 (mmm)
REVERT: B  643 GLU cc_start: 0.9201 (tt0) cc_final: 0.8958 (tp30)
REVERT: B  777 MET cc_start: 0.8151 (tpt) cc_final: 0.7854 (tpt)
  outliers start: 43
  outliers final: 31
  residues processed: 139
  average time/residue: 0.0858
  time to fit residues: 17.3964
Evaluate side-chains
  133 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 100
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ASP
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  313 HIS
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  478 ASN
Chi-restraints excluded: chain B residue   18 GLN
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  185 CYS
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  382 LEU
Chi-restraints excluded: chain B residue  422 THR
Chi-restraints excluded: chain B residue  456 MET
Chi-restraints excluded: chain B residue  465 GLU
Chi-restraints excluded: chain B residue  490 LEU
Chi-restraints excluded: chain B residue  519 ILE
Chi-restraints excluded: chain B residue  594 ILE
Chi-restraints excluded: chain B residue  609 TYR
Chi-restraints excluded: chain B residue  618 VAL
Chi-restraints excluded: chain B residue  708 VAL
Chi-restraints excluded: chain B residue  788 ASP
Chi-restraints excluded: chain B residue  808 THR
Chi-restraints excluded: chain B residue  852 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 10 optimal weight:    9.9990
   chunk 69 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 98 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   chunk 14 optimal weight:    7.9990
   chunk 63 optimal weight:   10.0000
   chunk 57 optimal weight:    0.3980
   chunk 99 optimal weight:    0.1980
   chunk 29 optimal weight:    6.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    2.7186

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

Flipped N/Q/H residues before XYZ refinement:
A 313 HIS
B 442 HIS
B 598 GLN
** B 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.078857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.063778 restraints weight = 42281.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.066010 restraints weight = 25072.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.067512 restraints weight = 16557.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.068523 restraints weight = 12213.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.069254 restraints weight = 9749.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.3827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10114  Z= 0.179
  Angle     :  0.704   9.327  13662  Z= 0.358
  Chirality :  0.044   0.156   1474
  Planarity :  0.005   0.061   1749
  Dihedral  :  6.655  58.548   1363
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 16.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.76 %
    Favored  : 91.24 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 17.66 %
    Favored  : 77.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.19 (0.23), residues: 1221
  helix: -0.31 (0.22), residues: 524
  sheet: -1.55 (0.52), residues: 97
  loop : -2.55 (0.24), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 775 
 TYR   0.022   0.002   TYR A 507 
 PHE   0.024   0.002   PHE A 504 
 TRP   0.022   0.002   TRP B 539 
 HIS   0.013   0.002   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 (10109)
  covalent geometry    : angle       0.70438 (13662)
  hydrogen bonds       : bond        0.04004 (  404)
  hydrogen bonds       : angle       5.81770 ( 1155)
  metal coordination   : bond        0.00269 (    5)

