Starting phenix.real_space_refine
on Thu Jul  2 19:11:59 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8bwr_16295/07_2026/8bwr_16295.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8bwr_16295/07_2026/8bwr_16295.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8bwr_16295/07_2026/8bwr_16295.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8bwr_16295/07_2026/8bwr_16295.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8bwr_16295/07_2026/8bwr_16295.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8bwr_16295/07_2026/8bwr_16295.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8bwr_16295/07_2026/8bwr_16295.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8bwr_16295/07_2026/8bwr_16295.map"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.031
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      43      5.16       5
     C    6221      2.51       5
     N    1602      2.21       5
     O    1704      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9570
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9545
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1195, 9545
          Classifications: {'peptide': 1195}
          Link IDs: {'PTRANS': 37, 'TRANS': 1157}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'P2E': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.11, per 1000 atoms: 0.22
  Number of scatterers: 9570
  At special positions: 0
  Unit cell: (74.048, 108.992, 143.936, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      43     16.00
     O    1704      8.00
     N    1602      7.00
     C    6221      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.93
  Conformation dependent library (CDL) restraints added in 343.7 milliseconds
  

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2266

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 4 sheets defined
      73.6% alpha, 6.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 15
    Processing helix  chain 'A' and resid 19 through 24
      removed outlier: 3.693A  pdb=" N   PHE A  23 " --> pdb=" O   CYS A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 28 through 37
      removed outlier: 3.771A  pdb=" N   LYS A  32 " --> pdb=" O   ASN A  28 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   LYS A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 51
    Processing helix  chain 'A' and resid 52 through 74
      removed outlier: 3.627A  pdb=" N   PHE A  63 " --> pdb=" O   GLU A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 122
      removed outlier: 5.131A  pdb=" N   LYS A  90 " --> pdb=" O   LYS A  86 " (cutoff:3.500A)
      removed outlier: 5.165A  pdb=" N   SER A  91 " --> pdb=" O   CYS A  87 " (cutoff:3.500A)
      removed outlier: 5.165A  pdb=" N   VAL A  94 " --> pdb=" O   LYS A  90 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   LEU A  95 " --> pdb=" O   SER A  91 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   GLY A  96 " --> pdb=" O   TYR A  92 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   PHE A  98 " --> pdb=" O   VAL A  94 " (cutoff:3.500A)
      Proline residue:  A 110  - end of helix
      removed outlier: 3.604A  pdb=" N   PHE A 120 " --> pdb=" O   ILE A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 150
      removed outlier: 3.600A  pdb=" N   LEU A 148 " --> pdb=" O   CYS A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 180
      removed outlier: 3.856A  pdb=" N   TYR A 157 " --> pdb=" O   HIS A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 188
    Processing helix  chain 'A' and resid 190 through 200
    Processing helix  chain 'A' and resid 203 through 210
      removed outlier: 3.982A  pdb=" N   GLN A 207 " --> pdb=" O   ASN A 203 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   THR A 209 " --> pdb=" O   PHE A 205 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   VAL A 210 " --> pdb=" O   ASP A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 234
      Proline residue:  A 219  - end of helix
    Processing helix  chain 'A' and resid 236 through 290
      removed outlier: 4.141A  pdb=" N   GLY A 240 " --> pdb=" O   SER A 236 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   VAL A 243 " --> pdb=" O   ALA A 239 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   LEU A 248 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
      Proline residue:  A 249  - end of helix
      removed outlier: 3.528A  pdb=" N   LYS A 256 " --> pdb=" O   SER A 252 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   THR A 267 " --> pdb=" O   SER A 263 " (cutoff:3.500A)
      removed outlier: 4.866A  pdb=" N   PHE A 268 " --> pdb=" O   LYS A 264 " (cutoff:3.500A)
      removed outlier: 5.735A  pdb=" N   ARG A 284 " --> pdb=" O   ILE A 280 " (cutoff:3.500A)
      removed outlier: 5.917A  pdb=" N   ILE A 285 " --> pdb=" O   THR A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 342
      removed outlier: 3.784A  pdb=" N   LYS A 309 " --> pdb=" O   LYS A 305 " (cutoff:3.500A)
      removed outlier: 4.622A  pdb=" N   ASN A 320 " --> pdb=" O   LEU A 316 " (cutoff:3.500A)
      removed outlier: 5.352A  pdb=" N   SER A 328 " --> pdb=" O   PHE A 324 " (cutoff:3.500A)
      removed outlier: 4.856A  pdb=" N   LYS A 329 " --> pdb=" O   PHE A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 367
      removed outlier: 4.151A  pdb=" N   LEU A 363 " --> pdb=" O   GLY A 359 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   THR A 364 " --> pdb=" O   ALA A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 391
      removed outlier: 3.552A  pdb=" N   VAL A 381 " --> pdb=" O   SER A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 452
      removed outlier: 4.019A  pdb=" N   SER A 452 " --> pdb=" O   ALA A 449 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 449 through 452'
    Processing helix  chain 'A' and resid 453 through 459
    Processing helix  chain 'A' and resid 488 through 495
    Processing helix  chain 'A' and resid 500 through 511
    Processing helix  chain 'A' and resid 512 through 521
      removed outlier: 3.649A  pdb=" N   ASP A 516 " --> pdb=" O   ALA A 512 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   LEU A 519 " --> pdb=" O   LYS A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 529 through 533
    Processing helix  chain 'A' and resid 536 through 552
      removed outlier: 3.652A  pdb=" N   LEU A 545 " --> pdb=" O   ALA A 541 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 562 through 566
    Processing helix  chain 'A' and resid 567 through 574
    Processing helix  chain 'A' and resid 593 through 598
    Processing helix  chain 'A' and resid 616 through 620
    Processing helix  chain 'A' and resid 697 through 707
      removed outlier: 4.164A  pdb=" N   TYR A 701 " --> pdb=" O   GLY A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 712 through 745
      removed outlier: 3.771A  pdb=" N   ASP A 732 " --> pdb=" O   TYR A 728 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LEU A 745 " --> pdb=" O   LYS A 741 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 760 through 808
      removed outlier: 4.006A  pdb=" N   GLY A 766 " --> pdb=" O   ASN A 762 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   PHE A 787 " --> pdb=" O   SER A 783 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LEU A 806 " --> pdb=" O   PHE A 802 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 809 through 816
      removed outlier: 4.063A  pdb=" N   PHE A 813 " --> pdb=" O   PRO A 809 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 817 through 827
