Starting phenix.real_space_refine
on Wed Sep 17 21:00:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8z5r_39779/09_2025/8z5r_39779.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8z5r_39779/09_2025/8z5r_39779.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.52
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8z5r_39779/09_2025/8z5r_39779.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8z5r_39779/09_2025/8z5r_39779.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8z5r_39779/09_2025/8z5r_39779.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8z5r_39779/09_2025/8z5r_39779.map"
  }
  resolution = 3.52
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.050
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      11      5.49       5
     S      55      5.16       5
     C    7151      2.51       5
     N    1909      2.21       5
     O    2147      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 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: 11273
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 7812
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 993, 7812
          Classifications: {'peptide': 993}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 43, 'TRANS': 949}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 104
          Unresolved non-hydrogen angles: 143
          Unresolved non-hydrogen dihedrals: 78
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'GLN:plan1': 1, 'TPO:plan-1': 2, 'ARG:plan': 2, 'PHE:plan': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 54
    Chain: "C"
      Number of atoms: 2788
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 372, 2788
          Classifications: {'peptide': 372}
          Incomplete info: {'truncation_to_alanine': 60}
          Link IDs: {'PTRANS': 19, 'TRANS': 352}
          Unresolved non-hydrogen bonds: 264
          Unresolved non-hydrogen angles: 322
          Unresolved non-hydrogen dihedrals: 221
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 6, 'PHE:plan': 2, 'TYR:plan': 3, 'GLU:plan': 15, 'ARG:plan': 11, 'ASP:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 189
    Chain: "D"
      Number of atoms: 642
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 642
          Classifications: {'peptide': 97}
          Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 28}
          Link IDs: {'PTRANS': 2, 'TRANS': 94}
          Unresolved non-hydrogen bonds: 129
          Unresolved non-hydrogen angles: 156
          Unresolved non-hydrogen dihedrals: 112
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 9, 'GLN:plan1': 1, 'PHE:plan': 5, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 81
    Chain: "C"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.71, per 1000 atoms: 0.24
  Number of scatterers: 11273
  At special positions: 0
  Unit cell: (119.355, 147.825, 109.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      55     16.00
     P      11     15.00
     O    2147      8.00
     N    1909      7.00
     C    7151      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: 0.96
  Conformation dependent library (CDL) restraints added in 536.7 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2746

  Finding SS restraints...
    Secondary structure from input PDB file:
      71 helices and 13 sheets defined
      57.9% alpha, 5.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 22
    Processing helix  chain 'A' and resid 23 through 26
    Processing helix  chain 'A' and resid 44 through 64
      removed outlier: 3.617A  pdb=" N   LEU A  52 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   ALA A  53 " --> pdb=" O   TYR A  49 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   VAL A  54 " --> pdb=" O   SER A  50 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LYS A  63 " --> pdb=" O   LEU A  59 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   ASN A  64 " --> pdb=" O   ALA A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 94
    Processing helix  chain 'A' and resid 95 through 104
      removed outlier: 3.692A  pdb=" N   LYS A 103 " --> pdb=" O   VAL A  99 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   TYR A 104 " --> pdb=" O   GLU A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 152
      removed outlier: 3.908A  pdb=" N   THR A 138 " --> pdb=" O   GLN A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 173
    Processing helix  chain 'A' and resid 174 through 178
      removed outlier: 3.767A  pdb=" N   LYS A 177 " --> pdb=" O   ALA A 174 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   THR A 178 " --> pdb=" O   ALA A 175 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 174 through 178'
    Processing helix  chain 'A' and resid 198 through 212
      removed outlier: 3.549A  pdb=" N   VAL A 202 " --> pdb=" O   ASN A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 222
      removed outlier: 3.938A  pdb=" N   LYS A 221 " --> pdb=" O   PHE A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 227
      removed outlier: 4.083A  pdb=" N   VAL A 227 " --> pdb=" O   PRO A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 246
      removed outlier: 4.328A  pdb=" N   VAL A 235 " --> pdb=" O   LEU A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 262
      removed outlier: 3.570A  pdb=" N   LEU A 260 " --> pdb=" O   ALA A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 287
    Processing helix  chain 'A' and resid 329 through 342
      removed outlier: 3.599A  pdb=" N   SER A 342 " --> pdb=" O   ASP A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 359
      removed outlier: 3.810A  pdb=" N   ALA A 357 " --> pdb=" O   GLU A 353 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   VAL A 358 " --> pdb=" O   ALA A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 365
      No H-bonds generated for 'chain 'A' and resid 363 through 365'
    Processing helix  chain 'A' and resid 380 through 386
    Processing helix  chain 'A' and resid 400 through 415
    Processing helix  chain 'A' and resid 419 through 424
      removed outlier: 4.042A  pdb=" N   ILE A 423 " --> pdb=" O   ALA A 419 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ASP A 424 " --> pdb=" O   PRO A 420 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 419 through 424'
    Processing helix  chain 'A' and resid 428 through 433
      removed outlier: 4.552A  pdb=" N   THR A 432 " --> pdb=" O   ARG A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 458
    Processing helix  chain 'A' and resid 475 through 484
      removed outlier: 3.845A  pdb=" N   LEU A 479 " --> pdb=" O   PRO A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 522 through 526
      removed outlier: 3.591A  pdb=" N   ILE A 525 " --> pdb=" O   PRO A 522 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ASP A 526 " --> pdb=" O   GLN A 523 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 522 through 526'
    Processing helix  chain 'A' and resid 530 through 534
      removed outlier: 4.045A  pdb=" N   ALA A 533 " --> pdb=" O   PHE A 530 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 553
      removed outlier: 3.548A  pdb=" N   ARG A 553 " --> pdb=" O   TYR A 549 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 571
      removed outlier: 3.940A  pdb=" N   MET A 570 " --> pdb=" O   SER A 567 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   LEU A 571 " --> pdb=" O   HIS A 568 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 567 through 571'
    Processing helix  chain 'A' and resid 579 through 591
    Processing helix  chain 'A' and resid 603 through 609
      removed outlier: 3.748A  pdb=" N   THR A 609 " --> pdb=" O   SER A 605 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 617 through 620
    Processing helix  chain 'A' and resid 763 through 773
    Processing helix  chain 'A' and resid 775 through 790
    Processing helix  chain 'A' and resid 805 through 821
      removed outlier: 3.534A  pdb=" N   GLU A 819 " --> pdb=" O   GLY A 815 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ILE A 820 " --> pdb=" O   LYS A 816 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 825 through 834
    Processing helix  chain 'A' and resid 839 through 849
    Processing helix  chain 'A' and resid 872 through 885
    Processing helix  chain 'A' and resid 888 through 908
      removed outlier: 3.784A  pdb=" N   ILE A 892 " --> pdb=" O   MET A 888 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ARG A 906 " --> pdb=" O   ALA A 902 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   THR A 907 " --> pdb=" O   MET A 903 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 920 through 936
    Processing helix  chain 'A' and resid 938 through 949
    Processing helix  chain 'A' and resid 950 through 964
    Processing helix  chain 'A' and resid 1054 through 1064
    Processing helix  chain 'A' and resid 1070 through 1082
    Processing helix  chain 'A' and resid 1095 through 1100
      removed outlier: 4.120A  pdb=" N   GLU A1099 " --> pdb=" O   SER A1095 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1104 through 1116
      removed outlier: 3.717A  pdb=" N   SER A1108 " --> pdb=" O   GLU A1104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1120 through 1141
    Processing helix  chain 'A' and resid 1151 through 1170
    Processing helix  chain 'A' and resid 1185 through 1191
    Processing helix  chain 'A' and resid 1198 through 1214
      removed outlier: 3.714A  pdb=" N   TYR A1202 " --> pdb=" O   GLY A1198 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 13 through 20
    Processing helix  chain 'C' and resid 60 through 81
      removed outlier: 3.581A  pdb=" N   VAL C  64 " --> pdb=" O   SER C  60 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 111 through 120
    Processing helix  chain 'C' and resid 123 through 144
      removed outlier: 3.504A  pdb=" N   LEU C 144 " --> pdb=" O   THR C 140 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 152 through 154
      No H-bonds generated for 'chain 'C' and resid 152 through 154'
    Processing helix  chain 'C' and resid 192 through 199
      removed outlier: 3.747A  pdb=" N   ILE C 196 " --> pdb=" O   ALA C 192 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 210 through 226
    Processing helix  chain 'C' and resid 234 through 245
    Processing helix  chain 'C' and resid 250 through 255
    Processing helix  chain 'C' and resid 258 through 269
      removed outlier: 3.665A  pdb=" N   LYS C 262 " --> pdb=" O   SER C 258 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 278 through 284
    Processing helix  chain 'C' and resid 300 through 320
    Processing helix  chain 'C' and resid 321 through 325
      removed outlier: 3.511A  pdb=" N   VAL C 325 " --> pdb=" O   TYR C 322 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 329 through 336
    Processing helix  chain 'C' and resid 340 through 355
    Processing helix  chain 'C' and resid 366 through 371
    Processing helix  chain 'C' and resid 377 through 381
    Processing helix  chain 'D' and resid 6 through 21
      removed outlier: 3.921A  pdb=" N   ASP D  21 " --> pdb=" O   PHE D  17 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 29 through 41
    Processing helix  chain 'D' and resid 45 through 57
    Processing helix  chain 'D' and resid 65 through 74
    Processing helix  chain 'D' and resid 79 through 94
    Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 43
    Processing sheet with id=AA2, first strand: chain 'A' and resid 288 through 289
      removed outlier: 3.996A  pdb=" N   GLY A 292 " --> pdb=" O   GLY A 289 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 360 through 361
      removed outlier: 3.541A  pdb=" N   ILE A 360 " --> pdb=" O   LEU A 368 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 374
    Processing sheet with id=AA5, first strand: chain 'A' and resid 463 through 464
      removed outlier: 4.018A  pdb=" N   GLU A 463 " --> pdb=" O   ILE A 444 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 463 through 464
      removed outlier: 4.018A  pdb=" N   GLU A 463 " --> pdb=" O   ILE A 444 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   VAL A 442 " --> pdb=" O   GLN A 600 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 471 through 474
      removed outlier: 5.812A  pdb=" N   ARG A 472 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 488 through 489
    Processing sheet with id=AA9, first strand: chain 'A' and resid 853 through 855
      removed outlier: 6.314A  pdb=" N   HIS A 853 " --> pdb=" O   LEU A 918 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1092 through 1093
      removed outlier: 3.637A  pdb=" N   LEU A1092 " --> pdb=" O   LEU A1085 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   LEU A1085 " --> pdb=" O   LEU A1092 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ILE A1149 " --> pdb=" O   GLY A1084 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 25 through 28
      removed outlier: 6.726A  pdb=" N   VAL C  34 " --> pdb=" O   LEU C  26 " (cutoff:3.500A)
      removed outlier: 4.974A  pdb=" N   ARG C  28 " --> pdb=" O   SER C  32 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   SER C  32 " --> pdb=" O   ARG C  28 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ILE C  51 " --> pdb=" O   PHE C 100 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   PHE C 100 " --> pdb=" O   ILE C  51 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   ASP C  92 " --> pdb=" O   VAL C 103 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 146 through 147
      removed outlier: 4.147A  pdb=" N   VAL C 147 " --> pdb=" O   CYS C 173 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   CYS C 173 " --> pdb=" O   VAL C 147 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'C' and resid 156 through 158
      removed outlier: 3.786A  pdb=" N   LEU C 157 " --> pdb=" O   LYS C 165 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   LYS C 165 " --> pdb=" O   LEU C 157 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4

