Starting phenix.real_space_refine
on Thu Sep 18 00:57:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dus_47176/09_2025/9dus_47176.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dus_47176/09_2025/9dus_47176.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.12
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dus_47176/09_2025/9dus_47176.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dus_47176/09_2025/9dus_47176.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dus_47176/09_2025/9dus_47176.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dus_47176/09_2025/9dus_47176.cif"
  }
  resolution = 3.12
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.017
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      62      5.16       5
     C    8101      2.51       5
     N    2201      2.21       5
     O    2338      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12702
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 10069
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1253, 10069
          Classifications: {'peptide': 1253}
          Link IDs: {'PTRANS': 52, 'TRANS': 1200}
          Chain breaks: 6
    Chain: "B"
      Number of atoms: 576
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 74, 570
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 4, 'TRANS': 69}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 74, 570
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 4, 'TRANS': 69}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 567
    Chain: "C"
      Number of atoms: 1039
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 1039
          Classifications: {'peptide': 132}
          Link IDs: {'PTRANS': 4, 'TRANS': 127}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 442
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 442
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 1, 'TRANS': 55}
    Chain: "E"
      Number of atoms: 576
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 74, 571
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 5, 'TRANS': 68}
      Conformer: "B"
        Number of residues, atoms: 74, 571
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 5, 'TRANS': 68}
          bond proxies already assigned to first conformer: 571
  Time building chain proxies: 2.62, per 1000 atoms: 0.21
  Number of scatterers: 12702
  At special positions: 0
  Unit cell: (99.1573, 107.125, 165.557, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      62     16.00
     O    2338      8.00
     N    2201      7.00
     C    8101      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: 0.92
  Conformation dependent library (CDL) restraints added in 564.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3012

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 7 sheets defined
      61.9% alpha, 5.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 32
      removed outlier: 4.009A  pdb=" N   ILE A  25 " --> pdb=" O   VAL A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 56
      removed outlier: 4.440A  pdb=" N   LYS A  50 " --> pdb=" O   CYS A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 77
      removed outlier: 3.758A  pdb=" N   GLU A  67 " --> pdb=" O   ILE A  63 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   VAL A  68 " --> pdb=" O   ASN A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 95
    Processing helix  chain 'A' and resid 103 through 135
      removed outlier: 3.584A  pdb=" N   ARG A 107 " --> pdb=" O   THR A 103 " (cutoff:3.500A)
      removed outlier: 5.246A  pdb=" N   ASP A 122 " --> pdb=" O   SER A 118 " (cutoff:3.500A)
      removed outlier: 5.401A  pdb=" N   LYS A 123 " --> pdb=" O   LYS A 119 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   LEU A 135 " --> pdb=" O   THR A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 151
      removed outlier: 4.041A  pdb=" N   GLU A 147 " --> pdb=" O   GLU A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 158
    Processing helix  chain 'A' and resid 161 through 183
      removed outlier: 3.696A  pdb=" N   PHE A 167 " --> pdb=" O   GLU A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 248
    Processing helix  chain 'A' and resid 251 through 273
      removed outlier: 3.734A  pdb=" N   GLY A 256 " --> pdb=" O   THR A 252 " (cutoff:3.500A)
      Proline residue:  A 270  - end of helix
    Processing helix  chain 'A' and resid 275 through 293
      removed outlier: 4.034A  pdb=" N   ILE A 279 " --> pdb=" O   PRO A 275 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   GLU A 284 " --> pdb=" O   VAL A 280 " (cutoff:3.500A)
      Proline residue:  A 285  - end of helix
      removed outlier: 4.336A  pdb=" N   LEU A 288 " --> pdb=" O   GLU A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 319
      removed outlier: 3.787A  pdb=" N   ASN A 306 " --> pdb=" O   GLY A 302 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   HIS A 307 " --> pdb=" O   ALA A 303 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ASN A 319 " --> pdb=" O   VAL A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 339
      removed outlier: 3.824A  pdb=" N   TYR A 327 " --> pdb=" O   ASP A 323 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   HIS A 328 " --> pdb=" O   GLU A 324 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ILE A 339 " --> pdb=" O   ASP A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 353
      removed outlier: 3.745A  pdb=" N   ILE A 349 " --> pdb=" O   THR A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 375
      removed outlier: 4.020A  pdb=" N   ALA A 366 " --> pdb=" O   GLU A 362 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 404
    Processing helix  chain 'A' and resid 418 through 428
    Processing helix  chain 'A' and resid 432 through 439
    Processing helix  chain 'A' and resid 440 through 444
      removed outlier: 3.529A  pdb=" N   PHE A 443 " --> pdb=" O   TRP A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 476 through 480
      removed outlier: 4.244A  pdb=" N   VAL A 479 " --> pdb=" O   TRP A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 485
      removed outlier: 3.523A  pdb=" N   LEU A 485 " --> pdb=" O   LYS A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 505
      removed outlier: 3.622A  pdb=" N   VAL A 501 " --> pdb=" O   ARG A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 519
      removed outlier: 3.904A  pdb=" N   VAL A 513 " --> pdb=" O   ASP A 509 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ILE A 514 " --> pdb=" O   PRO A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 550 through 567
    Processing helix  chain 'A' and resid 568 through 573
      removed outlier: 3.680A  pdb=" N   PHE A 572 " --> pdb=" O   ILE A 568 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LYS A 573 " --> pdb=" O   GLY A 569 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 568 through 573'
    Processing helix  chain 'A' and resid 666 through 671
      removed outlier: 3.682A  pdb=" N   ASN A 670 " --> pdb=" O   LYS A 666 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 688
      removed outlier: 4.827A  pdb=" N   LEU A 678 " --> pdb=" O   GLU A 674 " (cutoff:3.500A)
      removed outlier: 5.004A  pdb=" N   PHE A 679 " --> pdb=" O   THR A 675 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 694 through 701
      removed outlier: 3.664A  pdb=" N   LYS A 698 " --> pdb=" O   GLN A 694 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 721 through 725
    Processing helix  chain 'A' and resid 743 through 763
      Proline residue:  A 753  - end of helix
    Processing helix  chain 'A' and resid 788 through 815
      removed outlier: 3.698A  pdb=" N   LYS A 792 " --> pdb=" O   PRO A 788 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   LYS A 793 " --> pdb=" O   TYR A 789 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ARG A 794 " --> pdb=" O   ASN A 790 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ILE A 814 " --> pdb=" O   ARG A 810 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 846 through 852
      removed outlier: 4.376A  pdb=" N   ILE A 850 " --> pdb=" O   SER A 846 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 863 through 882
      removed outlier: 3.642A  pdb=" N   ALA A 867 " --> pdb=" O   GLU A 863 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 884 through 906
    Processing helix  chain 'A' and resid 913 through 923
      removed outlier: 3.608A  pdb=" N   ILE A 918 " --> pdb=" O   ARG A 914 " (cutoff:3.500A)
      Proline residue:  A 919  - end of helix
    Processing helix  chain 'A' and resid 923 through 933
      removed outlier: 3.654A  pdb=" N   LEU A 927 " --> pdb=" O   ASN A 923 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 934 through 938
    Processing helix  chain 'A' and resid 955 through 970
    Processing helix  chain 'A' and resid 975 through 983
      removed outlier: 3.897A  pdb=" N   HIS A 979 " --> pdb=" O   GLU A 975 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 990 through 997
    Processing helix  chain 'A' and resid 1008 through 1024
    Processing helix  chain 'A' and resid 1027 through 1031
      removed outlier: 4.059A  pdb=" N   LYS A1031 " --> pdb=" O   PRO A1028 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1037 through 1050
      removed outlier: 3.640A  pdb=" N   GLU A1041 " --> pdb=" O   ASP A1037 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1056 through 1067
      removed outlier: 3.734A  pdb=" N   ALA A1060 " --> pdb=" O   VAL A1056 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1067 through 1079
      removed outlier: 3.695A  pdb=" N   LEU A1079 " --> pdb=" O   ILE A1075 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1081 through 1093
      removed outlier: 3.884A  pdb=" N   ILE A1086 " --> pdb=" O   THR A1082 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1096 through 1104
    Processing helix  chain 'A' and resid 1105 through 1120
    Processing helix  chain 'A' and resid 1132 through 1145
    Processing helix  chain 'A' and resid 1145 through 1150
    Processing helix  chain 'A' and resid 1161 through 1165
    Processing helix  chain 'A' and resid 1176 through 1183
      removed outlier: 3.649A  pdb=" N   CYS A1180 " --> pdb=" O   THR A1176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1232 through 1249
    Processing helix  chain 'A' and resid 1252 through 1264
      removed outlier: 3.749A  pdb=" N   ASN A1257 " --> pdb=" O   ASP A1253 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   GLU A1258 " --> pdb=" O   SER A1254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1270 through 1278
    Processing helix  chain 'A' and resid 1304 through 1309
    Processing helix  chain 'A' and resid 1330 through 1348
    Processing helix  chain 'B' and resid 326 through 340
      removed outlier: 3.558A  pdb=" N   SER B 338 " --> pdb=" O   SER B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 342 through 368
    Processing helix  chain 'B' and resid 405 through 410
    Processing helix  chain 'C' and resid 324 through 371
      removed outlier: 3.992A  pdb=" N   GLY C 344 " --> pdb=" O   LEU C 340 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   GLU C 345 " --> pdb=" O   LEU C 341 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 457 through 470
      removed outlier: 4.087A  pdb=" N   ARG C 461 " --> pdb=" O   GLY C 457 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   SER C 462 " --> pdb=" O   PRO C 458 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 474 through 488
    Processing helix  chain 'C' and resid 490 through 507
    Processing helix  chain 'D' and resid 325 through 369
      removed outlier: 3.834A  pdb=" N   GLY D 344 " --> pdb=" O   LEU D 340 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   GLU D 345 " --> pdb=" O   LEU D 341 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 325 through 341
      removed outlier: 4.260A  pdb=" N   SER E 338 " --> pdb=" O   SER E 334 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   LEU E 339 " --> pdb=" O   LYS E 335 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 341 through 374
      removed outlier: 4.040A  pdb=" N   GLU E 345 " --> pdb=" O   LEU E 341 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ILE E 358 " --> pdb=" O   ASN E 354 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   ILE E 372 " --> pdb=" O   SER E 368 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 383 through 387
      removed outlier: 3.574A  pdb=" N   ASP E 387 " --> pdb=" O   PRO E 384 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.384A  pdb=" N   SER A  83 " --> pdb=" O   VAL A 220 " (cutoff:3.500A)
      removed outlier: 8.339A  pdb=" N   TYR A 222 " --> pdb=" O   SER A  83 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   HIS A 219 " --> pdb=" O   SER A 214 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 378 through 381
      removed outlier: 6.888A  pdb=" N   ILE B 398 " --> pdb=" O   ALA D 373 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 411 through 412
      removed outlier: 3.559A  pdb=" N   LYS A 447 " --> pdb=" O   THR A 412 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 545 through 549
      removed outlier: 3.958A  pdb=" N   TYR A 706 " --> pdb=" O   LEU A 530 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 765 through 770
      removed outlier: 3.544A  pdb=" N   VAL A 656 " --> pdb=" O   LYS A 781 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 829 through 831
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1166 through 1171
      removed outlier: 3.657A  pdb=" N   VAL A1360 " --> pdb=" O   ILE A1171 " (cutoff:3.500A)