      removed outlier: 3.564A  pdb=" N   ILE A 821 " --> pdb=" O   PRO A 817 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   ARG A 824 " --> pdb=" O   ARG A 820 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 827 through 835
      removed outlier: 3.806A  pdb=" N   LEU A 832 " --> pdb=" O   ASP A 828 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 835 through 861
      removed outlier: 3.693A  pdb=" N   GLN A 849 " --> pdb=" O   GLN A 845 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 864 through 910
      removed outlier: 3.597A  pdb=" N   LEU A 868 " --> pdb=" O   ILE A 864 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   VAL A 869 " --> pdb=" O   ALA A 865 " (cutoff:3.500A)
      Proline residue:  A 870  - end of helix
      removed outlier: 3.754A  pdb=" N   THR A 885 " --> pdb=" O   TYR A 881 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   ASP A 888 " --> pdb=" O   GLU A 884 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   SER A 898 " --> pdb=" O   SER A 894 " (cutoff:3.500A)
      Proline residue:  A 899  - end of helix
    Processing helix  chain 'A' and resid 910 through 917
    Processing helix  chain 'A' and resid 919 through 970
      removed outlier: 4.722A  pdb=" N   ILE A 955 " --> pdb=" O   ARG A 951 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 975 through 1018
      removed outlier: 3.687A  pdb=" N   GLY A 980 " --> pdb=" O   ALA A 976 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   THR A 988 " --> pdb=" O   SER A 984 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   MET A 990 " --> pdb=" O   ALA A 986 " (cutoff:3.500A)
      removed outlier: 4.870A  pdb=" N   GLY A 991 " --> pdb=" O   LEU A 987 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   MET A 992 " --> pdb=" O   THR A 988 " (cutoff:3.500A)
      removed outlier: 5.369A  pdb=" N   GLN A 994 " --> pdb=" O   MET A 990 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   TRP A 995 " --> pdb=" O   GLY A 991 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   VAL A 997 " --> pdb=" O   PHE A 993 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   ILE A1008 " --> pdb=" O   GLU A1004 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   SER A1009 " --> pdb=" O   ASN A1005 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   VAL A1010 " --> pdb=" O   MET A1006 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   TYR A1016 " --> pdb=" O   ARG A1012 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   THR A1017 " --> pdb=" O   VAL A1013 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   ASP A1018 " --> pdb=" O   ILE A1014 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1034 through 1038
      removed outlier: 3.894A  pdb=" N   GLU A1038 " --> pdb=" O   TRP A1035 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1076 through 1089
      removed outlier: 5.175A  pdb=" N   SER A1082 " --> pdb=" O   GLY A1078 " (cutoff:3.500A)
      removed outlier: 4.867A  pdb=" N   SER A1083 " --> pdb=" O   ALA A1079 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   LEU A1084 " --> pdb=" O   GLY A1080 " (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 1160
    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 1194
    Processing helix  chain 'A' and resid 1202 through 1207
      removed outlier: 3.671A  pdb=" N   ALA A1205 " --> pdb=" O   GLU A1202 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   ASN A1206 " --> pdb=" O   ALA A1203 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   VAL A1207 " --> pdb=" O   THR A1204 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1202 through 1207'
    Processing helix  chain 'A' and resid 1208 through 1223
    Processing helix  chain 'A' and resid 1234 through 1238
    Processing helix  chain 'A' and resid 1248 through 1251
    Processing helix  chain 'A' and resid 1257 through 1264
    Processing helix  chain 'A' and resid 1267 through 1275
    Processing helix  chain 'A' and resid 1276 through 1278
      No H-bonds generated for 'chain 'A' and resid 1276 through 1278'
    Processing helix  chain 'A' and resid 1279 through 1292
      removed outlier: 3.618A  pdb=" N   ALA A1283 " --> pdb=" O   ALA A1279 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   VAL A1291 " --> pdb=" O   THR A1287 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   TYR A1292 " --> pdb=" O   ALA A1288 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 431 through 435
      removed outlier: 5.330A  pdb=" N   LEU A 431 " --> pdb=" O   ASP A 414 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   VAL A 410 " --> pdb=" O   VAL A 435 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 475 through 478
      removed outlier: 6.186A  pdb=" N   TYR A 556 " --> pdb=" O   ILE A 588 " (cutoff:3.500A)
      removed outlier: 7.433A  pdb=" N   VAL A 590 " --> pdb=" O   TYR A 556 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   LEU A 558 " --> pdb=" O   VAL A 590 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   LYS A 607 " --> pdb=" O   MET A 611 " (cutoff:3.500A)
      removed outlier: 5.205A  pdb=" N   MET A 611 " --> pdb=" O   LYS A 607 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1056 through 1065
      removed outlier: 6.583A  pdb=" N   VAL A1057 " --> pdb=" O   MET A1049 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   MET A1049 " --> pdb=" O   VAL A1057 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   LYS A1059 " --> pdb=" O   ASN A1047 " (cutoff:3.500A)
      removed outlier: 5.782A  pdb=" N   ASN A1047 " --> pdb=" O   LYS A1059 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   LEU A1061 " --> pdb=" O   ASN A1045 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   VAL A1046 " --> pdb=" O   GLU A1095 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   GLU A1095 " --> pdb=" O   VAL A1046 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1117 through 1120
      removed outlier: 6.026A  pdb=" N   SER A1118 " --> pdb=" O   ILE A1199 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   LYS A1243 " --> pdb=" O   LYS A1070 " (cutoff:3.500A)

    627 hydrogen bonds defined for protein.
    1815 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.76

  Time building geometry restraints manager: 1.21 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1550
        1.32 -     1.44: 2579
        1.44 -     1.56: 5575
        1.56 -     1.69: 0
        1.69 -     1.81: 70
  Bond restraints: 9774
  Sorted by residual:
  bond pdb=" C7  P2E A1401 "
       pdb=" C8  P2E A1401 "
    ideal  model  delta    sigma   weight residual
    1.529  1.480  0.049 2.00e-02 2.50e+03 6.03e+00
  bond pdb=" CB  PHE A 843 "
       pdb=" CG  PHE A 843 "
    ideal  model  delta    sigma   weight residual
    1.502  1.451  0.051 2.30e-02 1.89e+03 4.86e+00
  bond pdb=" CB  PHE A 336 "
       pdb=" CG  PHE A 336 "
    ideal  model  delta    sigma   weight residual
    1.502  1.452  0.050 2.30e-02 1.89e+03 4.82e+00
  bond pdb=" CB  TRP A 291 "
       pdb=" CG  TRP A 291 "
    ideal  model  delta    sigma   weight residual
    1.498  1.430  0.068 3.10e-02 1.04e+03 4.76e+00
  bond pdb=" CB  PHE A 802 "
       pdb=" CG  PHE A 802 "
    ideal  model  delta    sigma   weight residual
    1.502  1.453  0.049 2.30e-02 1.89e+03 4.56e+00
  ... (remaining 9769 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.03: 12686
        2.03 -     4.06: 479
        4.06 -     6.09: 58
        6.09 -     8.12: 16