    573 hydrogen bonds defined for protein.
    1656 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: 1.82

  Time building geometry restraints manager: 1.27 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: 3683
        1.34 -     1.46: 1617
        1.46 -     1.58: 6079
        1.58 -     1.70: 33
        1.70 -     1.81: 89
  Bond restraints: 11501
  Sorted by residual:
  bond pdb=" OG1 TPO A1174 "
       pdb=" P   TPO A1174 "
    ideal  model  delta    sigma   weight residual
    1.717  1.610  0.107 2.00e-02 2.50e+03 2.88e+01
  bond pdb=" O1P SEP A 101 "
       pdb=" P   SEP A 101 "
    ideal  model  delta    sigma   weight residual
    1.610  1.504  0.106 2.00e-02 2.50e+03 2.82e+01
  bond pdb=" O2P SEP A 101 "
       pdb=" P   SEP A 101 "
    ideal  model  delta    sigma   weight residual
    1.610  1.504  0.106 2.00e-02 2.50e+03 2.79e+01
  bond pdb=" O3P SEP A 101 "
       pdb=" P   SEP A 101 "
    ideal  model  delta    sigma   weight residual
    1.610  1.505  0.105 2.00e-02 2.50e+03 2.77e+01
  bond pdb=" CA  SEP A 101 "
       pdb=" C   SEP A 101 "
    ideal  model  delta    sigma   weight residual
    1.525  1.435  0.090 2.10e-02 2.27e+03 1.83e+01
  ... (remaining 11496 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.38: 15482
        2.38 -     4.75: 132
        4.75 -     7.13: 25
        7.13 -     9.50: 9
        9.50 -    11.88: 1
  Bond angle restraints: 15649
  Sorted by residual:
  angle pdb=" O   GLU A 100 "
        pdb=" C   GLU A 100 "
        pdb=" N   SEP A 101 "
      ideal   model   delta    sigma   weight residual
     123.00  115.95    7.05 1.60e+00 3.91e-01 1.94e+01
  angle pdb=" N   VAL A 262 "
        pdb=" CA  VAL A 262 "
        pdb=" C   VAL A 262 "
      ideal   model   delta    sigma   weight residual
     112.96  108.98    3.98 1.00e+00 1.00e+00 1.58e+01
  angle pdb=" CB  TPO A1174 "
        pdb=" OG1 TPO A1174 "
        pdb=" P   TPO A1174 "
      ideal   model   delta    sigma   weight residual
     119.31  107.43   11.88 3.00e+00 1.11e-01 1.57e+01
  angle pdb=" CA  GLU A 306 "
        pdb=" CB  GLU A 306 "
        pdb=" CG  GLU A 306 "
      ideal   model   delta    sigma   weight residual
     114.10  121.96   -7.86 2.00e+00 2.50e-01 1.54e+01
  angle pdb=" C   PRO A 266 "
        pdb=" N   ALA A 267 "
        pdb=" CA  ALA A 267 "
      ideal   model   delta    sigma   weight residual
     121.54  128.91   -7.37 1.91e+00 2.74e-01 1.49e+01
  ... (remaining 15644 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 5926
       17.97 -    35.93: 707
       35.93 -    53.90: 224
       53.90 -    71.86: 63
       71.86 -    89.83: 18
  Dihedral angle restraints: 6938
    sinusoidal: 2680
      harmonic: 4258
  Sorted by residual:
  dihedral pdb=" CA  PRO A 859 "
           pdb=" C   PRO A 859 "
           pdb=" N   PRO A 860 "
           pdb=" CA  PRO A 860 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.79   30.21     0      5.00e+00 4.00e-02 3.65e+01
  dihedral pdb=" CA  LEU A 246 "
           pdb=" C   LEU A 246 "
           pdb=" N   PRO A 247 "
           pdb=" CA  PRO A 247 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.29   25.71     0      5.00e+00 4.00e-02 2.64e+01
  dihedral pdb=" CA  MET C 200 "
           pdb=" C   MET C 200 "
           pdb=" N   ASN C 201 "
           pdb=" CA  ASN C 201 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.49   21.51     0      5.00e+00 4.00e-02 1.85e+01
  ... (remaining 6935 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 1355
       0.039 -    0.079: 334
       0.079 -    0.118: 99
       0.118 -    0.157: 7
       0.157 -    0.197: 3
  Chirality restraints: 1798
  Sorted by residual:
  chirality pdb=" CB  ILE C 138 "
            pdb=" CA  ILE C 138 "
            pdb=" CG1 ILE C 138 "
            pdb=" CG2 ILE C 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.20 2.00e-01 2.50e+01 9.66e-01
  chirality pdb=" CA  GLU A 306 "
            pdb=" N   GLU A 306 "
            pdb=" C   GLU A 306 "
            pdb=" CB  GLU A 306 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.87e-01
  chirality pdb=" CB  ILE A1142 "
            pdb=" CA  ILE A1142 "
            pdb=" CG1 ILE A1142 "
            pdb=" CG2 ILE A1142 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.63e-01
  ... (remaining 1795 not shown)

