Starting phenix.real_space_refine
on Sat Aug 23 05:00:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8bwr_16295/08_2025/8bwr_16295.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8bwr_16295/08_2025/8bwr_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8bwr_16295/08_2025/8bwr_16295.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8bwr_16295/08_2025/8bwr_16295.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8bwr_16295/08_2025/8bwr_16295.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8bwr_16295/08_2025/8bwr_16295.cif"
  }
  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-2.0-5787/lib/python3.9/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: 1.74, per 1000 atoms: 0.18
  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: 0.63
  Conformation dependent library (CDL) restraints added in 253.3 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.38
  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: 1.56

  Time building geometry restraints manager: 0.90 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: 5355
       17.56 -    35.12: 394
       35.12 -    52.68: 77
       52.68 -    70.24: 19
       70.24 -    87.80: 8
  Dihedral angle restraints: 5853
    sinusoidal: 2359
      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 5850 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:             3.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.250
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
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  : 13.672  87.802   3587
  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 aren 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
  covalent geometry    : bond        0.00979 ( 9774)
  covalent geometry    : angle       0.93300 (13244)
  hydrogen bonds       : bond        0.23996 (  627)
  hydrogen bonds       : angle       8.82135 ( 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  : 0.262 
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: 0.7381 (mm)
REVERT: A  167 ARG cc_start: 0.8572 (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: 0.7915 (p90)
REVERT: A  278 GLU cc_start: 0.8408 (mt-10) cc_final: 0.7923 (mm-30)
REVERT: A  309 LYS cc_start: 0.9206 (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: 0.8882 (m-10) cc_final: 0.8636 (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: 0.7973 (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: 0.9483 (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: 0.1013
  time to fit residues: 33.0301
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  : 0.228 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4071 r_free = 0.4071 target = 0.147498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.107142 restraints weight = 21568.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.107025 restraints weight = 13471.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.109195 restraints weight = 9002.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.109823 restraints weight = 6926.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.109937 restraints weight = 6657.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.3153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9774  Z= 0.169
  Angle     :  0.653   7.010  13244  Z= 0.347
  Chirality :  0.043   0.232   1541
  Planarity :  0.004   0.047   1644
  Dihedral  :  6.914  58.526   1332
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  :  9.40 %
    Favored  : 87.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.24), residues: 1187
  helix:  0.66 (0.18), residues: 760
  sheet:  0.52 (0.52), residues: 82
  loop :  0.19 (0.37), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 503 
 TYR   0.014   0.002   TYR A  92 
 PHE   0.015   0.002   PHE A 714 
 TRP   0.016   0.001   TRP A  89 
 HIS   0.007   0.001   HIS A 798 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 9774)
  covalent geometry    : angle       0.65264 (13244)
  hydrogen bonds       : bond        0.05340 (  627)
  hydrogen bonds       : angle       5.41058 ( 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  : 0.344 
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: 0.5143 (OUTLIER) cc_final: 0.4524 (t-100)
REVERT: A  143 PHE cc_start: 0.8089 (m-10) cc_final: 0.7365 (t80)
REVERT: A  201 ASP cc_start: 0.8621 (t0) cc_final: 0.8322 (t0)
REVERT: A  309 LYS cc_start: 0.8906 (mttp) cc_final: 0.8508 (mtpt)
REVERT: A  363 LEU cc_start: 0.8740 (mm) cc_final: 0.8333 (mt)
REVERT: A  849 GLN cc_start: 0.8687 (mm-40) cc_final: 0.8298 (mm-40)