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

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

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 106
  time to evaluate  : 0.299 
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
TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it.
REVERT: A  238 TRP cc_start: 0.8244 (t-100) cc_final: 0.8017 (t-100)
REVERT: A  365 ARG cc_start: 0.7801 (ptt-90) cc_final: 0.7590 (pmt-80)
REVERT: A  389 GLU cc_start: 0.8848 (pt0) cc_final: 0.8530 (pm20)
REVERT: B  131 ASP cc_start: 0.8971 (t0) cc_final: 0.8711 (t0)
REVERT: B  344 MET cc_start: 0.5970 (mtt) cc_final: 0.5377 (ppp)
REVERT: B  777 MET cc_start: 0.8136 (tpt) cc_final: 0.7837 (tpt)
  outliers start: 50
  outliers final: 37
  residues processed: 146
  average time/residue: 0.0898
  time to fit residues: 18.8156
Evaluate side-chains
  135 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 98
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  207 ASP
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  313 HIS
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  478 ASN
Chi-restraints excluded: chain B residue   18 GLN
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  157 GLU
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  382 LEU
Chi-restraints excluded: chain B residue  422 THR
Chi-restraints excluded: chain B residue  456 MET
Chi-restraints excluded: chain B residue  490 LEU
Chi-restraints excluded: chain B residue  495 GLU
Chi-restraints excluded: chain B residue  594 ILE
Chi-restraints excluded: chain B residue  609 TYR
Chi-restraints excluded: chain B residue  619 VAL
Chi-restraints excluded: chain B residue  708 VAL
Chi-restraints excluded: chain B residue  736 LEU
Chi-restraints excluded: chain B residue  788 ASP
Chi-restraints excluded: chain B residue  808 THR
Chi-restraints excluded: chain B residue  852 LEU
Chi-restraints excluded: chain B residue  853 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 25 optimal weight:    6.9990
   chunk 61 optimal weight:    9.9990
   chunk 67 optimal weight:    0.0060
   chunk 20 optimal weight:    4.9990
   chunk 88 optimal weight:    2.9990
   chunk 111 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 75 optimal weight:    8.9990
   chunk 60 optimal weight:    8.9990
   chunk 32 optimal weight:    6.9990
   chunk 26 optimal weight:    8.9990
   overall best weight:    2.0002

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

Flipped N/Q/H residues before XYZ refinement:
A 313 HIS
** B 855 HIS ** 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 = 0.3808 r_free = 0.3808 target = 0.079490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.064401 restraints weight = 42031.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.066651 restraints weight = 24033.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.068164 restraints weight = 15943.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.069251 restraints weight = 11687.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.070008 restraints weight = 9266.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.4137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10114  Z= 0.149
  Angle     :  0.682   7.190  13662  Z= 0.345
  Chirality :  0.043   0.159   1474
  Planarity :  0.004   0.061   1749
  Dihedral  :  6.470  57.538   1363
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 13.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.53 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 17.85 %
    Favored  : 77.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.97 (0.23), residues: 1221
  helix: -0.08 (0.23), residues: 523
  sheet: -1.44 (0.54), residues: 97
  loop : -2.48 (0.24), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 310 
 TYR   0.016   0.002   TYR B 187 
 PHE   0.026   0.002   PHE A 504 
 TRP   0.020   0.001   TRP B 539 
 HIS   0.013   0.001   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (10109)
  covalent geometry    : angle       0.68212 (13662)
  hydrogen bonds       : bond        0.03836 (  404)
  hydrogen bonds       : angle       5.61391 ( 1155)
  metal coordination   : bond        0.00225 (    5)

