Starting phenix.real_space_refine
on Wed Mar  4 05:52:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7lcc_23271/03_2026/7lcc_23271.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7lcc_23271/03_2026/7lcc_23271.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.66
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7lcc_23271/03_2026/7lcc_23271.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7lcc_23271/03_2026/7lcc_23271.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7lcc_23271/03_2026/7lcc_23271.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7lcc_23271/03_2026/7lcc_23271.cif"
  }
  resolution = 3.66
  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=   1.000
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: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P      17      5.49       5
     S      74      5.16       5
     C    7100      2.51       5
     N    1977      2.21       5
     O    2112      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11281
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 10931
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1369, 10931
          Classifications: {'peptide': 1369}
          Link IDs: {'PTRANS': 63, 'TRANS': 1305}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 349
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 349
          Classifications: {'DNA': 17}
          Link IDs: {'rna3p': 16}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    116  SG  CYS A 125      41.692  14.661  64.944  1.00 42.22           S
  ATOM    142  SG  CYS A 128      41.329  16.565  68.156  1.00 47.79           S
  ATOM    284  SG  CYS A 146      43.235  17.512  64.552  1.00 33.37           S
  ATOM    290  SG  CYS A 147      44.974  16.501  67.153  1.00 38.33           S

  Time building chain proxies: 2.64, per 1000 atoms: 0.23
  Number of scatterers: 11281
  At special positions: 0
  Unit cell: (113.4, 104.76, 110.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     S      74     16.00
     P      17     15.00
     O    2112      8.00
     N    1977      7.00
     C    7100      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: 0.95
  Conformation dependent library (CDL) restraints added in 561.7 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1501 "
        pdb="ZN    ZN A1501 " - pdb=" SG  CYS A 147 "
        pdb="ZN    ZN A1501 " - pdb=" SG  CYS A 146 "
        pdb="ZN    ZN A1501 " - pdb=" SG  CYS A 128 "
        pdb="ZN    ZN A1501 " - pdb=" SG  CYS A 125 "
      Number of angles added : 6


  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2586

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 13 sheets defined
      43.4% alpha, 12.1% beta
      0 base pairs and 4 stacking pairs defined.
    Time for finding SS restraints: 1.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 133 through 137
    Processing helix  chain 'A' and resid 143 through 148
      removed outlier: 4.028A  pdb=" N   CYS A 147 " --> pdb=" O   PHE A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 171
    Processing helix  chain 'A' and resid 176 through 183
    Processing helix  chain 'A' and resid 183 through 192
    Processing helix  chain 'A' and resid 202 through 206
      removed outlier: 3.667A  pdb=" N   TYR A 206 " --> pdb=" O   PRO A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 245
      No H-bonds generated for 'chain 'A' and resid 243 through 245'
    Processing helix  chain 'A' and resid 246 through 252
    Processing helix  chain 'A' and resid 260 through 274
    Processing helix  chain 'A' and resid 275 through 280
      removed outlier: 4.221A  pdb=" N   SER A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 298
    Processing helix  chain 'A' and resid 369 through 375
    Processing helix  chain 'A' and resid 384 through 388
    Processing helix  chain 'A' and resid 413 through 422
    Processing helix  chain 'A' and resid 435 through 460
      removed outlier: 3.714A  pdb=" N   GLN A 439 " --> pdb=" O   GLY A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 478
    Processing helix  chain 'A' and resid 500 through 519
      removed outlier: 3.509A  pdb=" N   ILE A 514 " --> pdb=" O   ASP A 510 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   VAL A 515 " --> pdb=" O   ALA A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 533 through 540
      removed outlier: 3.740A  pdb=" N   ASN A 539 " --> pdb=" O   ASP A 535 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   LEU A 540 " --> pdb=" O   ILE A 536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 549 through 570
      removed outlier: 4.529A  pdb=" N   VAL A 553 " --> pdb=" O   ARG A 549 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 602 through 605
    Processing helix  chain 'A' and resid 608 through 616
    Processing helix  chain 'A' and resid 626 through 637
    Processing helix  chain 'A' and resid 652 through 657
      removed outlier: 3.580A  pdb=" N   CYS A 657 " --> pdb=" O   GLU A 653 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 697 through 699
      No H-bonds generated for 'chain 'A' and resid 697 through 699'
    Processing helix  chain 'A' and resid 703 through 710
    Processing helix  chain 'A' and resid 721 through 729
      removed outlier: 3.544A  pdb=" N   VAL A 725 " --> pdb=" O   SER A 721 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   TYR A 727 " --> pdb=" O   LYS A 723 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 730 through 733
    Processing helix  chain 'A' and resid 765 through 773
    Processing helix  chain 'A' and resid 803 through 814
      removed outlier: 3.861A  pdb=" N   VAL A 807 " --> pdb=" O   ASP A 803 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   LEU A 808 " --> pdb=" O   PHE A 804 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ASP A 809 " --> pdb=" O   ALA A 805 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   LYS A 812 " --> pdb=" O   LEU A 808 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   ARG A 813 " --> pdb=" O   ASP A 809 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 816 through 828
    Processing helix  chain 'A' and resid 829 through 834
    Processing helix  chain 'A' and resid 835 through 837
      No H-bonds generated for 'chain 'A' and resid 835 through 837'
    Processing helix  chain 'A' and resid 838 through 842
      removed outlier: 3.977A  pdb=" N   HIS A 842 " --> pdb=" O   GLU A 838 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 838 through 842'
    Processing helix  chain 'A' and resid 871 through 884
    Processing helix  chain 'A' and resid 889 through 895
    Processing helix  chain 'A' and resid 903 through 912
    Processing helix  chain 'A' and resid 917 through 931
    Processing helix  chain 'A' and resid 932 through 947
      removed outlier: 3.566A  pdb=" N   LEU A 936 " --> pdb=" O   MET A 932 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 951 through 959
      removed outlier: 3.907A  pdb=" N   LEU A 955 " --> pdb=" O   ALA A 951 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 959 through 972
      removed outlier: 3.526A  pdb=" N   PHE A 963 " --> pdb=" O   ASN A 959 " (cutoff:3.500A)
      removed outlier: 5.166A  pdb=" N   ASP A 966 " --> pdb=" O   HIS A 962 " (cutoff:3.500A)
      removed outlier: 5.739A  pdb=" N   PHE A 967 " --> pdb=" O   PHE A 963 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 980 through 997
      removed outlier: 4.159A  pdb=" N   VAL A 992 " --> pdb=" O   GLU A 988 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   PHE A 993 " --> pdb=" O   ILE A 989 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   HIS A 996 " --> pdb=" O   VAL A 992 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 999 through 1004
    Processing helix  chain 'A' and resid 1018 through 1033
      removed outlier: 3.535A  pdb=" N   SER A1032 " --> pdb=" O   VAL A1028 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   LEU A1033 " --> pdb=" O   LEU A1029 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1034 through 1050
    Processing helix  chain 'A' and resid 1065 through 1082
      removed outlier: 4.278A  pdb=" N   THR A1069 " --> pdb=" O   GLY A1065 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   LEU A1071 " --> pdb=" O   GLY A1067 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   TYR A1072 " --> pdb=" O   GLN A1068 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1092 through 1099
      removed outlier: 3.759A  pdb=" N   LEU A1098 " --> pdb=" O   ILE A1094 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   LEU A1099 " --> pdb=" O   ALA A1095 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1104 through 1109
    Processing helix  chain 'A' and resid 1127 through 1136
    Processing helix  chain 'A' and resid 1148 through 1163
    Processing helix  chain 'A' and resid 1167 through 1172
    Processing helix  chain 'A' and resid 1191 through 1199
      removed outlier: 3.948A  pdb=" N   GLN A1197 " --> pdb=" O   SER A1193 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   THR A1198 " --> pdb=" O   ALA A1194 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   SER A1199 " --> pdb=" O   ILE A1195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1200 through 1209
      removed outlier: 5.950A  pdb=" N   ASN A1204 " --> pdb=" O   LYS A1201 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   VAL A1205 " --> pdb=" O   TYR A1202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1222 through 1235
      removed outlier: 3.541A  pdb=" N   SER A1226 " --> pdb=" O   ASP A1222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1259 through 1266
      removed outlier: 3.552A  pdb=" N   ALA A1263 " --> pdb=" O   SER A1259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1286 through 1301
    Processing helix  chain 'A' and resid 1320 through 1325
      removed outlier: 3.653A  pdb=" N   ASN A1324 " --> pdb=" O   ALA A1320 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   PHE A1325 " --> pdb=" O   GLU A1321 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1320 through 1325'
    Processing helix  chain 'A' and resid 1326 through 1333
      removed outlier: 3.586A  pdb=" N   SER A1332 " --> pdb=" O   GLU A1328 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE A1333 " --> pdb=" O   PHE A1329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1427 through 1429
      No H-bonds generated for 'chain 'A' and resid 1427 through 1429'
    Processing helix  chain 'A' and resid 1449 through 1457
      removed outlier: 3.619A  pdb=" N   ARG A1457 " --> pdb=" O   VAL A1453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1460 through 1462
      No H-bonds generated for 'chain 'A' and resid 1460 through 1462'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 153 through 154
      removed outlier: 3.741A  pdb=" N   CYS A 153 " --> pdb=" O   LEU A 392 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 213
      removed outlier: 7.321A  pdb=" N   VAL A 217 " --> pdb=" O   ALA A 194 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   MET A 196 " --> pdb=" O   VAL A 217 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   LEU A 344 " --> pdb=" O   ILE A 363 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 237 through 240
      removed outlier: 3.751A  pdb=" N   ASP A 737 " --> pdb=" O   TYR A 762 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   ASN A 740 " --> pdb=" O   LYS A 309 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 489 through 491
      removed outlier: 4.666A  pdb=" N   LEU A 464 " --> pdb=" O   ILE A 491 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 714 through 718
      removed outlier: 3.540A  pdb=" N   ALA A 579 " --> pdb=" O   ILE A 599 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 686 through 689
    Processing sheet with id=AA7, first strand: chain 'A' and resid 843 through 846
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1086 through 1089
      removed outlier: 4.064A  pdb=" N   ILE A1140 " --> pdb=" O   LEU A1087 " (cutoff:3.500A)
      removed outlier: 7.209A  pdb=" N   LEU A1139 " --> pdb=" O   LEU A1175 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   CYS A1057 " --> pdb=" O   ARG A1210 " (cutoff:3.500A)
      removed outlier: 7.675A  pdb=" N   LEU A1212 " --> pdb=" O   CYS A1057 " (cutoff:3.500A)
      removed outlier: 6.172A  pdb=" N   PHE A1059 " --> pdb=" O   LEU A1212 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1247 through 1249
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1423 through 1425
      removed outlier: 6.202A  pdb=" N   ILE A1282 " --> pdb=" O   MET A1424 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1306 through 1308
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1311 through 1314
      removed outlier: 3.919A  pdb=" N   ASP A1311 " --> pdb=" O   ARG A1414 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLN A1415 " --> pdb=" O   ILE A1398 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ILE A1398 " --> pdb=" O   GLN A1415 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 1392 through 1395
      removed outlier: 3.705A  pdb=" N   ILE A1379 " --> pdb=" O   ILE A1395 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   ILE A1378 " --> pdb=" O   LEU A1374 " (cutoff:3.500A)
      removed outlier: 5.475A  pdb=" N   LEU A1374 " --> pdb=" O   ILE A1378 " (cutoff:3.500A)
      removed outlier: 7.128A  pdb=" N   GLU A1380 " --> pdb=" O   LYS A1372 " (cutoff:3.500A)