        8.12 -    10.15: 5
  Bond angle restraints: 13244
  Sorted by residual:
  angle pdb=" N   ASN A  28 "
        pdb=" CA  ASN A  28 "
        pdb=" C   ASN A  28 "
      ideal   model   delta    sigma   weight residual
     109.81  117.75   -7.94 2.21e+00 2.05e-01 1.29e+01
  angle pdb=" C   LEU A  27 "
        pdb=" N   ASN A  28 "
        pdb=" CA  ASN A  28 "
      ideal   model   delta    sigma   weight residual
     121.80  129.95   -8.15 2.44e+00 1.68e-01 1.11e+01
  angle pdb=" N   PHE A 205 "
        pdb=" CA  PHE A 205 "
        pdb=" C   PHE A 205 "
      ideal   model   delta    sigma   weight residual
     111.82  115.57   -3.75 1.16e+00 7.43e-01 1.04e+01
  angle pdb=" CA  LEU A 357 "
        pdb=" CB  LEU A 357 "
        pdb=" CG  LEU A 357 "
      ideal   model   delta    sigma   weight residual
     116.30  106.15   10.15 3.50e+00 8.16e-02 8.41e+00
  angle pdb=" CA  TYR A 881 "
        pdb=" CB  TYR A 881 "
        pdb=" CG  TYR A 881 "
      ideal   model   delta    sigma   weight residual
     113.90  118.81   -4.91 1.80e+00 3.09e-01 7.43e+00
  ... (remaining 13239 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.56: 5348
       17.56 -    35.12: 382
       35.12 -    52.68: 74
       52.68 -    70.24: 19
       70.24 -    87.80: 8
  Dihedral angle restraints: 5831
    sinusoidal: 2337
      harmonic: 3494
  Sorted by residual:
  dihedral pdb=" CA  ASP A 834 "
           pdb=" C   ASP A 834 "
           pdb=" N   LEU A 835 "
           pdb=" CA  LEU A 835 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.64  -29.36     0      5.00e+00 4.00e-02 3.45e+01
  dihedral pdb=" CA  VAL A1057 "
           pdb=" C   VAL A1057 "
           pdb=" N   LEU A1058 "
           pdb=" CA  LEU A1058 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.98   28.02     0      5.00e+00 4.00e-02 3.14e+01
  dihedral pdb=" CA  ARG A  37 "
           pdb=" C   ARG A  37 "
           pdb=" N   ARG A  38 "
           pdb=" CA  ARG A  38 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.85   27.15     0      5.00e+00 4.00e-02 2.95e+01
  ... (remaining 5828 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 936
       0.044 -    0.088: 448
       0.088 -    0.131: 131
       0.131 -    0.175: 19
       0.175 -    0.219: 7
  Chirality restraints: 1541
  Sorted by residual:
  chirality pdb=" C15 P2E A1401 "
            pdb=" C14 P2E A1401 "
            pdb=" C16 P2E A1401 "
            pdb=" O5  P2E A1401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.23    2.44   -0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CA  HIS A 158 "
            pdb=" N   HIS A 158 "
            pdb=" C   HIS A 158 "
            pdb=" CB  HIS A 158 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" CA  PRO A 110 "
            pdb=" N   PRO A 110 "
            pdb=" C   PRO A 110 "
            pdb=" CB  PRO A 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.53    0.19 2.00e-01 2.50e+01 9.28e-01
  ... (remaining 1538 not shown)

  Planarity restraints: 1644
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 358 "    0.006 2.00e-02 2.50e+03   2.16e-02 9.29e+00
        pdb=" CG  TYR A 358 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 358 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 358 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 358 "    0.029 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 358 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 358 "    0.031 2.00e-02 2.50e+03
        pdb=" OH  TYR A 358 "   -0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 547 "    0.217 9.50e-02 1.11e+02   9.76e-02 6.79e+00
        pdb=" NE  ARG A 547 "   -0.019 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 547 "    0.015 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 547 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 547 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 782 "   -0.226 9.50e-02 1.11e+02   1.02e-01 6.42e+00
        pdb=" NE  ARG A 782 "    0.015 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 782 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 782 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 782 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 1641 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1356
        2.74 -     3.28: 10807
        3.28 -     3.82: 15956
        3.82 -     4.36: 19572
        4.36 -     4.90: 31589
  Nonbonded interactions: 79280
  Sorted by model distance:
  nonbonded pdb=" O   LYS A 498 "
            pdb=" OH  TYR A 550 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" O   ILE A 223 "
            pdb=" OG1 THR A 226 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" NH1 ARG A1076 "
            pdb=" OD1 ASP A1248 "
     model   vdw
     2.274 3.120
  nonbonded pdb=" O   ARG A1234 "
            pdb=" OG1 THR A1237 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" O   ALA A 379 "
            pdb=" OG  SER A 382 "
     model   vdw
     2.291 3.040
  ... (remaining 79275 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 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:             5.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     10.340
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
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      :  0.010   0.068   9774  Z= 0.428
  Angle     :  0.933  10.148  13244  Z= 0.499
  Chirality :  0.053   0.219   1541
  Planarity :  0.008   0.102   1644
  Dihedral  : 13.540  87.802   3565
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  3.74 %
    Favored  : 95.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.63 (0.22), residues: 1187
  helix: -1.43 (0.15), residues: 723
  sheet:  0.25 (0.49), residues: 80
  loop : -0.18 (0.33), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.003   ARG A 167 
 TYR   0.032   0.004   TYR A 358 
 PHE   0.034   0.004   PHE A 336 
 TRP   0.022   0.003   TRP A1025 
 HIS   0.015   0.002   HIS A 798 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00979 /  0.43 ( 9774)
  covalent geometry    : angle       0.93300 /  0.50 (13244)
  hydrogen bonds       : bond        0.23996 / 16.06 (  627)
  hydrogen bonds       : angle       8.82135 /  6.38 ( 1815)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 237
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 TRP cc_start: 0.5585 (OUTLIER) cc_final: 0.5009 (t-100)
REVERT: A   44 MET cc_start: 0.8220 (ptp) cc_final: 0.7446 (ptp)
REVERT: A  143 PHE cc_start: 0.8136 (m-10) cc_final: 0.7274 (t80)
REVERT: A  146 LEU cc_start: 0.7612 (mm) cc_final: 0.7382 (mm)
REVERT: A  167 ARG cc_start: 0.8573 (ttp80) cc_final: 0.8322 (ttt-90)
REVERT: A  201 ASP cc_start: 0.8801 (t0) cc_final: 0.8545 (t0)
REVERT: A  221 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7959 (tp-100)
REVERT: A  258 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7916 (p90)
REVERT: A  278 GLU cc_start: 0.8408 (mt-10) cc_final: 0.7923 (mm-30)
REVERT: A  309 LYS cc_start: 0.9207 (mttp) cc_final: 0.8895 (mttp)
REVERT: A  312 ARG cc_start: 0.8548 (ttp-110) cc_final: 0.8078 (tpt170)
REVERT: A  336 PHE cc_start: 0.8580 (m-80) cc_final: 0.8266 (m-80)
REVERT: A  352 PHE cc_start: 0.7713 (m-80) cc_final: 0.7401 (m-80)
REVERT: A  363 LEU cc_start: 0.8541 (mm) cc_final: 0.8261 (mt)
REVERT: A  368 PHE cc_start: 0.8883 (m-10) cc_final: 0.8635 (m-80)
REVERT: A  387 GLN cc_start: 0.9159 (tt0) cc_final: 0.8753 (tt0)
REVERT: A  505 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8218 (pt0)