    708 hydrogen bonds defined for protein.
    2053 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: 1.69

  Time building geometry restraints manager: 1.28 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4094
        1.34 -     1.46: 2065
        1.46 -     1.58: 6687
        1.58 -     1.69: 0
        1.69 -     1.81: 103
  Bond restraints: 12949
  Sorted by residual:
  bond pdb=" C   PHE A 269 "
       pdb=" N   PRO A 270 "
    ideal  model  delta    sigma   weight residual
    1.335  1.363 -0.027 1.36e-02 5.41e+03 4.04e+00
  bond pdb=" N   ILE A 752 "
       pdb=" CA  ILE A 752 "
    ideal  model  delta    sigma   weight residual
    1.464  1.486 -0.022 1.23e-02 6.61e+03 3.18e+00
  bond pdb=" C   ILE A 918 "
       pdb=" N   PRO A 919 "
    ideal  model  delta    sigma   weight residual
    1.335  1.357 -0.022 1.28e-02 6.10e+03 3.02e+00
  bond pdb=" C   ILE A 752 "
       pdb=" N   PRO A 753 "
    ideal  model  delta    sigma   weight residual
    1.335  1.357 -0.022 1.28e-02 6.10e+03 3.01e+00
  bond pdb=" CA  ILE A 752 "
       pdb=" C   ILE A 752 "
    ideal  model  delta    sigma   weight residual
    1.520  1.534 -0.014 8.80e-03 1.29e+04 2.70e+00
  ... (remaining 12944 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.98: 17062
        1.98 -     3.97: 369
        3.97 -     5.95: 47
        5.95 -     7.93: 20
        7.93 -     9.91: 3
  Bond angle restraints: 17501
  Sorted by residual:
  angle pdb=" C   THR A1082 "
        pdb=" CA  THR A1082 "
        pdb=" CB  THR A1082 "
      ideal   model   delta    sigma   weight residual
     115.79  110.22    5.57 1.19e+00 7.06e-01 2.19e+01
  angle pdb=" C   LEU E 394 "
        pdb=" N   LYS E 395 "
        pdb=" CA  LYS E 395 "
      ideal   model   delta    sigma   weight residual
     121.80  131.40   -9.60 2.44e+00 1.68e-01 1.55e+01
  angle pdb=" C   ALA C 373 "
        pdb=" N   ILE C 374 "
        pdb=" CA  ILE C 374 "
      ideal   model   delta    sigma   weight residual
     122.13  128.79   -6.66 1.85e+00 2.92e-01 1.29e+01
  angle pdb=" C   GLY A 741 "
        pdb=" N   TYR A 742 "
        pdb=" CA  TYR A 742 "
      ideal   model   delta    sigma   weight residual
     121.54  128.23   -6.69 1.91e+00 2.74e-01 1.23e+01
  angle pdb=" C   PRO E 392 "
        pdb=" N   ASP E 393 "
        pdb=" CA  ASP E 393 "
      ideal   model   delta    sigma   weight residual
     121.54  128.21   -6.67 1.91e+00 2.74e-01 1.22e+01
  ... (remaining 17496 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.99: 7240
       14.99 -    29.97: 525
       29.97 -    44.96: 119
       44.96 -    59.95: 9
       59.95 -    74.94: 7
  Dihedral angle restraints: 7900
    sinusoidal: 3248
      harmonic: 4652
  Sorted by residual:
  dihedral pdb=" CA  ILE E 390 "
           pdb=" C   ILE E 390 "
           pdb=" N   ASN E 391 "
           pdb=" CA  ASN E 391 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.22   25.78     0      5.00e+00 4.00e-02 2.66e+01
  dihedral pdb=" CA  HIS A1174 "
           pdb=" C   HIS A1174 "
           pdb=" N   GLU A1175 "
           pdb=" CA  GLU A1175 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.57   25.43     0      5.00e+00 4.00e-02 2.59e+01
  dihedral pdb=" CA  ILE A 766 "
           pdb=" C   ILE A 766 "
           pdb=" N   ALA A 767 "
           pdb=" CA  ALA A 767 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.14   21.86     0      5.00e+00 4.00e-02 1.91e+01
  ... (remaining 7897 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.095: 1880
       0.095 -    0.190: 114
       0.190 -    0.286: 5
       0.286 -    0.381: 0
       0.381 -    0.476: 1
  Chirality restraints: 2000
  Sorted by residual:
  chirality pdb=" CG  LEU A 705 "
            pdb=" CB  LEU A 705 "
            pdb=" CD1 LEU A 705 "
            pdb=" CD2 LEU A 705 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.11   -0.48 2.00e-01 2.50e+01 5.67e+00
  chirality pdb=" CB  ILE E 372 "
            pdb=" CA  ILE E 372 "
            pdb=" CG1 ILE E 372 "
            pdb=" CG2 ILE E 372 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.86   -0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  ASP A 466 "
            pdb=" N   ASP A 466 "
            pdb=" C   ASP A 466 "
            pdb=" CB  ASP A 466 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.55e-01
  ... (remaining 1997 not shown)

