Starting phenix.real_space_refine
on Tue Jul 29 11:48:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8z5r_39779/07_2025/8z5r_39779.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8z5r_39779/07_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8z5r_39779/07_2025/8z5r_39779.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8z5r_39779/07_2025/8z5r_39779.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8z5r_39779/07_2025/8z5r_39779.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8z5r_39779/07_2025/8z5r_39779.cif"
  }
  resolution = 3.52
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'TPO:plan-1': 2, 'TYR:plan': 1, 'ASP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2}
          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, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 11}
          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: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 5, 'GLU:plan': 9, 'ARG: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: 8.77, per 1000 atoms: 0.78
  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: 2.94
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  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: 1.56
  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: 3.70

  Time building geometry restraints manager: 3.47 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:             9.810
  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:             0.020
  Extract box with map and model:          0.490
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     30.780
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.050
  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:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.260
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.010   0.001   TRP C 254 
 HIS   0.002   0.000   HIS C 285 
 PHE   0.016   0.001   PHE C 287 
 TYR   0.050   0.001   TYR A 313 
 ARG   0.003   0.000   ARG A  10 

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

*********************** 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  : 1.340 
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: 0.1903
  time to fit residues: 48.2192
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  : 1.225 
-------------------------------------------------------------------------------
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 122 optimal weight:    7.9990
   chunk 109 optimal weight:    0.4980
   chunk 60 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9980
   chunk 58 optimal weight:    0.7980
   chunk 113 optimal weight:    5.9990
   chunk 43 optimal weight:    0.2980
   chunk 69 optimal weight:    2.9990
   chunk 84 optimal weight:    3.9990
   chunk 131 optimal weight:    1.9990
   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 427 ASN
A 895 GLN
** C  39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 145 ASN
C 174 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.178926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.130839 restraints weight = 19618.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.132583 restraints weight = 11930.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.133213 restraints weight = 7778.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.1611

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= 0.144
  Angle     :  0.582  10.002  15649  Z= 0.291
  Chirality :  0.040   0.204   1798
  Planarity :  0.005   0.062   1999
  Dihedral  :  6.831  88.100   1642
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.38 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 24.38 %
    Favored  : 72.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.23), residues: 1411
  helix:  2.42 (0.19), residues: 748
  sheet:  1.07 (0.70), residues: 62
  loop : -1.00 (0.25), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 328 
 HIS   0.003   0.001   HIS A 822 
 PHE   0.018   0.001   PHE C 100 
 TYR   0.019   0.001   TYR A 171 
 ARG   0.004   0.000   ARG A  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03773 (  572)
  hydrogen bonds       : angle       3.84000 ( 1656)
  covalent geometry    : bond        0.00331 (11501)
  covalent geometry    : angle       0.58220 (15649)

*********************** 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
  194 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 159
  time to evaluate  : 2.274 
Fit side-chains
   revert: symmetry clash
REVERT: A  313 TYR cc_start: 0.6463 (t80) cc_final: 0.6243 (t80)
REVERT: A  491 ARG cc_start: 0.3398 (ttt180) cc_final: 0.2832 (ttt180)
REVERT: A  828 TYR cc_start: 0.6409 (OUTLIER) cc_final: 0.5297 (t80)
REVERT: A  916 PHE cc_start: 0.7267 (t80) cc_final: 0.6896 (t80)
REVERT: A 1060 LEU cc_start: 0.8323 (mt) cc_final: 0.7796 (tp)
REVERT: C  150 ASP cc_start: 0.7592 (OUTLIER) cc_final: 0.7020 (t0)
REVERT: C  207 TYR cc_start: 0.4322 (m-80) cc_final: 0.4087 (m-80)
  outliers start: 35
  outliers final: 18
  residues processed: 184
  average time/residue: 0.2310
  time to fit residues: 64.7272
Evaluate side-chains
  162 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 142
  time to evaluate  : 2.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 LYS
Chi-restraints excluded: chain A residue  138 THR
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  465 ILE
Chi-restraints excluded: chain A residue  517 ILE
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  961 ILE
Chi-restraints excluded: chain A residue 1061 ASP
Chi-restraints excluded: chain A residue 1137 LEU
Chi-restraints excluded: chain A residue 1159 ASN
Chi-restraints excluded: chain C residue   51 ILE
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  184 VAL
Chi-restraints excluded: chain C residue  259 ASP
Chi-restraints excluded: chain C residue  354 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 81 optimal weight:    0.8980
   chunk 99 optimal weight:    0.8980
   chunk 128 optimal weight:    9.9990
   chunk 129 optimal weight:    2.9990
   chunk 75 optimal weight:    0.6980
   chunk 100 optimal weight:    6.9990
   chunk 118 optimal weight:    0.0270
   chunk 40 optimal weight:    0.5980
   chunk 34 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.5638