  Planarity restraints: 1999
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 313 "    0.014 2.00e-02 2.50e+03   2.05e-02 8.39e+00
        pdb=" CG  TYR A 313 "   -0.050 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 313 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 313 "    0.019 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 313 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 313 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 313 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 313 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C 227 "    0.046 5.00e-02 4.00e+02   6.98e-02 7.79e+00
        pdb=" N   PRO C 228 "   -0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO C 228 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO C 228 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A1067 "   -0.040 5.00e-02 4.00e+02   6.12e-02 5.99e+00
        pdb=" N   PRO A1068 "    0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO A1068 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A1068 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 1996 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1984
        2.77 -     3.30: 10988
        3.30 -     3.83: 18364
        3.83 -     4.37: 19460
        4.37 -     4.90: 34843
  Nonbonded interactions: 85639
  Sorted by model distance:
  nonbonded pdb=" O   VAL A 504 "
            pdb=" OG  SER A 508 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" O   VAL C 378 "
            pdb=" OG  SER C 381 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O   GLY A 506 "
            pdb=" OH  TYR A 511 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" OH  TYR A  14 "
            pdb=" OG  SER A 411 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" O   SER A 226 "
            pdb=" OG  SER A 226 "
     model   vdw
     2.294 3.040
  ... (remaining 85634 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             8.530
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.200
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7183
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.107  11501  Z= 0.168
  Angle     :  0.590  11.880  15649  Z= 0.294
  Chirality :  0.038   0.197   1798
  Planarity :  0.004   0.070   1999
  Dihedral  : 18.190  89.829   4192
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  : 26.27 %
    Favored  : 73.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    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:  1.59 (0.23), residues: 1411
  helix:  2.63 (0.20), residues: 723
  sheet:  1.65 (0.78), residues: 57
  loop : -0.96 (0.24), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  10 
 TYR   0.050   0.001   TYR A 313 
 PHE   0.016   0.001   PHE C 287 
 TRP   0.010   0.001   TRP C 254 
 HIS   0.002   0.000   HIS C 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (11501)
  covalent geometry    : angle       0.59041 (15649)
  hydrogen bonds       : bond        0.13209 (  572)
  hydrogen bonds       : angle       5.14554 ( 1656)

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

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

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 160
  time to evaluate  : 0.438 
Fit side-chains
REVERT: A  483 TYR cc_start: 0.8541 (OUTLIER) cc_final: 0.7145 (t80)
  outliers start: 7
  outliers final: 3
  residues processed: 162
  average time/residue: 0.0863
  time to fit residues: 21.8516
Evaluate side-chains
  155 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 151
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  483 TYR
Chi-restraints excluded: chain C residue   77 ILE
Chi-restraints excluded: chain C residue  158 LEU
Chi-restraints excluded: chain C residue  203 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    0.7980
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    8.9990
   chunk 91 optimal weight:    9.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
A  25 HIS
A 427 ASN
** C  39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 145 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.173130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.124173 restraints weight = 19607.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.127121 restraints weight = 11338.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.126978 restraints weight = 8282.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.128234 restraints weight = 6840.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.128229 restraints weight = 6304.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.2337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.072  11501  Z= 0.291
  Angle     :  0.730  11.687  15649  Z= 0.371
  Chirality :  0.045   0.209   1798
  Planarity :  0.006   0.063   1999
  Dihedral  :  7.389  88.212   1642
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 23.95 %
    Favored  : 71.67 %
  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:  0.90 (0.23), residues: 1411
  helix:  2.00 (0.19), residues: 747
  sheet:  0.59 (0.66), residues: 62
  loop : -1.28 (0.24), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  45 
 TYR   0.026   0.002   TYR A 171 
 PHE   0.020   0.002   PHE A 218 
 TRP   0.019   0.002   TRP A 328 
 HIS   0.005   0.001   HIS A 400 

Details of bonding type rmsd
  covalent geometry    : bond        0.00690 (11501)
  covalent geometry    : angle       0.73025 (15649)
  hydrogen bonds       : bond        0.05077 (  572)
  hydrogen bonds       : angle       4.29055 ( 1656)