  Planarity restraints: 2212
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 274 "    0.055 5.00e-02 4.00e+02   8.15e-02 1.06e+01
        pdb=" N   PRO A 275 "   -0.141 5.00e-02 4.00e+02
        pdb=" CA  PRO A 275 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 275 "    0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 408 "   -0.016 2.00e-02 2.50e+03   2.03e-02 1.03e+01
        pdb=" CG  TRP A 408 "    0.049 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 408 "   -0.035 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 408 "    0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 408 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 408 "    0.010 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 408 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 408 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 408 "   -0.013 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 408 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 752 "    0.049 5.00e-02 4.00e+02   7.32e-02 8.57e+00
        pdb=" N   PRO A 753 "   -0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO A 753 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 753 "    0.041 5.00e-02 4.00e+02
  ... (remaining 2209 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 3580
        2.83 -     3.34: 11524
        3.34 -     3.86: 20296
        3.86 -     4.38: 24016
        4.38 -     4.90: 41638
  Nonbonded interactions: 101054
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 290 "
            pdb=" OD1 ASP A 335 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" O   TRP A 747 "
            pdb=" OG1 THR A 751 "
     model   vdw
     2.328 3.040
  nonbonded pdb=" OH  TYR A 673 "
            pdb=" OE1 GLN A 694 "
     model   vdw
     2.355 3.040
  nonbonded pdb=" O   LEU A1274 "
            pdb=" OG1 THR A1278 "
     model   vdw
     2.361 3.040
  nonbonded pdb=" O   ALA A 796 "
            pdb=" OG1 THR A 800 "
     model   vdw
     2.365 3.040
  ... (remaining 101049 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.800
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     10.410
  Find NCS groups from input model:        0.060
  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:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7393
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      :  0.004   0.068  12949  Z= 0.186
  Angle     :  0.731   9.915  17501  Z= 0.402
  Chirality :  0.048   0.476   2000
  Planarity :  0.008   0.082   2212
  Dihedral  : 11.116  74.935   4888
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.34 (0.18), residues: 1566
  helix: -0.60 (0.14), residues: 873
  sheet:  0.98 (0.59), residues: 80
  loop : -1.43 (0.22), residues: 613

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 403 
 TYR   0.026   0.002   TYR A 522 
 PHE   0.029   0.002   PHE A 304 
 TRP   0.049   0.002   TRP A 408 
 HIS   0.008   0.001   HIS A 812 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 (12949)
  covalent geometry    : angle       0.73148 (17501)
  hydrogen bonds       : bond        0.18792 (  708)
  hydrogen bonds       : angle       6.45483 ( 2053)

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

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

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 304
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 ARG cc_start: 0.7376 (mtt90) cc_final: 0.7115 (mtt180)
REVERT: A   50 LYS cc_start: 0.8240 (ttmt) cc_final: 0.8002 (mtpp)
REVERT: A   62 ILE cc_start: 0.7905 (mm) cc_final: 0.7471 (mt)
REVERT: A  111 LYS cc_start: 0.7553 (ttmt) cc_final: 0.7335 (ttmm)
REVERT: A  355 SER cc_start: 0.8255 (m) cc_final: 0.7989 (p)
REVERT: A  361 LEU cc_start: 0.8234 (mt) cc_final: 0.7991 (mt)
REVERT: A  435 GLN cc_start: 0.8520 (mt0) cc_final: 0.8281 (mt0)
REVERT: A  500 ASP cc_start: 0.6941 (t0) cc_final: 0.6491 (t70)
REVERT: A  516 TYR cc_start: 0.8101 (t80) cc_final: 0.7788 (t80)
REVERT: A  533 SER cc_start: 0.7921 (t) cc_final: 0.7495 (p)
REVERT: A  535 LYS cc_start: 0.8135 (tppt) cc_final: 0.7927 (mmtp)
REVERT: A  546 PHE cc_start: 0.7164 (p90) cc_final: 0.6677 (p90)
REVERT: A  559 ILE cc_start: 0.8339 (mt) cc_final: 0.7932 (mt)
REVERT: A  563 LEU cc_start: 0.7655 (mt) cc_final: 0.7399 (mp)
REVERT: A  570 LYS cc_start: 0.8022 (mttt) cc_final: 0.7769 (mttt)
REVERT: A  573 LYS cc_start: 0.7532 (mtpp) cc_final: 0.7324 (mtpp)
REVERT: A  861 VAL cc_start: 0.7413 (t) cc_final: 0.7136 (m)
REVERT: A  923 ASN cc_start: 0.8299 (t0) cc_final: 0.7986 (t0)
REVERT: A  925 ASP cc_start: 0.7296 (m-30) cc_final: 0.7015 (m-30)
REVERT: A 1019 ARG cc_start: 0.7635 (mtp85) cc_final: 0.7337 (mtp85)
REVERT: A 1090 MET cc_start: 0.7006 (ttt) cc_final: 0.6648 (ttt)
REVERT: A 1144 MET cc_start: 0.8124 (mmm) cc_final: 0.7841 (mmm)
REVERT: A 1240 ARG cc_start: 0.7386 (tpt170) cc_final: 0.7169 (mmm160)
REVERT: A 1352 LYS cc_start: 0.7286 (mttt) cc_final: 0.7011 (mttt)
REVERT: C  371 MET cc_start: 0.6812 (ptp) cc_final: 0.6579 (ptp)
REVERT: C  460 SER cc_start: 0.7749 (p) cc_final: 0.7450 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 304
  average time/residue: 0.1195
  time to fit residues: 50.3116
Evaluate side-chains
  258 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 258
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    0.5980
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    0.7980
   chunk 77 optimal weight:    0.2980
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9990
   chunk 149 optimal weight:    0.5980
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 307 HIS
A 809 GLN
B 329 ASN
E 329 ASN
E 356 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.150444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.118078 restraints weight = 41293.476|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 3.63
r_work: 0.3193 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3192
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3192 r_free = 0.3192    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3192 r_free = 0.3192    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3192
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.1697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12949  Z= 0.187
  Angle     :  0.574   6.850  17501  Z= 0.309
  Chirality :  0.042   0.183   2000
  Planarity :  0.006   0.047   2212
  Dihedral  :  4.492  24.300   1735
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  :  5.70 %
    Favored  : 93.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.62 (0.20), residues: 1566
  helix:  1.33 (0.17), residues: 897
  sheet:  1.16 (0.54), residues: 97
  loop : -1.21 (0.23), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  77 
 TYR   0.022   0.002   TYR A 516 
 PHE   0.022   0.002   PHE A 304 
 TRP   0.024   0.002   TRP A 408 
 HIS   0.012   0.001   HIS A 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 (12949)
  covalent geometry    : angle       0.57397 (17501)
  hydrogen bonds       : bond        0.06545 (  708)
  hydrogen bonds       : angle       4.48794 ( 2053)

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

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

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 277
  time to evaluate  : 0.480 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7600 (mtt90) cc_final: 0.7334 (mtt-85)
REVERT: A   50 LYS cc_start: 0.8564 (ttmt) cc_final: 0.8214 (mtpp)
REVERT: A  355 SER cc_start: 0.8491 (m) cc_final: 0.8251 (p)
REVERT: A  361 LEU cc_start: 0.8321 (mt) cc_final: 0.8113 (mt)
REVERT: A  500 ASP cc_start: 0.6970 (t0) cc_final: 0.6586 (t70)
REVERT: A  535 LYS cc_start: 0.8178 (tppt) cc_final: 0.7963 (mmtp)
REVERT: A  559 ILE cc_start: 0.8420 (mt) cc_final: 0.8050 (mt)
REVERT: A  563 LEU cc_start: 0.8051 (mt) cc_final: 0.7850 (mp)
REVERT: A  570 LYS cc_start: 0.8149 (mttt) cc_final: 0.7878 (mttt)
REVERT: A  573 LYS cc_start: 0.7572 (mtpp) cc_final: 0.7355 (mtpp)
REVERT: A  752 ILE cc_start: 0.8588 (mt) cc_final: 0.8332 (mp)
REVERT: A  780 THR cc_start: 0.7956 (m) cc_final: 0.7683 (p)
REVERT: A  803 TYR cc_start: 0.8225 (t80) cc_final: 0.7958 (t80)
REVERT: A  861 VAL cc_start: 0.7644 (t) cc_final: 0.7345 (m)
REVERT: A  923 ASN cc_start: 0.8336 (t0) cc_final: 0.7919 (t0)
REVERT: A  925 ASP cc_start: 0.7400 (m-30) cc_final: 0.7147 (m-30)
REVERT: A  930 MET cc_start: 0.7922 (ttp) cc_final: 0.7700 (ttp)
REVERT: A  969 LEU cc_start: 0.8400 (tp) cc_final: 0.8190 (tt)
REVERT: A 1019 ARG cc_start: 0.7750 (mtp85) cc_final: 0.7416 (mtp85)
REVERT: A 1062 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7342 (mm-30)
REVERT: A 1090 MET cc_start: 0.7087 (ttt) cc_final: 0.6761 (ttt)
REVERT: A 1144 MET cc_start: 0.8309 (mmm) cc_final: 0.7854 (mmm)
REVERT: A 1150 ARG cc_start: 0.7525 (mtm110) cc_final: 0.7295 (mtp180)
REVERT: A 1240 ARG cc_start: 0.7586 (tpt170) cc_final: 0.7263 (mmm160)
REVERT: A 1352 LYS cc_start: 0.7475 (mttt) cc_final: 0.7180 (mttt)
REVERT: A 1400 ASP cc_start: 0.7187 (t0) cc_final: 0.6904 (t0)
REVERT: C  446 MET cc_start: 0.5960 (mmt) cc_final: 0.5742 (mmt)
REVERT: C  460 SER cc_start: 0.7833 (p) cc_final: 0.7565 (m)
  outliers start: 16
  outliers final: 14
  residues processed: 282
  average time/residue: 0.1157
  time to fit residues: 45.0894
Evaluate side-chains
  275 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 261
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 GLN
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  483 GLU
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  730 ILE
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue 1132 CYS
Chi-restraints excluded: chain A residue 1312 THR
Chi-restraints excluded: chain A residue 1397 LEU
Chi-restraints excluded: chain C residue  448 SER
Chi-restraints excluded: chain C residue  462 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 5 optimal weight:    0.4980
   chunk 25 optimal weight:    0.9990
   chunk 131 optimal weight:    5.9990
   chunk 96 optimal weight:    0.0570
   chunk 132 optimal weight:    8.9990
   chunk 149 optimal weight:    0.9980
   chunk 48 optimal weight:    0.7980
   chunk 146 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 109 optimal weight:    0.0050
   chunk 116 optimal weight:    0.0470
   overall best weight:    0.2810