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

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

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 107
  time to evaluate  : 0.339 
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
TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it.
REVERT: A  365 ARG cc_start: 0.7837 (ptt-90) cc_final: 0.7633 (pmt-80)
REVERT: A  389 GLU cc_start: 0.8842 (pt0) cc_final: 0.8482 (pm20)
REVERT: B  344 MET cc_start: 0.6021 (mtt) cc_final: 0.5476 (ppp)
REVERT: B  777 MET cc_start: 0.8074 (tpt) cc_final: 0.7791 (tpt)
  outliers start: 49
  outliers final: 39
  residues processed: 143
  average time/residue: 0.0808
  time to fit residues: 16.9890
Evaluate side-chains
  133 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 94
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  207 ASP
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  313 HIS
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  478 ASN
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  157 GLU
Chi-restraints excluded: chain B residue  185 CYS
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  382 LEU
Chi-restraints excluded: chain B residue  422 THR
Chi-restraints excluded: chain B residue  456 MET
Chi-restraints excluded: chain B residue  490 LEU
Chi-restraints excluded: chain B residue  495 GLU
Chi-restraints excluded: chain B residue  594 ILE
Chi-restraints excluded: chain B residue  606 VAL
Chi-restraints excluded: chain B residue  609 TYR
Chi-restraints excluded: chain B residue  618 VAL
Chi-restraints excluded: chain B residue  619 VAL
Chi-restraints excluded: chain B residue  718 LEU
Chi-restraints excluded: chain B residue  736 LEU
Chi-restraints excluded: chain B residue  788 ASP
Chi-restraints excluded: chain B residue  808 THR
Chi-restraints excluded: chain B residue  852 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 97 optimal weight:    0.3980
   chunk 65 optimal weight:    0.9990
   chunk 100 optimal weight:    5.9990
   chunk 107 optimal weight:    6.9990
   chunk 105 optimal weight:    6.9990
   chunk 118 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 17 optimal weight:    9.9990
   chunk 1 optimal weight:    0.9990
   chunk 79 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 313 HIS
B 652 ASN
** B 855 HIS ** 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 = 0.3837 r_free = 0.3837 target = 0.080933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.066010 restraints weight = 41767.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.068256 restraints weight = 24465.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.069766 restraints weight = 16095.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.070838 restraints weight = 11853.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.071613 restraints weight = 9411.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.4429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10114  Z= 0.128
  Angle     :  0.677   9.729  13662  Z= 0.337
  Chirality :  0.043   0.165   1474
  Planarity :  0.004   0.061   1749
  Dihedral  :  6.241  58.106   1363
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 12.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 19.26 %
    Favored  : 76.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.78 (0.24), residues: 1221
  helix:  0.04 (0.23), residues: 532
  sheet: -1.27 (0.59), residues: 86
  loop : -2.38 (0.24), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 310 
 TYR   0.015   0.001   TYR B 187 
 PHE   0.024   0.002   PHE A 504 
 TRP   0.034   0.002   TRP B 539 
 HIS   0.008   0.001   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (10109)
  covalent geometry    : angle       0.67698 (13662)
  hydrogen bonds       : bond        0.03697 (  404)
  hydrogen bonds       : angle       5.46797 ( 1155)
  metal coordination   : bond        0.00125 (    5)

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

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

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 110
  time to evaluate  : 0.364 
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
TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it.
REVERT: A  365 ARG cc_start: 0.7925 (ptt-90) cc_final: 0.7673 (pmt-80)
REVERT: A  389 GLU cc_start: 0.8753 (pt0) cc_final: 0.8444 (pm20)
REVERT: B  344 MET cc_start: 0.6093 (mtt) cc_final: 0.5633 (ppp)
REVERT: B  777 MET cc_start: 0.8007 (tpt) cc_final: 0.7634 (tpt)
REVERT: B  826 MET cc_start: 0.8039 (tpt) cc_final: 0.7837 (tpp)
  outliers start: 40
  outliers final: 37
  residues processed: 137
  average time/residue: 0.0911
  time to fit residues: 17.7648
Evaluate side-chains
  139 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 102
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  313 HIS
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  478 ASN
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  157 GLU
Chi-restraints excluded: chain B residue  185 CYS
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  382 LEU
Chi-restraints excluded: chain B residue  422 THR
Chi-restraints excluded: chain B residue  456 MET
Chi-restraints excluded: chain B residue  490 LEU
Chi-restraints excluded: chain B residue  594 ILE
Chi-restraints excluded: chain B residue  609 TYR
Chi-restraints excluded: chain B residue  618 VAL
Chi-restraints excluded: chain B residue  619 VAL
Chi-restraints excluded: chain B residue  660 MET
Chi-restraints excluded: chain B residue  718 LEU
Chi-restraints excluded: chain B residue  736 LEU
Chi-restraints excluded: chain B residue  739 ARG
Chi-restraints excluded: chain B residue  808 THR
Chi-restraints excluded: chain B residue  852 LEU
Chi-restraints excluded: chain B residue  869 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 89 optimal weight:    0.8980
   chunk 38 optimal weight:    5.9990
   chunk 95 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 17 optimal weight:    5.9990
   chunk 20 optimal weight:    0.8980
   chunk 69 optimal weight:    5.9990
   chunk 33 optimal weight:    8.9990
   chunk 46 optimal weight:   10.0000
   chunk 23 optimal weight:   20.0000
   chunk 51 optimal weight:    0.9980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 242 GLN
A 313 HIS
B 605 GLN
** B 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.081414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.066725 restraints weight = 42050.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.068956 restraints weight = 23992.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.070461 restraints weight = 15935.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.071512 restraints weight = 11706.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.072272 restraints weight = 9274.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.4690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10114  Z= 0.121
  Angle     :  0.681  12.668  13662  Z= 0.334
  Chirality :  0.042   0.155   1474
  Planarity :  0.004   0.061   1749
  Dihedral  :  6.085  58.675   1363
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.55 %
    Favored  : 93.45 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 19.45 %
    Favored  : 76.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.69 (0.24), residues: 1221
  helix:  0.17 (0.23), residues: 531
  sheet: -1.86 (0.50), residues: 109
  loop : -2.26 (0.24), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 310 
 TYR   0.019   0.001   TYR A 402 
 PHE   0.026   0.002   PHE A 504 
 TRP   0.036   0.001   TRP A 238 
 HIS   0.009   0.001   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (10109)
  covalent geometry    : angle       0.68107 (13662)
  hydrogen bonds       : bond        0.03562 (  404)
  hydrogen bonds       : angle       5.31978 ( 1155)
  metal coordination   : bond        0.00115 (    5)