REVERT: A  711 TRP cc_start: 0.7228 (p-90) cc_final: 0.6979 (t-100)
REVERT: A  712 ILE cc_start: 0.7954 (mm) cc_final: 0.7450 (mm)
REVERT: A  741 LYS cc_start: 0.8634 (mmmt) cc_final: 0.8394 (tppt)
REVERT: A  744 MET cc_start: 0.8871 (mpm) cc_final: 0.8648 (mpp)
REVERT: A  908 LEU cc_start: 0.9316 (tp) cc_final: 0.9058 (pp)
REVERT: A  925 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8590 (tp30)
REVERT: A  970 LEU cc_start: 0.9396 (mt) cc_final: 0.9173 (mp)
REVERT: A 1011 GLU cc_start: 0.7972 (tt0) cc_final: 0.7669 (tm-30)
REVERT: A 1043 PHE cc_start: 0.9336 (m-80) cc_final: 0.8977 (m-80)
REVERT: A 1217 LYS cc_start: 0.9566 (tttt) cc_final: 0.9221 (ttpp)
REVERT: A 1238 ILE cc_start: 0.9484 (pt) cc_final: 0.9236 (pt)
REVERT: A 1245 MET cc_start: 0.9281 (mtp) cc_final: 0.8893 (mtt)
  outliers start: 10
  outliers final: 3
  residues processed: 244
  average time/residue: 0.1167
  time to fit residues: 38.3103
Evaluate side-chains
  158 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 152
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 TRP
Chi-restraints excluded: chain A residue  221 GLN
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  922 ARG
Chi-restraints excluded: chain A residue 1010 VAL
Chi-restraints excluded: chain A residue 1248 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:    0.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    4.9990
   chunk 117 optimal weight:    0.9990
   overall best weight:    0.9586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 122 ASN
A 203 ASN
A 703 ASN
A 903 HIS
** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.149343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.109970 restraints weight = 21890.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.110126 restraints weight = 13306.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.111043 restraints weight = 10212.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.111669 restraints weight = 8412.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.111848 restraints weight = 8035.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.3169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9774  Z= 0.168
  Angle     :  0.648   7.078  13244  Z= 0.344
  Chirality :  0.043   0.241   1541
  Planarity :  0.004   0.046   1644
  Dihedral  :  6.578  58.509   1310
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  :  9.31 %
    Favored  : 87.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.66 (0.24), residues: 1187
  helix:  0.67 (0.18), residues: 760
  sheet:  0.51 (0.52), residues: 82
  loop :  0.19 (0.37), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 503 
 TYR   0.014   0.002   TYR A  92 
 PHE   0.016   0.002   PHE A1048 
 TRP   0.017   0.001   TRP A  89 
 HIS   0.006   0.001   HIS A 798 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00364 /  0.17 ( 9774)
  covalent geometry    : angle       0.64787 /  0.34 (13244)
  hydrogen bonds       : bond        0.05297 /  3.55 (  627)
  hydrogen bonds       : angle       5.39880 /  3.92 ( 1815)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 191
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 TRP cc_start: 0.5154 (OUTLIER) cc_final: 0.4530 (t-100)
REVERT: A  143 PHE cc_start: 0.8110 (m-10) cc_final: 0.7360 (t80)
REVERT: A  201 ASP cc_start: 0.8599 (t0) cc_final: 0.8309 (t0)
REVERT: A  309 LYS cc_start: 0.8903 (mttp) cc_final: 0.8506 (mtpt)
REVERT: A  363 LEU cc_start: 0.8804 (mm) cc_final: 0.8419 (mt)
REVERT: A  849 GLN cc_start: 0.8688 (mm-40) cc_final: 0.8297 (mm-40)
REVERT: A  873 ILE cc_start: 0.8958 (mm) cc_final: 0.8755 (mt)
REVERT: A  890 LYS cc_start: 0.9515 (OUTLIER) cc_final: 0.9300 (mtmm)
REVERT: A  911 LEU cc_start: 0.9269 (mt) cc_final: 0.9052 (mt)
REVERT: A  915 ARG cc_start: 0.9013 (ptp-110) cc_final: 0.8649 (ptp90)
REVERT: A  921 GLU cc_start: 0.8676 (pm20) cc_final: 0.8428 (pm20)
REVERT: A 1131 MET cc_start: 0.8805 (mmm) cc_final: 0.8581 (mmt)
REVERT: A 1134 ASN cc_start: 0.8612 (OUTLIER) cc_final: 0.7861 (t0)
  outliers start: 30
  outliers final: 13
  residues processed: 211
  average time/residue: 0.1001
  time to fit residues: 29.5778
Evaluate side-chains
  151 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 135
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   26 TRP
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  374 GLU
Chi-restraints excluded: chain A residue  759 LEU
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  775 THR
Chi-restraints excluded: chain A residue  866 ILE
Chi-restraints excluded: chain A residue  890 LYS
Chi-restraints excluded: chain A residue  955 ILE
Chi-restraints excluded: chain A residue  979 VAL
Chi-restraints excluded: chain A residue 1010 VAL
Chi-restraints excluded: chain A residue 1071 VAL
Chi-restraints excluded: chain A residue 1091 LEU
Chi-restraints excluded: chain A residue 1134 ASN
Chi-restraints excluded: chain A residue 1197 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 116 optimal weight:    6.9990
   chunk 38 optimal weight:    0.4980
   chunk 84 optimal weight:    0.5980
   chunk 90 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 108 optimal weight:    0.6980
   chunk 92 optimal weight:    0.3980
   chunk 111 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1233 HIS ** 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 = 0.4093 r_free = 0.4093 target = 0.149324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.109654 restraints weight = 21942.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.108318 restraints weight = 14895.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.109888 restraints weight = 10785.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.111222 restraints weight = 8448.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.111332 restraints weight = 7325.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.4202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9774  Z= 0.136
  Angle     :  0.608  10.860  13244  Z= 0.313
  Chirality :  0.041   0.376   1541
  Planarity :  0.003   0.047   1644
  Dihedral  :  5.493  56.932   1299
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 13.05 %
    Favored  : 83.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.13 (0.24), residues: 1187
  helix:  1.10 (0.19), residues: 764
  sheet:  0.77 (0.53), residues: 81
  loop :  0.16 (0.36), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 262 
 TYR   0.013   0.001   TYR A1292 
 PHE   0.034   0.002   PHE A 352 
 TRP   0.026   0.001   TRP A1147 
 HIS   0.009   0.001   HIS A1233 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.14 ( 9774)
  covalent geometry    : angle       0.60818 /  0.31 (13244)
  hydrogen bonds       : bond        0.04608 /  3.11 (  627)
  hydrogen bonds       : angle       4.82111 /  3.50 ( 1815)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 173
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 TRP cc_start: 0.5068 (OUTLIER) cc_final: 0.4371 (t-100)
REVERT: A  143 PHE cc_start: 0.8241 (m-10) cc_final: 0.7472 (t80)
REVERT: A  201 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.8190 (t0)
REVERT: A  352 PHE cc_start: 0.7818 (m-80) cc_final: 0.7592 (m-80)
REVERT: A  849 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8012 (mt0)
REVERT: A  915 ARG cc_start: 0.9095 (ptp-110) cc_final: 0.8552 (mtt-85)
REVERT: A  921 GLU cc_start: 0.8644 (pm20) cc_final: 0.8431 (pm20)
REVERT: A  922 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7954 (mmm-85)
REVERT: A 1134 ASN cc_start: 0.8668 (OUTLIER) cc_final: 0.7766 (t0)