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

Flipped N/Q/H residues before XYZ refinement:
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 504 ASN
A 809 GLN
A1186 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.151991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.119431 restraints weight = 40862.826|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 3.67
r_work: 0.3226 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3228
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3228
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7511
moved from start:          0.2027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  12949  Z= 0.120
  Angle     :  0.485   7.138  17501  Z= 0.258
  Chirality :  0.039   0.150   2000
  Planarity :  0.004   0.042   2212
  Dihedral  :  4.160  23.385   1735
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  7.89 %
    Favored  : 91.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.36 (0.21), residues: 1566
  helix:  2.14 (0.17), residues: 889
  sheet:  1.11 (0.53), residues: 97
  loop : -1.17 (0.24), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 782 
 TYR   0.016   0.001   TYR A 789 
 PHE   0.017   0.001   PHE A 392 
 TRP   0.017   0.001   TRP A1189 
 HIS   0.012   0.001   HIS A 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (12949)
  covalent geometry    : angle       0.48460 (17501)
  hydrogen bonds       : bond        0.05109 (  708)
  hydrogen bonds       : angle       4.14460 ( 2053)

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

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

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 269
  time to evaluate  : 0.479 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7558 (mtt90) cc_final: 0.7253 (mtt-85)
REVERT: A   50 LYS cc_start: 0.8547 (ttmt) cc_final: 0.8191 (mtpp)
REVERT: A  257 ARG cc_start: 0.8086 (mtm110) cc_final: 0.7689 (mtm180)
REVERT: A  355 SER cc_start: 0.8484 (m) cc_final: 0.8235 (p)
REVERT: A  361 LEU cc_start: 0.8294 (mt) cc_final: 0.8075 (mt)
REVERT: A  435 GLN cc_start: 0.8426 (mt0) cc_final: 0.8193 (mt0)
REVERT: A  504 ASN cc_start: 0.6893 (m-40) cc_final: 0.6355 (t0)
REVERT: A  535 LYS cc_start: 0.8192 (tppt) cc_final: 0.7960 (mmtp)
REVERT: A  546 PHE cc_start: 0.7279 (p90) cc_final: 0.6940 (p90)
REVERT: A  559 ILE cc_start: 0.8367 (mt) cc_final: 0.7985 (mt)
REVERT: A  563 LEU cc_start: 0.8039 (mt) cc_final: 0.7743 (mp)
REVERT: A  570 LYS cc_start: 0.8148 (mttt) cc_final: 0.7876 (mttt)
REVERT: A  573 LYS cc_start: 0.7494 (mtpp) cc_final: 0.7253 (mtpp)
REVERT: A  780 THR cc_start: 0.7970 (m) cc_final: 0.7708 (p)
REVERT: A  803 TYR cc_start: 0.8223 (t80) cc_final: 0.7889 (t80)
REVERT: A  861 VAL cc_start: 0.7612 (t) cc_final: 0.7311 (m)
REVERT: A  923 ASN cc_start: 0.8358 (t0) cc_final: 0.7937 (t0)
REVERT: A  925 ASP cc_start: 0.7350 (m-30) cc_final: 0.7098 (m-30)
REVERT: A  930 MET cc_start: 0.7914 (ttp) cc_final: 0.7698 (ttp)
REVERT: A 1090 MET cc_start: 0.7072 (ttt) cc_final: 0.6769 (ttt)
REVERT: A 1110 GLN cc_start: 0.7296 (mt0) cc_final: 0.6986 (mt0)
REVERT: A 1112 ARG cc_start: 0.7800 (ttp80) cc_final: 0.7589 (ttm-80)
REVERT: A 1150 ARG cc_start: 0.7439 (mtm110) cc_final: 0.7215 (mtp180)
REVERT: A 1240 ARG cc_start: 0.7564 (tpt170) cc_final: 0.7261 (mmm160)
REVERT: A 1352 LYS cc_start: 0.7410 (mttt) cc_final: 0.7145 (mttt)
REVERT: C  446 MET cc_start: 0.5987 (mmt) cc_final: 0.5787 (mmt)
REVERT: C  460 SER cc_start: 0.7806 (p) cc_final: 0.7538 (m)
  outliers start: 11
  outliers final: 9
  residues processed: 271
  average time/residue: 0.1238
  time to fit residues: 46.4912
Evaluate side-chains
  268 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 259
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 GLN
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  483 GLU
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  730 ILE
Chi-restraints excluded: chain A residue 1186 ASN
Chi-restraints excluded: chain A residue 1392 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9980
   chunk 154 optimal weight:    0.9990
   chunk 138 optimal weight:    3.9990
   chunk 134 optimal weight:    2.9990
   chunk 92 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 116 optimal weight:    0.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 809 GLN
A1053 HIS
** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.148443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.116781 restraints weight = 29295.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 3.05
r_work: 0.3240 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3241
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3241 r_free = 0.3241    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3241 r_free = 0.3241    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3241
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
moved from start:          0.2428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  12949  Z= 0.227
  Angle     :  0.583   6.431  17501  Z= 0.307
  Chirality :  0.044   0.151   2000
  Planarity :  0.005   0.039   2212
  Dihedral  :  4.434  23.772   1735
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  :  9.01 %
    Favored  : 89.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.15 (0.21), residues: 1566
  helix:  1.99 (0.17), residues: 889
  sheet:  0.80 (0.52), residues: 96
  loop : -1.25 (0.24), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 301 
 TYR   0.025   0.002   TYR A 516 
 PHE   0.020   0.002   PHE A 991 
 TRP   0.029   0.002   TRP A 408 
 HIS   0.010   0.001   HIS A 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00544 (12949)
  covalent geometry    : angle       0.58291 (17501)
  hydrogen bonds       : bond        0.06281 (  708)
  hydrogen bonds       : angle       4.37159 ( 2053)

