Starting phenix.real_space_refine
on Mon May 19 19:41:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8swn_40821/05_2025/8swn_40821_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8swn_40821/05_2025/8swn_40821.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8swn_40821/05_2025/8swn_40821.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8swn_40821/05_2025/8swn_40821.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8swn_40821/05_2025/8swn_40821_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8swn_40821/05_2025/8swn_40821_trim.cif"
  }
  resolution = 3.1
  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=   0.003 sd=   0.075
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: 7
    Type Number    sf(0)   Gaussians
     P       7      5.49       5
     Mg      2      5.21       5
     S      36      5.16       5
     C    5934      2.51       5
     N    1529      2.21       5
     O    1645      1.98       5
     H    9269      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 58 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 18422
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 18308
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1135, 18308
          Classifications: {'peptide': 1135}
          Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 1100}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 114
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 114
          Unusual residues: {' MG': 2, 'ATP': 2, 'PTY': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
  Time building chain proxies: 8.25, per 1000 atoms: 0.45
  Number of scatterers: 18422
  At special positions: 0
  Unit cell: (72.558, 90.906, 147.618, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      36     16.00
     P       7     15.00
     Mg      2     11.99
     O    1645      8.00
     N    1529      7.00
     C    5934      6.00
     H    9269      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.32
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2144