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

Flipped N/Q/H residues before XYZ refinement:
A 427 ASN
A 795 ASN
** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.179306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.135347 restraints weight = 19409.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.134691 restraints weight = 12149.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.134708 restraints weight = 8096.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.3657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.1832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  11501  Z= 0.107
  Angle     :  0.539  11.440  15649  Z= 0.266
  Chirality :  0.039   0.246   1798
  Planarity :  0.005   0.065   1999
  Dihedral  :  6.580  86.345   1636
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.95 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 24.38 %
    Favored  : 72.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.23), residues: 1411
  helix:  2.45 (0.19), residues: 746
  sheet:  0.81 (0.70), residues: 62
  loop : -1.07 (0.25), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 358 
 HIS   0.002   0.000   HIS A 822 
 PHE   0.013   0.001   PHE C 100 
 TYR   0.011   0.001   TYR A 171 
 ARG   0.006   0.000   ARG A  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02986 (  572)
  hydrogen bonds       : angle       3.59189 ( 1656)
  covalent geometry    : bond        0.00240 (11501)
  covalent geometry    : angle       0.53873 (15649)

*********************** 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
  195 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 153
  time to evaluate  : 1.254 
Fit side-chains
   revert: symmetry clash
REVERT: A  491 ARG cc_start: 0.3493 (ttt180) cc_final: 0.2837 (ttt180)
REVERT: A  828 TYR cc_start: 0.6589 (OUTLIER) cc_final: 0.5504 (t80)
REVERT: A  916 PHE cc_start: 0.7281 (t80) cc_final: 0.6922 (t80)
REVERT: A  954 MET cc_start: 0.7942 (tpp) cc_final: 0.7259 (ttp)
REVERT: A 1099 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8076 (tm-30)
REVERT: A 1100 MET cc_start: 0.8090 (mmm) cc_final: 0.7343 (mmm)
REVERT: C   46 TYR cc_start: 0.6314 (OUTLIER) cc_final: 0.5736 (m-10)
REVERT: C  207 TYR cc_start: 0.4331 (m-80) cc_final: 0.4019 (m-80)
REVERT: C  289 GLN cc_start: 0.4756 (pp30) cc_final: 0.3753 (pt0)
  outliers start: 42
  outliers final: 21
  residues processed: 184
  average time/residue: 0.2322
  time to fit residues: 66.0985
Evaluate side-chains
  167 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 144
  time to evaluate  : 2.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  119 LYS
Chi-restraints excluded: chain A residue  138 THR
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  194 ILE
Chi-restraints excluded: chain A residue  413 MET
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  828 TYR
Chi-restraints excluded: chain A residue  891 SER
Chi-restraints excluded: chain A residue  931 LEU
Chi-restraints excluded: chain A residue  956 ASN
Chi-restraints excluded: chain A residue  961 ILE
Chi-restraints excluded: chain A residue 1137 LEU
Chi-restraints excluded: chain A residue 1144 SER
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   93 THR
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  259 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 51 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 117 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 71 optimal weight:    4.9990
   chunk 65 optimal weight:    5.9990
   chunk 129 optimal weight:    8.9990
   chunk 112 optimal weight:    5.9990
   chunk 62 optimal weight:    0.7980
   chunk 7 optimal weight:    0.0980
   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  25 HIS
** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.177620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.129311 restraints weight = 19341.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.132340 restraints weight = 11136.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.132574 restraints weight = 7899.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.2189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11501  Z= 0.125
  Angle     :  0.563  10.803  15649  Z= 0.278
  Chirality :  0.040   0.242   1798
  Planarity :  0.005   0.068   1999
  Dihedral  :  6.547  86.973   1636
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.31 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 23.78 %
    Favored  : 71.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.23), residues: 1411
  helix:  2.33 (0.19), residues: 748
  sheet:  0.49 (0.69), residues: 62
  loop : -1.16 (0.25), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 328 
 HIS   0.003   0.001   HIS A1156 
 PHE   0.012   0.001   PHE C 100 
 TYR   0.015   0.001   TYR A 171 
 ARG   0.007   0.000   ARG A  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03318 (  572)
  hydrogen bonds       : angle       3.59061 ( 1656)
  covalent geometry    : bond        0.00287 (11501)
  covalent geometry    : angle       0.56344 (15649)