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

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

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 274
  time to evaluate  : 0.441 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7554 (mtt90) cc_final: 0.7350 (mtt180)
REVERT: A   50 LYS cc_start: 0.8519 (ttmt) cc_final: 0.8185 (mtpp)
REVERT: A  250 ARG cc_start: 0.8274 (ttp-170) cc_final: 0.8044 (ttp80)
REVERT: A  435 GLN cc_start: 0.8370 (mt0) cc_final: 0.8076 (mt0)
REVERT: A  533 SER cc_start: 0.8137 (t) cc_final: 0.7846 (p)
REVERT: A  535 LYS cc_start: 0.8098 (tppt) cc_final: 0.7844 (mmtp)
REVERT: A  559 ILE cc_start: 0.8408 (mt) cc_final: 0.8076 (mt)
REVERT: A  563 LEU cc_start: 0.7988 (mt) cc_final: 0.7717 (mp)
REVERT: A  570 LYS cc_start: 0.8114 (mttt) cc_final: 0.7706 (mttt)
REVERT: A  573 LYS cc_start: 0.7479 (mtpp) cc_final: 0.7217 (mtpp)
REVERT: A  780 THR cc_start: 0.7909 (m) cc_final: 0.7629 (p)
REVERT: A  803 TYR cc_start: 0.8242 (t80) cc_final: 0.7875 (t80)
REVERT: A  861 VAL cc_start: 0.7693 (t) cc_final: 0.7427 (m)
REVERT: A  887 LEU cc_start: 0.8158 (mt) cc_final: 0.7949 (mt)
REVERT: A  923 ASN cc_start: 0.8333 (t0) cc_final: 0.7923 (t0)
REVERT: A  925 ASP cc_start: 0.7211 (m-30) cc_final: 0.6980 (m-30)
REVERT: A  930 MET cc_start: 0.7889 (ttp) cc_final: 0.7661 (ttp)
REVERT: A 1012 LEU cc_start: 0.7936 (mt) cc_final: 0.7684 (mm)
REVERT: A 1019 ARG cc_start: 0.7671 (mtp85) cc_final: 0.7299 (mtp85)
REVERT: A 1090 MET cc_start: 0.6920 (ttt) cc_final: 0.6652 (ttt)
REVERT: A 1110 GLN cc_start: 0.7221 (mt0) cc_final: 0.6923 (mt0)
REVERT: A 1150 ARG cc_start: 0.7381 (mtm110) cc_final: 0.7141 (mtp-110)
REVERT: A 1240 ARG cc_start: 0.7452 (tpt170) cc_final: 0.7126 (mmm160)
REVERT: A 1352 LYS cc_start: 0.7614 (mttt) cc_final: 0.7263 (mttt)
REVERT: C  446 MET cc_start: 0.5939 (mmt) cc_final: 0.5734 (mmt)
REVERT: C  460 SER cc_start: 0.7725 (p) cc_final: 0.7490 (m)
  outliers start: 24
  outliers final: 23
  residues processed: 283
  average time/residue: 0.1284
  time to fit residues: 50.1791
Evaluate side-chains
  294 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 271
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 GLN
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  483 GLU
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  730 ILE
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue 1053 HIS
Chi-restraints excluded: chain A residue 1236 ARG
Chi-restraints excluded: chain A residue 1312 THR
Chi-restraints excluded: chain A residue 1392 LEU
Chi-restraints excluded: chain A residue 1397 LEU
Chi-restraints excluded: chain C residue  448 SER
Chi-restraints excluded: chain C residue  462 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 86 optimal weight:    0.5980
   chunk 138 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 135 optimal weight:    4.9990
   chunk 15 optimal weight:    0.5980
   chunk 1 optimal weight:    0.1980
   chunk 68 optimal weight:    3.9990
   chunk 16 optimal weight:    0.5980
   chunk 94 optimal weight:    0.7980
   chunk 60 optimal weight:    0.8980
   chunk 134 optimal weight:    0.9980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 126 GLN
A 404 HIS
A 504 ASN
A 562 ASN
A 809 GLN
A 812 HIS
A1053 HIS
** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.149448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.116550 restraints weight = 49776.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 4.05
r_work: 0.3166 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3167
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3167 r_free = 0.3167    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3167 r_free = 0.3167    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3167
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.2545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12949  Z= 0.163
  Angle     :  0.526   6.886  17501  Z= 0.280
  Chirality :  0.041   0.154   2000
  Planarity :  0.004   0.036   2212
  Dihedral  :  4.308  23.509   1735
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  :  9.86 %
    Favored  : 88.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.29 (0.21), residues: 1566
  helix:  2.16 (0.17), residues: 892
  sheet:  0.74 (0.52), residues: 96
  loop : -1.30 (0.24), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 403 
 TYR   0.019   0.002   TYR A 516 
 PHE   0.016   0.002   PHE A1191 
 TRP   0.017   0.002   TRP A 408 
 HIS   0.008   0.001   HIS A 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 (12949)
  covalent geometry    : angle       0.52641 (17501)
  hydrogen bonds       : bond        0.05586 (  708)
  hydrogen bonds       : angle       4.23742 ( 2053)

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

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

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 268
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 ARG cc_start: 0.7611 (mtt90) cc_final: 0.7380 (mtt180)
REVERT: A   50 LYS cc_start: 0.8646 (ttmt) cc_final: 0.8313 (mtpp)
REVERT: A  175 MET cc_start: 0.8738 (ttt) cc_final: 0.8381 (ttt)
REVERT: A  250 ARG cc_start: 0.8333 (ttp-170) cc_final: 0.8091 (ttp80)
REVERT: A  329 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7373 (mt-10)
REVERT: A  435 GLN cc_start: 0.8424 (mt0) cc_final: 0.8143 (mt0)
REVERT: A  535 LYS cc_start: 0.8185 (tppt) cc_final: 0.7951 (mmtp)
REVERT: A  563 LEU cc_start: 0.7977 (mt) cc_final: 0.7776 (mp)
REVERT: A  570 LYS cc_start: 0.8145 (mttt) cc_final: 0.7903 (mttt)
REVERT: A  573 LYS cc_start: 0.7563 (mtpp) cc_final: 0.7291 (mtpp)
REVERT: A  780 THR cc_start: 0.8030 (m) cc_final: 0.7730 (p)
REVERT: A  803 TYR cc_start: 0.8271 (t80) cc_final: 0.7886 (t80)
REVERT: A  861 VAL cc_start: 0.7701 (t) cc_final: 0.7417 (m)
REVERT: A  923 ASN cc_start: 0.8334 (t0) cc_final: 0.7857 (t0)
REVERT: A  925 ASP cc_start: 0.7311 (m-30) cc_final: 0.7090 (m-30)
REVERT: A  930 MET cc_start: 0.7995 (ttp) cc_final: 0.7776 (ttp)
REVERT: A 1012 LEU cc_start: 0.7959 (mt) cc_final: 0.7708 (mm)
REVERT: A 1019 ARG cc_start: 0.7817 (mtp85) cc_final: 0.7454 (mtp85)
REVERT: A 1090 MET cc_start: 0.7065 (ttt) cc_final: 0.6741 (ttt)
REVERT: A 1110 GLN cc_start: 0.7309 (mt0) cc_final: 0.6958 (mt0)
REVERT: A 1150 ARG cc_start: 0.7518 (mtm110) cc_final: 0.7253 (mtp180)
REVERT: A 1240 ARG cc_start: 0.7548 (tpt170) cc_final: 0.7189 (mmm160)
REVERT: A 1352 LYS cc_start: 0.7663 (mttt) cc_final: 0.7317 (mttt)
REVERT: C  446 MET cc_start: 0.6045 (mmt) cc_final: 0.5839 (mmt)
REVERT: C  460 SER cc_start: 0.7702 (p) cc_final: 0.7473 (m)
  outliers start: 24
  outliers final: 22
  residues processed: 276
  average time/residue: 0.1288
  time to fit residues: 48.6612
Evaluate side-chains
  287 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 265
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 GLN
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  483 GLU
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  730 ILE
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue 1053 HIS
Chi-restraints excluded: chain A residue 1236 ARG
Chi-restraints excluded: chain A residue 1312 THR
Chi-restraints excluded: chain A residue 1379 ARG
Chi-restraints excluded: chain A residue 1392 LEU
Chi-restraints excluded: chain C residue  448 SER
Chi-restraints excluded: chain C residue  462 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 135 optimal weight:    4.9990
   chunk 87 optimal weight:    0.9980
   chunk 103 optimal weight:    0.9980
   chunk 107 optimal weight:    0.8980
   chunk 66 optimal weight:    0.0980
   chunk 154 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 34 optimal weight:    0.5980
   chunk 96 optimal weight:    0.3980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 404 HIS
A 557 GLN
A 562 ASN
A 809 GLN
A 812 HIS
A1053 HIS
** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.153853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.120481 restraints weight = 41812.434|
|-----------------------------------------------------------------------------|
r_work (start): 0.3400 rms_B_bonded: 3.86
r_work: 0.3188 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3190
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3190 r_free = 0.3190    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3190 r_free = 0.3190    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3190
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
moved from start:          0.2653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12949  Z= 0.157
  Angle     :  0.522   7.534  17501  Z= 0.275
  Chirality :  0.040   0.152   2000
  Planarity :  0.004   0.036   2212
  Dihedral  :  4.250  23.239   1735
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 10.49 %
    Favored  : 87.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.35 (0.21), residues: 1566
  helix:  2.25 (0.17), residues: 892
  sheet:  0.57 (0.52), residues: 98
  loop : -1.31 (0.24), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1147 
 TYR   0.019   0.002   TYR A 516 
 PHE   0.017   0.002   PHE A 392 
 TRP   0.015   0.001   TRP A 408 
 HIS   0.008   0.001   HIS A1053 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 (12949)
  covalent geometry    : angle       0.52193 (17501)
  hydrogen bonds       : bond        0.05419 (  708)
  hydrogen bonds       : angle       4.19392 ( 2053)