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

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

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 109
  time to evaluate  : 0.322 
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
TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it.
REVERT: A  389 GLU cc_start: 0.8753 (pt0) cc_final: 0.8424 (pm20)
REVERT: B   32 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7825 (pp)
REVERT: B  135 MET cc_start: 0.8464 (mmp) cc_final: 0.7886 (mmp)
REVERT: B  219 MET cc_start: 0.7921 (mmm) cc_final: 0.7492 (mmm)
REVERT: B  344 MET cc_start: 0.6062 (mtt) cc_final: 0.5651 (ppp)
REVERT: B  734 ASP cc_start: 0.7953 (t0) cc_final: 0.7697 (t0)
REVERT: B  826 MET cc_start: 0.8007 (tpt) cc_final: 0.7800 (tpp)
  outliers start: 38
  outliers final: 33
  residues processed: 136
  average time/residue: 0.0782
  time to fit residues: 15.6226
Evaluate side-chains
  133 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 99
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  207 ASP
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  313 HIS
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  478 ASN
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  185 CYS
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  382 LEU
Chi-restraints excluded: chain B residue  422 THR
Chi-restraints excluded: chain B residue  456 MET
Chi-restraints excluded: chain B residue  490 LEU
Chi-restraints excluded: chain B residue  594 ILE
Chi-restraints excluded: chain B residue  606 VAL
Chi-restraints excluded: chain B residue  618 VAL
Chi-restraints excluded: chain B residue  619 VAL
Chi-restraints excluded: chain B residue  736 LEU
Chi-restraints excluded: chain B residue  739 ARG
Chi-restraints excluded: chain B residue  808 THR
Chi-restraints excluded: chain B residue  852 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 45 optimal weight:    0.0040
   chunk 87 optimal weight:    5.9990
   chunk 8 optimal weight:    5.9990
   chunk 24 optimal weight:   10.0000
   chunk 111 optimal weight:    0.7980
   chunk 75 optimal weight:   10.0000
   chunk 100 optimal weight:    0.8980
   chunk 18 optimal weight:    3.9990
   chunk 56 optimal weight:    4.9990
   chunk 117 optimal weight:    6.9990
   chunk 96 optimal weight:    0.7980
   overall best weight:    1.2994