*********************** 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
  204 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 152
  time to evaluate  : 2.283 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 THR cc_start: 0.8668 (OUTLIER) cc_final: 0.8264 (t)
REVERT: A  435 LYS cc_start: 0.7072 (tmtt) cc_final: 0.6624 (mmtt)
REVERT: A  491 ARG cc_start: 0.3438 (ttt180) cc_final: 0.2830 (ttt180)
REVERT: A  828 TYR cc_start: 0.7021 (OUTLIER) cc_final: 0.6056 (t80)
REVERT: A  916 PHE cc_start: 0.7505 (t80) cc_final: 0.7159 (t80)
REVERT: A  954 MET cc_start: 0.7906 (tpp) cc_final: 0.7250 (ttp)
REVERT: A 1100 MET cc_start: 0.8059 (mmm) cc_final: 0.7655 (mmm)
REVERT: C   46 TYR cc_start: 0.6171 (OUTLIER) cc_final: 0.5485 (m-10)
REVERT: C  238 MET cc_start: 0.6889 (OUTLIER) cc_final: 0.6454 (ptp)
  outliers start: 52
  outliers final: 33
  residues processed: 191
  average time/residue: 0.2571
  time to fit residues: 77.7453
Evaluate side-chains
  179 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 142
  time to evaluate  : 2.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  124 VAL
Chi-restraints excluded: chain A residue  138 THR
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  261 SER
Chi-restraints excluded: chain A residue  275 LEU
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  557 THR
Chi-restraints excluded: chain A residue  828 TYR
Chi-restraints excluded: chain A residue  891 SER
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  154 GLU
Chi-restraints excluded: chain C residue  158 LEU
Chi-restraints excluded: chain C residue  184 VAL
Chi-restraints excluded: chain C residue  238 MET
Chi-restraints excluded: chain C residue  263 ASP
Chi-restraints excluded: chain C residue  277 TYR
Chi-restraints excluded: chain C residue  354 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 41 optimal weight:    0.0970
   chunk 88 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 106 optimal weight:    0.4980
   chunk 109 optimal weight:    0.8980
   chunk 108 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9990
   chunk 125 optimal weight:    3.9990
   chunk 47 optimal weight:    0.2980
   chunk 121 optimal weight:    0.3980
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.3978

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

Flipped N/Q/H residues before XYZ refinement:
C 142 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.179729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.132937 restraints weight = 19680.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.133943 restraints weight = 12191.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.133834 restraints weight = 7959.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.2231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  11501  Z= 0.101
  Angle     :  0.551  10.160  15649  Z= 0.271
  Chirality :  0.039   0.209   1798
  Planarity :  0.005   0.071   1999
  Dihedral  :  6.354  87.386   1636
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.02 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 25.41 %
    Favored  : 71.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.23), residues: 1411
  helix:  2.39 (0.19), residues: 748
  sheet:  0.35 (0.68), residues: 62
  loop : -1.17 (0.25), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 358 
 HIS   0.002   0.000   HIS A 960 
 PHE   0.016   0.001   PHE A 763 
 TYR   0.010   0.001   TYR A 787 
 ARG   0.007   0.000   ARG A 598 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02752 (  572)
  hydrogen bonds       : angle       3.46563 ( 1656)
  covalent geometry    : bond        0.00224 (11501)
  covalent geometry    : angle       0.55118 (15649)