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

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

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 270
  time to evaluate  : 0.488 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 ARG cc_start: 0.7591 (mtt90) cc_final: 0.7367 (mtt180)
REVERT: A   50 LYS cc_start: 0.8622 (ttmt) cc_final: 0.8286 (mtpp)
REVERT: A  114 ASN cc_start: 0.8288 (OUTLIER) cc_final: 0.7995 (m-40)
REVERT: A  157 HIS cc_start: 0.8368 (m90) cc_final: 0.7984 (m90)
REVERT: A  194 VAL cc_start: 0.8427 (m) cc_final: 0.8159 (t)
REVERT: A  250 ARG cc_start: 0.8306 (ttp-170) cc_final: 0.8062 (ttp80)
REVERT: A  329 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7353 (mt-10)
REVERT: A  435 GLN cc_start: 0.8418 (mt0) cc_final: 0.8175 (mt0)
REVERT: A  535 LYS cc_start: 0.8089 (tppt) cc_final: 0.7849 (mmtp)
REVERT: A  570 LYS cc_start: 0.8114 (mttt) cc_final: 0.7881 (mttt)
REVERT: A  573 LYS cc_start: 0.7554 (mtpp) cc_final: 0.7278 (mtpp)
REVERT: A  775 GLN cc_start: 0.7681 (tt0) cc_final: 0.7478 (tt0)
REVERT: A  780 THR cc_start: 0.7996 (m) cc_final: 0.7697 (p)
REVERT: A  803 TYR cc_start: 0.8234 (t80) cc_final: 0.7857 (t80)
REVERT: A  861 VAL cc_start: 0.7715 (t) cc_final: 0.7447 (m)
REVERT: A  923 ASN cc_start: 0.8329 (t0) cc_final: 0.7841 (t0)
REVERT: A  925 ASP cc_start: 0.7299 (m-30) cc_final: 0.7082 (m-30)
REVERT: A  930 MET cc_start: 0.7981 (ttp) cc_final: 0.7760 (ttp)
REVERT: A 1012 LEU cc_start: 0.7917 (mt) cc_final: 0.7672 (mm)
REVERT: A 1090 MET cc_start: 0.7058 (ttt) cc_final: 0.6729 (ttt)
REVERT: A 1110 GLN cc_start: 0.7271 (mt0) cc_final: 0.6918 (mt0)
REVERT: A 1112 ARG cc_start: 0.7720 (ttp80) cc_final: 0.7403 (ttm-80)
REVERT: A 1150 ARG cc_start: 0.7511 (mtm110) cc_final: 0.7242 (mtp180)
REVERT: A 1240 ARG cc_start: 0.7540 (tpt170) cc_final: 0.7180 (mmm160)
REVERT: A 1352 LYS cc_start: 0.7676 (mttt) cc_final: 0.7310 (mttt)
REVERT: C  446 MET cc_start: 0.6024 (mmt) cc_final: 0.5808 (mmt)
REVERT: C  460 SER cc_start: 0.7664 (p) cc_final: 0.7423 (m)
  outliers start: 27
  outliers final: 23
  residues processed: 280
  average time/residue: 0.1329
  time to fit residues: 50.8565
Evaluate side-chains
  287 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 263
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 ASN
Chi-restraints excluded: chain A residue  160 GLN
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  483 GLU
Chi-restraints excluded: chain A residue  500 ASP
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  730 ILE
Chi-restraints excluded: chain A residue  791 LEU
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue 1053 HIS
Chi-restraints excluded: chain A residue 1236 ARG
Chi-restraints excluded: chain A residue 1312 THR
Chi-restraints excluded: chain A residue 1392 LEU
Chi-restraints excluded: chain C residue  448 SER
Chi-restraints excluded: chain C residue  462 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 101 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   chunk 121 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   chunk 50 optimal weight:    0.0980
   chunk 81 optimal weight:    0.5980
   chunk 60 optimal weight:    0.6980
   chunk 110 optimal weight:    0.0470
   overall best weight:    0.4078

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

Flipped N/Q/H residues before XYZ refinement:
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 404 HIS
A 557 GLN
A 809 GLN
A 812 HIS
A1053 HIS
** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.154460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.121249 restraints weight = 35982.479|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 3.58
r_work: 0.3235 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3233
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3233
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
moved from start:          0.2713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12949  Z= 0.135
  Angle     :  0.506   8.931  17501  Z= 0.266
  Chirality :  0.039   0.153   2000
  Planarity :  0.004   0.036   2212
  Dihedral  :  4.162  22.888   1735
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 10.92 %
    Favored  : 87.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.48 (0.21), residues: 1566
  helix:  2.37 (0.17), residues: 892
  sheet:  0.59 (0.52), residues: 98
  loop : -1.28 (0.24), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1147 
 TYR   0.017   0.001   TYR A 516 
 PHE   0.016   0.001   PHE A 392 
 TRP   0.015   0.001   TRP A1189 
 HIS   0.011   0.001   HIS A1053 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (12949)
  covalent geometry    : angle       0.50602 (17501)
  hydrogen bonds       : bond        0.05070 (  708)
  hydrogen bonds       : angle       4.10865 ( 2053)

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

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

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 268
  time to evaluate  : 0.481 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7537 (mtt90) cc_final: 0.7302 (mtt180)
REVERT: A   50 LYS cc_start: 0.8566 (ttmt) cc_final: 0.8223 (mtpp)
REVERT: A  114 ASN cc_start: 0.8242 (OUTLIER) cc_final: 0.7928 (m-40)
REVERT: A  157 HIS cc_start: 0.8337 (m90) cc_final: 0.7965 (m90)
REVERT: A  175 MET cc_start: 0.8651 (ttt) cc_final: 0.8274 (ttt)
REVERT: A  194 VAL cc_start: 0.8406 (m) cc_final: 0.8148 (t)
REVERT: A  250 ARG cc_start: 0.8274 (ttp-170) cc_final: 0.8021 (ttp80)
REVERT: A  329 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7290 (mt-10)
REVERT: A  435 GLN cc_start: 0.8402 (mt0) cc_final: 0.8174 (mt0)
REVERT: A  535 LYS cc_start: 0.8057 (tppt) cc_final: 0.7816 (mmtp)
REVERT: A  570 LYS cc_start: 0.8124 (mttt) cc_final: 0.7881 (mttt)
REVERT: A  573 LYS cc_start: 0.7504 (mtpp) cc_final: 0.7224 (mtpp)
REVERT: A  775 GLN cc_start: 0.7644 (tt0) cc_final: 0.7442 (tt0)
REVERT: A  780 THR cc_start: 0.7932 (m) cc_final: 0.7642 (p)
REVERT: A  803 TYR cc_start: 0.8258 (t80) cc_final: 0.7978 (t80)
REVERT: A  861 VAL cc_start: 0.7701 (t) cc_final: 0.7440 (m)
REVERT: A  923 ASN cc_start: 0.8313 (t0) cc_final: 0.7831 (t0)
REVERT: A  925 ASP cc_start: 0.7241 (m-30) cc_final: 0.7033 (m-30)
REVERT: A  930 MET cc_start: 0.7933 (ttp) cc_final: 0.7704 (ttp)
REVERT: A 1012 LEU cc_start: 0.7877 (mt) cc_final: 0.7623 (mm)
REVERT: A 1090 MET cc_start: 0.7001 (ttt) cc_final: 0.6695 (ttt)
REVERT: A 1110 GLN cc_start: 0.7187 (mt0) cc_final: 0.6825 (mt0)
REVERT: A 1112 ARG cc_start: 0.7662 (ttp80) cc_final: 0.7328 (ttm-80)
REVERT: A 1150 ARG cc_start: 0.7469 (mtm110) cc_final: 0.7197 (mtp180)
REVERT: A 1240 ARG cc_start: 0.7449 (tpt170) cc_final: 0.7101 (mmm160)
REVERT: A 1352 LYS cc_start: 0.7661 (mttt) cc_final: 0.7284 (mttt)
REVERT: C  446 MET cc_start: 0.5970 (mmt) cc_final: 0.5752 (mmt)
  outliers start: 26
  outliers final: 18
  residues processed: 275
  average time/residue: 0.1323
  time to fit residues: 49.8284
Evaluate side-chains
  282 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 263
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 ASN
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  483 GLU
Chi-restraints excluded: chain A residue  500 ASP
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  791 LEU
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue 1107 ASP
Chi-restraints excluded: chain A residue 1236 ARG
Chi-restraints excluded: chain A residue 1392 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 65 optimal weight:    0.0060
   chunk 7 optimal weight:    1.9990
   chunk 150 optimal weight:    6.9990
   chunk 3 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 145 optimal weight:    0.7980
   chunk 130 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9980
   chunk 154 optimal weight:    0.2980
   chunk 114 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9990
   overall best weight:    0.5996