REVERT: A  890 LYS cc_start: 0.9508 (OUTLIER) cc_final: 0.9292 (mtmm)
REVERT: A  911 LEU cc_start: 0.9318 (mt) cc_final: 0.9111 (mt)
REVERT: A  915 ARG cc_start: 0.9102 (ptp-110) cc_final: 0.8731 (ptp90)
REVERT: A  921 GLU cc_start: 0.8773 (pm20) cc_final: 0.8496 (pm20)
REVERT: A 1108 ILE cc_start: 0.8582 (mm) cc_final: 0.8370 (tp)
REVERT: A 1131 MET cc_start: 0.8968 (mmm) cc_final: 0.8733 (mmt)
REVERT: A 1134 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.7856 (t0)
  outliers start: 30
  outliers final: 13
  residues processed: 211
  average time/residue: 0.0847
  time to fit residues: 24.9880
Evaluate side-chains
  155 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 139
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 84 optimal weight:    0.6980
   chunk 90 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 108 optimal weight:    0.6980
   chunk 92 optimal weight:    0.2980
   chunk 111 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1236 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 = 0.4058 r_free = 0.4058 target = 0.146661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.107417 restraints weight = 21632.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.106339 restraints weight = 14223.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.107646 restraints weight = 9717.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.109497 restraints weight = 7983.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.109456 restraints weight = 6686.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.4102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9774  Z= 0.154
  Angle     :  0.618  10.512  13244  Z= 0.319
  Chirality :  0.042   0.343   1541
  Planarity :  0.003   0.049   1644
  Dihedral  :  5.907  55.493   1321
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 12.76 %
    Favored  : 83.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.07 (0.24), residues: 1187
  helix:  1.05 (0.18), residues: 766
  sheet:  0.71 (0.52), residues: 81
  loop :  0.14 (0.36), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 262 
 TYR   0.013   0.001   TYR A1292 
 PHE   0.038   0.002   PHE A 352 
 TRP   0.025   0.001   TRP A1147 
 HIS   0.009   0.001   HIS A1233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 9774)
  covalent geometry    : angle       0.61812 (13244)
  hydrogen bonds       : bond        0.04722 (  627)
  hydrogen bonds       : angle       4.92608 ( 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
  208 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 171
  time to evaluate  : 0.303 
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: 0.5133 (OUTLIER) cc_final: 0.4471 (t-100)
REVERT: A  143 PHE cc_start: 0.8250 (m-10) cc_final: 0.7466 (t80)
REVERT: A  173 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8486 (mtt)
REVERT: A  201 ASP cc_start: 0.8443 (t0) cc_final: 0.8177 (t0)
REVERT: A  210 VAL cc_start: 0.9208 (m) cc_final: 0.8990 (p)
REVERT: A  352 PHE cc_start: 0.7928 (m-80) cc_final: 0.7642 (m-80)
REVERT: A  387 GLN cc_start: 0.8765 (tt0) cc_final: 0.8553 (tp40)
REVERT: A  849 GLN cc_start: 0.8587 (mm-40) cc_final: 0.8187 (mm-40)
REVERT: A  887 ARG cc_start: 0.7215 (ttm170) cc_final: 0.6924 (tpp-160)
REVERT: A  890 LYS cc_start: 0.9495 (OUTLIER) cc_final: 0.9279 (mtmm)
REVERT: A  915 ARG cc_start: 0.9104 (ptp-110) cc_final: 0.8614 (mtt-85)
REVERT: A  922 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7994 (mmm-85)
REVERT: A 1134 ASN cc_start: 0.8645 (OUTLIER) cc_final: 0.7769 (t0)
  outliers start: 37
  outliers final: 19
  residues processed: 193
  average time/residue: 0.0784
  time to fit residues: 21.5736
Evaluate side-chains
  161 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 137
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
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   89 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  173 MET
Chi-restraints excluded: chain A residue  583 HIS
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  776 VAL
Chi-restraints excluded: chain A residue  866 ILE
Chi-restraints excluded: chain A residue  890 LYS
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 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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 59 optimal weight:    8.9990
   chunk 109 optimal weight:    6.9990
   chunk 105 optimal weight:    4.9990
   chunk 21 optimal weight:    0.6980
   chunk 102 optimal weight:    0.0970
   chunk 30 optimal weight:    6.9990
   chunk 107 optimal weight:    0.3980
   chunk 61 optimal weight:    0.8980