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 5 sheets defined
      72.3% alpha, 8.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 48 through 52
    Processing helix  chain 'A' and resid 57 through 75
      removed outlier: 3.596A  pdb=" N   GLU A  72 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LYS A  73 " --> pdb=" O   LEU A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 93
      removed outlier: 5.817A  pdb=" N   LYS A  90 " --> pdb=" O   LYS A  86 " (cutoff:3.500A)
      removed outlier: 5.910A  pdb=" N   SER A  91 " --> pdb=" O   CYS A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 121
      removed outlier: 3.643A  pdb=" N   THR A  99 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   VAL A 107 " --> pdb=" O   GLU A 103 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   VAL A 108 " --> pdb=" O   SER A 104 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLN A 109 " --> pdb=" O   THR A 105 " (cutoff:3.500A)
      Proline residue:  A 110  - end of helix
      removed outlier: 3.526A  pdb=" N   LYS A 115 " --> pdb=" O   ILE A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 181
      removed outlier: 3.503A  pdb=" N   HIS A 153 " --> pdb=" O   ALA A 149 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   HIS A 158 " --> pdb=" O   LEU A 154 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   GLN A 160 " --> pdb=" O   PHE A 156 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ARG A 180 " --> pdb=" O   ARG A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 189
    Processing helix  chain 'A' and resid 190 through 200
    Processing helix  chain 'A' and resid 201 through 203
      No H-bonds generated for 'chain 'A' and resid 201 through 203'
    Processing helix  chain 'A' and resid 204 through 212
      removed outlier: 4.254A  pdb=" N   THR A 209 " --> pdb=" O   PHE A 205 " (cutoff:3.500A)
      removed outlier: 4.729A  pdb=" N   ILE A 210 " --> pdb=" O   ASP A 206 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   PHE A 211 " --> pdb=" O   GLN A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 234
      Proline residue:  A 219  - end of helix
      removed outlier: 3.774A  pdb=" N   MET A 231 " --> pdb=" O   ALA A 227 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLU A 232 " --> pdb=" O   LEU A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 254
      removed outlier: 3.910A  pdb=" N   VAL A 243 " --> pdb=" O   ALA A 239 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   ILE A 246 " --> pdb=" O   ALA A 242 " (cutoff:3.500A)
      Proline residue:  A 249  - end of helix
    Processing helix  chain 'A' and resid 254 through 290
      removed outlier: 3.538A  pdb=" N   PHE A 258 " --> pdb=" O   ILE A 254 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   PHE A 268 " --> pdb=" O   LYS A 264 " (cutoff:3.500A)
      removed outlier: 5.928A  pdb=" N   ARG A 284 " --> pdb=" O   ILE A 280 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   ILE A 285 " --> pdb=" O   THR A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 342
      removed outlier: 3.561A  pdb=" N   PHE A 295 " --> pdb=" O   TRP A 291 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   LYS A 309 " --> pdb=" O   LYS A 305 " (cutoff:3.500A)
      removed outlier: 5.305A  pdb=" N   SER A 328 " --> pdb=" O   PHE A 324 " (cutoff:3.500A)
      removed outlier: 4.773A  pdb=" N   LYS A 329 " --> pdb=" O   PHE A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 367
      removed outlier: 4.820A  pdb=" N   LEU A 363 " --> pdb=" O   GLY A 359 " (cutoff:3.500A)
      removed outlier: 5.695A  pdb=" N   THR A 364 " --> pdb=" O   ALA A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 391
      removed outlier: 3.998A  pdb=" N   VAL A 381 " --> pdb=" O   SER A 377 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   SER A 382 " --> pdb=" O   GLU A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 459
    Processing helix  chain 'A' and resid 489 through 495
    Processing helix  chain 'A' and resid 500 through 511
    Processing helix  chain 'A' and resid 513 through 520
    Processing helix  chain 'A' and resid 522 through 525
    Processing helix  chain 'A' and resid 536 through 551
      removed outlier: 3.750A  pdb=" N   ALA A 548 " --> pdb=" O   ASN A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 577
    Processing helix  chain 'A' and resid 593 through 600
      removed outlier: 4.825A  pdb=" N   LYS A 598 " --> pdb=" O   GLN A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 697 through 707
      removed outlier: 3.755A  pdb=" N   TYR A 701 " --> pdb=" O   GLY A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 710 through 745
      removed outlier: 3.653A  pdb=" N   ASP A 732 " --> pdb=" O   TYR A 728 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 760 through 807
      removed outlier: 3.747A  pdb=" N   PHE A 787 " --> pdb=" O   SER A 783 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 809 through 816
      removed outlier: 3.870A  pdb=" N   PHE A 813 " --> pdb=" O   PRO A 809 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 817 through 834
      removed outlier: 3.904A  pdb=" N   ARG A 824 " --> pdb=" O   ARG A 820 " (cutoff:3.500A)
      removed outlier: 4.988A  pdb=" N   ILE A 829 " --> pdb=" O   PHE A 825 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 834 through 861
      removed outlier: 4.372A  pdb=" N   LEU A 838 " --> pdb=" O   ASP A 834 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 864 through 882
      removed outlier: 3.502A  pdb=" N   VAL A 869 " --> pdb=" O   ALA A 865 " (cutoff:3.500A)
      Proline residue:  A 870  - end of helix
    Processing helix  chain 'A' and resid 900 through 910
    Processing helix  chain 'A' and resid 910 through 917
    Processing helix  chain 'A' and resid 919 through 970
      removed outlier: 3.755A  pdb=" N   ARG A 951 " --> pdb=" O   TRP A 947 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ALA A 954 " --> pdb=" O   VAL A 950 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   LEU A 968 " --> pdb=" O   ALA A 964 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 971 through 974
    Processing helix  chain 'A' and resid 975 through 1018
      removed outlier: 4.370A  pdb=" N   MET A 990 " --> pdb=" O   ALA A 986 " (cutoff:3.500A)
      removed outlier: 5.130A  pdb=" N   GLY A 991 " --> pdb=" O   LEU A 987 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   ILE A1008 " --> pdb=" O   GLU A1004 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   SER A1009 " --> pdb=" O   ASN A1005 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   VAL A1010 " --> pdb=" O   MET A1006 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   TYR A1016 " --> pdb=" O   ARG A1012 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ASP A1018 " --> pdb=" O   ILE A1014 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1080 through 1089
      removed outlier: 3.845A  pdb=" N   ILE A1085 " --> pdb=" O   LYS A1081 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1106 through 1108
      No H-bonds generated for 'chain 'A' and resid 1106 through 1108'
    Processing helix  chain 'A' and resid 1109 through 1115
    Processing helix  chain 'A' and resid 1130 through 1136
    Processing helix  chain 'A' and resid 1142 through 1153
    Processing helix  chain 'A' and resid 1155 through 1161
    Processing helix  chain 'A' and resid 1164 through 1168
    Processing helix  chain 'A' and resid 1171 through 1175
    Processing helix  chain 'A' and resid 1178 through 1193
    Processing helix  chain 'A' and resid 1208 through 1223
      removed outlier: 3.929A  pdb=" N   LEU A1214 " --> pdb=" O   ARG A1210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1234 through 1238
    Processing helix  chain 'A' and resid 1257 through 1264
      removed outlier: 3.508A  pdb=" N   ASN A1264 " --> pdb=" O   VAL A1260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1267 through 1276
      removed outlier: 3.563A  pdb=" N   LYS A1271 " --> pdb=" O   SER A1267 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   LEU A1276 " --> pdb=" O   MET A1272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1277 through 1297
    Processing sheet with id=AA1, first strand: chain 'A' and resid 428 through 435
      removed outlier: 6.698A  pdb=" N   GLN A 429 " --> pdb=" O   THR A 416 " (cutoff:3.500A)
      removed outlier: 6.271A  pdb=" N   THR A 416 " --> pdb=" O   GLN A 429 " (cutoff:3.500A)
      removed outlier: 5.224A  pdb=" N   LEU A 431 " --> pdb=" O   ASP A 414 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ILE A 409 " --> pdb=" O   HIS A 472 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   PHE A 415 " --> pdb=" O   GLN A 466 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   GLN A 466 " --> pdb=" O   PHE A 415 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 475 through 478
      removed outlier: 6.473A  pdb=" N   ALA A 476 " --> pdb=" O   LEU A 557 " (cutoff:3.500A)
      removed outlier: 7.400A  pdb=" N   ASP A 559 " --> pdb=" O   ALA A 476 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   VAL A 478 " --> pdb=" O   ASP A 559 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   LEU A 441 " --> pdb=" O   LEU A 589 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   LEU A 440 " --> pdb=" O   GLN A 602 " (cutoff:3.500A)
      removed outlier: 7.881A  pdb=" N   LEU A 604 " --> pdb=" O   LEU A 440 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   ALA A 442 " --> pdb=" O   LEU A 604 " (cutoff:3.500A)
      removed outlier: 7.502A  pdb=" N   LEU A 606 " --> pdb=" O   ALA A 442 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   VAL A 444 " --> pdb=" O   LEU A 606 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   ILE A 603 " --> pdb=" O   LYS A 614 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   LYS A 614 " --> pdb=" O   ILE A 603 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   ILE A 605 " --> pdb=" O   VAL A 612 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 488
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1058 through 1065
      removed outlier: 6.774A  pdb=" N   LYS A1059 " --> pdb=" O   ASN A1047 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   ASN A1047 " --> pdb=" O   LYS A1059 " (cutoff:3.500A)
      removed outlier: 5.174A  pdb=" N   LEU A1061 " --> pdb=" O   ASN A1045 " (cutoff:3.500A)
      removed outlier: 5.574A  pdb=" N   PHE A1043 " --> pdb=" O   TRP A1099 " (cutoff:3.500A)
      removed outlier: 7.154A  pdb=" N   TRP A1099 " --> pdb=" O   PHE A1043 " (cutoff:3.500A)
      removed outlier: 5.128A  pdb=" N   ASN A1045 " --> pdb=" O   LYS A1097 " (cutoff:3.500A)
      removed outlier: 5.003A  pdb=" N   LYS A1097 " --> pdb=" O   ASN A1045 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1117 through 1120
      removed outlier: 6.605A  pdb=" N   LYS A1070 " --> pdb=" O   LYS A1243 " (cutoff:3.500A)
      removed outlier: 7.917A  pdb=" N   MET A1245 " --> pdb=" O   LYS A1070 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   GLY A1072 " --> pdb=" O   MET A1245 " (cutoff:3.500A)
      removed outlier: 7.704A  pdb=" N   LEU A1247 " --> pdb=" O   GLY A1072 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   VAL A1074 " --> pdb=" O   LEU A1247 " (cutoff:3.500A)
      removed outlier: 6.019A  pdb=" N   ILE A1244 " --> pdb=" O   TYR A1255 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   TYR A1255 " --> pdb=" O   ILE A1244 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   VAL A1246 " --> pdb=" O   LYS A1253 " (cutoff:3.500A)