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

Flipped N/Q/H residues before XYZ refinement:
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 404 HIS
A 557 GLN
A 812 HIS
A1053 HIS
** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.153246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.120263 restraints weight = 41852.877|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 3.81
r_work: 0.3175 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3173
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3173 r_free = 0.3173    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3173 r_free = 0.3173    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3173
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.2845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12949  Z= 0.167
  Angle     :  0.536   8.245  17501  Z= 0.281
  Chirality :  0.041   0.151   2000
  Planarity :  0.004   0.038   2212
  Dihedral  :  4.224  22.854   1735
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 11.55 %
    Favored  : 86.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.39 (0.21), residues: 1566
  helix:  2.32 (0.17), residues: 891
  sheet:  0.50 (0.52), residues: 98
  loop : -1.33 (0.24), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1147 
 TYR   0.019   0.002   TYR A 516 
 PHE   0.017   0.002   PHE A 392 
 TRP   0.016   0.002   TRP A 408 
 HIS   0.008   0.001   HIS A 812 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 (12949)
  covalent geometry    : angle       0.53648 (17501)
  hydrogen bonds       : bond        0.05385 (  708)
  hydrogen bonds       : angle       4.16159 ( 2053)

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

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

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 269
  time to evaluate  : 0.332 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7632 (mtt90) cc_final: 0.7404 (mtt180)
REVERT: A   50 LYS cc_start: 0.8633 (ttmt) cc_final: 0.8319 (mtpp)
REVERT: A  104 ARG cc_start: 0.7769 (mtm-85) cc_final: 0.7479 (mtp85)
REVERT: A  114 ASN cc_start: 0.8313 (m110) cc_final: 0.7956 (m-40)
REVERT: A  157 HIS cc_start: 0.8361 (m90) cc_final: 0.7974 (m90)
REVERT: A  175 MET cc_start: 0.8715 (ttt) cc_final: 0.8338 (ttt)
REVERT: A  194 VAL cc_start: 0.8428 (m) cc_final: 0.8191 (t)
REVERT: A  250 ARG cc_start: 0.8299 (ttp-170) cc_final: 0.8056 (ttp80)
REVERT: A  329 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7373 (mt-10)
REVERT: A  435 GLN cc_start: 0.8412 (mt0) cc_final: 0.8130 (mt0)
REVERT: A  535 LYS cc_start: 0.8073 (tppt) cc_final: 0.7837 (mmtp)
REVERT: A  570 LYS cc_start: 0.8174 (mttt) cc_final: 0.7926 (mttt)
REVERT: A  573 LYS cc_start: 0.7524 (mtpp) cc_final: 0.7274 (mtpp)
REVERT: A  780 THR cc_start: 0.7971 (m) cc_final: 0.7693 (p)
REVERT: A  803 TYR cc_start: 0.8266 (t80) cc_final: 0.8039 (t80)
REVERT: A  861 VAL cc_start: 0.7739 (t) cc_final: 0.7482 (m)
REVERT: A  923 ASN cc_start: 0.8348 (t0) cc_final: 0.7863 (t0)
REVERT: A  925 ASP cc_start: 0.7300 (m-30) cc_final: 0.7085 (m-30)
REVERT: A  930 MET cc_start: 0.8005 (ttp) cc_final: 0.7792 (ttp)
REVERT: A 1012 LEU cc_start: 0.7955 (mt) cc_final: 0.7701 (mm)
REVERT: A 1090 MET cc_start: 0.7006 (ttt) cc_final: 0.6693 (ttt)
REVERT: A 1110 GLN cc_start: 0.7290 (mt0) cc_final: 0.7021 (mt0)
REVERT: A 1112 ARG cc_start: 0.7757 (ttp80) cc_final: 0.7353 (ttm-80)
REVERT: A 1116 VAL cc_start: 0.8527 (t) cc_final: 0.8289 (t)
REVERT: A 1135 GLN cc_start: 0.7491 (tm-30) cc_final: 0.7117 (tm-30)
REVERT: A 1150 ARG cc_start: 0.7534 (mtm110) cc_final: 0.7272 (mtp180)
REVERT: A 1240 ARG cc_start: 0.7589 (tpt170) cc_final: 0.7219 (mmm160)
REVERT: A 1392 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7257 (mt)
REVERT: C  446 MET cc_start: 0.6065 (mmt) cc_final: 0.5841 (mmt)
REVERT: C  460 SER cc_start: 0.7649 (p) cc_final: 0.7408 (m)
  outliers start: 25
  outliers final: 21
  residues processed: 278
  average time/residue: 0.1291
  time to fit residues: 49.2162
Evaluate side-chains
  288 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 266
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 GLN
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  483 GLU
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  730 ILE
Chi-restraints excluded: chain A residue  791 LEU
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue  971 SER
Chi-restraints excluded: chain A residue 1107 ASP
Chi-restraints excluded: chain A residue 1236 ARG
Chi-restraints excluded: chain A residue 1392 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 36 optimal weight:    0.5980
   chunk 84 optimal weight:    0.4980
   chunk 85 optimal weight:    0.4980
   chunk 140 optimal weight:    1.9990
   chunk 143 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 42 optimal weight:    0.3980
   chunk 75 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 126 GLN
A 404 HIS
A 504 ASN
A 557 GLN
A 809 GLN
A 812 HIS
** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.153243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.120268 restraints weight = 39370.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 3.70
r_work: 0.3192 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3194
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3194 r_free = 0.3194    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3194 r_free = 0.3194    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3194
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.2927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12949  Z= 0.163
  Angle     :  0.533   8.279  17501  Z= 0.280
  Chirality :  0.041   0.153   2000
  Planarity :  0.004   0.036   2212
  Dihedral  :  4.227  22.659   1735
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 11.48 %
    Favored  : 86.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.37 (0.21), residues: 1566
  helix:  2.31 (0.17), residues: 891
  sheet:  0.47 (0.51), residues: 98
  loop : -1.37 (0.24), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1147 
 TYR   0.019   0.002   TYR A 516 
 PHE   0.017   0.002   PHE A 392 
 TRP   0.013   0.002   TRP A1189 
 HIS   0.007   0.001   HIS A 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 (12949)
  covalent geometry    : angle       0.53271 (17501)
  hydrogen bonds       : bond        0.05277 (  708)
  hydrogen bonds       : angle       4.14751 ( 2053)