   chunk 33 optimal weight:    0.3980
   chunk 103 optimal weight:    0.7980
   chunk 62 optimal weight:    4.9990
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4098 r_free = 0.4098 target = 0.149736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.110908 restraints weight = 22201.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.110807 restraints weight = 13279.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.111901 restraints weight = 10529.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.112808 restraints weight = 8523.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.112899 restraints weight = 7905.255|
|-----------------------------------------------------------------------------|
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.4692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9774  Z= 0.131
  Angle     :  0.607  12.417  13244  Z= 0.310
  Chirality :  0.042   0.396   1541
  Planarity :  0.003   0.045   1644
  Dihedral  :  5.667  59.138   1321
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 15.93 %
    Favored  : 81.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.27 (0.24), residues: 1187
  helix:  1.24 (0.19), residues: 765
  sheet:  0.85 (0.53), residues: 81
  loop :  0.13 (0.36), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 176 
 TYR   0.022   0.001   TYR A1270 
 PHE   0.031   0.001   PHE A 352 
 TRP   0.017   0.001   TRP A1147 
 HIS   0.005   0.001   HIS A1233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 9774)
  covalent geometry    : angle       0.60690 (13244)
  hydrogen bonds       : bond        0.04349 (  627)
  hydrogen bonds       : angle       4.67746 ( 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
  194 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 164
  time to evaluate  : 0.265 
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: 0.8501 (OUTLIER) cc_final: 0.8138 (tt)
REVERT: A   26 TRP cc_start: 0.4933 (OUTLIER) cc_final: 0.4136 (t-100)
REVERT: A  143 PHE cc_start: 0.8272 (m-10) cc_final: 0.7441 (t80)
REVERT: A  161 CYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7932 (t)
REVERT: A  849 GLN cc_start: 0.8449 (mm-40) cc_final: 0.8041 (mt0)
REVERT: A  915 ARG cc_start: 0.9023 (ptp-110) cc_final: 0.8459 (mtt180)
REVERT: A 1134 ASN cc_start: 0.8469 (OUTLIER) cc_final: 0.7745 (t0)
REVERT: A 1270 TYR cc_start: 0.8705 (t80) cc_final: 0.7986 (t80)
  outliers start: 30
  outliers final: 14
  residues processed: 181
  average time/residue: 0.0835
  time to fit residues: 21.2497
Evaluate side-chains
  163 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 145
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
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  161 CYS
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  866 ILE
Chi-restraints excluded: chain A residue  913 THR
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 1119 ILE
Chi-restraints excluded: chain A residue 1134 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9980
   chunk 117 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 81 optimal weight:    0.8980
   chunk 54 optimal weight:   30.0000
   chunk 45 optimal weight:    8.9990
   chunk 73 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 71 optimal weight:    0.6980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A  61 GLN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.148972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.110101 restraints weight = 22265.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.110186 restraints weight = 13220.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.111119 restraints weight = 10455.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.111572 restraints weight = 8192.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.111643 restraints weight = 7986.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.4921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9774  Z= 0.158
  Angle     :  0.609  11.069  13244  Z= 0.312
  Chirality :  0.042   0.393   1541
  Planarity :  0.003   0.044   1644
  Dihedral  :  5.634  56.723   1321
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 12.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 17.37 %
    Favored  : 79.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.22 (0.24), residues: 1187
  helix:  1.18 (0.18), residues: 771
  sheet:  1.08 (0.56), residues: 76
  loop :  0.08 (0.35), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 180 
 TYR   0.024   0.002   TYR A 289 
 PHE   0.024   0.002   PHE A1048 