    424 hydrogen bonds defined for protein.
    1182 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      4 stacking parallelities
  Total time for adding SS restraints: 1.79

  Time building geometry restraints manager: 1.30 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1855
        1.32 -     1.44: 3103
        1.44 -     1.57: 6462
        1.57 -     1.69: 33
        1.69 -     1.81: 112
  Bond restraints: 11565
  Sorted by residual:
  bond pdb=" N   ARG A1375 "
       pdb=" CA  ARG A1375 "
    ideal  model  delta    sigma   weight residual
    1.453  1.488 -0.035 9.20e-03 1.18e+04 1.44e+01
  bond pdb=" N   GLU A1443 "
       pdb=" CA  GLU A1443 "
    ideal  model  delta    sigma   weight residual
    1.453  1.487 -0.034 9.20e-03 1.18e+04 1.36e+01
  bond pdb=" N   ILE A 390 "
       pdb=" CA  ILE A 390 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 9.10e-03 1.21e+04 1.31e+01
  bond pdb=" N   ILE A1282 "
       pdb=" CA  ILE A1282 "
    ideal  model  delta    sigma   weight residual
    1.458  1.498 -0.040 1.14e-02 7.69e+03 1.25e+01
  bond pdb=" CA  SER A 781 "
       pdb=" CB  SER A 781 "
    ideal  model  delta    sigma   weight residual
    1.528  1.474  0.055 1.56e-02 4.11e+03 1.24e+01
  ... (remaining 11560 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.51: 10755
        1.51 -     3.02: 4097
        3.02 -     4.53: 786
        4.53 -     6.04: 63
        6.04 -     7.55: 7
  Bond angle restraints: 15708
  Sorted by residual:
  angle pdb=" CA  PHE A 865 "
        pdb=" C   PHE A 865 "
        pdb=" O   PHE A 865 "
      ideal   model   delta    sigma   weight residual
     121.99  117.44    4.55 1.14e+00 7.69e-01 1.59e+01
  angle pdb=" CA  TYR A 835 "
        pdb=" C   TYR A 835 "
        pdb=" O   TYR A 835 "
      ideal   model   delta    sigma   weight residual
     121.94  117.35    4.59 1.15e+00 7.56e-01 1.59e+01
  angle pdb=" CA  VAL A 327 "
        pdb=" C   VAL A 327 "
        pdb=" O   VAL A 327 "
      ideal   model   delta    sigma   weight residual
     121.19  117.10    4.09 1.03e+00 9.43e-01 1.58e+01
  angle pdb=" CA  GLY A1177 "
        pdb=" C   GLY A1177 "
        pdb=" O   GLY A1177 "
      ideal   model   delta    sigma   weight residual
     121.41  117.92    3.49 8.80e-01 1.29e+00 1.58e+01
  angle pdb=" CA  ALA A 783 "
        pdb=" C   ALA A 783 "
        pdb=" O   ALA A 783 "
      ideal   model   delta    sigma   weight residual
     121.94  117.37    4.57 1.15e+00 7.56e-01 1.58e+01
  ... (remaining 15703 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.75: 6303
       17.75 -    35.49: 504
       35.49 -    53.24: 135
       53.24 -    70.98: 42
       70.98 -    88.73: 5
  Dihedral angle restraints: 6989
    sinusoidal: 2989
      harmonic: 4000
  Sorted by residual:
  dihedral pdb=" C   THR A 669 "
           pdb=" N   THR A 669 "
           pdb=" CA  THR A 669 "
           pdb=" CB  THR A 669 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -135.89   13.89     0      2.50e+00 1.60e-01 3.09e+01
  dihedral pdb=" C   TYR A 731 "
           pdb=" N   TYR A 731 "
           pdb=" CA  TYR A 731 "
           pdb=" CB  TYR A 731 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -135.46   12.86     0      2.50e+00 1.60e-01 2.64e+01
  dihedral pdb=" N   THR A 669 "
           pdb=" C   THR A 669 "
           pdb=" CA  THR A 669 "
           pdb=" CB  THR A 669 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  133.81  -10.41     0      2.50e+00 1.60e-01 1.73e+01
  ... (remaining 6986 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.087: 920
       0.087 -    0.175: 600
       0.175 -    0.262: 192
       0.262 -    0.350: 12
       0.350 -    0.437: 3
  Chirality restraints: 1727
  Sorted by residual:
  chirality pdb=" CA  THR A 669 "
            pdb=" N   THR A 669 "
            pdb=" C   THR A 669 "
            pdb=" CB  THR A 669 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.09    0.44 2.00e-01 2.50e+01 4.77e+00
  chirality pdb=" CA  TYR A 731 "
            pdb=" N   TYR A 731 "
            pdb=" C   TYR A 731 "
            pdb=" CB  TYR A 731 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 3.93e+00
  chirality pdb=" CA  ILE A 492 "
            pdb=" N   ILE A 492 "
            pdb=" C   ILE A 492 "
            pdb=" CB  ILE A 492 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.79   -0.35 2.00e-01 2.50e+01 3.13e+00
  ... (remaining 1724 not shown)