REVERT: A 1270 TYR cc_start: 0.8621 (t80) cc_final: 0.8380 (t80)
  outliers start: 32
  outliers final: 13
  residues processed: 190
  average time/residue: 0.0928
  time to fit residues: 25.4939
Evaluate side-chains
  158 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 141
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   26 TRP
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  201 ASP
Chi-restraints excluded: chain A residue  583 HIS
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  866 ILE
Chi-restraints excluded: chain A residue  913 THR
Chi-restraints excluded: chain A residue  922 ARG
Chi-restraints excluded: chain A residue  955 ILE
Chi-restraints excluded: chain A residue  963 VAL
Chi-restraints excluded: chain A residue 1010 VAL
Chi-restraints excluded: chain A residue 1091 LEU
Chi-restraints excluded: chain A residue 1119 ILE
Chi-restraints excluded: chain A residue 1134 ASN
Chi-restraints excluded: chain A residue 1159 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 59 optimal weight:   10.0000
   chunk 109 optimal weight:    6.9990
   chunk 105 optimal weight:    9.9990
   chunk 21 optimal weight:    0.7980
   chunk 102 optimal weight:    0.1980
   chunk 30 optimal weight:    2.9990
   chunk 107 optimal weight:    3.9990
   chunk 61 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   chunk 103 optimal weight:    0.8980
   chunk 62 optimal weight:    3.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 602 GLN
** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1233 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.148259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.110141 restraints weight = 21925.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.110481 restraints weight = 12397.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.111444 restraints weight = 9659.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.111825 restraints weight = 7451.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.111865 restraints weight = 7202.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.4754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9774  Z= 0.137
  Angle     :  0.611  11.749  13244  Z= 0.312
  Chirality :  0.042   0.381   1541
  Planarity :  0.003   0.045   1644
  Dihedral  :  5.293  57.567   1299
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 15.16 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.24), residues: 1187
  helix:  1.27 (0.19), residues: 765
  sheet:  0.96 (0.54), residues: 81
  loop :  0.11 (0.36), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1132 
 TYR   0.015   0.001   TYR A1292 
 PHE   0.033   0.002   PHE A 352 
 TRP   0.026   0.001   TRP A  89 
 HIS   0.005   0.001   HIS A1233 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00303 /  0.14 ( 9774)
  covalent geometry    : angle       0.61135 /  0.31 (13244)
  hydrogen bonds       : bond        0.04310 /  2.88 (  627)
  hydrogen bonds       : angle       4.64574 /  3.38 ( 1815)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 154
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8135 (tt)
REVERT: A   26 TRP cc_start: 0.4952 (OUTLIER) cc_final: 0.4153 (t-100)
REVERT: A  352 PHE cc_start: 0.7842 (m-80) cc_final: 0.7621 (m-80)
REVERT: A  849 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8095 (mt0)
REVERT: A  915 ARG cc_start: 0.9043 (ptp-110) cc_final: 0.8334 (mtt-85)
REVERT: A 1134 ASN cc_start: 0.8445 (OUTLIER) cc_final: 0.7736 (t0)
REVERT: A 1146 LEU cc_start: 0.8754 (mt) cc_final: 0.8464 (mm)
REVERT: A 1166 MET cc_start: 0.7474 (mpp) cc_final: 0.7168 (pmm)
  outliers start: 31
  outliers final: 20
  residues processed: 173
  average time/residue: 0.0963
  time to fit residues: 23.6960
Evaluate side-chains
  160 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 137
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   26 TRP
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  583 HIS
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  772 THR
Chi-restraints excluded: chain A residue  775 THR
Chi-restraints excluded: chain A residue  866 ILE
Chi-restraints excluded: chain A residue  913 THR
Chi-restraints excluded: chain A residue  922 ARG
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue  955 ILE
Chi-restraints excluded: chain A residue 1010 VAL
Chi-restraints excluded: chain A residue 1084 LEU
Chi-restraints excluded: chain A residue 1091 LEU
Chi-restraints excluded: chain A residue 1119 ILE
Chi-restraints excluded: chain A residue 1134 ASN
Chi-restraints excluded: chain A residue 1268 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 77 optimal weight:    0.8980
   chunk 117 optimal weight:    0.4980
   chunk 8 optimal weight:    3.9990
   chunk 97 optimal weight:    0.9990
   chunk 81 optimal weight:    2.9990
   chunk 54 optimal weight:   30.0000
   chunk 45 optimal weight:    6.9990
   chunk 73 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   overall best weight:    0.8182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1037 HIS
** A1183 GLN ** 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 = 0.4087 r_free = 0.4087 target = 0.148896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.109779 restraints weight = 21906.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.110306 restraints weight = 13407.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.111166 restraints weight = 10329.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.111486 restraints weight = 8274.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.111525 restraints weight = 8034.407|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.5049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9774  Z= 0.141
  Angle     :  0.593  10.721  13244  Z= 0.304
  Chirality :  0.042   0.376   1541
  Planarity :  0.003   0.044   1644
  Dihedral  :  5.207  57.034   1299
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 17.95 %
    Favored  : 78.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.24), residues: 1187
  helix:  1.24 (0.18), residues: 777
  sheet:  1.06 (0.56), residues: 78
  loop :  0.13 (0.36), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1234 
 TYR   0.023   0.001   TYR A 289 
 PHE   0.031   0.002   PHE A 352 
 TRP   0.014   0.001   TRP A  89 
 HIS   0.006   0.001   HIS A1037 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00312 /  0.14 ( 9774)
  covalent geometry    : angle       0.59314 /  0.30 (13244)
  hydrogen bonds       : bond        0.04155 /  2.77 (  627)
  hydrogen bonds       : angle       4.47966 /  3.26 ( 1815)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 159
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8177 (tt)
REVERT: A   26 TRP cc_start: 0.4964 (OUTLIER) cc_final: 0.4157 (t-100)
REVERT: A   89 TRP cc_start: 0.7899 (p-90) cc_final: 0.7697 (p-90)
REVERT: A  177 LYS cc_start: 0.9144 (mmmt) cc_final: 0.8749 (mmtt)
REVERT: A  352 PHE cc_start: 0.7937 (m-80) cc_final: 0.7628 (m-80)
REVERT: A  701 TYR cc_start: 0.8835 (m-80) cc_final: 0.8612 (m-80)
REVERT: A  744 MET cc_start: 0.8445 (mmm) cc_final: 0.8155 (tpp)
REVERT: A  849 GLN cc_start: 0.8664 (mm-40) cc_final: 0.8343 (mm-40)
REVERT: A  915 ARG cc_start: 0.8817 (ptp-110) cc_final: 0.8281 (mtt180)
REVERT: A 1006 MET cc_start: 0.8512 (ttm) cc_final: 0.7884 (mtm)
  outliers start: 35
  outliers final: 22
  residues processed: 178
  average time/residue: 0.0929
  time to fit residues: 23.8344
Evaluate side-chains
  164 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 140