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

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

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 145
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
REVERT: A  491 ARG cc_start: 0.3777 (ttt180) cc_final: 0.3055 (ttt180)
REVERT: A  544 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.6848 (ptm160)
REVERT: A  828 TYR cc_start: 0.6835 (OUTLIER) cc_final: 0.6042 (t80)
REVERT: A  916 PHE cc_start: 0.7443 (t80) cc_final: 0.7134 (t80)
REVERT: A  954 MET cc_start: 0.8012 (tpp) cc_final: 0.7346 (ttp)
REVERT: A 1060 LEU cc_start: 0.8178 (mt) cc_final: 0.7784 (tt)
REVERT: A 1100 MET cc_start: 0.8114 (mmm) cc_final: 0.7652 (mmm)
REVERT: A 1152 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7548 (tm-30)
REVERT: C   46 TYR cc_start: 0.6276 (OUTLIER) cc_final: 0.5673 (m-10)
REVERT: C  131 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8322 (tpp)
REVERT: C  150 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7088 (t0)
  outliers start: 51
  outliers final: 29
  residues processed: 187
  average time/residue: 0.0827
  time to fit residues: 23.7642
Evaluate side-chains
  176 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 141
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 CYS
Chi-restraints excluded: chain A residue   66 ASP
Chi-restraints excluded: chain A residue  119 LYS
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  341 PHE
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain A residue  465 ILE
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain A residue  544 ARG
Chi-restraints excluded: chain A residue  828 TYR
Chi-restraints excluded: chain A residue  864 GLU
Chi-restraints excluded: chain A residue  891 SER
Chi-restraints excluded: chain A residue  949 LEU
Chi-restraints excluded: chain A residue  956 ASN
Chi-restraints excluded: chain A residue  961 ILE
Chi-restraints excluded: chain A residue 1061 ASP
Chi-restraints excluded: chain A residue 1137 LEU
Chi-restraints excluded: chain A residue 1152 GLU
Chi-restraints excluded: chain A residue 1156 HIS
Chi-restraints excluded: chain A residue 1159 ASN
Chi-restraints excluded: chain C residue   46 TYR
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   93 THR
Chi-restraints excluded: chain C residue  131 MET
Chi-restraints excluded: chain C residue  150 ASP
Chi-restraints excluded: chain C residue  154 GLU
Chi-restraints excluded: chain C residue  158 LEU
Chi-restraints excluded: chain C residue  163 ASN
Chi-restraints excluded: chain C residue  184 VAL
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  318 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 77 optimal weight:    0.5980
   chunk 92 optimal weight:    0.9990
   chunk 82 optimal weight:    0.9990
   chunk 130 optimal weight:    9.9990
   chunk 86 optimal weight:    2.9990
   chunk 104 optimal weight:    6.9990
   chunk 113 optimal weight:    4.9990
   chunk 46 optimal weight:    0.6980
   chunk 89 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 63 optimal weight:    5.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 795 ASN
A 895 GLN
C  97 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.176317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.127252 restraints weight = 19896.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.129351 restraints weight = 12168.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.129939 restraints weight = 8396.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.130363 restraints weight = 7166.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.130573 restraints weight = 6969.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.2384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11501  Z= 0.134
  Angle     :  0.579  11.666  15649  Z= 0.288
  Chirality :  0.040   0.259   1798
  Planarity :  0.005   0.061   1999
  Dihedral  :  6.977  85.265   1636
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.73 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 24.29 %
    Favored  : 71.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.12 %
    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:  1.02 (0.23), residues: 1411
  helix:  2.16 (0.19), residues: 747
  sheet:  0.23 (0.66), residues: 62
  loop : -1.26 (0.24), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1059 
 TYR   0.013   0.001   TYR A 171 
 PHE   0.019   0.001   PHE A 763 
 TRP   0.012   0.001   TRP C 358 
 HIS   0.003   0.001   HIS A 960 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (11501)
  covalent geometry    : angle       0.57869 (15649)
  hydrogen bonds       : bond        0.03610 (  572)
  hydrogen bonds       : angle       3.83552 ( 1656)

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

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

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 147
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
REVERT: A  491 ARG cc_start: 0.3568 (ttt180) cc_final: 0.2766 (ttt180)
REVERT: A  544 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.6838 (ptm160)
REVERT: A  828 TYR cc_start: 0.6748 (OUTLIER) cc_final: 0.5999 (t80)
REVERT: A  916 PHE cc_start: 0.7543 (t80) cc_final: 0.7275 (t80)
REVERT: A  917 ARG cc_start: 0.8523 (ptp-110) cc_final: 0.7772 (ptm160)
REVERT: A  954 MET cc_start: 0.7936 (tpp) cc_final: 0.7304 (ttp)
REVERT: C   46 TYR cc_start: 0.6184 (OUTLIER) cc_final: 0.5464 (m-10)
REVERT: C  165 LYS cc_start: 0.5613 (OUTLIER) cc_final: 0.5230 (ptpp)
REVERT: C  289 GLN cc_start: 0.4896 (pp30) cc_final: 0.3997 (pt0)
  outliers start: 44
  outliers final: 25
  residues processed: 180
  average time/residue: 0.0940
  time to fit residues: 25.2849
Evaluate side-chains
  167 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 138
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  119 LYS
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  194 ILE
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  544 ARG
Chi-restraints excluded: chain A residue  828 TYR
Chi-restraints excluded: chain A residue  864 GLU
Chi-restraints excluded: chain A residue  891 SER
Chi-restraints excluded: chain A residue  956 ASN
Chi-restraints excluded: chain A residue  961 ILE
Chi-restraints excluded: chain A residue 1061 ASP
Chi-restraints excluded: chain A residue 1137 LEU
Chi-restraints excluded: chain A residue 1144 SER
Chi-restraints excluded: chain A residue 1156 HIS
Chi-restraints excluded: chain A residue 1159 ASN
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   46 TYR
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue  154 GLU
Chi-restraints excluded: chain C residue  158 LEU
Chi-restraints excluded: chain C residue  165 LYS
Chi-restraints excluded: chain C residue  213 MET
Chi-restraints excluded: chain C residue  268 PHE
Chi-restraints excluded: chain C residue  318 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 94 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 34 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9990
   chunk 103 optimal weight:    0.0470
   chunk 32 optimal weight:    1.9990
   chunk 129 optimal weight:    7.9990
   chunk 73 optimal weight:    0.7980
   chunk 105 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 47 optimal weight:    0.4980
   overall best weight:    0.6078

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.179886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.131663 restraints weight = 19859.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.133900 restraints weight = 11861.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.134454 restraints weight = 7536.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.134447 restraints weight = 7186.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.134751 restraints weight = 6988.654|
|-----------------------------------------------------------------------------|
r_work (final): 0.3649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.2469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  11501  Z= 0.114
  Angle     :  0.550  11.420  15649  Z= 0.275
  Chirality :  0.039   0.270   1798
  Planarity :  0.005   0.072   1999
  Dihedral  :  6.751  85.244   1636
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.52 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 25.06 %
    Favored  : 70.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.12 %
    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:  1.03 (0.23), residues: 1411
  helix:  2.20 (0.19), residues: 747
  sheet:  0.14 (0.66), residues: 62
  loop : -1.30 (0.24), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  10 
 TYR   0.011   0.001   TYR A 171 
 PHE   0.014   0.001   PHE C 100 
 TRP   0.011   0.001   TRP C 358 
 HIS   0.002   0.000   HIS A 960 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 (11501)
  covalent geometry    : angle       0.55038 (15649)
  hydrogen bonds       : bond        0.03167 (  572)
  hydrogen bonds       : angle       3.65333 ( 1656)