  Planarity restraints: 1974
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 668 "    0.011 2.00e-02 2.50e+03   2.25e-02 5.06e+00
        pdb=" C   ALA A 668 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   ALA A 668 "    0.014 2.00e-02 2.50e+03
        pdb=" N   THR A 669 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 257 "   -0.011 2.00e-02 2.50e+03   2.20e-02 4.84e+00
        pdb=" C   GLY A 257 "    0.038 2.00e-02 2.50e+03
        pdb=" O   GLY A 257 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   CYS A 258 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A1447 "    0.010 2.00e-02 2.50e+03   2.01e-02 4.03e+00
        pdb=" C   ALA A1447 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   ALA A1447 "    0.013 2.00e-02 2.50e+03
        pdb=" N   HIS A1448 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1971 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 27
        2.60 -     3.18: 8949
        3.18 -     3.75: 15851
        3.75 -     4.33: 22652
        4.33 -     4.90: 35676
  Nonbonded interactions: 83155
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 727 "
            pdb=" P    DT B   1 "
     model   vdw
     2.026 3.400
  nonbonded pdb=" CB  ARG A1375 "
            pdb=" NE  ARG A1375 "
     model   vdw
     2.467 2.816
  nonbonded pdb=" O5'  DA B  17 "
            pdb=" O4'  DA B  17 "
     model   vdw
     2.476 2.432
  nonbonded pdb=" N   GLN A 795 "
            pdb=" O   GLN A 795 "
     model   vdw
     2.536 2.496
  nonbonded pdb=" N   MET A1191 "
            pdb=" O   MET A1191 "
     model   vdw
     2.541 2.496
  ... (remaining 83150 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.010
  Process input model:                     13.880
  Find NCS groups from input model:        0.030
  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:0.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
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      :  0.012   0.055  11569  Z= 0.927
  Angle     :  1.574  28.814  15714  Z= 1.193
  Chirality :  0.111   0.437   1727
  Planarity :  0.004   0.027   1974
  Dihedral  : 14.395  88.729   4403
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  6.10 %
    Allowed  :  7.17 %
    Favored  : 86.73 %
  Cbeta Deviations :  0.23 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.96 (0.22), residues: 1365
  helix:  3.15 (0.22), residues: 454
  sheet:  1.68 (0.42), residues: 159
  loop :  0.07 (0.21), residues: 752

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 681 
 TYR   0.026   0.002   TYR A 762 
 PHE   0.020   0.002   PHE A1369 
 TRP   0.020   0.002   TRP A 850 
 HIS   0.009   0.001   HIS A 582 

Details of bonding type rmsd
  covalent geometry    : bond        0.01220 (11565)
  covalent geometry    : angle       1.53351 (15708)
  hydrogen bonds       : bond        0.28020 (  424)
  hydrogen bonds       : angle       6.95016 ( 1182)
  metal coordination   : bond        0.01141 (    4)
  metal coordination   : angle      18.14638 (    6)

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

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

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  361 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 287
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  188 ASN cc_start: 0.8657 (t0) cc_final: 0.8333 (t0)
REVERT: A  233 LYS cc_start: 0.8042 (tptt) cc_final: 0.7750 (tptp)
REVERT: A  343 ASP cc_start: 0.7911 (t0) cc_final: 0.7617 (p0)
REVERT: A  361 LYS cc_start: 0.7951 (mttt) cc_final: 0.7692 (tttm)
REVERT: A  390 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7949 (tp)
REVERT: A  487 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8628 (tp)
REVERT: A  669 THR cc_start: 0.8201 (t) cc_final: 0.6824 (t)
REVERT: A  967 PHE cc_start: 0.8796 (m-80) cc_final: 0.8487 (m-80)
REVERT: A 1021 TYR cc_start: 0.8145 (t80) cc_final: 0.7935 (t80)
REVERT: A 1196 VAL cc_start: 0.9222 (m) cc_final: 0.8672 (t)
REVERT: A 1352 MET cc_start: 0.8369 (ttm) cc_final: 0.8070 (ttp)
REVERT: A 1426 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8931 (mt)
  outliers start: 74
  outliers final: 21
  residues processed: 337
  average time/residue: 0.0972
  time to fit residues: 46.8014
Evaluate side-chains
  160 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 136
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  258 CYS
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  582 HIS
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain A residue  656 LYS
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain A residue  672 ASN
Chi-restraints excluded: chain A residue  698 TRP
Chi-restraints excluded: chain A residue  729 PHE
Chi-restraints excluded: chain A residue  751 HIS
Chi-restraints excluded: chain A residue  860 VAL
Chi-restraints excluded: chain A residue  913 LEU
Chi-restraints excluded: chain A residue  972 HIS
Chi-restraints excluded: chain A residue  974 ARG
Chi-restraints excluded: chain A residue  986 LEU
Chi-restraints excluded: chain A residue 1145 THR
Chi-restraints excluded: chain A residue 1156 ASP
Chi-restraints excluded: chain A residue 1205 VAL
Chi-restraints excluded: chain A residue 1426 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 98 optimal weight:    0.0980
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    0.8980
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9980
   chunk 55 optimal weight:    0.2980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 284 HIS
A 347 HIS
A 433 ASN
A 509 GLN
** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 666 GLN
A 672 ASN
A 742 GLN
A 782 HIS
A 790 HIS
A 987 ASN
A 996 HIS
A1166 ASN
A1289 HIS
A1365 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.149122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.110844 restraints weight = 16883.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.116650 restraints weight = 9841.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.118959 restraints weight = 5955.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.119267 restraints weight = 5040.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.119702 restraints weight = 4936.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.3022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11569  Z= 0.130
  Angle     :  0.590   9.626  15714  Z= 0.319
  Chirality :  0.042   0.189   1727
  Planarity :  0.004   0.044   1974
  Dihedral  : 12.431  88.120   1735
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 12.61 %
    Favored  : 83.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.49 (0.21), residues: 1365
  helix:  2.35 (0.23), residues: 468
  sheet:  2.16 (0.41), residues: 148
  loop : -0.14 (0.21), residues: 749

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 502 
 TYR   0.020   0.002   TYR A 762 
 PHE   0.015   0.001   PHE A 630 
 TRP   0.010   0.001   TRP A 770 
 HIS   0.007   0.001   HIS A 582 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (11565)
  covalent geometry    : angle       0.57982 (15708)
  hydrogen bonds       : bond        0.04923 (  424)
  hydrogen bonds       : angle       4.97842 ( 1182)
  metal coordination   : bond        0.00951 (    4)
  metal coordination   : angle       5.63594 (    6)