*********************** 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
  190 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 153
  time to evaluate  : 1.223 
Fit side-chains
   revert: symmetry clash
REVERT: A  491 ARG cc_start: 0.3384 (ttt180) cc_final: 0.2770 (ttt180)
REVERT: A  828 TYR cc_start: 0.6964 (OUTLIER) cc_final: 0.6012 (t80)
REVERT: A  916 PHE cc_start: 0.7501 (t80) cc_final: 0.7121 (t80)
REVERT: A  954 MET cc_start: 0.7806 (tpp) cc_final: 0.7185 (ttp)
REVERT: A 1100 MET cc_start: 0.8062 (mmm) cc_final: 0.7590 (mmm)
REVERT: C   46 TYR cc_start: 0.6029 (OUTLIER) cc_final: 0.5388 (m-10)
REVERT: C  150 ASP cc_start: 0.7505 (OUTLIER) cc_final: 0.7120 (t0)
REVERT: C  289 GLN cc_start: 0.4738 (pp30) cc_final: 0.3840 (pt0)
  outliers start: 37
  outliers final: 23
  residues processed: 182
  average time/residue: 0.1868
  time to fit residues: 51.8145
Evaluate side-chains
  169 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 143
  time to evaluate  : 1.242 
-------------------------------------------------------------------------------
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  124 VAL
Chi-restraints excluded: chain A residue  138 THR
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  358 VAL
Chi-restraints excluded: chain A residue  828 TYR
Chi-restraints excluded: chain A residue  931 LEU
Chi-restraints excluded: chain A residue  956 ASN
Chi-restraints excluded: chain A residue  961 ILE
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   93 THR
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  184 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 52 optimal weight:    0.8980
   chunk 73 optimal weight:    3.9990
   chunk 134 optimal weight:    0.0010
   chunk 37 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   chunk 111 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 136 optimal weight:    0.8980
   chunk 56 optimal weight:    0.6980
   chunk 124 optimal weight:    4.9990
   chunk 12 optimal weight:    4.9990
   overall best weight:    0.6586

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN
C 145 ASN
C 148 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.178022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.132212 restraints weight = 19357.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.133433 restraints weight = 11840.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.133205 restraints weight = 7602.889|
|-----------------------------------------------------------------------------|
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.2462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11501  Z= 0.117
  Angle     :  0.558  10.152  15649  Z= 0.276
  Chirality :  0.039   0.240   1798
  Planarity :  0.005   0.074   1999
  Dihedral  :  6.309  89.405   1636
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.52 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 24.64 %
    Favored  : 71.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.23), residues: 1411
  helix:  2.34 (0.19), residues: 748
  sheet:  0.25 (0.68), residues: 62
  loop : -1.24 (0.25), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 328 
 HIS   0.002   0.001   HIS A1156 
 PHE   0.015   0.001   PHE A 763 
 TYR   0.013   0.001   TYR A 171 
 ARG   0.006   0.000   ARG A  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03154 (  572)
  hydrogen bonds       : angle       3.51557 ( 1656)
  covalent geometry    : bond        0.00266 (11501)
  covalent geometry    : angle       0.55840 (15649)