 TRP   0.026   0.001   TRP A  89 
 HIS   0.007   0.001   HIS A1037 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 9774)
  covalent geometry    : angle       0.60853 (13244)
  hydrogen bonds       : bond        0.04317 (  627)
  hydrogen bonds       : angle       4.61473 ( 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
  184 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 150
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8241 (tt)
REVERT: A   26 TRP cc_start: 0.4996 (OUTLIER) cc_final: 0.4227 (t-100)
REVERT: A  143 PHE cc_start: 0.8388 (m-10) cc_final: 0.7498 (t80)
REVERT: A  161 CYS cc_start: 0.8297 (OUTLIER) cc_final: 0.8090 (t)
REVERT: A  744 MET cc_start: 0.8476 (mmm) cc_final: 0.8160 (tpp)
REVERT: A  849 GLN cc_start: 0.8661 (mm-40) cc_final: 0.8330 (mm-40)
REVERT: A  915 ARG cc_start: 0.8877 (ptp-110) cc_final: 0.8438 (mtt-85)
REVERT: A 1134 ASN cc_start: 0.8395 (OUTLIER) cc_final: 0.7728 (t0)
  outliers start: 34
  outliers final: 21
  residues processed: 172
  average time/residue: 0.0793
  time to fit residues: 20.0343
Evaluate side-chains
  159 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 134
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
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  161 CYS
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  761 LEU
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  940 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 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 1198 LEU
Chi-restraints excluded: chain A residue 1268 LEU
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:    0.0020
   chunk 100 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9980
   chunk 67 optimal weight:    0.8980
   chunk 113 optimal weight:    4.9990
   chunk 56 optimal weight:    8.9990
   chunk 117 optimal weight:    3.9990
   chunk 57 optimal weight:    0.0370
   chunk 91 optimal weight:    0.9980
   chunk 103 optimal weight:    2.9990
   overall best weight:    0.5466

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4109 r_free = 0.4109 target = 0.150435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.112275 restraints weight = 22082.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.108982 restraints weight = 16291.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.110477 restraints weight = 12293.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.110976 restraints weight = 10038.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.111179 restraints weight = 9107.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.5288

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= 0.128
  Angle     :  0.602  12.581  13244  Z= 0.306
  Chirality :  0.042   0.400   1541
  Planarity :  0.003   0.043   1644
  Dihedral  :  5.575  59.474   1321
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 18.33 %
    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 aren not related in a simple way.
  whole:  1.29 (0.24), residues: 1187
  helix:  1.23 (0.18), residues: 772
  sheet:  0.98 (0.54), residues: 83
  loop :  0.14 (0.36), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 180 
 TYR   0.023   0.001   TYR A 289 
 PHE   0.018   0.001   PHE A1043 
 TRP   0.033   0.001   TRP A  89 
 HIS   0.003   0.001   HIS A 934 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 9774)
  covalent geometry    : angle       0.60245 (13244)
  hydrogen bonds       : bond        0.04174 (  627)
  hydrogen bonds       : angle       4.51066 ( 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
  185 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 154
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8120 (tt)
REVERT: A   26 TRP cc_start: 0.4907 (OUTLIER) cc_final: 0.4160 (t-100)
REVERT: A  744 MET cc_start: 0.8320 (mmm) cc_final: 0.8071 (tpp)
REVERT: A  849 GLN cc_start: 0.8389 (mm-40) cc_final: 0.7900 (mt0)
REVERT: A  915 ARG cc_start: 0.8906 (ptp-110) cc_final: 0.8388 (mtt-85)
REVERT: A 1134 ASN cc_start: 0.8288 (OUTLIER) cc_final: 0.7712 (t0)
  outliers start: 31
  outliers final: 20
  residues processed: 172
  average time/residue: 0.0675
  time to fit residues: 17.3727
Evaluate side-chains
  161 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 138
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
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  161 CYS
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  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  775 THR
Chi-restraints excluded: chain A residue  866 ILE
Chi-restraints excluded: chain A residue  913 THR