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

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

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 162
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 LEU cc_start: 0.8662 (mt) cc_final: 0.8441 (tp)
REVERT: A  188 ASN cc_start: 0.8386 (t0) cc_final: 0.7883 (t0)
REVERT: A  233 LYS cc_start: 0.7759 (tptt) cc_final: 0.7548 (tptp)
REVERT: A  263 MET cc_start: 0.8543 (tpt) cc_final: 0.8310 (tpt)
REVERT: A  306 MET cc_start: 0.8181 (mtt) cc_final: 0.7962 (mtp)
REVERT: A  343 ASP cc_start: 0.7719 (t0) cc_final: 0.6844 (p0)
REVERT: A  361 LYS cc_start: 0.6778 (mttt) cc_final: 0.6565 (mtpt)
REVERT: A  390 ILE cc_start: 0.8556 (tp) cc_final: 0.8229 (tp)
REVERT: A  487 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8378 (tp)
REVERT: A  490 MET cc_start: 0.7910 (ttp) cc_final: 0.7700 (ptm)
REVERT: A  512 MET cc_start: 0.8177 (tpp) cc_final: 0.7769 (mmt)
REVERT: A  547 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6738 (mt-10)
REVERT: A  665 PHE cc_start: 0.8264 (t80) cc_final: 0.7804 (t80)
REVERT: A  679 TYR cc_start: 0.7997 (m-80) cc_final: 0.7657 (m-80)
REVERT: A  775 MET cc_start: 0.8741 (mtt) cc_final: 0.8471 (mmt)
REVERT: A  913 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8104 (pp)
REVERT: A  989 ILE cc_start: 0.8742 (mt) cc_final: 0.8450 (mm)
REVERT: A 1074 VAL cc_start: 0.8816 (t) cc_final: 0.8584 (p)
REVERT: A 1218 MET cc_start: 0.5673 (mmm) cc_final: 0.3914 (mtm)
REVERT: A 1232 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8264 (tp)
REVERT: A 1481 SER cc_start: 0.8632 (t) cc_final: 0.8369 (p)
  outliers start: 51
  outliers final: 28
  residues processed: 199
  average time/residue: 0.0906
  time to fit residues: 26.7203
Evaluate side-chains
  156 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 124
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  547 GLU
Chi-restraints excluded: chain A residue  559 ILE
Chi-restraints excluded: chain A residue  582 HIS
Chi-restraints excluded: chain A residue  593 HIS
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain A residue  656 LYS
Chi-restraints excluded: chain A residue  661 TYR
Chi-restraints excluded: chain A residue  689 ILE
Chi-restraints excluded: chain A residue  698 TRP
Chi-restraints excluded: chain A residue  751 HIS
Chi-restraints excluded: chain A residue  759 ASP
Chi-restraints excluded: chain A residue  806 GLU
Chi-restraints excluded: chain A residue  913 LEU
Chi-restraints excluded: chain A residue  914 LEU
Chi-restraints excluded: chain A residue  972 HIS
Chi-restraints excluded: chain A residue  974 ARG
Chi-restraints excluded: chain A residue 1029 LEU
Chi-restraints excluded: chain A residue 1086 VAL
Chi-restraints excluded: chain A residue 1145 THR
Chi-restraints excluded: chain A residue 1156 ASP
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1205 VAL
Chi-restraints excluded: chain A residue 1232 LEU
Chi-restraints excluded: chain A residue 1395 ILE
Chi-restraints excluded: chain A residue 1477 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 113 optimal weight:    0.8980
   chunk 46 optimal weight:    7.9990
   chunk 89 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9980
   chunk 63 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   chunk 51 optimal weight:    8.9990
   chunk 9 optimal weight:    7.9990
   chunk 83 optimal weight:    0.9990
   chunk 131 optimal weight:    0.7980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 333 ASN
A 593 HIS
A1054 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.144883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.106560 restraints weight = 17053.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.110849 restraints weight = 10430.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.112375 restraints weight = 6584.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.113178 restraints weight = 5847.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.113669 restraints weight = 5520.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.3566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11569  Z= 0.130
  Angle     :  0.541   8.113  15714  Z= 0.290
  Chirality :  0.042   0.144   1727
  Planarity :  0.004   0.049   1974
  Dihedral  : 11.887  89.306   1719
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 14.34 %
    Favored  : 81.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.19 (0.22), residues: 1365
  helix:  2.08 (0.23), residues: 471
  sheet:  1.55 (0.41), residues: 166
  loop : -0.25 (0.21), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1459 
 TYR   0.019   0.001   TYR A 762 
 PHE   0.014   0.001   PHE A 630 
 TRP   0.009   0.001   TRP A 770 
 HIS   0.008   0.001   HIS A1054 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (11565)
  covalent geometry    : angle       0.53244 (15708)
  hydrogen bonds       : bond        0.04446 (  424)
  hydrogen bonds       : angle       4.67941 ( 1182)
  metal coordination   : bond        0.00838 (    4)
  metal coordination   : angle       4.84251 (    6)

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

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

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 140
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 LEU cc_start: 0.8705 (mt) cc_final: 0.8484 (tp)
REVERT: A  233 LYS cc_start: 0.7794 (tptt) cc_final: 0.7463 (tptp)
REVERT: A  306 MET cc_start: 0.8382 (mtt) cc_final: 0.8049 (mtp)
REVERT: A  343 ASP cc_start: 0.7693 (t0) cc_final: 0.7027 (p0)
REVERT: A  390 ILE cc_start: 0.8578 (tp) cc_final: 0.8298 (tp)
REVERT: A  547 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6845 (mt-10)
REVERT: A  665 PHE cc_start: 0.8350 (t80) cc_final: 0.7849 (t80)
REVERT: A  913 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8298 (pp)
REVERT: A  989 ILE cc_start: 0.8789 (mt) cc_final: 0.8509 (mm)
REVERT: A 1074 VAL cc_start: 0.8818 (t) cc_final: 0.8581 (p)
REVERT: A 1146 MET cc_start: 0.9414 (mmm) cc_final: 0.9130 (mmm)
REVERT: A 1218 MET cc_start: 0.5941 (mmm) cc_final: 0.4147 (mtp)
REVERT: A 1318 ASP cc_start: 0.8198 (t0) cc_final: 0.7888 (m-30)
REVERT: A 1481 SER cc_start: 0.8644 (t) cc_final: 0.8414 (p)
REVERT: A 1493 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7171 (pt0)
  outliers start: 49
  outliers final: 32
  residues processed: 176
  average time/residue: 0.0840
  time to fit residues: 22.6753
Evaluate side-chains
  157 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 122
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  333 ASN
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  533 TRP
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  547 GLU
Chi-restraints excluded: chain A residue  559 ILE
Chi-restraints excluded: chain A residue  582 HIS
Chi-restraints excluded: chain A residue  661 TYR
Chi-restraints excluded: chain A residue  689 ILE
Chi-restraints excluded: chain A residue  698 TRP
Chi-restraints excluded: chain A residue  738 CYS
Chi-restraints excluded: chain A residue  743 ILE
Chi-restraints excluded: chain A residue  751 HIS
Chi-restraints excluded: chain A residue  759 ASP
Chi-restraints excluded: chain A residue  806 GLU
Chi-restraints excluded: chain A residue  913 LEU
Chi-restraints excluded: chain A residue  931 ASN
Chi-restraints excluded: chain A residue  972 HIS
Chi-restraints excluded: chain A residue  974 ARG
Chi-restraints excluded: chain A residue 1086 VAL
Chi-restraints excluded: chain A residue 1104 THR
Chi-restraints excluded: chain A residue 1144 CYS
Chi-restraints excluded: chain A residue 1145 THR
Chi-restraints excluded: chain A residue 1156 ASP
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1193 SER
Chi-restraints excluded: chain A residue 1229 LEU
Chi-restraints excluded: chain A residue 1240 SER
Chi-restraints excluded: chain A residue 1395 ILE
Chi-restraints excluded: chain A residue 1493 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 81 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 84 optimal weight:    7.9990
   chunk 122 optimal weight:    3.9990
   chunk 116 optimal weight:    4.9990
   chunk 71 optimal weight:    3.9990
   chunk 130 optimal weight:    1.9990
   chunk 21 optimal weight:    0.2980
   chunk 22 optimal weight:    2.9990
   chunk 41 optimal weight:    0.2980
   chunk 30 optimal weight:    6.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 333 ASN
** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1054 HIS
A1432 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.144446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.104484 restraints weight = 17788.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.108817 restraints weight = 10760.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.111935 restraints weight = 7102.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.111833 restraints weight = 5982.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.112452 restraints weight = 5835.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.3911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11569  Z= 0.138
  Angle     :  0.526   8.007  15714  Z= 0.280
  Chirality :  0.041   0.143   1727
  Planarity :  0.004   0.045   1974
  Dihedral  : 11.499  86.995   1710
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 14.84 %
    Favored  : 80.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.05 (0.22), residues: 1365
  helix:  1.99 (0.23), residues: 474
  sheet:  1.47 (0.41), residues: 166
  loop : -0.36 (0.21), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1459 
 TYR   0.017   0.001   TYR A 661 
 PHE   0.012   0.001   PHE A1105 
 TRP   0.009   0.001   TRP A 850 
 HIS   0.006   0.001   HIS A 582 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (11565)
  covalent geometry    : angle       0.51779 (15708)
  hydrogen bonds       : bond        0.04171 (  424)
  hydrogen bonds       : angle       4.61867 ( 1182)
  metal coordination   : bond        0.00854 (    4)
  metal coordination   : angle       4.76729 (    6)