*********************** 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
  193 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 143
  time to evaluate  : 1.422 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8220 (t)
REVERT: A  491 ARG cc_start: 0.3409 (ttt180) cc_final: 0.2735 (ttt180)
REVERT: A  828 TYR cc_start: 0.6761 (OUTLIER) cc_final: 0.6128 (t80)
REVERT: A  916 PHE cc_start: 0.7546 (t80) cc_final: 0.7201 (t80)
REVERT: A  954 MET cc_start: 0.7798 (tpp) cc_final: 0.7100 (ttp)
REVERT: A 1077 LYS cc_start: 0.8457 (mptt) cc_final: 0.8246 (mmmt)
REVERT: A 1099 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8268 (tm-30)
REVERT: A 1100 MET cc_start: 0.8034 (mmm) cc_final: 0.7438 (mmm)
REVERT: C   46 TYR cc_start: 0.6278 (OUTLIER) cc_final: 0.5585 (m-10)
REVERT: C  238 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.6683 (ptp)
  outliers start: 50
  outliers final: 31
  residues processed: 182
  average time/residue: 0.2149
  time to fit residues: 59.7100
Evaluate side-chains
  174 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 139
  time to evaluate  : 1.307 
-------------------------------------------------------------------------------
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  119 LYS
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  138 THR
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  275 LEU
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  783 LEU
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  956 ASN
Chi-restraints excluded: chain A residue  961 ILE
Chi-restraints excluded: chain A residue 1061 ASP
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   77 ILE
Chi-restraints excluded: chain C residue   93 THR
Chi-restraints excluded: chain C residue  158 LEU
Chi-restraints excluded: chain C residue  184 VAL
Chi-restraints excluded: chain C residue  238 MET
Chi-restraints excluded: chain C residue  318 ILE
Chi-restraints excluded: chain C residue  354 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 112 optimal weight:    0.9990
   chunk 118 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 144 optimal weight:    9.9990
   chunk 104 optimal weight:    0.8980
   chunk 88 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 116 optimal weight:    2.9990
   chunk 122 optimal weight:    1.9990
   overall best weight:    0.9384

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.179293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.131086 restraints weight = 19918.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.132700 restraints weight = 12545.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.133630 restraints weight = 8035.340|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.2722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11501  Z= 0.143
  Angle     :  0.587  10.566  15649  Z= 0.292
  Chirality :  0.040   0.222   1798
  Planarity :  0.005   0.080   1999
  Dihedral  :  6.436  89.145   1636
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.95 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 25.32 %
    Favored  : 70.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.23), residues: 1411
  helix:  2.19 (0.19), residues: 749
  sheet:  0.03 (0.67), residues: 62
  loop : -1.32 (0.25), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP C 358 
 HIS   0.002   0.001   HIS A1156 
 PHE   0.013   0.001   PHE A 763 
 TYR   0.015   0.001   TYR A 171 
 ARG   0.007   0.000   ARG A  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03513 (  572)
  hydrogen bonds       : angle       3.63839 ( 1656)
  covalent geometry    : bond        0.00336 (11501)
  covalent geometry    : angle       0.58735 (15649)

*********************** 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
  190 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 141
  time to evaluate  : 1.058 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 THR cc_start: 0.8899 (OUTLIER) cc_final: 0.8446 (t)
REVERT: A  491 ARG cc_start: 0.3555 (ttt180) cc_final: 0.2870 (ttt180)
REVERT: A  828 TYR cc_start: 0.6749 (OUTLIER) cc_final: 0.6153 (t80)
REVERT: A  916 PHE cc_start: 0.7573 (t80) cc_final: 0.7225 (t80)
REVERT: A  954 MET cc_start: 0.7856 (tpp) cc_final: 0.7159 (ttp)
REVERT: A 1077 LYS cc_start: 0.8429 (mptt) cc_final: 0.8165 (mmmt)
REVERT: A 1152 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7314 (tm-30)
REVERT: C   46 TYR cc_start: 0.6163 (OUTLIER) cc_final: 0.5317 (m-10)
REVERT: C  238 MET cc_start: 0.6965 (OUTLIER) cc_final: 0.6598 (ptp)
REVERT: C  289 GLN cc_start: 0.5037 (pp30) cc_final: 0.4027 (pt0)
  outliers start: 49
  outliers final: 36
  residues processed: 177
  average time/residue: 0.1952
  time to fit residues: 54.5242
Evaluate side-chains
  180 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 139
  time to evaluate  : 1.501 
-------------------------------------------------------------------------------
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   33 LEU
Chi-restraints excluded: chain A residue   93 ILE
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  275 LEU
Chi-restraints excluded: chain A residue  279 THR
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  783 LEU
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 1152 GLU
Chi-restraints excluded: chain A residue 1156 HIS
Chi-restraints excluded: chain A residue 1159 ASN
Chi-restraints excluded: chain A residue 1182 SER
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  158 LEU
Chi-restraints excluded: chain C residue  164 ILE
Chi-restraints excluded: chain C residue  184 VAL
Chi-restraints excluded: chain C residue  238 MET
Chi-restraints excluded: chain C residue  263 ASP
Chi-restraints excluded: chain C residue  318 ILE
Chi-restraints excluded: chain C residue  354 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 77 optimal weight:    0.7980
   chunk 128 optimal weight:    1.9990
   chunk 97 optimal weight:    0.8980
   chunk 86 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 129 optimal weight:   20.0000
   chunk 101 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   overall best weight:    1.0982