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 1119 ILE
Chi-restraints excluded: chain A residue 1134 ASN
Chi-restraints excluded: chain A residue 1268 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 107 optimal weight:    0.9990
   chunk 18 optimal weight:    8.9990
   chunk 52 optimal weight:    8.9990
   chunk 78 optimal weight:    2.9990
   chunk 34 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 83 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 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 = 0.4107 r_free = 0.4107 target = 0.149787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.109566 restraints weight = 21151.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.109208 restraints weight = 12907.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.109660 restraints weight = 9969.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.110307 restraints weight = 8564.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.110346 restraints weight = 8111.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.5462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9774  Z= 0.138
  Angle     :  0.610  12.137  13244  Z= 0.306
  Chirality :  0.042   0.402   1541
  Planarity :  0.003   0.042   1644
  Dihedral  :  5.560  57.289   1321
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 18.71 %
    Favored  : 78.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.39 (0.25), residues: 1187
  helix:  1.29 (0.19), residues: 771
  sheet:  1.06 (0.56), residues: 83
  loop :  0.22 (0.36), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A1234 
 TYR   0.023   0.001   TYR A 289 
 PHE   0.016   0.001   PHE A1043 
 TRP   0.022   0.001   TRP A  89 
 HIS   0.004   0.001   HIS A 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 9774)
  covalent geometry    : angle       0.60962 (13244)
  hydrogen bonds       : bond        0.04089 (  627)
  hydrogen bonds       : angle       4.44680 ( 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
  178 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 148
  time to evaluate  : 0.260 
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: 0.8514 (OUTLIER) cc_final: 0.8202 (tt)
REVERT: A   26 TRP cc_start: 0.4865 (OUTLIER) cc_final: 0.4168 (t-100)
REVERT: A  225 VAL cc_start: 0.7889 (p) cc_final: 0.7638 (p)
REVERT: A  849 GLN cc_start: 0.8553 (mm-40) cc_final: 0.8118 (mt0)
REVERT: A  915 ARG cc_start: 0.8812 (ptp-110) cc_final: 0.8266 (mtt-85)
REVERT: A 1134 ASN cc_start: 0.8272 (OUTLIER) cc_final: 0.7750 (t0)
  outliers start: 30
  outliers final: 21
  residues processed: 169
  average time/residue: 0.0767
  time to fit residues: 18.9250
Evaluate side-chains
  161 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 137
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
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   39 LEU
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  161 CYS
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  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  775 THR
Chi-restraints excluded: chain A residue  866 ILE
Chi-restraints excluded: chain A residue  913 THR
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 1119 ILE
Chi-restraints excluded: chain A residue 1134 ASN
Chi-restraints excluded: chain A residue 1268 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 54 optimal weight:   20.0000
   chunk 39 optimal weight:    9.9990
   chunk 97 optimal weight:    0.7980
   chunk 98 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 102 optimal weight:    0.7980
   chunk 71 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 387 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.148685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.109414 restraints weight = 21215.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.108548 restraints weight = 12929.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.109210 restraints weight = 12197.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.109735 restraints weight = 8734.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.110036 restraints weight = 7921.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.5565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9774  Z= 0.160
  Angle     :  0.658  12.286  13244  Z= 0.326
  Chirality :  0.042   0.412   1541
  Planarity :  0.003   0.042   1644
  Dihedral  :  5.632  59.772   1321
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 19.10 %
    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 aren not related in a simple way.