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

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

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 128
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 LEU cc_start: 0.8728 (mt) cc_final: 0.8482 (tp)
REVERT: A  233 LYS cc_start: 0.7797 (tptt) cc_final: 0.7453 (tptp)
REVERT: A  306 MET cc_start: 0.8473 (mtt) cc_final: 0.8145 (mtp)
REVERT: A  343 ASP cc_start: 0.7544 (t0) cc_final: 0.6894 (p0)
REVERT: A  390 ILE cc_start: 0.8598 (tp) cc_final: 0.8334 (tp)
REVERT: A  547 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6976 (mt-10)
REVERT: A  665 PHE cc_start: 0.8303 (t80) cc_final: 0.7842 (t80)
REVERT: A  913 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8392 (pp)
REVERT: A  989 ILE cc_start: 0.8742 (mt) cc_final: 0.8469 (mm)
REVERT: A 1074 VAL cc_start: 0.8789 (t) cc_final: 0.8546 (p)
REVERT: A 1252 HIS cc_start: 0.7218 (p-80) cc_final: 0.6388 (t70)
REVERT: A 1481 SER cc_start: 0.8657 (t) cc_final: 0.8432 (p)
REVERT: A 1493 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7241 (pt0)
  outliers start: 53
  outliers final: 38
  residues processed: 167
  average time/residue: 0.0893
  time to fit residues: 22.7715
Evaluate side-chains
  164 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 123
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 MET
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  333 ASN
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  533 TRP
Chi-restraints excluded: chain A residue  547 GLU
Chi-restraints excluded: chain A residue  559 ILE
Chi-restraints excluded: chain A residue  582 HIS
Chi-restraints excluded: chain A residue  639 HIS
Chi-restraints excluded: chain A residue  661 TYR
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain A residue  689 ILE
Chi-restraints excluded: chain A residue  698 TRP
Chi-restraints excluded: chain A residue  738 CYS
Chi-restraints excluded: chain A residue  743 ILE
Chi-restraints excluded: chain A residue  751 HIS
Chi-restraints excluded: chain A residue  759 ASP
Chi-restraints excluded: chain A residue  806 GLU
Chi-restraints excluded: chain A residue  913 LEU
Chi-restraints excluded: chain A residue  931 ASN
Chi-restraints excluded: chain A residue  943 ILE
Chi-restraints excluded: chain A residue  972 HIS
Chi-restraints excluded: chain A residue  974 ARG
Chi-restraints excluded: chain A residue 1086 VAL
Chi-restraints excluded: chain A residue 1091 SER
Chi-restraints excluded: chain A residue 1104 THR
Chi-restraints excluded: chain A residue 1144 CYS
Chi-restraints excluded: chain A residue 1145 THR
Chi-restraints excluded: chain A residue 1156 ASP
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1193 SER
Chi-restraints excluded: chain A residue 1240 SER
Chi-restraints excluded: chain A residue 1395 ILE
Chi-restraints excluded: chain A residue 1477 LEU
Chi-restraints excluded: chain A residue 1493 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 120 optimal weight:    0.3980
   chunk 49 optimal weight:    3.9990
   chunk 90 optimal weight:    9.9990
   chunk 40 optimal weight:    0.9980
   chunk 35 optimal weight:    0.5980
   chunk 8 optimal weight:    8.9990
   chunk 50 optimal weight:    2.9990
   chunk 3 optimal weight:    9.9990
   chunk 126 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 114 optimal weight:    1.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A 333 ASN
A 506 GLN
A 636 ASN
A 666 GLN
A1054 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.144168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.104224 restraints weight = 17592.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.108719 restraints weight = 10761.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.111159 restraints weight = 7005.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.111437 restraints weight = 6098.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.111736 restraints weight = 5769.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.4145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11569  Z= 0.129
  Angle     :  0.514   8.152  15714  Z= 0.273
  Chirality :  0.041   0.140   1727
  Planarity :  0.004   0.042   1974
  Dihedral  : 11.361  84.939   1710
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 15.58 %
    Favored  : 80.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.99 (0.22), residues: 1365
  helix:  1.91 (0.23), residues: 486
  sheet:  1.36 (0.41), residues: 166
  loop : -0.39 (0.22), residues: 713

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1459 
 TYR   0.017   0.001   TYR A 661 
 PHE   0.012   0.001   PHE A1369 
 TRP   0.008   0.001   TRP A 850 
 HIS   0.006   0.001   HIS A 582 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (11565)
  covalent geometry    : angle       0.50589 (15708)
  hydrogen bonds       : bond        0.03922 (  424)
  hydrogen bonds       : angle       4.52200 ( 1182)
  metal coordination   : bond        0.00789 (    4)
  metal coordination   : angle       4.63300 (    6)

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

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

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 130
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 LEU cc_start: 0.8744 (mt) cc_final: 0.8501 (tp)
REVERT: A  233 LYS cc_start: 0.7853 (tptt) cc_final: 0.7507 (tptp)
REVERT: A  343 ASP cc_start: 0.7526 (t0) cc_final: 0.6778 (p0)
REVERT: A  390 ILE cc_start: 0.8590 (tp) cc_final: 0.8337 (tp)
REVERT: A  547 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6930 (mt-10)
REVERT: A  665 PHE cc_start: 0.8357 (t80) cc_final: 0.7910 (t80)
REVERT: A  913 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8483 (pp)
REVERT: A  989 ILE cc_start: 0.8744 (mt) cc_final: 0.8484 (mm)
REVERT: A 1074 VAL cc_start: 0.8794 (t) cc_final: 0.8552 (p)
REVERT: A 1218 MET cc_start: 0.5085 (mmm) cc_final: 0.3499 (mtp)
REVERT: A 1252 HIS cc_start: 0.7233 (p-80) cc_final: 0.6418 (t70)
REVERT: A 1318 ASP cc_start: 0.8179 (t0) cc_final: 0.7723 (m-30)
REVERT: A 1481 SER cc_start: 0.8594 (t) cc_final: 0.8372 (p)
REVERT: A 1493 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7218 (pt0)
  outliers start: 51
  outliers final: 38
  residues processed: 163
  average time/residue: 0.0803
  time to fit residues: 20.3883
Evaluate side-chains
  164 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 123
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  200 ILE
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  333 ASN
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  547 GLU
Chi-restraints excluded: chain A residue  582 HIS
Chi-restraints excluded: chain A residue  593 HIS
Chi-restraints excluded: chain A residue  629 LEU
Chi-restraints excluded: chain A residue  661 TYR
Chi-restraints excluded: chain A residue  698 TRP
Chi-restraints excluded: chain A residue  738 CYS
Chi-restraints excluded: chain A residue  743 ILE
Chi-restraints excluded: chain A residue  751 HIS
Chi-restraints excluded: chain A residue  759 ASP
Chi-restraints excluded: chain A residue  777 MET
Chi-restraints excluded: chain A residue  806 GLU
Chi-restraints excluded: chain A residue  913 LEU
Chi-restraints excluded: chain A residue  931 ASN
Chi-restraints excluded: chain A residue  943 ILE
Chi-restraints excluded: chain A residue  972 HIS
Chi-restraints excluded: chain A residue 1048 ILE
Chi-restraints excluded: chain A residue 1054 HIS
Chi-restraints excluded: chain A residue 1086 VAL
Chi-restraints excluded: chain A residue 1091 SER
Chi-restraints excluded: chain A residue 1104 THR
Chi-restraints excluded: chain A residue 1144 CYS
Chi-restraints excluded: chain A residue 1145 THR
Chi-restraints excluded: chain A residue 1156 ASP
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1193 SER
Chi-restraints excluded: chain A residue 1338 MET
Chi-restraints excluded: chain A residue 1387 SER
Chi-restraints excluded: chain A residue 1395 ILE
Chi-restraints excluded: chain A residue 1477 LEU
Chi-restraints excluded: chain A residue 1493 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 25 optimal weight:    6.9990
   chunk 122 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 55 optimal weight:    4.9990
   chunk 117 optimal weight:    2.9990
   chunk 70 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 60 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 98 optimal weight:    0.0470
   overall best weight:    2.4086