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.177652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.126266 restraints weight = 19697.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.129215 restraints weight = 10458.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.131226 restraints weight = 7010.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.2986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  11501  Z= 0.160
  Angle     :  0.611  11.206  15649  Z= 0.305
  Chirality :  0.041   0.215   1798
  Planarity :  0.005   0.085   1999
  Dihedral  :  6.642  85.043   1636
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.80 %
    Favored  : 93.13 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 25.84 %
    Favored  : 69.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.23), residues: 1411
  helix:  2.07 (0.19), residues: 748
  sheet: -0.32 (0.66), residues: 62
  loop : -1.44 (0.24), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 358 
 HIS   0.004   0.001   HIS A 960 
 PHE   0.012   0.001   PHE A 763 
 TYR   0.016   0.001   TYR A 171 
 ARG   0.006   0.000   ARG A  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03841 (  572)
  hydrogen bonds       : angle       3.75234 ( 1656)
  covalent geometry    : bond        0.00379 (11501)
  covalent geometry    : angle       0.61062 (15649)

*********************** 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
  195 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 145
  time to evaluate  : 1.216 
Fit side-chains
REVERT: A   30 THR cc_start: 0.8712 (OUTLIER) cc_final: 0.8334 (t)
REVERT: A  491 ARG cc_start: 0.3463 (ttt180) cc_final: 0.2806 (ttt180)
REVERT: A  828 TYR cc_start: 0.7096 (OUTLIER) cc_final: 0.6565 (t80)
REVERT: A  916 PHE cc_start: 0.7685 (t80) cc_final: 0.7400 (t80)
REVERT: A  954 MET cc_start: 0.7864 (tpp) cc_final: 0.7235 (ttp)
REVERT: A  965 LYS cc_start: 0.7315 (mmtt) cc_final: 0.6788 (mtpp)
REVERT: A 1077 LYS cc_start: 0.8642 (mptt) cc_final: 0.8320 (mmmt)
REVERT: A 1152 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7288 (tm-30)
REVERT: C   46 TYR cc_start: 0.6449 (OUTLIER) cc_final: 0.5588 (m-10)
REVERT: C  131 MET cc_start: 0.8627 (tpp) cc_final: 0.8402 (tpp)
REVERT: C  238 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.6938 (ptp)
REVERT: C  289 GLN cc_start: 0.4764 (pp30) cc_final: 0.3918 (pt0)
  outliers start: 50
  outliers final: 41
  residues processed: 184
  average time/residue: 0.1907
  time to fit residues: 53.7219
Evaluate side-chains
  184 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 138
  time to evaluate  : 1.231 
-------------------------------------------------------------------------------
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   33 LEU
Chi-restraints excluded: chain A residue   66 ASP
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  119 LYS
Chi-restraints excluded: chain A residue  138 THR
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  220 VAL
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  279 THR
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  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 1152 GLU
Chi-restraints excluded: chain A residue 1156 HIS
Chi-restraints excluded: chain A residue 1159 ASN
Chi-restraints excluded: chain A residue 1182 SER
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  158 LEU
Chi-restraints excluded: chain C residue  184 VAL
Chi-restraints excluded: chain C residue  213 MET
Chi-restraints excluded: chain C residue  238 MET
Chi-restraints excluded: chain C residue  263 ASP
Chi-restraints excluded: chain C residue  318 ILE
Chi-restraints excluded: chain C residue  354 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 88 optimal weight:    6.9990
   chunk 33 optimal weight:    0.7980
   chunk 67 optimal weight:    2.9990
   chunk 103 optimal weight:    9.9990
   chunk 87 optimal weight:    0.1980
   chunk 60 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9980
   chunk 131 optimal weight:    4.9990
   chunk 89 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9990
   overall best weight:    0.7984