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

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

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 144
  time to evaluate  : 0.449 
Fit side-chains
REVERT: A  491 ARG cc_start: 0.3462 (ttt180) cc_final: 0.2600 (ttt180)
REVERT: A  544 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.6866 (ptm160)
REVERT: A  828 TYR cc_start: 0.6736 (OUTLIER) cc_final: 0.6045 (t80)
REVERT: A  916 PHE cc_start: 0.7566 (t80) cc_final: 0.7304 (t80)
REVERT: A  917 ARG cc_start: 0.8469 (ptp-110) cc_final: 0.7715 (ptm160)
REVERT: A  954 MET cc_start: 0.7870 (tpp) cc_final: 0.7217 (ttp)
REVERT: C   46 TYR cc_start: 0.6321 (OUTLIER) cc_final: 0.5623 (m-10)
REVERT: C  100 PHE cc_start: 0.7221 (m-80) cc_final: 0.6993 (m-80)
REVERT: C  150 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7049 (t0)
  outliers start: 48
  outliers final: 30
  residues processed: 182
  average time/residue: 0.0887
  time to fit residues: 24.6190
Evaluate side-chains
  171 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 137
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASP
Chi-restraints excluded: chain A residue   24 CYS
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  119 LYS
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  194 ILE
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain A residue  465 ILE
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  544 ARG
Chi-restraints excluded: chain A residue  828 TYR
Chi-restraints excluded: chain A residue  891 SER
Chi-restraints excluded: chain A residue  914 GLU
Chi-restraints excluded: chain A residue  931 LEU
Chi-restraints excluded: chain A residue  949 LEU
Chi-restraints excluded: chain A residue  956 ASN
Chi-restraints excluded: chain A residue  961 ILE
Chi-restraints excluded: chain A residue 1061 ASP
Chi-restraints excluded: chain A residue 1156 HIS
Chi-restraints excluded: chain A residue 1159 ASN
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   46 TYR
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   77 ILE
Chi-restraints excluded: chain C residue   93 THR
Chi-restraints excluded: chain C residue  150 ASP
Chi-restraints excluded: chain C residue  158 LEU
Chi-restraints excluded: chain C residue  184 VAL
Chi-restraints excluded: chain C residue  263 ASP
Chi-restraints excluded: chain C residue  277 TYR
Chi-restraints excluded: chain C residue  318 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   chunk 123 optimal weight:    0.3980
   chunk 43 optimal weight:    0.9990
   chunk 75 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 38 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 97 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.179119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.128997 restraints weight = 19765.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.132310 restraints weight = 11653.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.133031 restraints weight = 7991.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.133832 restraints weight = 6403.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.134081 restraints weight = 6394.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.2634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11501  Z= 0.126
  Angle     :  0.573  11.318  15649  Z= 0.284
  Chirality :  0.040   0.241   1798
  Planarity :  0.005   0.075   1999
  Dihedral  :  6.715  86.984   1636
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.73 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 25.49 %
    Favored  : 69.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.12 %
    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:  1.01 (0.23), residues: 1411
  helix:  2.21 (0.19), residues: 748
  sheet: -0.03 (0.65), residues: 62
  loop : -1.34 (0.24), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  10 
 TYR   0.014   0.001   TYR A 171 
 PHE   0.013   0.001   PHE C 287 
 TRP   0.013   0.001   TRP C 358 
 HIS   0.002   0.001   HIS A 960 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (11501)
  covalent geometry    : angle       0.57279 (15649)
  hydrogen bonds       : bond        0.03344 (  572)
  hydrogen bonds       : angle       3.65960 ( 1656)

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

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

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 141
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
REVERT: A  491 ARG cc_start: 0.3272 (ttt180) cc_final: 0.2365 (ttt180)
REVERT: A  544 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.6877 (ptm160)
REVERT: A  828 TYR cc_start: 0.6810 (OUTLIER) cc_final: 0.6164 (t80)
REVERT: A  916 PHE cc_start: 0.7623 (t80) cc_final: 0.7368 (t80)
REVERT: A  917 ARG cc_start: 0.8453 (ptp-110) cc_final: 0.7799 (ptm160)
REVERT: A  954 MET cc_start: 0.7882 (tpp) cc_final: 0.7248 (ttp)
REVERT: A 1060 LEU cc_start: 0.8235 (mt) cc_final: 0.7927 (tt)
REVERT: C   46 TYR cc_start: 0.6337 (OUTLIER) cc_final: 0.5565 (m-10)
REVERT: C  100 PHE cc_start: 0.7185 (m-80) cc_final: 0.6964 (m-80)
REVERT: C  150 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.7019 (t0)
REVERT: C  289 GLN cc_start: 0.5092 (pp30) cc_final: 0.3961 (pt0)
  outliers start: 53
  outliers final: 37
  residues processed: 183
  average time/residue: 0.0909
  time to fit residues: 25.2528
Evaluate side-chains
  177 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 136
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 CYS
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  119 LYS
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  194 ILE
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain A residue  465 ILE
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  544 ARG
Chi-restraints excluded: chain A residue  828 TYR
Chi-restraints excluded: chain A residue  891 SER
Chi-restraints excluded: chain A residue  914 GLU
Chi-restraints excluded: chain A residue  931 LEU
Chi-restraints excluded: chain A residue  949 LEU
Chi-restraints excluded: chain A residue  956 ASN
Chi-restraints excluded: chain A residue  961 ILE
Chi-restraints excluded: chain A residue 1061 ASP
Chi-restraints excluded: chain A residue 1137 LEU
Chi-restraints excluded: chain A residue 1156 HIS
Chi-restraints excluded: chain A residue 1159 ASN
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   46 TYR
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   77 ILE
Chi-restraints excluded: chain C residue   93 THR
Chi-restraints excluded: chain C residue  150 ASP
Chi-restraints excluded: chain C residue  158 LEU
Chi-restraints excluded: chain C residue  184 VAL
Chi-restraints excluded: chain C residue  213 MET
Chi-restraints excluded: chain C residue  251 SER
Chi-restraints excluded: chain C residue  263 ASP
Chi-restraints excluded: chain C residue  268 PHE
Chi-restraints excluded: chain C residue  277 TYR
Chi-restraints excluded: chain C residue  318 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 38 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    2.9990
   chunk 118 optimal weight:    7.9990
   chunk 77 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 86 optimal weight:    0.2980
   chunk 40 optimal weight:    0.9990
   chunk 65 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
C  86 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.178673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.128561 restraints weight = 19775.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.131478 restraints weight = 11562.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.132696 restraints weight = 8348.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.133309 restraints weight = 6348.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.133564 restraints weight = 6448.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.2767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  11501  Z= 0.133
  Angle     :  0.578  11.378  15649  Z= 0.288
  Chirality :  0.040   0.215   1798
  Planarity :  0.005   0.079   1999
  Dihedral  :  6.690  88.459   1636
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.87 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  5.24 %
    Allowed  : 25.15 %
    Favored  : 69.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.12 %
    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:  0.92 (0.23), residues: 1411
  helix:  2.14 (0.19), residues: 749
  sheet: -0.16 (0.65), residues: 62
  loop : -1.38 (0.24), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1059 
 TYR   0.014   0.001   TYR A 171 
 PHE   0.013   0.001   PHE C 287 
 TRP   0.014   0.001   TRP C 358 
 HIS   0.002   0.001   HIS A 960 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (11501)
  covalent geometry    : angle       0.57784 (15649)
  hydrogen bonds       : bond        0.03438 (  572)
  hydrogen bonds       : angle       3.69433 ( 1656)