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

Flipped N/Q/H residues before XYZ refinement:
A 116 HIS
A 333 ASN
** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 646 ASN
A1054 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.139967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.099773 restraints weight = 17957.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.104004 restraints weight = 11150.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.106125 restraints weight = 7355.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.106496 restraints weight = 6546.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.107181 restraints weight = 6335.936|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.4269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  11569  Z= 0.213
  Angle     :  0.590   8.524  15714  Z= 0.314
  Chirality :  0.044   0.144   1727
  Planarity :  0.004   0.040   1974
  Dihedral  : 11.463  83.058   1705
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  5.61 %
    Allowed  : 14.26 %
    Favored  : 80.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.77 (0.22), residues: 1365
  helix:  1.62 (0.23), residues: 483
  sheet:  1.20 (0.41), residues: 170
  loop : -0.43 (0.22), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 974 
 TYR   0.019   0.002   TYR A 702 
 PHE   0.014   0.002   PHE A 574 
 TRP   0.011   0.001   TRP A 850 
 HIS   0.009   0.001   HIS A1054 

Details of bonding type rmsd
  covalent geometry    : bond        0.00514 (11565)
  covalent geometry    : angle       0.58089 (15708)
  hydrogen bonds       : bond        0.04959 (  424)
  hydrogen bonds       : angle       4.80287 ( 1182)
  metal coordination   : bond        0.01299 (    4)
  metal coordination   : angle       5.35792 (    6)

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

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

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 126
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 LEU cc_start: 0.8861 (mt) cc_final: 0.8564 (tp)
REVERT: A  233 LYS cc_start: 0.7920 (tptt) cc_final: 0.7568 (tptp)
REVERT: A  343 ASP cc_start: 0.7507 (t0) cc_final: 0.6776 (p0)
REVERT: A  390 ILE cc_start: 0.8634 (tp) cc_final: 0.8366 (tp)
REVERT: A  547 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6931 (mt-10)
REVERT: A  665 PHE cc_start: 0.8374 (t80) cc_final: 0.8022 (t80)
REVERT: A  913 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8698 (pp)
REVERT: A  973 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7188 (tpt90)
REVERT: A  974 ARG cc_start: 0.7777 (tpm170) cc_final: 0.7522 (tpm170)
REVERT: A 1117 GLU cc_start: 0.7610 (pt0) cc_final: 0.7399 (pt0)
REVERT: A 1252 HIS cc_start: 0.7342 (p-80) cc_final: 0.6532 (t70)
REVERT: A 1318 ASP cc_start: 0.8253 (t0) cc_final: 0.7887 (m-30)
REVERT: A 1481 SER cc_start: 0.8561 (t) cc_final: 0.8345 (p)
  outliers start: 68
  outliers final: 55
  residues processed: 170
  average time/residue: 0.0928
  time to fit residues: 23.5798
Evaluate side-chains
  177 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 119
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  200 ILE
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  321 SER
Chi-restraints excluded: chain A residue  333 ASN
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  415 MET
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  454 ILE
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  516 THR
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  533 TRP
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  547 GLU
Chi-restraints excluded: chain A residue  559 ILE
Chi-restraints excluded: chain A residue  582 HIS
Chi-restraints excluded: chain A residue  629 LEU
Chi-restraints excluded: chain A residue  639 HIS
Chi-restraints excluded: chain A residue  661 TYR
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain A residue  698 TRP
Chi-restraints excluded: chain A residue  729 PHE
Chi-restraints excluded: chain A residue  738 CYS
Chi-restraints excluded: chain A residue  743 ILE
Chi-restraints excluded: chain A residue  751 HIS
Chi-restraints excluded: chain A residue  759 ASP
Chi-restraints excluded: chain A residue  777 MET
Chi-restraints excluded: chain A residue  806 GLU
Chi-restraints excluded: chain A residue  913 LEU
Chi-restraints excluded: chain A residue  931 ASN
Chi-restraints excluded: chain A residue  943 ILE
Chi-restraints excluded: chain A residue  972 HIS
Chi-restraints excluded: chain A residue  973 ARG
Chi-restraints excluded: chain A residue 1030 ILE
Chi-restraints excluded: chain A residue 1048 ILE
Chi-restraints excluded: chain A residue 1054 HIS
Chi-restraints excluded: chain A residue 1086 VAL
Chi-restraints excluded: chain A residue 1091 SER
Chi-restraints excluded: chain A residue 1104 THR
Chi-restraints excluded: chain A residue 1144 CYS
Chi-restraints excluded: chain A residue 1145 THR
Chi-restraints excluded: chain A residue 1156 ASP
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1193 SER
Chi-restraints excluded: chain A residue 1195 ILE
Chi-restraints excluded: chain A residue 1205 VAL
Chi-restraints excluded: chain A residue 1240 SER
Chi-restraints excluded: chain A residue 1338 MET
Chi-restraints excluded: chain A residue 1387 SER
Chi-restraints excluded: chain A residue 1395 ILE
Chi-restraints excluded: chain A residue 1477 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 30 optimal weight:    3.9990
   chunk 25 optimal weight:    6.9990
   chunk 21 optimal weight:    0.7980
   chunk 11 optimal weight:   10.0000
   chunk 68 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 60 optimal weight:    0.5980
   chunk 103 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 333 ASN
A 421 HIS
** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1054 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.142748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.103675 restraints weight = 17175.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.108413 restraints weight = 10287.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.111020 restraints weight = 6487.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.111238 restraints weight = 5440.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.111499 restraints weight = 5297.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.4442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11569  Z= 0.111
  Angle     :  0.521   8.787  15714  Z= 0.273
  Chirality :  0.040   0.140   1727
  Planarity :  0.003   0.040   1974
  Dihedral  : 11.229  82.582   1705
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 16.49 %
    Favored  : 79.72 %
  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 are not related in a simple way.
  whole:  0.78 (0.22), residues: 1365
  helix:  1.72 (0.24), residues: 480
  sheet:  1.14 (0.42), residues: 166
  loop : -0.44 (0.22), residues: 719

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 332 
 TYR   0.018   0.001   TYR A 702 
 PHE   0.014   0.001   PHE A 630 
 TRP   0.009   0.001   TRP A 850 
 HIS   0.014   0.001   HIS A1054 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (11565)
  covalent geometry    : angle       0.51433 (15708)
  hydrogen bonds       : bond        0.03695 (  424)
  hydrogen bonds       : angle       4.52764 ( 1182)
  metal coordination   : bond        0.00628 (    4)
  metal coordination   : angle       4.14456 (    6)

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

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

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 125
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
REVERT: A  169 LEU cc_start: 0.8774 (mt) cc_final: 0.8543 (tp)
REVERT: A  233 LYS cc_start: 0.7928 (tptt) cc_final: 0.7581 (tptp)
REVERT: A  343 ASP cc_start: 0.7504 (t0) cc_final: 0.6758 (p0)
REVERT: A  390 ILE cc_start: 0.8588 (tp) cc_final: 0.8337 (tp)
REVERT: A  467 GLU cc_start: 0.8542 (tp30) cc_final: 0.7807 (tp30)
REVERT: A  547 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6975 (mt-10)
REVERT: A  587 GLN cc_start: 0.7317 (tp40) cc_final: 0.7034 (tp40)
REVERT: A  665 PHE cc_start: 0.8444 (t80) cc_final: 0.8040 (t80)
REVERT: A  913 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8693 (pp)
REVERT: A 1117 GLU cc_start: 0.7599 (pt0) cc_final: 0.7379 (pt0)
REVERT: A 1218 MET cc_start: 0.4936 (mmm) cc_final: 0.3375 (mtp)
REVERT: A 1252 HIS cc_start: 0.7270 (p-80) cc_final: 0.6375 (t70)
  outliers start: 46
  outliers final: 37
  residues processed: 156
  average time/residue: 0.0868
  time to fit residues: 20.7195
Evaluate side-chains
  160 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 121
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  321 SER
Chi-restraints excluded: chain A residue  333 ASN
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  547 GLU
Chi-restraints excluded: chain A residue  582 HIS
Chi-restraints excluded: chain A residue  593 HIS
Chi-restraints excluded: chain A residue  629 LEU
Chi-restraints excluded: chain A residue  661 TYR
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain A residue  698 TRP
Chi-restraints excluded: chain A residue  733 TYR
Chi-restraints excluded: chain A residue  738 CYS
Chi-restraints excluded: chain A residue  743 ILE
Chi-restraints excluded: chain A residue  759 ASP
Chi-restraints excluded: chain A residue  777 MET
Chi-restraints excluded: chain A residue  806 GLU
Chi-restraints excluded: chain A residue  913 LEU
Chi-restraints excluded: chain A residue  931 ASN
Chi-restraints excluded: chain A residue  943 ILE
Chi-restraints excluded: chain A residue  972 HIS
Chi-restraints excluded: chain A residue 1030 ILE
Chi-restraints excluded: chain A residue 1048 ILE
Chi-restraints excluded: chain A residue 1086 VAL
Chi-restraints excluded: chain A residue 1091 SER
Chi-restraints excluded: chain A residue 1104 THR
Chi-restraints excluded: chain A residue 1144 CYS
Chi-restraints excluded: chain A residue 1145 THR
Chi-restraints excluded: chain A residue 1156 ASP
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1240 SER
Chi-restraints excluded: chain A residue 1338 MET
Chi-restraints excluded: chain A residue 1387 SER
Chi-restraints excluded: chain A residue 1395 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 108 optimal weight:    5.9990
   chunk 98 optimal weight:    0.0970
   chunk 124 optimal weight:    0.9980
   chunk 77 optimal weight:    6.9990
   chunk 80 optimal weight:    2.9990
   chunk 126 optimal weight:    0.9990
   chunk 57 optimal weight:    3.9990
   chunk 74 optimal weight:    0.8980
   chunk 113 optimal weight:    3.9990
   chunk 18 optimal weight:    9.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 333 ASN
A 421 HIS
** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1054 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.144640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.104696 restraints weight = 17681.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.109077 restraints weight = 10828.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.111757 restraints weight = 7129.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.111941 restraints weight = 6148.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.112611 restraints weight = 6057.932|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.4555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  11569  Z= 0.108
  Angle     :  0.512   8.157  15714  Z= 0.267
  Chirality :  0.040   0.140   1727
  Planarity :  0.003   0.037   1974
  Dihedral  : 11.079  82.440   1703
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 16.16 %
    Favored  : 79.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.79 (0.22), residues: 1365
  helix:  1.69 (0.24), residues: 486
  sheet:  1.16 (0.42), residues: 166
  loop : -0.45 (0.22), residues: 713