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

Flipped N/Q/H residues before XYZ refinement:
A 313 HIS
** B 855 HIS ** 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 = 0.3846 r_free = 0.3846 target = 0.081345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.066422 restraints weight = 42654.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.068693 restraints weight = 24020.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.070229 restraints weight = 15875.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.071281 restraints weight = 11636.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.072059 restraints weight = 9212.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.4808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10114  Z= 0.126
  Angle     :  0.686  12.023  13662  Z= 0.337
  Chirality :  0.043   0.149   1474
  Planarity :  0.004   0.060   1749
  Dihedral  :  5.849  58.802   1361
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 20.40 %
    Favored  : 75.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.61 (0.24), residues: 1221
  helix:  0.23 (0.23), residues: 532
  sheet: -1.85 (0.50), residues: 111
  loop : -2.20 (0.25), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 310 
 TYR   0.014   0.001   TYR B 187 
 PHE   0.026   0.002   PHE A 504 
 TRP   0.040   0.002   TRP A 238 
 HIS   0.009   0.001   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (10109)
  covalent geometry    : angle       0.68612 (13662)
  hydrogen bonds       : bond        0.03527 (  404)
  hydrogen bonds       : angle       5.29912 ( 1155)
  metal coordination   : bond        0.00173 (    5)

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

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

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 106
  time to evaluate  : 0.358 
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
TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it.
REVERT: A  389 GLU cc_start: 0.8745 (pt0) cc_final: 0.8414 (pm20)
REVERT: B   32 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7838 (pp)
REVERT: B  104 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8352 (m)
REVERT: B  135 MET cc_start: 0.8507 (mmp) cc_final: 0.8114 (mmp)
REVERT: B  219 MET cc_start: 0.7943 (mmm) cc_final: 0.7552 (mmm)
REVERT: B  344 MET cc_start: 0.6112 (mtt) cc_final: 0.5715 (ppp)
REVERT: B  523 MET cc_start: 0.8361 (mmm) cc_final: 0.8140 (mmt)
  outliers start: 39
  outliers final: 31
  residues processed: 132
  average time/residue: 0.0825
  time to fit residues: 16.0409
Evaluate side-chains
  137 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 104
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  207 ASP
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  313 HIS
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  478 ASN
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  185 CYS
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  382 LEU
Chi-restraints excluded: chain B residue  422 THR
Chi-restraints excluded: chain B residue  456 MET
Chi-restraints excluded: chain B residue  490 LEU
Chi-restraints excluded: chain B residue  594 ILE
Chi-restraints excluded: chain B residue  606 VAL
Chi-restraints excluded: chain B residue  618 VAL
Chi-restraints excluded: chain B residue  736 LEU
Chi-restraints excluded: chain B residue  808 THR
Chi-restraints excluded: chain B residue  852 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 65 optimal weight:    0.6980
   chunk 66 optimal weight:    0.6980
   chunk 112 optimal weight:    1.9990
   chunk 29 optimal weight:    7.9990
   chunk 4 optimal weight:   10.0000
   chunk 87 optimal weight:    7.9990
   chunk 48 optimal weight:    0.0040
   chunk 24 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0070
   chunk 122 optimal weight:    7.9990
   chunk 61 optimal weight:   10.0000
   overall best weight:    0.6812

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

Flipped N/Q/H residues before XYZ refinement:
A 313 HIS
** B 855 HIS ** 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 = 0.3873 r_free = 0.3873 target = 0.082735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.067779 restraints weight = 41773.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.070144 restraints weight = 24158.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.071669 restraints weight = 15886.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.072733 restraints weight = 11667.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.073515 restraints weight = 9255.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.5010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10114  Z= 0.116
  Angle     :  0.692  12.104  13662  Z= 0.335
  Chirality :  0.043   0.251   1474
  Planarity :  0.004   0.061   1749
  Dihedral  :  5.544  59.040   1359
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 11.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 21.53 %
    Favored  : 75.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.49 (0.24), residues: 1221
  helix:  0.29 (0.23), residues: 538
  sheet: -1.77 (0.50), residues: 111
  loop : -2.12 (0.25), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 310 
 TYR   0.029   0.001   TYR A 507 
 PHE   0.030   0.002   PHE A 504 
 TRP   0.045   0.001   TRP A 238 
 HIS   0.014   0.001   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (10109)
  covalent geometry    : angle       0.69207 (13662)
  hydrogen bonds       : bond        0.03424 (  404)
  hydrogen bonds       : angle       5.20392 ( 1155)
  metal coordination   : bond        0.00081 (    5)