    607 hydrogen bonds defined for protein.
    1761 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: 7.12

  Time building geometry restraints manager: 5.25 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 8227
        1.03 -     1.23: 1128
        1.23 -     1.43: 4018
        1.43 -     1.62: 5182
        1.62 -     1.82: 59
  Bond restraints: 18614
  Sorted by residual:
  bond pdb=" ND1 HIS A 158 "
       pdb=" CE1 HIS A 158 "
    ideal  model  delta    sigma   weight residual
    1.321  1.235  0.086 1.00e-02 1.00e+04 7.42e+01
  bond pdb=" N   TYR A 358 "
       pdb=" H   TYR A 358 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.73e+01
  bond pdb=" CE1 HIS A 158 "
       pdb=" HE1 HIS A 158 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.72e+01
  bond pdb=" N   ILE A 233 "
       pdb=" H   ILE A 233 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.71e+01
  bond pdb=" CE1 PHE A 211 "
       pdb=" HE1 PHE A 211 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.71e+01
  ... (remaining 18609 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.78: 32674
        4.78 -     9.56: 969
        9.56 -    14.34: 21
       14.34 -    19.13: 0
       19.13 -    23.91: 4
  Bond angle restraints: 33668
  Sorted by residual:
  angle pdb=" PB  ATP A1404 "
        pdb=" O3B ATP A1404 "
        pdb=" PG  ATP A1404 "
      ideal   model   delta    sigma   weight residual
     139.87  115.96   23.91 1.00e+00 1.00e+00 5.72e+02
  angle pdb=" PB  ATP A1405 "
        pdb=" O3B ATP A1405 "
        pdb=" PG  ATP A1405 "
      ideal   model   delta    sigma   weight residual
     139.87  116.17   23.70 1.00e+00 1.00e+00 5.62e+02
  angle pdb=" PA  ATP A1404 "
        pdb=" O3A ATP A1404 "
        pdb=" PB  ATP A1404 "
      ideal   model   delta    sigma   weight residual
     136.83  113.83   23.00 1.00e+00 1.00e+00 5.29e+02
  angle pdb=" PA  ATP A1405 "
        pdb=" O3A ATP A1405 "
        pdb=" PB  ATP A1405 "
      ideal   model   delta    sigma   weight residual
     136.83  115.96   20.87 1.00e+00 1.00e+00 4.36e+02
  angle pdb=" C5' ATP A1404 "
        pdb=" O5' ATP A1404 "
        pdb=" PA  ATP A1404 "
      ideal   model   delta    sigma   weight residual
     121.27  109.68   11.59 1.00e+00 1.00e+00 1.34e+02
  ... (remaining 33663 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.63: 8142
       21.63 -    43.25: 311
       43.25 -    64.88: 223
       64.88 -    86.50: 46
       86.50 -   108.13: 2
  Dihedral angle restraints: 8724
    sinusoidal: 4769
      harmonic: 3955
  Sorted by residual:
  dihedral pdb=" CA  ARG A  76 "
           pdb=" C   ARG A  76 "
           pdb=" N   GLU A  77 "
           pdb=" CA  GLU A  77 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.08   30.92     0      5.00e+00 4.00e-02 3.82e+01
  dihedral pdb=" C   PHE A 156 "
           pdb=" N   PHE A 156 "
           pdb=" CA  PHE A 156 "
           pdb=" CB  PHE A 156 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.50   14.90     0      2.50e+00 1.60e-01 3.55e+01
  dihedral pdb=" CA  HIS A  55 "
           pdb=" C   HIS A  55 "
           pdb=" N   LEU A  56 "
           pdb=" CA  LEU A  56 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.39   28.61     0      5.00e+00 4.00e-02 3.27e+01
  ... (remaining 8721 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.149: 1280
       0.149 -    0.298: 17
       0.298 -    0.447: 11
       0.447 -    0.596: 92
       0.596 -    0.745: 64
  Chirality restraints: 1464
  Sorted by residual:
  chirality pdb=" CA  PHE A 156 "
            pdb=" N   PHE A 156 "
            pdb=" C   PHE A 156 "
            pdb=" CB  PHE A 156 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.77    0.74 2.00e-01 2.50e+01 1.39e+01
  chirality pdb=" CB  VAL A 208 "
            pdb=" CA  VAL A 208 "
            pdb=" CG1 VAL A 208 "
            pdb=" CG2 VAL A 208 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -1.91   -0.72 2.00e-01 2.50e+01 1.29e+01
  chirality pdb=" CB  ILE A  84 "
            pdb=" CA  ILE A  84 "
            pdb=" CG1 ILE A  84 "
            pdb=" CG2 ILE A  84 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    1.93    0.71 2.00e-01 2.50e+01 1.27e+01
  ... (remaining 1461 not shown)