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 589 
 TYR   0.018   0.001   TYR A 702 
 PHE   0.014   0.001   PHE A 630 
 TRP   0.011   0.001   TRP A 837 
 HIS   0.009   0.001   HIS A1054 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 (11565)
  covalent geometry    : angle       0.50658 (15708)
  hydrogen bonds       : bond        0.03484 (  424)
  hydrogen bonds       : angle       4.42598 ( 1182)
  metal coordination   : bond        0.00554 (    4)
  metal coordination   : angle       3.89336 (    6)

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

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

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 125
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
REVERT: A  169 LEU cc_start: 0.8837 (mt) cc_final: 0.8612 (tp)
REVERT: A  233 LYS cc_start: 0.7925 (tptt) cc_final: 0.7590 (tptp)
REVERT: A  343 ASP cc_start: 0.7505 (t0) cc_final: 0.6712 (p0)
REVERT: A  390 ILE cc_start: 0.8621 (tp) cc_final: 0.8387 (tp)
REVERT: A  512 MET cc_start: 0.8479 (tpp) cc_final: 0.8257 (tpp)
REVERT: A  547 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6962 (mt-10)
REVERT: A  587 GLN cc_start: 0.7364 (tp40) cc_final: 0.7057 (tp40)
REVERT: A  637 MET cc_start: 0.7819 (mtm) cc_final: 0.7285 (mtt)
REVERT: A  665 PHE cc_start: 0.8465 (t80) cc_final: 0.8066 (t80)
REVERT: A  759 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7925 (t0)
REVERT: A  913 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8676 (pp)
REVERT: A  973 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7034 (tpt90)
REVERT: A 1117 GLU cc_start: 0.7626 (pt0) cc_final: 0.7397 (pt0)
REVERT: A 1218 MET cc_start: 0.4953 (mmm) cc_final: 0.3390 (mtp)
REVERT: A 1252 HIS cc_start: 0.7205 (p-80) cc_final: 0.6311 (t70)
REVERT: A 1367 THR cc_start: 0.9188 (m) cc_final: 0.8926 (m)
  outliers start: 49
  outliers final: 37
  residues processed: 159
  average time/residue: 0.0842
  time to fit residues: 20.6558
Evaluate side-chains
  161 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 120
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  321 SER
Chi-restraints excluded: chain A residue  333 ASN
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  547 GLU
Chi-restraints excluded: chain A residue  582 HIS
Chi-restraints excluded: chain A residue  593 HIS
Chi-restraints excluded: chain A residue  629 LEU
Chi-restraints excluded: chain A residue  661 TYR
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain A residue  698 TRP
Chi-restraints excluded: chain A residue  738 CYS
Chi-restraints excluded: chain A residue  743 ILE
Chi-restraints excluded: chain A residue  751 HIS
Chi-restraints excluded: chain A residue  759 ASP
Chi-restraints excluded: chain A residue  777 MET
Chi-restraints excluded: chain A residue  806 GLU
Chi-restraints excluded: chain A residue  913 LEU
Chi-restraints excluded: chain A residue  931 ASN
Chi-restraints excluded: chain A residue  943 ILE
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue  972 HIS
Chi-restraints excluded: chain A residue  973 ARG
Chi-restraints excluded: chain A residue 1086 VAL
Chi-restraints excluded: chain A residue 1091 SER
Chi-restraints excluded: chain A residue 1104 THR
Chi-restraints excluded: chain A residue 1144 CYS
Chi-restraints excluded: chain A residue 1145 THR
Chi-restraints excluded: chain A residue 1156 ASP
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1195 ILE
Chi-restraints excluded: chain A residue 1205 VAL
Chi-restraints excluded: chain A residue 1240 SER
Chi-restraints excluded: chain A residue 1338 MET
Chi-restraints excluded: chain A residue 1387 SER
Chi-restraints excluded: chain A residue 1395 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 93 optimal weight:    0.8980
   chunk 47 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0010
   chunk 3 optimal weight:    6.9990
   chunk 85 optimal weight:    5.9990
   chunk 130 optimal weight:    0.7980
   chunk 100 optimal weight:    5.9990
   chunk 128 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 107 optimal weight:    6.9990
   overall best weight:    1.0788

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

Flipped N/Q/H residues before XYZ refinement:
A 333 ASN
A 421 HIS
** A 587 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 = 0.3810 r_free = 0.3810 target = 0.144084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.103994 restraints weight = 17817.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.108698 restraints weight = 10977.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.111214 restraints weight = 7099.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.111386 restraints weight = 6157.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.111671 restraints weight = 5892.348|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.4617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11569  Z= 0.121
  Angle     :  0.514   7.318  15714  Z= 0.269
  Chirality :  0.040   0.139   1727
  Planarity :  0.003   0.036   1974
  Dihedral  : 11.057  82.074   1703
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 16.74 %
    Favored  : 79.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.76 (0.22), residues: 1365
  helix:  1.69 (0.24), residues: 487
  sheet:  1.15 (0.41), residues: 172
  loop : -0.50 (0.22), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1459 
 TYR   0.018   0.001   TYR A 702 
 PHE   0.014   0.001   PHE A 630 
 TRP   0.020   0.001   TRP A 837 
 HIS   0.006   0.001   HIS A 582 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (11565)
  covalent geometry    : angle       0.50841 (15708)
  hydrogen bonds       : bond        0.03642 (  424)
  hydrogen bonds       : angle       4.43502 ( 1182)
  metal coordination   : bond        0.00654 (    4)
  metal coordination   : angle       3.92159 (    6)