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   26 TRP
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  288 MET
Chi-restraints excluded: chain A residue  583 HIS
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  759 LEU
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  772 THR
Chi-restraints excluded: chain A residue  775 THR
Chi-restraints excluded: chain A residue  866 ILE
Chi-restraints excluded: chain A residue  913 THR
Chi-restraints excluded: chain A residue  922 ARG
Chi-restraints excluded: chain A residue  955 ILE
Chi-restraints excluded: chain A residue  984 SER
Chi-restraints excluded: chain A residue 1010 VAL
Chi-restraints excluded: chain A residue 1027 TYR
Chi-restraints excluded: chain A residue 1091 LEU
Chi-restraints excluded: chain A residue 1119 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 90 optimal weight:    0.7980
   chunk 109 optimal weight:    0.6980
   chunk 100 optimal weight:    0.9980
   chunk 28 optimal weight:    0.3980
   chunk 67 optimal weight:    0.9990
   chunk 113 optimal weight:    1.9990
   chunk 56 optimal weight:   10.0000
   chunk 117 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0170
   chunk 91 optimal weight:    0.0980
   chunk 103 optimal weight:    0.0870
   overall best weight:    0.2596

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.152225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.112244 restraints weight = 22110.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.112453 restraints weight = 14691.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.113357 restraints weight = 9384.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.113871 restraints weight = 8392.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.114011 restraints weight = 7644.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.5568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9774  Z= 0.116
  Angle     :  0.593  13.269  13244  Z= 0.297
  Chirality :  0.041   0.375   1541
  Planarity :  0.003   0.043   1644
  Dihedral  :  4.981  57.065   1299
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 19.39 %
    Favored  : 78.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.50 (0.25), residues: 1187
  helix:  1.37 (0.18), residues: 774
  sheet:  1.15 (0.56), residues: 83
  loop :  0.23 (0.37), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1132 
 TYR   0.021   0.001   TYR A1270 
 PHE   0.029   0.001   PHE A1048 
 TRP   0.011   0.001   TRP A1147 
 HIS   0.003   0.001   HIS A1037 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00242 /  0.12 ( 9774)
  covalent geometry    : angle       0.59254 /  0.30 (13244)
  hydrogen bonds       : bond        0.03952 /  2.63 (  627)
  hydrogen bonds       : angle       4.32509 /  3.15 ( 1815)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 164
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8060 (tt)
REVERT: A   89 TRP cc_start: 0.7871 (p-90) cc_final: 0.7431 (p-90)
REVERT: A  309 LYS cc_start: 0.8586 (mtpt) cc_final: 0.8307 (ptmt)
REVERT: A  352 PHE cc_start: 0.7821 (m-80) cc_final: 0.7543 (m-80)
REVERT: A  542 ARG cc_start: 0.8600 (ptm160) cc_final: 0.8301 (ptm160)
REVERT: A  701 TYR cc_start: 0.8764 (m-80) cc_final: 0.8448 (m-80)
REVERT: A  744 MET cc_start: 0.8385 (mmm) cc_final: 0.8174 (tpp)
REVERT: A  849 GLN cc_start: 0.8375 (mm-40) cc_final: 0.8083 (mt0)
REVERT: A  915 ARG cc_start: 0.8883 (ptp-110) cc_final: 0.8347 (mtt-85)
REVERT: A  962 ILE cc_start: 0.8830 (mm) cc_final: 0.8362 (tp)
REVERT: A 1006 MET cc_start: 0.8450 (ttm) cc_final: 0.7925 (mtm)
  outliers start: 22
  outliers final: 17
  residues processed: 178
  average time/residue: 0.0938
  time to fit residues: 24.0934
Evaluate side-chains
  157 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 139
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  288 MET
Chi-restraints excluded: chain A residue  299 ILE
Chi-restraints excluded: chain A residue  583 HIS
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  866 ILE
Chi-restraints excluded: chain A residue  913 THR
Chi-restraints excluded: chain A residue  922 ARG
Chi-restraints excluded: chain A residue  955 ILE
Chi-restraints excluded: chain A residue 1007 MET
Chi-restraints excluded: chain A residue 1027 TYR
Chi-restraints excluded: chain A residue 1084 LEU
Chi-restraints excluded: chain A residue 1159 ILE
Chi-restraints excluded: chain A residue 1166 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 107 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 52 optimal weight:    7.9990
   chunk 78 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0070
   chunk 19 optimal weight:    0.8980
   chunk 83 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.7398

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 387 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.150130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.110170 restraints weight = 21262.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.110328 restraints weight = 12970.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.111110 restraints weight = 9646.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.111527 restraints weight = 7871.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.111616 restraints weight = 7315.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.5700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9774  Z= 0.136
  Angle     :  0.624  11.121  13244  Z= 0.311
  Chirality :  0.041   0.220   1541
  Planarity :  0.003   0.041   1644
  Dihedral  :  4.812  58.252   1296
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 20.06 %
    Favored  : 77.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.52 (0.25), residues: 1187
  helix:  1.38 (0.19), residues: 777
  sheet:  1.16 (0.57), residues: 83
  loop :  0.25 (0.37), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1234 
 TYR   0.022   0.001   TYR A 289 
 PHE   0.028   0.001   PHE A 352 
 TRP   0.022   0.001   TRP A1147 
 HIS   0.004   0.001   HIS A 798 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.14 ( 9774)
  covalent geometry    : angle       0.62375 /  0.31 (13244)
  hydrogen bonds       : bond        0.03973 /  2.64 (  627)
  hydrogen bonds       : angle       4.38626 /  3.20 ( 1815)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 143
  time to evaluate  : 0.432 
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   13 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8167 (tt)
REVERT: A   26 TRP cc_start: 0.4766 (OUTLIER) cc_final: 0.4073 (t-100)
REVERT: A   89 TRP cc_start: 0.7935 (p-90) cc_final: 0.7532 (p-90)
REVERT: A  177 LYS cc_start: 0.9267 (mmmt) cc_final: 0.8852 (mmtt)
REVERT: A  225 VAL cc_start: 0.7922 (p) cc_final: 0.7639 (p)
REVERT: A  352 PHE cc_start: 0.8018 (m-80) cc_final: 0.7745 (m-80)
REVERT: A  542 ARG cc_start: 0.8584 (ptm160) cc_final: 0.8298 (ptm160)
REVERT: A  701 TYR cc_start: 0.8878 (m-80) cc_final: 0.8569 (m-80)
REVERT: A  849 GLN cc_start: 0.8557 (mm-40) cc_final: 0.8158 (mt0)
REVERT: A  915 ARG cc_start: 0.8789 (ptp-110) cc_final: 0.8289 (mtt-85)
REVERT: A  926 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8364 (mm)
REVERT: A 1006 MET cc_start: 0.8449 (ttm) cc_final: 0.7892 (mtm)
REVERT: A 1234 ARG cc_start: 0.8065 (mtm110) cc_final: 0.7841 (ptp90)
  outliers start: 28
  outliers final: 21
  residues processed: 161
  average time/residue: 0.0927
  time to fit residues: 21.7284
Evaluate side-chains
  159 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 135