  Planarity restraints: 2656
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 216 "   -0.020 2.00e-02 2.50e+03   6.63e-02 1.76e+02
        pdb=" CG  TRP A 216 "    0.060 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 216 "    0.061 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 216 "    0.052 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 216 "    0.023 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 216 "    0.063 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 216 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 216 "    0.046 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 216 "   -0.010 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 216 "    0.027 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 216 "    0.010 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 216 "   -0.210 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 216 "   -0.071 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 216 "    0.018 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 216 "   -0.051 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 216 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  92 "    0.159 2.00e-02 2.50e+03   6.66e-02 1.33e+02
        pdb=" CG  TYR A  92 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  92 "   -0.055 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  92 "   -0.046 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  92 "   -0.041 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  92 "   -0.036 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  92 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A  92 "    0.130 2.00e-02 2.50e+03
        pdb=" HD1 TYR A  92 "   -0.031 2.00e-02 2.50e+03
        pdb=" HD2 TYR A  92 "   -0.031 2.00e-02 2.50e+03
        pdb=" HE1 TYR A  92 "   -0.005 2.00e-02 2.50e+03
        pdb=" HE2 TYR A  92 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A1295 "   -0.112 9.50e-02 1.11e+02   5.80e-02 4.57e+01
        pdb=" NE  ARG A1295 "    0.023 2.00e-02 2.50e+03
        pdb=" CZ  ARG A1295 "   -0.030 2.00e-02 2.50e+03
        pdb=" NH1 ARG A1295 "   -0.065 2.00e-02 2.50e+03
        pdb=" NH2 ARG A1295 "    0.055 2.00e-02 2.50e+03
        pdb="HH11 ARG A1295 "   -0.000 2.00e-02 2.50e+03
        pdb="HH12 ARG A1295 "    0.075 2.00e-02 2.50e+03
        pdb="HH21 ARG A1295 "    0.005 2.00e-02 2.50e+03
        pdb="HH22 ARG A1295 "   -0.058 2.00e-02 2.50e+03
  ... (remaining 2653 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.15: 607
        2.15 -     2.76: 34262
        2.76 -     3.37: 52584
        3.37 -     3.99: 66979
        3.99 -     4.60: 106283
  Nonbonded interactions: 260715
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 270 "
            pdb="HH22 ARG A 385 "
     model   vdw
     1.534 2.450
  nonbonded pdb="HD21 ASN A 196 "
            pdb=" OD1 ASP A 270 "
     model   vdw
     1.597 2.450
  nonbonded pdb=" OE1 GLU A 121 "
            pdb=" HG  SER A 349 "
     model   vdw
     1.611 2.450
  nonbonded pdb=" HG  SER A 259 "
            pdb=" O13 PTY A1403 "
     model   vdw
     1.623 2.450
  nonbonded pdb=" O   ARG A 362 "
            pdb=" HG1 THR A 366 "
     model   vdw
     1.637 2.450
  ... (remaining 260710 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.120
  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:             0.280
  Extract box with map and model:          0.610
  Check model and map are aligned:         0.110
  Set scattering table:                    0.190
  Process input model:                     37.730
  Find NCS groups from input model:        0.150
  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:             0.010
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
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      :  0.020   0.147   9345  Z= 1.015
  Angle     :  1.665  23.907  12669  Z= 1.142
  Chirality :  0.202   0.745   1464
  Planarity :  0.009   0.100   1559
  Dihedral  : 13.416 108.130   3463
  Min Nonbonded Distance : 1.789