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

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

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 140
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
REVERT: A  491 ARG cc_start: 0.3307 (ttt180) cc_final: 0.2666 (ttt180)
REVERT: A  544 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.6950 (ptm160)
REVERT: A  828 TYR cc_start: 0.6942 (OUTLIER) cc_final: 0.6361 (t80)
REVERT: A  916 PHE cc_start: 0.7644 (t80) cc_final: 0.7393 (t80)
REVERT: A  917 ARG cc_start: 0.8426 (ptp-110) cc_final: 0.7836 (ptm160)
REVERT: A  954 MET cc_start: 0.7859 (tpp) cc_final: 0.7212 (ttp)
REVERT: C   46 TYR cc_start: 0.6366 (OUTLIER) cc_final: 0.5582 (m-10)
REVERT: C  150 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7080 (t0)
REVERT: C  165 LYS cc_start: 0.5684 (OUTLIER) cc_final: 0.5461 (ptpp)
REVERT: C  207 TYR cc_start: 0.4780 (m-80) cc_final: 0.4404 (m-80)
  outliers start: 61
  outliers final: 44
  residues processed: 191
  average time/residue: 0.0835
  time to fit residues: 24.6791
Evaluate side-chains
  186 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 137
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASP
Chi-restraints excluded: chain A residue   24 CYS
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   61 TYR
Chi-restraints excluded: chain A residue   66 ASP
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  119 LYS
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  194 ILE
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain A residue  413 MET
Chi-restraints excluded: chain A residue  465 ILE
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  544 ARG
Chi-restraints excluded: chain A residue  828 TYR
Chi-restraints excluded: chain A residue  891 SER
Chi-restraints excluded: chain A residue  914 GLU
Chi-restraints excluded: chain A residue  931 LEU
Chi-restraints excluded: chain A residue  949 LEU
Chi-restraints excluded: chain A residue  952 SER
Chi-restraints excluded: chain A residue  956 ASN
Chi-restraints excluded: chain A residue  961 ILE
Chi-restraints excluded: chain A residue 1061 ASP
Chi-restraints excluded: chain A residue 1137 LEU
Chi-restraints excluded: chain A residue 1144 SER
Chi-restraints excluded: chain A residue 1156 HIS
Chi-restraints excluded: chain A residue 1159 ASN
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue   46 TYR
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   77 ILE
Chi-restraints excluded: chain C residue   93 THR
Chi-restraints excluded: chain C residue  150 ASP
Chi-restraints excluded: chain C residue  158 LEU
Chi-restraints excluded: chain C residue  165 LYS
Chi-restraints excluded: chain C residue  184 VAL
Chi-restraints excluded: chain C residue  213 MET
Chi-restraints excluded: chain C residue  251 SER
Chi-restraints excluded: chain C residue  263 ASP
Chi-restraints excluded: chain C residue  268 PHE
Chi-restraints excluded: chain C residue  318 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 114 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 102 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 46 optimal weight:    0.0030
   chunk 142 optimal weight:    4.9990
   chunk 96 optimal weight:    2.9990
   chunk 118 optimal weight:    1.9990
   chunk 119 optimal weight:    0.9990
   chunk 77 optimal weight:    0.7980
   overall best weight:    0.6992

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN
** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.178993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.129176 restraints weight = 19842.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.132298 restraints weight = 11633.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.132911 restraints weight = 8603.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.133999 restraints weight = 6523.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.134184 restraints weight = 6356.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.2851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11501  Z= 0.121
  Angle     :  0.571  11.141  15649  Z= 0.283
  Chirality :  0.040   0.210   1798
  Planarity :  0.005   0.082   1999
  Dihedral  :  6.631  89.936   1636
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.80 %
    Favored  : 93.13 %
  Rotamer:
    Outliers :  5.24 %
    Allowed  : 26.01 %
    Favored  : 68.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.12 %
    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:  0.95 (0.23), residues: 1411
  helix:  2.19 (0.19), residues: 749
  sheet: -0.29 (0.65), residues: 62
  loop : -1.37 (0.25), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1059 
 TYR   0.012   0.001   TYR A 171 
 PHE   0.024   0.001   PHE C 100 
 TRP   0.016   0.001   TRP C 358 
 HIS   0.006   0.001   HIS A 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (11501)
  covalent geometry    : angle       0.57081 (15649)
  hydrogen bonds       : bond        0.03254 (  572)
  hydrogen bonds       : angle       3.63004 ( 1656)

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

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

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 150
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  491 ARG cc_start: 0.3249 (ttt180) cc_final: 0.2335 (ttt180)
REVERT: A  544 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.6946 (ptm160)
REVERT: A  828 TYR cc_start: 0.7015 (OUTLIER) cc_final: 0.6445 (t80)
REVERT: A  842 GLU cc_start: 0.5963 (tp30) cc_final: 0.5542 (tp30)
REVERT: A  916 PHE cc_start: 0.7626 (t80) cc_final: 0.7385 (t80)
REVERT: A  917 ARG cc_start: 0.8400 (ptp-110) cc_final: 0.7791 (ptm160)
REVERT: A  954 MET cc_start: 0.7827 (tpp) cc_final: 0.7180 (ttp)
REVERT: A 1077 LYS cc_start: 0.8472 (mptt) cc_final: 0.8192 (mmmt)
REVERT: C   46 TYR cc_start: 0.6315 (OUTLIER) cc_final: 0.5540 (m-10)
REVERT: C  150 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.7109 (t0)
REVERT: C  207 TYR cc_start: 0.4697 (m-80) cc_final: 0.4276 (m-80)
REVERT: C  289 GLN cc_start: 0.4836 (pp30) cc_final: 0.3688 (pt0)
  outliers start: 61
  outliers final: 41
  residues processed: 201
  average time/residue: 0.0910
  time to fit residues: 27.3683
Evaluate side-chains
  186 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 141
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASP
Chi-restraints excluded: chain A residue   24 CYS
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   61 TYR
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  119 LYS
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  194 ILE
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain A residue  465 ILE
Chi-restraints excluded: chain A residue  484 SER
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  544 ARG
Chi-restraints excluded: chain A residue  828 TYR
Chi-restraints excluded: chain A residue  891 SER
Chi-restraints excluded: chain A residue  914 GLU
Chi-restraints excluded: chain A residue  931 LEU
Chi-restraints excluded: chain A residue  949 LEU
Chi-restraints excluded: chain A residue  952 SER
Chi-restraints excluded: chain A residue  956 ASN
Chi-restraints excluded: chain A residue  961 ILE
Chi-restraints excluded: chain A residue 1061 ASP
Chi-restraints excluded: chain A residue 1137 LEU
Chi-restraints excluded: chain A residue 1156 HIS
Chi-restraints excluded: chain A residue 1159 ASN
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue   46 TYR
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   77 ILE
Chi-restraints excluded: chain C residue   93 THR
Chi-restraints excluded: chain C residue  150 ASP
Chi-restraints excluded: chain C residue  184 VAL
Chi-restraints excluded: chain C residue  201 ASN
Chi-restraints excluded: chain C residue  213 MET
Chi-restraints excluded: chain C residue  251 SER
Chi-restraints excluded: chain C residue  260 THR
Chi-restraints excluded: chain C residue  263 ASP
Chi-restraints excluded: chain C residue  268 PHE
Chi-restraints excluded: chain C residue  318 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 2 optimal weight:    0.0050
   chunk 70 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 129 optimal weight:    5.9990
   chunk 126 optimal weight:    0.0970
   chunk 38 optimal weight:    4.9990
   chunk 90 optimal weight:    6.9990
   chunk 57 optimal weight:    1.9990
   chunk 94 optimal weight:    0.3980
   chunk 56 optimal weight:    0.6980
   chunk 58 optimal weight:    0.6980
   overall best weight:    0.3792