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

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

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 121
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
REVERT: A  169 LEU cc_start: 0.8772 (mt) cc_final: 0.8541 (tp)
REVERT: A  233 LYS cc_start: 0.7933 (tptt) cc_final: 0.7584 (tptp)
REVERT: A  343 ASP cc_start: 0.7466 (t0) cc_final: 0.6720 (p0)
REVERT: A  390 ILE cc_start: 0.8626 (tp) cc_final: 0.8388 (tp)
REVERT: A  512 MET cc_start: 0.8478 (tpp) cc_final: 0.8229 (tpp)
REVERT: A  547 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6988 (mt-10)
REVERT: A  587 GLN cc_start: 0.7300 (tp40) cc_final: 0.7079 (tp40)
REVERT: A  665 PHE cc_start: 0.8453 (t80) cc_final: 0.8087 (t80)
REVERT: A  913 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8684 (pp)
REVERT: A  973 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7052 (tpt90)
REVERT: A 1117 GLU cc_start: 0.7664 (pt0) cc_final: 0.7438 (pt0)
REVERT: A 1218 MET cc_start: 0.5019 (mmm) cc_final: 0.3467 (mtp)
REVERT: A 1252 HIS cc_start: 0.7231 (p-80) cc_final: 0.6321 (t70)
  outliers start: 45
  outliers final: 37
  residues processed: 153
  average time/residue: 0.0843
  time to fit residues: 20.0130
Evaluate side-chains
  156 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 116
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  321 SER
Chi-restraints excluded: chain A residue  333 ASN
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  547 GLU
Chi-restraints excluded: chain A residue  582 HIS
Chi-restraints excluded: chain A residue  593 HIS
Chi-restraints excluded: chain A residue  661 TYR
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain A residue  698 TRP
Chi-restraints excluded: chain A residue  738 CYS
Chi-restraints excluded: chain A residue  743 ILE
Chi-restraints excluded: chain A residue  751 HIS
Chi-restraints excluded: chain A residue  777 MET
Chi-restraints excluded: chain A residue  806 GLU
Chi-restraints excluded: chain A residue  913 LEU
Chi-restraints excluded: chain A residue  931 ASN
Chi-restraints excluded: chain A residue  943 ILE
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue  972 HIS
Chi-restraints excluded: chain A residue  973 ARG
Chi-restraints excluded: chain A residue 1086 VAL
Chi-restraints excluded: chain A residue 1091 SER
Chi-restraints excluded: chain A residue 1104 THR
Chi-restraints excluded: chain A residue 1144 CYS
Chi-restraints excluded: chain A residue 1145 THR
Chi-restraints excluded: chain A residue 1156 ASP
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1195 ILE
Chi-restraints excluded: chain A residue 1205 VAL
Chi-restraints excluded: chain A residue 1240 SER
Chi-restraints excluded: chain A residue 1338 MET
Chi-restraints excluded: chain A residue 1387 SER
Chi-restraints excluded: chain A residue 1395 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 94 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 8 optimal weight:    7.9990
   chunk 104 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 77 optimal weight:    6.9990
   chunk 72 optimal weight:    5.9990
   chunk 129 optimal weight:    0.7980
   chunk 90 optimal weight:   10.0000
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 333 ASN
A 421 HIS
** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 672 ASN
A1054 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.146669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.106755 restraints weight = 17743.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.111933 restraints weight = 10857.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.113587 restraints weight = 7043.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.113818 restraints weight = 6079.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.114178 restraints weight = 6231.728|
|-----------------------------------------------------------------------------|
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.4691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11569  Z= 0.110
  Angle     :  0.508   7.168  15714  Z= 0.265
  Chirality :  0.040   0.139   1727
  Planarity :  0.003   0.036   1974
  Dihedral  : 10.999  81.851   1703
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 16.82 %
    Favored  : 79.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.76 (0.22), residues: 1365
  helix:  1.71 (0.24), residues: 487
  sheet:  1.09 (0.40), residues: 172
  loop : -0.50 (0.22), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 786 
 TYR   0.017   0.001   TYR A 702 
 PHE   0.014   0.001   PHE A 630 
 TRP   0.016   0.001   TRP A 837 
 HIS   0.006   0.001   HIS A 582 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 (11565)
  covalent geometry    : angle       0.50237 (15708)
  hydrogen bonds       : bond        0.03473 (  424)
  hydrogen bonds       : angle       4.40253 ( 1182)
  metal coordination   : bond        0.00563 (    4)
  metal coordination   : angle       3.72520 (    6)

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

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

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 122
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 LEU cc_start: 0.8827 (mt) cc_final: 0.8602 (tp)
REVERT: A  233 LYS cc_start: 0.7883 (tptt) cc_final: 0.7537 (tptp)
REVERT: A  343 ASP cc_start: 0.7482 (t0) cc_final: 0.6707 (p0)
REVERT: A  390 ILE cc_start: 0.8584 (tp) cc_final: 0.8344 (tp)
REVERT: A  547 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.7030 (mt-10)
REVERT: A  637 MET cc_start: 0.7726 (mtm) cc_final: 0.7186 (mtt)
REVERT: A  665 PHE cc_start: 0.8464 (t80) cc_final: 0.8108 (t80)
REVERT: A  913 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8684 (pp)
REVERT: A  973 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7049 (tpt90)
REVERT: A 1117 GLU cc_start: 0.7686 (pt0) cc_final: 0.7440 (pt0)
REVERT: A 1218 MET cc_start: 0.5016 (mmm) cc_final: 0.3473 (mtp)
REVERT: A 1252 HIS cc_start: 0.7325 (p-80) cc_final: 0.6356 (t70)
REVERT: A 1367 THR cc_start: 0.9224 (m) cc_final: 0.8963 (m)
  outliers start: 44
  outliers final: 39
  residues processed: 150
  average time/residue: 0.0836
  time to fit residues: 19.4760
Evaluate side-chains
  163 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 121
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  321 SER
Chi-restraints excluded: chain A residue  333 ASN
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  547 GLU
Chi-restraints excluded: chain A residue  582 HIS
Chi-restraints excluded: chain A residue  593 HIS
Chi-restraints excluded: chain A residue  661 TYR
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain A residue  698 TRP
Chi-restraints excluded: chain A residue  738 CYS
Chi-restraints excluded: chain A residue  743 ILE
Chi-restraints excluded: chain A residue  751 HIS
Chi-restraints excluded: chain A residue  777 MET
Chi-restraints excluded: chain A residue  806 GLU
Chi-restraints excluded: chain A residue  913 LEU
Chi-restraints excluded: chain A residue  931 ASN
Chi-restraints excluded: chain A residue  943 ILE
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue  972 HIS
Chi-restraints excluded: chain A residue  973 ARG
Chi-restraints excluded: chain A residue 1048 ILE
Chi-restraints excluded: chain A residue 1054 HIS
Chi-restraints excluded: chain A residue 1086 VAL
Chi-restraints excluded: chain A residue 1091 SER
Chi-restraints excluded: chain A residue 1104 THR
Chi-restraints excluded: chain A residue 1144 CYS
Chi-restraints excluded: chain A residue 1145 THR
Chi-restraints excluded: chain A residue 1156 ASP
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1195 ILE
Chi-restraints excluded: chain A residue 1205 VAL
Chi-restraints excluded: chain A residue 1240 SER
Chi-restraints excluded: chain A residue 1338 MET
Chi-restraints excluded: chain A residue 1387 SER
Chi-restraints excluded: chain A residue 1395 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 104 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0980
   chunk 34 optimal weight:    0.9980
   chunk 68 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 126 optimal weight:    1.9990
   chunk 135 optimal weight:    3.9990
   chunk 37 optimal weight:    0.6980
   chunk 84 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 333 ASN
** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1054 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.147594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.107516 restraints weight = 18014.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.112523 restraints weight = 10994.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.114110 restraints weight = 7248.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.114221 restraints weight = 6311.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.114781 restraints weight = 6322.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.4747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  11569  Z= 0.103
  Angle     :  0.499   6.933  15714  Z= 0.261
  Chirality :  0.040   0.138   1727
  Planarity :  0.003   0.037   1974
  Dihedral  : 10.960  81.827   1703
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 16.74 %
    Favored  : 79.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.77 (0.22), residues: 1365
  helix:  1.73 (0.24), residues: 487
  sheet:  1.03 (0.41), residues: 166
  loop : -0.47 (0.22), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 786 
 TYR   0.017   0.001   TYR A 702 
 PHE   0.014   0.001   PHE A 630 
 TRP   0.013   0.001   TRP A 837 
 HIS   0.010   0.001   HIS A1054 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 (11565)
  covalent geometry    : angle       0.49442 (15708)
  hydrogen bonds       : bond        0.03360 (  424)
  hydrogen bonds       : angle       4.35999 ( 1182)
  metal coordination   : bond        0.00513 (    4)
  metal coordination   : angle       3.60188 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1665.69 seconds
wall clock time: 29 minutes 33.36 seconds (1773.36 seconds total)