Molprobity Statistics.
  All-atom Clashscore : 0.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Cbeta Deviations :  7.93 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.67 (0.23), residues: 1125
  helix: -0.66 (0.16), residues: 753
  sheet:  0.41 (0.52), residues: 84
  loop :  0.53 (0.36), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.006   TRP A 216 
 HIS   0.013   0.002   HIS A1233 
 PHE   0.034   0.004   PHE A 156 
 TYR   0.142   0.008   TYR A  92 
 ARG   0.026   0.002   ARG A1295 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20152 (  607)
  hydrogen bonds       : angle       7.66150 ( 1761)
  covalent geometry    : bond        0.02008 ( 9345)
  covalent geometry    : angle       1.66503 (12669)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 1.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  241 MET cc_start: 0.7562 (tpp) cc_final: 0.7004 (tpt)
REVERT: A  293 LYS cc_start: 0.8339 (mttm) cc_final: 0.7942 (ttpt)
REVERT: A 1018 ASP cc_start: 0.8257 (m-30) cc_final: 0.8055 (t0)
REVERT: A 1131 MET cc_start: 0.8564 (tpt) cc_final: 0.8243 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 193
  average time/residue: 0.7458
  time to fit residues: 182.7949
Evaluate side-chains
  104 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 1.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 95 optimal weight:    0.8980
   chunk 85 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   chunk 57 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 102 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 731 GLN
A 742 GLN
A 994 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.124976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.100355 restraints weight = 34393.666|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 2.12
r_work: 0.3031 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2908 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.2470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9345  Z= 0.160
  Angle     :  0.579   5.603  12669  Z= 0.331
  Chirality :  0.040   0.152   1464
  Planarity :  0.005   0.044   1559
  Dihedral  :  9.943 100.108   1335
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 1.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  :  4.48 %
    Favored  : 95.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.90 (0.24), residues: 1125
  helix:  0.78 (0.18), residues: 766
  sheet:  0.05 (0.56), residues: 78
  loop :  0.65 (0.36), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 711 
 HIS   0.002   0.001   HIS A1060 
 PHE   0.013   0.001   PHE A 993 
 TYR   0.014   0.001   TYR A 339 
 ARG   0.006   0.001   ARG A1012 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07161 (  607)
  hydrogen bonds       : angle       5.33734 ( 1761)
  covalent geometry    : bond        0.00314 ( 9345)
  covalent geometry    : angle       0.57890 (12669)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 116
  time to evaluate  : 1.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  595 GLN cc_start: 0.7800 (mp10) cc_final: 0.7551 (pm20)
REVERT: A 1002 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7757 (mm-30)
REVERT: A 1018 ASP cc_start: 0.8461 (m-30) cc_final: 0.8186 (t0)
REVERT: A 1133 LYS cc_start: 0.8068 (mmtt) cc_final: 0.7471 (tttt)
  outliers start: 5
  outliers final: 2
  residues processed: 117
  average time/residue: 0.6323
  time to fit residues: 96.8693
Evaluate side-chains
  93 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 91
  time to evaluate  : 1.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  815 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0170
   chunk 72 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 104 optimal weight:    0.9990
   overall best weight:    0.7822

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.123931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.101042 restraints weight = 35744.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 1.93
r_work: 0.3097 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2977 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.3367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9345  Z= 0.125
  Angle     :  0.490   5.083  12669  Z= 0.274
  Chirality :  0.038   0.144   1464
  Planarity :  0.004   0.058   1559
  Dihedral  :  8.616  81.524   1335
  Min Nonbonded Distance : 1.891

Molprobity Statistics.
  All-atom Clashscore : 1.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  5.80 %
    Favored  : 93.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  1.69 (0.25), residues: 1125
  helix:  1.55 (0.19), residues: 772
  sheet: -0.36 (0.54), residues: 79
  loop :  0.61 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 711 
 HIS   0.003   0.001   HIS A 710 
 PHE   0.014   0.001   PHE A 993 
 TYR   0.012   0.001   TYR A 737 
 ARG   0.006   0.001   ARG A 350 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05571 (  607)
  hydrogen bonds       : angle       4.69126 ( 1761)
  covalent geometry    : bond        0.00257 ( 9345)
  covalent geometry    : angle       0.49027 (12669)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 100
  time to evaluate  : 1.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  509 LYS cc_start: 0.8634 (ptmt) cc_final: 0.8294 (ttpt)
REVERT: A  711 TRP cc_start: 0.5926 (p-90) cc_final: 0.5706 (p-90)
REVERT: A  823 ASN cc_start: 0.7917 (m-40) cc_final: 0.7571 (m-40)
  outliers start: 7
  outliers final: 4
  residues processed: 106
  average time/residue: 0.5134
  time to fit residues: 75.2706
Evaluate side-chains
  86 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 82
  time to evaluate  : 1.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  292 GLU
Chi-restraints excluded: chain A residue  958 VAL
Chi-restraints excluded: chain A residue  962 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 89 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 112 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9990
   chunk 64 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
A 994 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.120867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.097842 restraints weight = 36722.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.3150 rms_B_bonded: 2.00
r_work: 0.3051 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2938 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.3713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9345  Z= 0.169
  Angle     :  0.503   6.407  12669  Z= 0.283
  Chirality :  0.039   0.143   1464
  Planarity :  0.004   0.039   1559
  Dihedral  :  8.356  88.886   1335
  Min Nonbonded Distance : 1.828