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

Flipped N/Q/H residues before XYZ refinement:
** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 145 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.181103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.131982 restraints weight = 19605.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.135294 restraints weight = 10669.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.135856 restraints weight = 8127.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.137180 restraints weight = 6011.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.137445 restraints weight = 5347.428|
|-----------------------------------------------------------------------------|
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.2808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  11501  Z= 0.103
  Angle     :  0.567  10.751  15649  Z= 0.279
  Chirality :  0.039   0.196   1798
  Planarity :  0.005   0.082   1999
  Dihedral  :  6.337  88.241   1634
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.52 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 28.41 %
    Favored  : 68.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.12 %
    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:  1.02 (0.23), residues: 1411
  helix:  2.25 (0.19), residues: 749
  sheet: -0.23 (0.66), residues: 62
  loop : -1.35 (0.24), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 598 
 TYR   0.009   0.001   TYR A 171 
 PHE   0.024   0.001   PHE C 100 
 TRP   0.018   0.001   TRP C 358 
 HIS   0.004   0.000   HIS A 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 (11501)
  covalent geometry    : angle       0.56671 (15649)
  hydrogen bonds       : bond        0.02785 (  572)
  hydrogen bonds       : angle       3.50520 ( 1656)

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

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

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 148
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  491 ARG cc_start: 0.3375 (ttt180) cc_final: 0.2714 (ttt180)
REVERT: A  544 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.6959 (ptm160)
REVERT: A  828 TYR cc_start: 0.6901 (OUTLIER) cc_final: 0.6289 (t80)
REVERT: A  842 GLU cc_start: 0.5952 (tp30) cc_final: 0.5443 (tp30)
REVERT: A  916 PHE cc_start: 0.7561 (t80) cc_final: 0.7349 (t80)
REVERT: A  954 MET cc_start: 0.7740 (tpp) cc_final: 0.7137 (ttp)
REVERT: A 1077 LYS cc_start: 0.8477 (mptt) cc_final: 0.8191 (mmmt)
REVERT: C  131 MET cc_start: 0.8542 (tpp) cc_final: 0.8268 (tpp)
REVERT: C  174 GLN cc_start: 0.7178 (pp30) cc_final: 0.6782 (pp30)
  outliers start: 35
  outliers final: 26
  residues processed: 179
  average time/residue: 0.0902
  time to fit residues: 24.9382
Evaluate side-chains
  171 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 143
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 TYR
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  119 LYS
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  194 ILE
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain A residue  484 SER
Chi-restraints excluded: chain A residue  544 ARG
Chi-restraints excluded: chain A residue  828 TYR
Chi-restraints excluded: chain A residue  914 GLU
Chi-restraints excluded: chain A residue  931 LEU
Chi-restraints excluded: chain A residue  952 SER
Chi-restraints excluded: chain A residue  956 ASN
Chi-restraints excluded: chain A residue  961 ILE
Chi-restraints excluded: chain A residue 1061 ASP
Chi-restraints excluded: chain A residue 1156 HIS
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   77 ILE
Chi-restraints excluded: chain C residue   93 THR
Chi-restraints excluded: chain C residue  184 VAL
Chi-restraints excluded: chain C residue  201 ASN
Chi-restraints excluded: chain C residue  251 SER
Chi-restraints excluded: chain C residue  263 ASP
Chi-restraints excluded: chain C residue  277 TYR
Chi-restraints excluded: chain C residue  318 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 120 optimal weight:    0.0980
   chunk 70 optimal weight:    3.9990
   chunk 103 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 137 optimal weight:    6.9990
   chunk 63 optimal weight:    3.9990
   chunk 12 optimal weight:    0.2980
   chunk 38 optimal weight:    3.9990
   chunk 111 optimal weight:    8.9990
   chunk 82 optimal weight:    3.9990
   chunk 62 optimal weight:    6.9990
   overall best weight:    2.0786

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

Flipped N/Q/H residues before XYZ refinement:
A 347 GLN
C 145 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.173841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.136933 restraints weight = 19757.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.132813 restraints weight = 16342.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.133646 restraints weight = 14663.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.134338 restraints weight = 9325.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.135928 restraints weight = 8373.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.3547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.064  11501  Z= 0.262
  Angle     :  0.724  13.225  15649  Z= 0.363
  Chirality :  0.044   0.189   1798
  Planarity :  0.006   0.096   1999
  Dihedral  :  7.125  84.930   1634
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.09 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 27.47 %
    Favored  : 68.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.12 %
    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:  0.45 (0.22), residues: 1411
  helix:  1.79 (0.19), residues: 749
  sheet: -0.61 (0.63), residues: 62
  loop : -1.63 (0.24), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 598 
 TYR   0.020   0.002   TYR A 171 
 PHE   0.020   0.002   PHE C 101 
 TRP   0.024   0.002   TRP C 358 
 HIS   0.008   0.001   HIS A 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00624 (11501)
  covalent geometry    : angle       0.72418 (15649)
  hydrogen bonds       : bond        0.04886 (  572)
  hydrogen bonds       : angle       4.07324 ( 1656)