  whole:  1.43 (0.25), residues: 1187
  helix:  1.31 (0.19), residues: 772
  sheet:  1.02 (0.57), residues: 83
  loop :  0.28 (0.36), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1234 
 TYR   0.020   0.002   TYR A 289 
 PHE   0.015   0.001   PHE A1043 
 TRP   0.027   0.001   TRP A  89 
 HIS   0.005   0.001   HIS A 798 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 9774)
  covalent geometry    : angle       0.65787 (13244)
  hydrogen bonds       : bond        0.04275 (  627)
  hydrogen bonds       : angle       4.48725 ( 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
  180 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 141
  time to evaluate  : 0.309 
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: 0.8507 (OUTLIER) cc_final: 0.8207 (tt)
REVERT: A   26 TRP cc_start: 0.4937 (OUTLIER) cc_final: 0.4212 (t-100)
REVERT: A  186 MET cc_start: 0.8964 (tmm) cc_final: 0.8683 (tpp)
REVERT: A  238 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7775 (tp)
REVERT: A  849 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8353 (mm-40)
REVERT: A  915 ARG cc_start: 0.8910 (ptp-110) cc_final: 0.8247 (mtt-85)
REVERT: A 1134 ASN cc_start: 0.8282 (OUTLIER) cc_final: 0.7800 (t0)
  outliers start: 39
  outliers final: 30
  residues processed: 164
  average time/residue: 0.0680
  time to fit residues: 16.0883
Evaluate side-chains
  167 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 133
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
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   39 LEU
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  161 CYS
Chi-restraints excluded: chain A residue  170 MET
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  238 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  361 VAL
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  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  913 THR
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 1050 TYR
Chi-restraints excluded: chain A residue 1057 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 1268 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 63 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9990
   chunk 71 optimal weight:    0.5980
   chunk 72 optimal weight:    0.3980
   chunk 62 optimal weight:    0.8980
   chunk 113 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 118 optimal weight:   10.0000
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 387 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.150027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.111331 restraints weight = 21223.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.109775 restraints weight = 13030.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.110791 restraints weight = 12643.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.111434 restraints weight = 8866.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.111788 restraints weight = 7964.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.5781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9774  Z= 0.135
  Angle     :  0.653  13.022  13244  Z= 0.322
  Chirality :  0.042   0.407   1541
  Planarity :  0.003   0.042   1644
  Dihedral  :  5.602  59.815   1321
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 19.96 %
    Favored  : 76.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.47 (0.25), residues: 1187
  helix:  1.32 (0.19), residues: 776
  sheet:  0.99 (0.58), residues: 83
  loop :  0.38 (0.36), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A1132 
 TYR   0.018   0.001   TYR A1292 
 PHE   0.021   0.001   PHE A 352 
 TRP   0.025   0.001   TRP A  89 
 HIS   0.004   0.001   HIS A 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 9774)
  covalent geometry    : angle       0.65341 (13244)
  hydrogen bonds       : bond        0.04091 (  627)
  hydrogen bonds       : angle       4.40260 ( 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
  171 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 138
  time to evaluate  : 0.381 
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: 0.8478 (OUTLIER) cc_final: 0.8185 (tt)
REVERT: A   26 TRP cc_start: 0.4873 (OUTLIER) cc_final: 0.4154 (t-100)
REVERT: A  186 MET cc_start: 0.8951 (tmm) cc_final: 0.8633 (tpp)
REVERT: A  238 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7754 (tp)
REVERT: A  849 GLN cc_start: 0.8549 (mm-40) cc_final: 0.8106 (mt0)
REVERT: A  915 ARG cc_start: 0.8820 (ptp-110) cc_final: 0.8204 (mtt-85)
REVERT: A 1134 ASN cc_start: 0.8249 (OUTLIER) cc_final: 0.7836 (t0)
  outliers start: 33
  outliers final: 21
  residues processed: 158
  average time/residue: 0.0907
  time to fit residues: 20.9805
Evaluate side-chains
  153 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 128
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
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  161 CYS
Chi-restraints excluded: chain A residue  170 MET
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  258 PHE
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  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  913 THR
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 1057 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 1268 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 58 optimal weight:    0.9980
   chunk 26 optimal weight:    0.6980