Molprobity Statistics.
  All-atom Clashscore : 2.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  5.80 %
    Favored  : 92.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  1.84 (0.25), residues: 1125
  helix:  1.70 (0.19), residues: 759
  sheet: -0.32 (0.54), residues: 79
  loop :  0.60 (0.37), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 711 
 HIS   0.003   0.001   HIS A 592 
 PHE   0.011   0.001   PHE A 214 
 TYR   0.012   0.001   TYR A 737 
 ARG   0.004   0.000   ARG A 350 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05680 (  607)
  hydrogen bonds       : angle       4.66028 ( 1761)
  covalent geometry    : bond        0.00387 ( 9345)
  covalent geometry    : angle       0.50326 (12669)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 1.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  509 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8401 (ttpt)
REVERT: A  602 GLN cc_start: 0.7412 (mt0) cc_final: 0.7143 (pt0)
REVERT: A  823 ASN cc_start: 0.7962 (m-40) cc_final: 0.7640 (m-40)
  outliers start: 12
  outliers final: 7
  residues processed: 91
  average time/residue: 0.5714
  time to fit residues: 69.7139
Evaluate side-chains
  86 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 78
  time to evaluate  : 1.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  292 GLU
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  509 LYS
Chi-restraints excluded: chain A residue  608 ASP
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain A residue  958 VAL
Chi-restraints excluded: chain A residue  962 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0870
   chunk 1 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 86 optimal weight:    0.7980
   chunk 72 optimal weight:    0.9980
   chunk 108 optimal weight:    3.9990
   chunk 88 optimal weight:    3.9990
   overall best weight:    0.7762

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.123586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.100743 restraints weight = 36538.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 1.99
r_work: 0.3079 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2965 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.3975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9345  Z= 0.114
  Angle     :  0.450   4.966  12669  Z= 0.251
  Chirality :  0.036   0.143   1464
  Planarity :  0.004   0.057   1559
  Dihedral  :  7.601  77.860   1335
  Min Nonbonded Distance : 1.874

Molprobity Statistics.
  All-atom Clashscore : 2.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  6.71 %
    Favored  : 92.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  2.31 (0.25), residues: 1125
  helix:  2.08 (0.19), residues: 753
  sheet: -0.33 (0.55), residues: 79
  loop :  0.78 (0.37), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 711 
 HIS   0.002   0.001   HIS A 798 
 PHE   0.007   0.001   PHE A 574 
 TYR   0.010   0.001   TYR A 737 
 ARG   0.009   0.000   ARG A 350 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04957 (  607)
  hydrogen bonds       : angle       4.38720 ( 1761)
  covalent geometry    : bond        0.00234 ( 9345)
  covalent geometry    : angle       0.45007 (12669)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 1.314 
Fit side-chains
   revert: symmetry clash
REVERT: A  509 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8370 (ttpt)
REVERT: A  602 GLN cc_start: 0.7418 (mt0) cc_final: 0.7175 (pt0)
REVERT: A  823 ASN cc_start: 0.7849 (m-40) cc_final: 0.7553 (m-40)
REVERT: A 1243 LYS cc_start: 0.7838 (mtpt) cc_final: 0.7615 (mttp)
  outliers start: 7
  outliers final: 6
  residues processed: 90
  average time/residue: 0.5189
  time to fit residues: 64.4235
Evaluate side-chains
  88 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 81
  time to evaluate  : 1.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  292 GLU
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  509 LYS
Chi-restraints excluded: chain A residue  958 VAL
Chi-restraints excluded: chain A residue  962 VAL
Chi-restraints excluded: chain A residue 1263 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 86 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   chunk 61 optimal weight:    0.5980
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A1216 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.120457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.097568 restraints weight = 37056.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.3144 rms_B_bonded: 1.99
r_work: 0.3046 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2933 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
moved from start:          0.4039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9345  Z= 0.166
  Angle     :  0.483   5.438  12669  Z= 0.271
  Chirality :  0.038   0.142   1464
  Planarity :  0.004   0.041   1559
  Dihedral  :  7.862  83.156   1335
  Min Nonbonded Distance : 1.797