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

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

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 138
  time to evaluate  : 0.451 
Fit side-chains
REVERT: A  491 ARG cc_start: 0.3806 (ttt180) cc_final: 0.2850 (ttt180)
REVERT: A  544 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.6756 (ptm160)
REVERT: A  828 TYR cc_start: 0.7408 (OUTLIER) cc_final: 0.6894 (t80)
REVERT: A  842 GLU cc_start: 0.6392 (tp30) cc_final: 0.6074 (tp30)
REVERT: A  916 PHE cc_start: 0.7620 (t80) cc_final: 0.7417 (t80)
REVERT: A  954 MET cc_start: 0.7946 (tpp) cc_final: 0.7379 (ttp)
REVERT: A 1077 LYS cc_start: 0.8715 (mptt) cc_final: 0.8345 (mmmt)
REVERT: C   46 TYR cc_start: 0.6453 (OUTLIER) cc_final: 0.5528 (m-10)
REVERT: C  174 GLN cc_start: 0.7283 (pp30) cc_final: 0.6234 (pm20)
REVERT: C  207 TYR cc_start: 0.5419 (m-80) cc_final: 0.5094 (m-80)
REVERT: C  289 GLN cc_start: 0.5287 (pp30) cc_final: 0.4206 (pt0)
REVERT: C  358 TRP cc_start: 0.7361 (m-10) cc_final: 0.4855 (t60)
REVERT: C  365 GLN cc_start: 0.6534 (mt0) cc_final: 0.6285 (pt0)
  outliers start: 45
  outliers final: 34
  residues processed: 176
  average time/residue: 0.0920
  time to fit residues: 24.5722
Evaluate side-chains
  169 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 132
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASP
Chi-restraints excluded: chain A residue   61 TYR
Chi-restraints excluded: chain A residue  119 LYS
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  194 ILE
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  338 ASP
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain A residue  465 ILE
Chi-restraints excluded: chain A residue  484 SER
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  544 ARG
Chi-restraints excluded: chain A residue  828 TYR
Chi-restraints excluded: chain A residue  914 GLU
Chi-restraints excluded: chain A residue  931 LEU
Chi-restraints excluded: chain A residue  949 LEU
Chi-restraints excluded: chain A residue  952 SER
Chi-restraints excluded: chain A residue  956 ASN
Chi-restraints excluded: chain A residue 1156 HIS
Chi-restraints excluded: chain A residue 1159 ASN
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   46 TYR
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   77 ILE
Chi-restraints excluded: chain C residue   93 THR
Chi-restraints excluded: chain C residue  184 VAL
Chi-restraints excluded: chain C residue  213 MET
Chi-restraints excluded: chain C residue  251 SER
Chi-restraints excluded: chain C residue  260 THR
Chi-restraints excluded: chain C residue  263 ASP
Chi-restraints excluded: chain C residue  268 PHE
Chi-restraints excluded: chain C residue  318 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 82 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 80 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 41 optimal weight:    0.6980
   chunk 43 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 102 optimal weight:    2.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 145 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.177017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.127368 restraints weight = 19889.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.129540 restraints weight = 12920.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.131588 restraints weight = 8636.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.131428 restraints weight = 6909.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.131639 restraints weight = 6849.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.3430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11501  Z= 0.142
  Angle     :  0.620  12.427  15649  Z= 0.307
  Chirality :  0.041   0.204   1798
  Planarity :  0.006   0.121   1999
  Dihedral  :  6.859  85.446   1634
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.80 %
    Favored  : 93.13 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 28.15 %
    Favored  : 68.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.23), residues: 1411
  helix:  1.99 (0.19), residues: 749
  sheet: -0.63 (0.64), residues: 62
  loop : -1.59 (0.24), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 598 
 TYR   0.017   0.001   TYR A 784 
 PHE   0.023   0.001   PHE C 100 
 TRP   0.028   0.002   TRP C 358 
 HIS   0.005   0.001   HIS A 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (11501)
  covalent geometry    : angle       0.62032 (15649)
  hydrogen bonds       : bond        0.03592 (  572)
  hydrogen bonds       : angle       3.77564 ( 1656)

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

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

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 140
  time to evaluate  : 0.449 
Fit side-chains
REVERT: A  491 ARG cc_start: 0.3504 (ttt180) cc_final: 0.2460 (ttt180)
REVERT: A  544 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.6906 (ptm160)
REVERT: A  828 TYR cc_start: 0.7388 (OUTLIER) cc_final: 0.7079 (t80)
REVERT: A  842 GLU cc_start: 0.6111 (tp30) cc_final: 0.5830 (tp30)
REVERT: A  954 MET cc_start: 0.7914 (tpp) cc_final: 0.7275 (ttp)
REVERT: A  965 LYS cc_start: 0.7704 (mtpp) cc_final: 0.6849 (mtmm)
REVERT: A 1077 LYS cc_start: 0.8507 (mptt) cc_final: 0.8149 (mmmt)
REVERT: C  174 GLN cc_start: 0.7357 (pp30) cc_final: 0.6384 (pm20)
REVERT: C  207 TYR cc_start: 0.4980 (m-80) cc_final: 0.4616 (m-80)
REVERT: C  289 GLN cc_start: 0.5289 (pp30) cc_final: 0.4288 (pt0)
REVERT: C  358 TRP cc_start: 0.7150 (m-10) cc_final: 0.4884 (t60)
  outliers start: 37
  outliers final: 33
  residues processed: 171
  average time/residue: 0.0899
  time to fit residues: 23.8078
Evaluate side-chains
  172 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 137
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASP
Chi-restraints excluded: chain A residue   24 CYS
Chi-restraints excluded: chain A residue   61 TYR
Chi-restraints excluded: chain A residue  119 LYS
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  194 ILE
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain A residue  484 SER
Chi-restraints excluded: chain A residue  544 ARG
Chi-restraints excluded: chain A residue  828 TYR
Chi-restraints excluded: chain A residue  914 GLU
Chi-restraints excluded: chain A residue  931 LEU
Chi-restraints excluded: chain A residue  952 SER
Chi-restraints excluded: chain A residue  956 ASN
Chi-restraints excluded: chain A residue 1078 VAL
Chi-restraints excluded: chain A residue 1137 LEU
Chi-restraints excluded: chain A residue 1156 HIS
Chi-restraints excluded: chain A residue 1159 ASN
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   77 ILE
Chi-restraints excluded: chain C residue   93 THR
Chi-restraints excluded: chain C residue  158 LEU
Chi-restraints excluded: chain C residue  166 LEU
Chi-restraints excluded: chain C residue  184 VAL
Chi-restraints excluded: chain C residue  251 SER
Chi-restraints excluded: chain C residue  260 THR
Chi-restraints excluded: chain C residue  263 ASP
Chi-restraints excluded: chain C residue  318 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 106 optimal weight:    0.7980
   chunk 124 optimal weight:    1.9990
   chunk 94 optimal weight:    8.9990
   chunk 5 optimal weight:    0.9990
   chunk 98 optimal weight:    0.8980
   chunk 137 optimal weight:    7.9990
   chunk 143 optimal weight:    8.9990
   chunk 112 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9980
   chunk 84 optimal weight:    3.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 590 GLN
C 145 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.176741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.127200 restraints weight = 19795.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.129255 restraints weight = 13153.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.131701 restraints weight = 8795.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.131314 restraints weight = 7017.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.131479 restraints weight = 6538.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.3505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11501  Z= 0.146
  Angle     :  0.625  12.551  15649  Z= 0.310
  Chirality :  0.041   0.200   1798
  Planarity :  0.006   0.114   1999
  Dihedral  :  6.793  83.702   1634
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.16 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 27.73 %
    Favored  : 68.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.12 %
    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:  0.63 (0.23), residues: 1411
  helix:  1.99 (0.19), residues: 748
  sheet: -0.63 (0.65), residues: 62
  loop : -1.60 (0.24), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 598 
 TYR   0.019   0.001   TYR A 784 
 PHE   0.022   0.001   PHE C 100 
 TRP   0.025   0.002   TRP C 358 
 HIS   0.005   0.001   HIS A 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 (11501)
  covalent geometry    : angle       0.62550 (15649)
  hydrogen bonds       : bond        0.03662 (  572)
  hydrogen bonds       : angle       3.80362 ( 1656)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2218.66 seconds
wall clock time: 39 minutes 1.17 seconds (2341.17 seconds total)