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   26 TRP
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  288 MET
Chi-restraints excluded: chain A residue  299 ILE
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  583 HIS
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  759 LEU
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  866 ILE
Chi-restraints excluded: chain A residue  913 THR
Chi-restraints excluded: chain A residue  922 ARG
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue  955 ILE
Chi-restraints excluded: chain A residue 1010 VAL
Chi-restraints excluded: chain A residue 1027 TYR
Chi-restraints excluded: chain A residue 1098 ILE
Chi-restraints excluded: chain A residue 1119 ILE
Chi-restraints excluded: chain A residue 1159 ILE
Chi-restraints excluded: chain A residue 1166 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 51 optimal weight:    5.9990
   chunk 54 optimal weight:   30.0000
   chunk 39 optimal weight:   10.0000
   chunk 97 optimal weight:    0.6980
   chunk 98 optimal weight:    0.5980
   chunk 2 optimal weight:    2.9990
   chunk 102 optimal weight:    0.0050
   chunk 71 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 96 optimal weight:    6.9990
   overall best weight:    0.6194

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.150880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.112079 restraints weight = 22269.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.111757 restraints weight = 14044.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.112696 restraints weight = 11215.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.113062 restraints weight = 8929.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.113289 restraints weight = 8544.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.5882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9774  Z= 0.128
  Angle     :  0.621  10.148  13244  Z= 0.308
  Chirality :  0.040   0.164   1541
  Planarity :  0.003   0.039   1644
  Dihedral  :  4.810  59.745   1296
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 19.96 %
    Favored  : 77.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.60 (0.25), residues: 1187
  helix:  1.45 (0.19), residues: 775
  sheet:  1.14 (0.58), residues: 83
  loop :  0.30 (0.37), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1234 
 TYR   0.017   0.001   TYR A1292 
 PHE   0.026   0.001   PHE A 352 
 TRP   0.015   0.001   TRP A1147 
 HIS   0.004   0.001   HIS A 158 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.13 ( 9774)
  covalent geometry    : angle       0.62123 /  0.31 (13244)
  hydrogen bonds       : bond        0.03951 /  2.63 (  627)
  hydrogen bonds       : angle       4.32393 /  3.14 ( 1815)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 141
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8151 (tt)
REVERT: A   89 TRP cc_start: 0.7965 (p-90) cc_final: 0.7439 (p-90)
REVERT: A  177 LYS cc_start: 0.9242 (mmmt) cc_final: 0.8742 (mmtt)
REVERT: A  186 MET cc_start: 0.8957 (tmm) cc_final: 0.8665 (tpp)
REVERT: A  309 LYS cc_start: 0.8664 (mtpt) cc_final: 0.8247 (ptmt)
REVERT: A  352 PHE cc_start: 0.7988 (m-80) cc_final: 0.7732 (m-80)
REVERT: A  542 ARG cc_start: 0.8539 (ptm160) cc_final: 0.8225 (ptm160)
REVERT: A  616 THR cc_start: 0.0846 (OUTLIER) cc_final: 0.0198 (p)
REVERT: A  701 TYR cc_start: 0.8924 (m-80) cc_final: 0.8660 (m-80)
REVERT: A  849 GLN cc_start: 0.8389 (mm-40) cc_final: 0.8099 (mt0)
REVERT: A  915 ARG cc_start: 0.8854 (ptp-110) cc_final: 0.8200 (mtt-85)
REVERT: A  926 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8376 (mm)
REVERT: A  962 ILE cc_start: 0.8872 (mm) cc_final: 0.8406 (tp)
REVERT: A 1006 MET cc_start: 0.8473 (ttm) cc_final: 0.7924 (mtm)
  outliers start: 31
  outliers final: 19
  residues processed: 159
  average time/residue: 0.0880
  time to fit residues: 20.0127
Evaluate side-chains
  152 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 130
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  583 HIS
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  616 THR
Chi-restraints excluded: chain A residue  759 LEU
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  866 ILE
Chi-restraints excluded: chain A residue  913 THR
Chi-restraints excluded: chain A residue  922 ARG
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue  955 ILE
Chi-restraints excluded: chain A residue  984 SER
Chi-restraints excluded: chain A residue 1007 MET
Chi-restraints excluded: chain A residue 1010 VAL
Chi-restraints excluded: chain A residue 1027 TYR
Chi-restraints excluded: chain A residue 1098 ILE
Chi-restraints excluded: chain A residue 1119 ILE
Chi-restraints excluded: chain A residue 1166 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 63 optimal weight:    0.5980
   chunk 14 optimal weight:    3.9990
   chunk 71 optimal weight:    0.8980
   chunk 72 optimal weight:    0.5980
   chunk 62 optimal weight:    0.8980
   chunk 113 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 118 optimal weight:    6.9990
   overall best weight:    0.7982

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.150198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.112173 restraints weight = 22275.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.111119 restraints weight = 14161.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.112081 restraints weight = 12714.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.112572 restraints weight = 9375.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.112798 restraints weight = 8729.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.5949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9774  Z= 0.141
  Angle     :  0.646   9.998  13244  Z= 0.322
  Chirality :  0.041   0.237   1541
  Planarity :  0.003   0.039   1644
  Dihedral  :  4.836  59.547   1296
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 19.77 %
    Favored  : 77.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.62 (0.25), residues: 1187
  helix:  1.44 (0.19), residues: 778
  sheet:  1.14 (0.58), residues: 83
  loop :  0.37 (0.37), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A1132 
 TYR   0.025   0.001   TYR A 289 
 PHE   0.026   0.001   PHE A 352 
 TRP   0.016   0.001   TRP A1035 
 HIS   0.004   0.001   HIS A 158 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00322 /  0.14 ( 9774)
  covalent geometry    : angle       0.64562 /  0.32 (13244)
  hydrogen bonds       : bond        0.04008 /  2.67 (  627)
  hydrogen bonds       : angle       4.39267 /  3.18 ( 1815)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 136
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8163 (tt)
REVERT: A   26 TRP cc_start: 0.4750 (OUTLIER) cc_final: 0.4079 (t-100)
REVERT: A   89 TRP cc_start: 0.8058 (p-90) cc_final: 0.7742 (p-90)
REVERT: A  177 LYS cc_start: 0.9185 (mmmt) cc_final: 0.8683 (mmtt)
REVERT: A  186 MET cc_start: 0.8925 (tmm) cc_final: 0.8638 (tpp)
REVERT: A  309 LYS cc_start: 0.8657 (mtpt) cc_final: 0.8229 (ptmt)
REVERT: A  374 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7766 (pp20)
REVERT: A  542 ARG cc_start: 0.8568 (ptm160) cc_final: 0.8269 (ptm160)
REVERT: A  616 THR cc_start: 0.0854 (OUTLIER) cc_final: 0.0214 (p)
REVERT: A  849 GLN cc_start: 0.8631 (mm-40) cc_final: 0.8176 (mt0)
REVERT: A  915 ARG cc_start: 0.8788 (ptp-110) cc_final: 0.8219 (mtt-85)
REVERT: A  926 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8337 (mm)
REVERT: A 1006 MET cc_start: 0.8416 (ttm) cc_final: 0.7880 (mtm)
  outliers start: 32