Molprobity Statistics.
  All-atom Clashscore : 2.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  :  7.02 %
    Favored  : 92.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  2.13 (0.25), residues: 1125
  helix:  1.95 (0.19), residues: 753
  sheet:  0.13 (0.59), residues: 67
  loop :  0.50 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 711 
 HIS   0.002   0.001   HIS A1233 
 PHE   0.010   0.001   PHE A 214 
 TYR   0.012   0.001   TYR A 339 
 ARG   0.005   0.000   ARG A 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05343 (  607)
  hydrogen bonds       : angle       4.46446 ( 1761)
  covalent geometry    : bond        0.00384 ( 9345)
  covalent geometry    : angle       0.48292 (12669)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 84
  time to evaluate  : 1.440 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  509 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8352 (ttpt)
REVERT: A  602 GLN cc_start: 0.7492 (mt0) cc_final: 0.7189 (pt0)
REVERT: A  823 ASN cc_start: 0.7874 (m-40) cc_final: 0.7545 (m-40)
REVERT: A 1243 LYS cc_start: 0.7860 (mtpt) cc_final: 0.7611 (mttp)
  outliers start: 9
  outliers final: 6
  residues processed: 91
  average time/residue: 0.5504
  time to fit residues: 68.4130
Evaluate side-chains
  87 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 1.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  292 GLU
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  509 LYS
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain A residue  958 VAL
Chi-restraints excluded: chain A residue  962 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 83 optimal weight:    1.9990
   chunk 105 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.120790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.098024 restraints weight = 36868.036|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 1.96
r_work: 0.3063 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2950 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.4158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9345  Z= 0.149
  Angle     :  0.470   5.744  12669  Z= 0.263
  Chirality :  0.037   0.144   1464
  Planarity :  0.004   0.047   1559
  Dihedral  :  7.781  82.738   1335
  Min Nonbonded Distance : 1.811

Molprobity Statistics.
  All-atom Clashscore : 2.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  7.83 %
    Favored  : 91.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  2.14 (0.25), residues: 1125
  helix:  1.98 (0.19), residues: 753
  sheet:  0.15 (0.58), residues: 67
  loop :  0.45 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 711 
 HIS   0.003   0.001   HIS A 798 
 PHE   0.009   0.001   PHE A 214 
 TYR   0.011   0.001   TYR A 339 
 ARG   0.006   0.000   ARG A 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05186 (  607)
  hydrogen bonds       : angle       4.42474 ( 1761)
  covalent geometry    : bond        0.00335 ( 9345)
  covalent geometry    : angle       0.47038 (12669)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 1.491 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  509 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8390 (ttpt)
REVERT: A  823 ASN cc_start: 0.7900 (m-40) cc_final: 0.7576 (m-40)
  outliers start: 8
  outliers final: 7
  residues processed: 89
  average time/residue: 0.5560
  time to fit residues: 68.0944
Evaluate side-chains
  90 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 1.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  292 GLU
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  509 LYS
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain A residue  958 VAL
Chi-restraints excluded: chain A residue  962 VAL
Chi-restraints excluded: chain A residue 1263 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 96 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 2 optimal weight:    0.5980
   chunk 43 optimal weight:    0.8980
   chunk 108 optimal weight:    3.9990
   chunk 98 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 18 optimal weight:    0.3980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.123052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.100253 restraints weight = 36708.775|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 1.98
r_work: 0.3086 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2972 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.4334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9345  Z= 0.108
  Angle     :  0.438   5.201  12669  Z= 0.244
  Chirality :  0.036   0.146   1464
  Planarity :  0.004   0.051   1559
  Dihedral  :  7.257  74.228   1335
  Min Nonbonded Distance : 1.845

Molprobity Statistics.
  All-atom Clashscore : 2.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  7.32 %
    Favored  : 91.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  2.45 (0.25), residues: 1125
  helix:  2.24 (0.19), residues: 755
  sheet:  0.15 (0.58), residues: 67
  loop :  0.51 (0.36), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 711 
 HIS   0.003   0.001   HIS A 710 
 PHE   0.008   0.001   PHE A 993 
 TYR   0.009   0.001   TYR A 339 
 ARG   0.007   0.000   ARG A 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04683 (  607)
  hydrogen bonds       : angle       4.23580 ( 1761)
  covalent geometry    : bond        0.00221 ( 9345)
  covalent geometry    : angle       0.43813 (12669)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 1.512 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  509 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8313 (ttpt)
REVERT: A  823 ASN cc_start: 0.7728 (m-40) cc_final: 0.7440 (m-40)
REVERT: A 1236 ASN cc_start: 0.8403 (OUTLIER) cc_final: 0.7881 (p0)
  outliers start: 11
  outliers final: 9
  residues processed: 98
  average time/residue: 0.5691
  time to fit residues: 76.5869
Evaluate side-chains
  95 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 1.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  292 GLU
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  509 LYS
Chi-restraints excluded: chain A residue  608 ASP
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  958 VAL
Chi-restraints excluded: chain A residue  962 VAL
Chi-restraints excluded: chain A residue 1236 ASN
Chi-restraints excluded: chain A residue 1263 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 112 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   chunk 111 optimal weight:    5.9990
   chunk 87 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0010
   chunk 69 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   overall best weight:    1.0790

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

Flipped N/Q/H residues before XYZ refinement:
A 994 GLN
A1216 GLN
A1263 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.121693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.098527 restraints weight = 37053.479|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 2.01
r_work: 0.3065 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2954 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.4377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9345  Z= 0.131
  Angle     :  0.454   5.390  12669  Z= 0.253
  Chirality :  0.037   0.202   1464
  Planarity :  0.004   0.047   1559
  Dihedral  :  7.352  71.234   1335
  Min Nonbonded Distance : 1.806