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

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

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 118
  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
TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it.
REVERT: A  298 ASP cc_start: 0.7097 (m-30) cc_final: 0.6859 (m-30)
REVERT: A  389 GLU cc_start: 0.8775 (pt0) cc_final: 0.8424 (pm20)
REVERT: A  478 ASN cc_start: 0.8012 (OUTLIER) cc_final: 0.7615 (p0)
REVERT: B   22 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.8039 (mt)
REVERT: B   32 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7771 (pp)
REVERT: B  104 THR cc_start: 0.8847 (t) cc_final: 0.8372 (m)
REVERT: B  135 MET cc_start: 0.8547 (mmp) cc_final: 0.8122 (mmp)
REVERT: B  344 MET cc_start: 0.6284 (mtt) cc_final: 0.5844 (ppp)
REVERT: B  523 MET cc_start: 0.8409 (mmm) cc_final: 0.8142 (mmt)
REVERT: B  558 MET cc_start: 0.7449 (ppp) cc_final: 0.7118 (ppp)
REVERT: B  623 ARG cc_start: 0.8921 (ttt180) cc_final: 0.8543 (ttt180)
REVERT: B  734 ASP cc_start: 0.7913 (t0) cc_final: 0.7673 (t0)
  outliers start: 28
  outliers final: 24
  residues processed: 137
  average time/residue: 0.0820
  time to fit residues: 16.6933
Evaluate side-chains
  136 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 109
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  207 ASP
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  478 ASN
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  185 CYS
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  422 THR
Chi-restraints excluded: chain B residue  456 MET
Chi-restraints excluded: chain B residue  490 LEU
Chi-restraints excluded: chain B residue  594 ILE
Chi-restraints excluded: chain B residue  618 VAL
Chi-restraints excluded: chain B residue  736 LEU
Chi-restraints excluded: chain B residue  808 THR
Chi-restraints excluded: chain B residue  852 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9990
   chunk 31 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9990
   chunk 82 optimal weight:    2.9990
   chunk 18 optimal weight:    7.9990
   chunk 70 optimal weight:    3.9990
   chunk 113 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   chunk 4 optimal weight:    4.9990
   chunk 9 optimal weight:    3.9990
   overall best weight:    1.3588

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

Flipped N/Q/H residues before XYZ refinement:
B 733 GLN
** B 855 HIS ** 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 = 0.3855 r_free = 0.3855 target = 0.081760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.066678 restraints weight = 42793.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.069021 restraints weight = 24288.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.070557 restraints weight = 15947.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.071636 restraints weight = 11716.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.072407 restraints weight = 9284.512|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.5056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10114  Z= 0.126
  Angle     :  0.698  13.057  13662  Z= 0.337
  Chirality :  0.043   0.211   1474
  Planarity :  0.004   0.060   1749
  Dihedral  :  5.525  59.223   1359
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 21.44 %
    Favored  : 75.54 %
  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 are not related in a simple way.
  whole: -1.47 (0.24), residues: 1221
  helix:  0.34 (0.23), residues: 533
  sheet: -2.07 (0.47), residues: 121
  loop : -2.04 (0.25), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 310 
 TYR   0.029   0.001   TYR A 507 
 PHE   0.028   0.002   PHE A 504 
 TRP   0.044   0.002   TRP A 238 
 HIS   0.006   0.001   HIS B 443 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (10109)
  covalent geometry    : angle       0.69814 (13662)
  hydrogen bonds       : bond        0.03392 (  404)
  hydrogen bonds       : angle       5.16697 ( 1155)
  metal coordination   : bond        0.00118 (    5)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1650.54 seconds
wall clock time: 29 minutes 17.32 seconds (1757.32 seconds total)