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

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

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 267
  time to evaluate  : 0.548 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7626 (mtt90) cc_final: 0.7386 (mtt180)
REVERT: A   50 LYS cc_start: 0.8593 (ttmt) cc_final: 0.8275 (mtpp)
REVERT: A  104 ARG cc_start: 0.7708 (mtm-85) cc_final: 0.7438 (mtp85)
REVERT: A  114 ASN cc_start: 0.8288 (OUTLIER) cc_final: 0.7900 (m-40)
REVERT: A  126 GLN cc_start: 0.8066 (tp-100) cc_final: 0.7529 (tp-100)
REVERT: A  157 HIS cc_start: 0.8340 (m90) cc_final: 0.7973 (m90)
REVERT: A  194 VAL cc_start: 0.8422 (m) cc_final: 0.8187 (t)
REVERT: A  250 ARG cc_start: 0.8277 (ttp-170) cc_final: 0.8033 (ttp80)
REVERT: A  329 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7313 (mt-10)
REVERT: A  435 GLN cc_start: 0.8409 (mt0) cc_final: 0.8130 (mt0)
REVERT: A  535 LYS cc_start: 0.8058 (tppt) cc_final: 0.7823 (mmtp)
REVERT: A  570 LYS cc_start: 0.8161 (mttt) cc_final: 0.7911 (mttt)
REVERT: A  573 LYS cc_start: 0.7487 (mtpp) cc_final: 0.7249 (mtpp)
REVERT: A  780 THR cc_start: 0.7964 (m) cc_final: 0.7671 (p)
REVERT: A  803 TYR cc_start: 0.8273 (t80) cc_final: 0.7964 (t80)
REVERT: A  861 VAL cc_start: 0.7740 (t) cc_final: 0.7492 (m)
REVERT: A  923 ASN cc_start: 0.8338 (t0) cc_final: 0.7844 (t0)
REVERT: A  925 ASP cc_start: 0.7265 (m-30) cc_final: 0.7053 (m-30)
REVERT: A  930 MET cc_start: 0.7990 (ttp) cc_final: 0.7772 (ttp)
REVERT: A 1012 LEU cc_start: 0.7932 (mt) cc_final: 0.7698 (mm)
REVERT: A 1090 MET cc_start: 0.7039 (ttt) cc_final: 0.6716 (ttt)
REVERT: A 1110 GLN cc_start: 0.7274 (mt0) cc_final: 0.6998 (mt0)
REVERT: A 1116 VAL cc_start: 0.8506 (t) cc_final: 0.8272 (t)
REVERT: A 1135 GLN cc_start: 0.7496 (tm-30) cc_final: 0.7137 (tm-30)
REVERT: A 1150 ARG cc_start: 0.7510 (mtm110) cc_final: 0.7247 (mtp180)
REVERT: A 1240 ARG cc_start: 0.7571 (tpt170) cc_final: 0.7206 (mmm160)
REVERT: A 1392 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7243 (mt)
REVERT: C  446 MET cc_start: 0.6052 (mmt) cc_final: 0.5833 (mmt)
REVERT: C  460 SER cc_start: 0.7661 (p) cc_final: 0.7414 (m)
  outliers start: 30
  outliers final: 23
  residues processed: 277
  average time/residue: 0.1363
  time to fit residues: 51.6853
Evaluate side-chains
  292 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 267
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 SER
Chi-restraints excluded: chain A residue  114 ASN
Chi-restraints excluded: chain A residue  160 GLN
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  483 GLU
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  730 ILE
Chi-restraints excluded: chain A residue  791 LEU
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue 1107 ASP
Chi-restraints excluded: chain A residue 1236 ARG
Chi-restraints excluded: chain A residue 1312 THR
Chi-restraints excluded: chain A residue 1392 LEU
Chi-restraints excluded: chain C residue  448 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 91 optimal weight:    0.0870
   chunk 3 optimal weight:    0.3980
   chunk 151 optimal weight:    0.2980
   chunk 35 optimal weight:    0.8980
   chunk 148 optimal weight:    0.6980
   chunk 132 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 98 optimal weight:    1.9990
   chunk 124 optimal weight:    0.3980
   chunk 122 optimal weight:    1.9990
   chunk 121 optimal weight:    0.5980
   overall best weight:    0.3558

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

Flipped N/Q/H residues before XYZ refinement:
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 404 HIS
A 557 GLN
A 812 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.154839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.121132 restraints weight = 42154.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 3.84
r_work: 0.3208 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3210
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3210 r_free = 0.3210    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3210 r_free = 0.3210    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3210
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7513
moved from start:          0.2954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12949  Z= 0.126
  Angle     :  0.504   8.568  17501  Z= 0.263
  Chirality :  0.039   0.151   2000
  Planarity :  0.004   0.034   2212
  Dihedral  :  4.060  22.036   1735
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 12.04 %
    Favored  : 86.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.62 (0.22), residues: 1566
  helix:  2.52 (0.17), residues: 892
  sheet:  0.62 (0.53), residues: 98
  loop : -1.27 (0.24), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1147 
 TYR   0.015   0.001   TYR A 516 
 PHE   0.017   0.001   PHE A 392 
 TRP   0.018   0.001   TRP A1189 
 HIS   0.008   0.001   HIS A 812 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (12949)
  covalent geometry    : angle       0.50396 (17501)
  hydrogen bonds       : bond        0.04676 (  708)
  hydrogen bonds       : angle       4.00850 ( 2053)

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

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

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 265
  time to evaluate  : 0.463 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7579 (mtt90) cc_final: 0.7338 (mtt180)
REVERT: A   50 LYS cc_start: 0.8610 (ttmt) cc_final: 0.8268 (mtpp)
REVERT: A  114 ASN cc_start: 0.8282 (OUTLIER) cc_final: 0.7889 (m-40)
REVERT: A  126 GLN cc_start: 0.7987 (tp-100) cc_final: 0.7431 (tp-100)
REVERT: A  157 HIS cc_start: 0.8334 (m90) cc_final: 0.7999 (m90)
REVERT: A  194 VAL cc_start: 0.8409 (m) cc_final: 0.8164 (t)
REVERT: A  250 ARG cc_start: 0.8231 (ttp-170) cc_final: 0.7983 (ttp80)
REVERT: A  329 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7280 (mt-10)
REVERT: A  435 GLN cc_start: 0.8423 (mt0) cc_final: 0.8149 (mt0)
REVERT: A  535 LYS cc_start: 0.8094 (tppt) cc_final: 0.7866 (mmtp)
REVERT: A  570 LYS cc_start: 0.8115 (mttt) cc_final: 0.7859 (mttt)
REVERT: A  573 LYS cc_start: 0.7435 (mtpp) cc_final: 0.7232 (mtpp)
REVERT: A  736 MET cc_start: 0.7345 (mmm) cc_final: 0.7138 (mmt)
REVERT: A  780 THR cc_start: 0.7956 (m) cc_final: 0.7671 (p)
REVERT: A  803 TYR cc_start: 0.8269 (t80) cc_final: 0.8019 (t80)
REVERT: A  861 VAL cc_start: 0.7725 (t) cc_final: 0.7489 (m)
REVERT: A  930 MET cc_start: 0.7982 (ttp) cc_final: 0.7766 (ttp)
REVERT: A 1012 LEU cc_start: 0.7908 (mt) cc_final: 0.7629 (mm)
REVERT: A 1090 MET cc_start: 0.7052 (ttt) cc_final: 0.6708 (ttt)
REVERT: A 1108 TYR cc_start: 0.7734 (t80) cc_final: 0.7502 (t80)
REVERT: A 1110 GLN cc_start: 0.7276 (mt0) cc_final: 0.6996 (mt0)
REVERT: A 1112 ARG cc_start: 0.7727 (ttp80) cc_final: 0.7400 (ttm-80)
REVERT: A 1135 GLN cc_start: 0.7512 (tm-30) cc_final: 0.7153 (tm-30)
REVERT: A 1150 ARG cc_start: 0.7511 (mtm110) cc_final: 0.7182 (mtp-110)
REVERT: A 1240 ARG cc_start: 0.7543 (tpt170) cc_final: 0.7180 (mmm160)
REVERT: C  446 MET cc_start: 0.6062 (mmt) cc_final: 0.5836 (mmt)
  outliers start: 21
  outliers final: 14
  residues processed: 271
  average time/residue: 0.1316
  time to fit residues: 49.1511
Evaluate side-chains
  277 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 262
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 ASN
Chi-restraints excluded: chain A residue  160 GLN
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  483 GLU
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  791 LEU
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue 1312 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 108 optimal weight:    0.0770
   chunk 78 optimal weight:    1.9990
   chunk 81 optimal weight:    0.7980
   chunk 84 optimal weight:    0.0970
   chunk 55 optimal weight:    0.9980
   chunk 64 optimal weight:    0.5980
   chunk 85 optimal weight:    0.7980
   chunk 56 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 129 optimal weight:    4.9990
   overall best weight:    0.4336

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

Flipped N/Q/H residues before XYZ refinement:
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 404 HIS
A 557 GLN
A 809 GLN
A 812 HIS
E 329 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.150153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.117553 restraints weight = 49108.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 4.08
r_work: 0.3181 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3181
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3181 r_free = 0.3181    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3181 r_free = 0.3181    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3181
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
moved from start:          0.3034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12949  Z= 0.138
  Angle     :  0.514   8.179  17501  Z= 0.268
  Chirality :  0.040   0.153   2000
  Planarity :  0.004   0.033   2212
  Dihedral  :  4.068  21.864   1735
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 12.46 %
    Favored  : 86.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.63 (0.22), residues: 1566
  helix:  2.53 (0.17), residues: 890
  sheet:  0.59 (0.52), residues: 98
  loop : -1.26 (0.24), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1147 
 TYR   0.017   0.001   TYR A 516 
 PHE   0.017   0.001   PHE A 392 
 TRP   0.015   0.001   TRP A1189 
 HIS   0.007   0.001   HIS A 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (12949)
  covalent geometry    : angle       0.51408 (17501)
  hydrogen bonds       : bond        0.04861 (  708)
  hydrogen bonds       : angle       4.02721 ( 2053)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3389.30 seconds
wall clock time: 58 minutes 47.58 seconds (3527.58 seconds total)