-------------------------------------------------------------------------------
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 = 0.4257 r_free = 0.4257 target = 0.178706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.128772 restraints weight = 19759.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.132476 restraints weight = 10868.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.132940 restraints weight = 7607.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.3004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11501  Z= 0.133
  Angle     :  0.597  11.411  15649  Z= 0.295
  Chirality :  0.040   0.212   1798
  Planarity :  0.005   0.087   1999
  Dihedral  :  6.542  83.855   1636
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.45 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 26.70 %
    Favored  : 69.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.23), residues: 1411
  helix:  2.13 (0.19), residues: 748
  sheet: -0.44 (0.66), residues: 62
  loop : -1.44 (0.24), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 254 
 HIS   0.003   0.001   HIS A 960 
 PHE   0.010   0.001   PHE A 763 
 TYR   0.035   0.001   TYR A 313 
 ARG   0.007   0.000   ARG A  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03386 (  572)
  hydrogen bonds       : angle       3.66249 ( 1656)
  covalent geometry    : bond        0.00310 (11501)
  covalent geometry    : angle       0.59734 (15649)

*********************** 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
  188 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 143
  time to evaluate  : 1.238 
Fit side-chains
   revert: symmetry clash
REVERT: A  491 ARG cc_start: 0.3323 (ttt180) cc_final: 0.2678 (ttt180)
REVERT: A  828 TYR cc_start: 0.7114 (OUTLIER) cc_final: 0.6569 (t80)
REVERT: A  916 PHE cc_start: 0.7645 (t80) cc_final: 0.7330 (t80)
REVERT: A  954 MET cc_start: 0.7899 (tpp) cc_final: 0.7233 (ttp)
REVERT: A 1077 LYS cc_start: 0.8545 (mptt) cc_final: 0.8204 (mmmt)
REVERT: A 1152 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7243 (tm-30)
REVERT: C   46 TYR cc_start: 0.6309 (OUTLIER) cc_final: 0.5516 (m-10)
REVERT: C  174 GLN cc_start: 0.7181 (pp30) cc_final: 0.6812 (pp30)
REVERT: C  238 MET cc_start: 0.6941 (OUTLIER) cc_final: 0.6567 (ptp)
REVERT: C  289 GLN cc_start: 0.4798 (pp30) cc_final: 0.4001 (pt0)
REVERT: C  334 ILE cc_start: 0.6398 (tp) cc_final: 0.6188 (tp)
  outliers start: 45
  outliers final: 40
  residues processed: 177
  average time/residue: 0.1966
  time to fit residues: 53.4974
Evaluate side-chains
  182 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 138
  time to evaluate  : 1.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 CYS
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   66 ASP
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  119 LYS
Chi-restraints excluded: chain A residue  138 THR
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  220 VAL
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain A residue  413 MET
Chi-restraints excluded: chain A residue  517 ILE
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 1152 GLU
Chi-restraints excluded: chain A residue 1156 HIS
Chi-restraints excluded: chain A residue 1159 ASN
Chi-restraints excluded: chain A residue 1182 SER
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  158 LEU
Chi-restraints excluded: chain C residue  164 ILE
Chi-restraints excluded: chain C residue  184 VAL
Chi-restraints excluded: chain C residue  238 MET
Chi-restraints excluded: chain C residue  263 ASP
Chi-restraints excluded: chain C residue  277 TYR
Chi-restraints excluded: chain C residue  318 ILE
Chi-restraints excluded: chain C residue  354 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 100 optimal weight:    0.0020
   chunk 126 optimal weight:    0.8980
   chunk 127 optimal weight:   10.0000
   chunk 45 optimal weight:    0.9980
   chunk 64 optimal weight:    0.7980
   chunk 122 optimal weight:    8.9990
   chunk 142 optimal weight:    0.0470
   chunk 48 optimal weight:    0.3980
   chunk 81 optimal weight:    0.7980
   chunk 89 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.4086