   chunk 116 optimal weight:   10.0000
   chunk 53 optimal weight:   10.0000
   chunk 24 optimal weight:    0.8980
   chunk 63 optimal weight:    0.5980
   chunk 103 optimal weight:    7.9990
   chunk 42 optimal weight:    5.9990
   chunk 104 optimal weight:    4.9990
   chunk 56 optimal weight:    6.9990
   chunk 83 optimal weight:    1.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 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 = 0.4077 r_free = 0.4077 target = 0.147588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.110208 restraints weight = 21748.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.108587 restraints weight = 13311.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.109621 restraints weight = 12787.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.110089 restraints weight = 8852.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.110458 restraints weight = 8111.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.5792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9774  Z= 0.160
  Angle     :  0.675  12.501  13244  Z= 0.333
  Chirality :  0.043   0.414   1541
  Planarity :  0.003   0.044   1644
  Dihedral  :  5.666  59.341   1321
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 19.87 %
    Favored  : 76.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.47 (0.25), residues: 1187
  helix:  1.35 (0.19), residues: 770
  sheet:  0.98 (0.58), residues: 83
  loop :  0.30 (0.36), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.000   ARG A1132 
 TYR   0.019   0.001   TYR A1292 
 PHE   0.017   0.002   PHE A 352 
 TRP   0.024   0.001   TRP A  89 
 HIS   0.005   0.001   HIS A 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 9774)
  covalent geometry    : angle       0.67506 (13244)
  hydrogen bonds       : bond        0.04168 (  627)
  hydrogen bonds       : angle       4.47093 ( 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
  169 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 135
  time to evaluate  : 0.376 
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: 0.8520 (OUTLIER) cc_final: 0.8229 (tt)
REVERT: A   26 TRP cc_start: 0.4912 (OUTLIER) cc_final: 0.4206 (t-100)
REVERT: A  177 LYS cc_start: 0.8890 (tptm) cc_final: 0.8076 (tppt)
REVERT: A  186 MET cc_start: 0.8977 (tmm) cc_final: 0.8598 (tpp)
REVERT: A  238 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7779 (tp)
REVERT: A  849 GLN cc_start: 0.8762 (mm-40) cc_final: 0.8381 (mm-40)
REVERT: A  915 ARG cc_start: 0.8867 (ptp-110) cc_final: 0.8321 (mtt-85)
REVERT: A 1134 ASN cc_start: 0.8308 (OUTLIER) cc_final: 0.7942 (t0)
  outliers start: 34
  outliers final: 27
  residues processed: 154
  average time/residue: 0.0923
  time to fit residues: 20.7846
Evaluate side-chains
  162 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 131
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
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  161 CYS
Chi-restraints excluded: chain A residue  170 MET
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  238 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  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  775 THR
Chi-restraints excluded: chain A residue  866 ILE
Chi-restraints excluded: chain A residue  913 THR
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 1050 TYR
Chi-restraints excluded: chain A residue 1057 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 1268 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 99 optimal weight:    0.8980
   chunk 43 optimal weight:    8.9990
   chunk 108 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 110 optimal weight:    0.8980
   chunk 88 optimal weight:    0.5980
   chunk 84 optimal weight:    0.9980
   chunk 83 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 172 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.148837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.111725 restraints weight = 21677.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.110685 restraints weight = 13072.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.111484 restraints weight = 12493.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.111985 restraints weight = 8795.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.112308 restraints weight = 8079.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.5936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9774  Z= 0.140
  Angle     :  0.682  12.721  13244  Z= 0.330
  Chirality :  0.042   0.394   1541
  Planarity :  0.003   0.044   1644
  Dihedral  :  5.705  59.836   1321
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 20.44 %
    Favored  : 76.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.47 (0.25), residues: 1187
  helix:  1.34 (0.19), residues: 771
  sheet:  0.95 (0.58), residues: 83
  loop :  0.33 (0.36), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG A1132 
 TYR   0.020   0.001   TYR A1292 
 PHE   0.017   0.001   PHE A 352 
 TRP   0.044   0.001   TRP A  89 
 HIS   0.004   0.001   HIS A 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 9774)
  covalent geometry    : angle       0.68198 (13244)
  hydrogen bonds       : bond        0.04082 (  627)
  hydrogen bonds       : angle       4.44718 ( 1815)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1485.05 seconds
wall clock time: 26 minutes 29.66 seconds (1589.66 seconds total)