  outliers final: 24
  residues processed: 153
  average time/residue: 0.0892
  time to fit residues: 19.7834
Evaluate side-chains
  157 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 128
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   26 TRP
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  170 MET
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  299 ILE
Chi-restraints excluded: chain A residue  374 GLU
Chi-restraints excluded: chain A residue  583 HIS
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  616 THR
Chi-restraints excluded: chain A residue  759 LEU
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  866 ILE
Chi-restraints excluded: chain A residue  913 THR
Chi-restraints excluded: chain A residue  922 ARG
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue  955 ILE
Chi-restraints excluded: chain A residue  984 SER
Chi-restraints excluded: chain A residue 1007 MET
Chi-restraints excluded: chain A residue 1010 VAL
Chi-restraints excluded: chain A residue 1027 TYR
Chi-restraints excluded: chain A residue 1035 TRP
Chi-restraints excluded: chain A residue 1091 LEU
Chi-restraints excluded: chain A residue 1098 ILE
Chi-restraints excluded: chain A residue 1119 ILE
Chi-restraints excluded: chain A residue 1166 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 58 optimal weight:    9.9990
   chunk 26 optimal weight:    0.7980
   chunk 116 optimal weight:    5.9990
   chunk 53 optimal weight:    5.9990
   chunk 24 optimal weight:    0.7980
   chunk 63 optimal weight:    0.7980
   chunk 103 optimal weight:    6.9990
   chunk 42 optimal weight:    7.9990
   chunk 104 optimal weight:    5.9990
   chunk 56 optimal weight:    6.9990
   chunk 83 optimal weight:    1.9990
   overall best weight:    2.0784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  35 HIS
A  76 GLN
A 152 HIS
A 699 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.145322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.107420 restraints weight = 22067.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.105759 restraints weight = 15039.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.106511 restraints weight = 14940.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.107045 restraints weight = 10379.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.107438 restraints weight = 9371.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.5670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.073   9774  Z= 0.261
  Angle     :  0.749   9.445  13244  Z= 0.379
  Chirality :  0.045   0.196   1541
  Planarity :  0.004   0.046   1644
  Dihedral  :  5.144  55.480   1296
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 14.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 19.67 %
    Favored  : 76.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.16 (0.25), residues: 1187
  helix:  1.08 (0.18), residues: 777
  sheet:  1.01 (0.58), residues: 83
  loop :  0.19 (0.36), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A1132 
 TYR   0.032   0.002   TYR A 289 
 PHE   0.032   0.002   PHE A 352 
 TRP   0.019   0.002   TRP A1035 
 HIS   0.008   0.001   HIS A 158 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00604 /  0.26 ( 9774)
  covalent geometry    : angle       0.74908 /  0.38 (13244)
  hydrogen bonds       : bond        0.04619 /  3.04 (  627)
  hydrogen bonds       : angle       4.78846 /  3.48 ( 1815)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 129
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8366 (tt)
REVERT: A   26 TRP cc_start: 0.4944 (OUTLIER) cc_final: 0.4254 (t-100)
REVERT: A  143 PHE cc_start: 0.8055 (m-10) cc_final: 0.6996 (t80)
REVERT: A  177 LYS cc_start: 0.9184 (mmmt) cc_final: 0.8790 (tptt)
REVERT: A  186 MET cc_start: 0.8972 (tmm) cc_final: 0.8662 (tpp)
REVERT: A  309 LYS cc_start: 0.8858 (mtpt) cc_final: 0.8264 (ptmt)
REVERT: A  616 THR cc_start: 0.0679 (OUTLIER) cc_final: -0.0044 (p)
REVERT: A  915 ARG cc_start: 0.8874 (ptp-110) cc_final: 0.8316 (mtt-85)
REVERT: A  926 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8409 (mm)
REVERT: A 1049 MET cc_start: 0.7659 (tpp) cc_final: 0.7233 (tpp)
  outliers start: 35
  outliers final: 26
  residues processed: 149
  average time/residue: 0.0873
  time to fit residues: 19.0696
Evaluate side-chains
  153 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 123
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   26 TRP
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  170 MET
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  299 ILE
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  374 GLU
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  583 HIS
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  616 THR
Chi-restraints excluded: chain A residue  759 LEU
Chi-restraints excluded: chain A residue  775 THR
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue  866 ILE
Chi-restraints excluded: chain A residue  922 ARG
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue  955 ILE
Chi-restraints excluded: chain A residue  984 SER
Chi-restraints excluded: chain A residue 1010 VAL
Chi-restraints excluded: chain A residue 1027 TYR
Chi-restraints excluded: chain A residue 1035 TRP
Chi-restraints excluded: chain A residue 1091 LEU
Chi-restraints excluded: chain A residue 1119 ILE
Chi-restraints excluded: chain A residue 1166 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 24 optimal weight:    0.4980
   chunk 99 optimal weight:    1.9990
   chunk 43 optimal weight:    9.9990
   chunk 108 optimal weight:    0.7980
   chunk 68 optimal weight:    0.4980
   chunk 15 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 110 optimal weight:    4.9990
   chunk 88 optimal weight:    0.5980
   chunk 84 optimal weight:    0.5980
   chunk 83 optimal weight:    0.8980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  35 HIS
A 472 HIS
A 699 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.149616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.111789 restraints weight = 21915.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.110186 restraints weight = 14114.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.111211 restraints weight = 12794.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.111736 restraints weight = 9514.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.111967 restraints weight = 8787.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.6018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9774  Z= 0.132
  Angle     :  0.665  12.055  13244  Z= 0.327
  Chirality :  0.041   0.191   1541
  Planarity :  0.003   0.053   1644
  Dihedral  :  5.013  58.794   1296
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 21.59 %
    Favored  : 76.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.49 (0.25), residues: 1187
  helix:  1.36 (0.19), residues: 775
  sheet:  1.09 (0.58), residues: 83
  loop :  0.27 (0.36), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG A1132 
 TYR   0.022   0.001   TYR A 289 
 PHE   0.026   0.001   PHE A 352 
 TRP   0.016   0.001   TRP A1035 
 HIS   0.003   0.001   HIS A 153 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00297 /  0.13 ( 9774)
  covalent geometry    : angle       0.66531 /  0.33 (13244)
  hydrogen bonds       : bond        0.04139 /  2.75 (  627)
  hydrogen bonds       : angle       4.46505 /  3.24 ( 1815)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1691.42 seconds
wall clock time: 30 minutes 10.98 seconds (1810.98 seconds total)