Molprobity Statistics.
  All-atom Clashscore : 2.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  7.83 %
    Favored  : 90.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  2.40 (0.25), residues: 1125
  helix:  2.20 (0.19), residues: 755
  sheet:  0.23 (0.59), residues: 67
  loop :  0.46 (0.36), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 733 
 HIS   0.004   0.001   HIS A 710 
 PHE   0.009   0.001   PHE A 214 
 TYR   0.010   0.001   TYR A 339 
 ARG   0.007   0.000   ARG A 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04848 (  607)
  hydrogen bonds       : angle       4.28829 ( 1761)
  covalent geometry    : bond        0.00289 ( 9345)
  covalent geometry    : angle       0.45397 (12669)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 1.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  509 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8263 (ttpt)
REVERT: A  602 GLN cc_start: 0.7553 (mt0) cc_final: 0.7303 (pt0)
REVERT: A  823 ASN cc_start: 0.7792 (m-40) cc_final: 0.7488 (m-40)
REVERT: A 1236 ASN cc_start: 0.8408 (OUTLIER) cc_final: 0.7882 (p0)
  outliers start: 12
  outliers final: 9
  residues processed: 92
  average time/residue: 0.5331
  time to fit residues: 66.8158
Evaluate side-chains
  93 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 1.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  292 GLU
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  509 LYS
Chi-restraints excluded: chain A residue  608 ASP
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  958 VAL
Chi-restraints excluded: chain A residue  962 VAL
Chi-restraints excluded: chain A residue 1236 ASN
Chi-restraints excluded: chain A residue 1263 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 90 optimal weight:    4.9990
   chunk 75 optimal weight:    0.9980
   chunk 13 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 29 optimal weight:    0.4980
   chunk 78 optimal weight:    3.9990
   chunk 102 optimal weight:    0.0470
   chunk 105 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.6078

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

Flipped N/Q/H residues before XYZ refinement:
** A1263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.123950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.099608 restraints weight = 35413.103|
|-----------------------------------------------------------------------------|
r_work (start): 0.3172 rms_B_bonded: 2.14
r_work: 0.3066 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2943 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.4452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9345  Z= 0.107
  Angle     :  0.443   5.167  12669  Z= 0.246
  Chirality :  0.037   0.174   1464
  Planarity :  0.004   0.050   1559
  Dihedral  :  7.170  73.435   1335
  Min Nonbonded Distance : 1.829

Molprobity Statistics.
  All-atom Clashscore : 2.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  7.83 %
    Favored  : 90.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  2.48 (0.25), residues: 1125
  helix:  2.27 (0.19), residues: 756
  sheet:  0.26 (0.59), residues: 67
  loop :  0.47 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 733 
 HIS   0.003   0.001   HIS A 152 
 PHE   0.007   0.001   PHE A 352 
 TYR   0.009   0.001   TYR A 339 
 ARG   0.005   0.000   ARG A 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04633 (  607)
  hydrogen bonds       : angle       4.22516 ( 1761)
  covalent geometry    : bond        0.00219 ( 9345)
  covalent geometry    : angle       0.44253 (12669)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 1.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  509 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8163 (ttpt)
REVERT: A  823 ASN cc_start: 0.7629 (m-40) cc_final: 0.7340 (m-40)
REVERT: A 1236 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.7922 (p0)
  outliers start: 12
  outliers final: 10
  residues processed: 91
  average time/residue: 0.5582
  time to fit residues: 70.3878
Evaluate side-chains
  94 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 1.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  292 GLU
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  509 LYS
Chi-restraints excluded: chain A residue  608 ASP
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  953 ASP
Chi-restraints excluded: chain A residue  958 VAL
Chi-restraints excluded: chain A residue  962 VAL
Chi-restraints excluded: chain A residue 1236 ASN
Chi-restraints excluded: chain A residue 1263 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 94 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 111 optimal weight:    0.4980
   chunk 19 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9980
   chunk 91 optimal weight:    0.8980
   chunk 105 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A1263 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.123082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.098951 restraints weight = 35366.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.3099 rms_B_bonded: 2.11
r_work: 0.2995 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2874 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.4472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9345  Z= 0.129
  Angle     :  0.451   5.371  12669  Z= 0.252
  Chirality :  0.037   0.154   1464
  Planarity :  0.004   0.049   1559
  Dihedral  :  7.236  70.840   1335
  Min Nonbonded Distance : 1.810

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  8.04 %
    Favored  : 90.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  2.43 (0.25), residues: 1125
  helix:  2.22 (0.19), residues: 756
  sheet:  0.52 (0.65), residues: 57
  loop :  0.41 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 995 
 HIS   0.003   0.001   HIS A 798 
 PHE   0.009   0.001   PHE A 214 
 TYR   0.010   0.001   TYR A 339 
 ARG   0.006   0.000   ARG A 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04799 (  607)
  hydrogen bonds       : angle       4.26584 ( 1761)
  covalent geometry    : bond        0.00284 ( 9345)
  covalent geometry    : angle       0.45106 (12669)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9051.32 seconds
wall clock time: 155 minutes 37.02 seconds (9337.02 seconds total)