-------------------------------------------------------------------------------
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 = 0.181081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.133842 restraints weight = 19588.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.135423 restraints weight = 11805.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.136708 restraints weight = 7486.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
moved from start:          0.2912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  11501  Z= 0.104
  Angle     :  0.559  10.799  15649  Z= 0.276
  Chirality :  0.039   0.210   1798
  Planarity :  0.005   0.085   1999
  Dihedral  :  6.277  83.056   1636
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.45 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 27.38 %
    Favored  : 69.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.23), residues: 1411
  helix:  2.26 (0.19), residues: 748
  sheet: -0.29 (0.68), residues: 62
  loop : -1.36 (0.25), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP C 358 
 HIS   0.002   0.000   HIS A 960 
 PHE   0.010   0.001   PHE A 524 
 TYR   0.017   0.001   TYR A 784 
 ARG   0.007   0.000   ARG A  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02828 (  572)
  hydrogen bonds       : angle       3.53200 ( 1656)
  covalent geometry    : bond        0.00233 (11501)
  covalent geometry    : angle       0.55905 (15649)

********************** 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
  186 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 150
  time to evaluate  : 1.228 
Fit side-chains
   revert: symmetry clash
REVERT: A  491 ARG cc_start: 0.3380 (ttt180) cc_final: 0.2724 (ttt180)
REVERT: A  828 TYR cc_start: 0.7003 (OUTLIER) cc_final: 0.6586 (t80)
REVERT: A  842 GLU cc_start: 0.5872 (tp30) cc_final: 0.5460 (tp30)
REVERT: A  916 PHE cc_start: 0.7616 (t80) cc_final: 0.7332 (t80)
REVERT: A 1077 LYS cc_start: 0.8590 (mptt) cc_final: 0.8237 (mmmt)
REVERT: C   46 TYR cc_start: 0.6353 (OUTLIER) cc_final: 0.5583 (m-10)
REVERT: C  107 MET cc_start: 0.7663 (mtp) cc_final: 0.7414 (mtp)
REVERT: C  174 GLN cc_start: 0.7167 (pp30) cc_final: 0.6204 (pm20)
REVERT: C  238 MET cc_start: 0.6960 (OUTLIER) cc_final: 0.6533 (ptp)
REVERT: C  334 ILE cc_start: 0.6513 (tp) cc_final: 0.6304 (tp)
  outliers start: 36
  outliers final: 30
  residues processed: 178
  average time/residue: 0.1864
  time to fit residues: 51.2969
Evaluate side-chains
  179 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 146
  time to evaluate  : 1.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 CYS
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  119 LYS
Chi-restraints excluded: chain A residue  138 THR
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  220 VAL
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain A residue  828 TYR
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 A residue 1182 SER
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  158 LEU
Chi-restraints excluded: chain C residue  184 VAL
Chi-restraints excluded: chain C residue  238 MET
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 105 optimal weight:    0.8980
   chunk 119 optimal weight:    0.9990
   chunk 77 optimal weight:    0.7980
   chunk 4 optimal weight:    0.4980
   chunk 94 optimal weight:    5.9990
   chunk 108 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 8 optimal weight:    0.4980
   chunk 46 optimal weight:    0.0970
   chunk 44 optimal weight:    0.9980
   chunk 113 optimal weight:    0.9990
   overall best weight:    0.5178

-------------------------------------------------------------------------------
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 = 0.4280 r_free = 0.4280 target = 0.180532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.131324 restraints weight = 19508.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.135618 restraints weight = 10690.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.135699 restraints weight = 7129.582|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.2992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11501  Z= 0.112
  Angle     :  0.577  10.914  15649  Z= 0.285
  Chirality :  0.039   0.208   1798
  Planarity :  0.005   0.083   1999
  Dihedral  :  6.206  81.696   1636
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.45 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 27.30 %
    Favored  : 69.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.23), residues: 1411
  helix:  2.25 (0.19), residues: 748
  sheet: -0.26 (0.68), residues: 62
  loop : -1.37 (0.25), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C 358 
 HIS   0.002   0.000   HIS A 960 
 PHE   0.010   0.001   PHE A 524 
 TYR   0.018   0.001   TYR A 312 
 ARG   0.007   0.000   ARG A  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02983 (  572)
  hydrogen bonds       : angle       3.56939 ( 1656)
  covalent geometry    : bond        0.00256 (11501)
  covalent geometry    : angle       0.57727 (15649)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4652.32 seconds
wall clock time: 83 minutes 46.16 seconds (5026.16 seconds total)