Starting phenix.real_space_refine
on Fri Feb 14 09:06:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6pza_20530/02_2025/6pza_20530_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6pza_20530/02_2025/6pza_20530.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.74
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6pza_20530/02_2025/6pza_20530.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6pza_20530/02_2025/6pza_20530.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6pza_20530/02_2025/6pza_20530_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6pza_20530/02_2025/6pza_20530_neut.cif"
  }
  resolution = 3.74
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
-------------------------------------------------------------------------------
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=   0.001 sd=   0.004
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
     P       3      5.49       5
     S      34      5.16       5
     Cl      1      4.86       5
     C    6209      2.51       5
     N    1717      2.21       5
     O    1695      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9659
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 9501
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1422, 9501
          Classifications: {'peptide': 1422}
          Incomplete info: {'truncation_to_alanine': 543}
          Link IDs: {'CIS': 1, 'PTRANS': 48, 'TRANS': 1372}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 1768
          Unresolved non-hydrogen angles: 2233
          Unresolved non-hydrogen dihedrals: 1378
          Unresolved non-hydrogen chiralities: 225
          Planarities with less than four sites: {'GLN:plan1': 32, 'ASP:plan': 41, 'TYR:plan': 2, 'ASN:plan1': 21, 'TRP:plan': 3, 'HIS:plan': 7, 'PHE:plan': 17, 'GLU:plan': 44, 'ARG:plan': 33}
          Unresolved non-hydrogen planarities: 833
    Chain: "D"
      Number of atoms: 94
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 94
          Classifications: {'peptide': 19}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 1, 'TRANS': 17}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 62
          Unresolved non-hydrogen angles: 78
          Unresolved non-hydrogen dihedrals: 50
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 29
    Chain: "C"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 64
          Unusual residues: {'ATP': 1, 'GBM': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 6.09, per 1000 atoms: 0.63
  Number of scatterers: 9659
  At special positions: 0
  Unit cell: (96.615, 110.295, 140.22, 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)
     Cl      1     17.00
     S      34     16.00
     P       3     15.00
     O    1695      8.00
     N    1717      7.00
     C    6209      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS C   6 " - pdb=" SG  CYS C  26 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.40
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2730

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 8 sheets defined
      66.3% alpha, 3.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.30
  Creating SS restraints...
    Processing helix  chain 'C' and resid 12 through 16
      removed outlier: 3.613A  pdb=" N   ARG C  16 " --> pdb=" O   ALA C  13 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 55
      removed outlier: 3.885A  pdb=" N   VAL C  34 " --> pdb=" O   ALA C  30 " (cutoff:3.500A)
      Proline residue:  C  35  - end of helix
      Proline residue:  C  45  - end of helix
    Processing helix  chain 'C' and resid 58 through 63
      removed outlier: 3.604A  pdb=" N   HIS C  61 " --> pdb=" O   VAL C  58 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   HIS C  62 " --> pdb=" O   HIS C  59 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 71 through 97
    Processing helix  chain 'C' and resid 108 through 130
      removed outlier: 3.599A  pdb=" N   TYR C 124 " --> pdb=" O   SER C 120 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   SER C 130 " --> pdb=" O   ASN C 126 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 132 through 135
    Processing helix  chain 'C' and resid 136 through 160
    Processing helix  chain 'C' and resid 166 through 194
      removed outlier: 3.993A  pdb=" N   CYS C 170 " --> pdb=" O   GLN C 166 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 207 through 212
    Processing helix  chain 'C' and resid 223 through 230
    Processing helix  chain 'C' and resid 232 through 238
      removed outlier: 4.019A  pdb=" N   PHE C 236 " --> pdb=" O   TRP C 232 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 239 through 242
    Processing helix  chain 'C' and resid 254 through 257
    Processing helix  chain 'C' and resid 258 through 277
    Processing helix  chain 'C' and resid 283 through 314
      removed outlier: 5.732A  pdb=" N   ARG C 297 " --> pdb=" O   HIS C 293 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   ARG C 298 " --> pdb=" O   ALA C 294 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   LEU C 301 " --> pdb=" O   ARG C 297 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 316 through 328
    Processing helix  chain 'C' and resid 329 through 332
      removed outlier: 3.897A  pdb=" N   HIS C 332 " --> pdb=" O   LYS C 329 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 329 through 332'
    Processing helix  chain 'C' and resid 347 through 352
    Processing helix  chain 'C' and resid 355 through 398
      removed outlier: 3.505A  pdb=" N   LEU C 368 " --> pdb=" O   LEU C 364 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   THR C 371 " --> pdb=" O   LEU C 367 " (cutoff:3.500A)
      removed outlier: 4.846A  pdb=" N   GLN C 374 " --> pdb=" O   ARG C 370 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 413 through 432
      removed outlier: 3.510A  pdb=" N   ILE C 417 " --> pdb=" O   THR C 413 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ASP C 424 " --> pdb=" O   LEU C 420 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   THR C 425 " --> pdb=" O   VAL C 421 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 436 through 456
      Proline residue:  C 442  - end of helix
    Processing helix  chain 'C' and resid 457 through 468
      removed outlier: 3.662A  pdb=" N   LEU C 461 " --> pdb=" O   GLY C 457 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 470 through 504
      removed outlier: 3.539A  pdb=" N   GLN C 474 " --> pdb=" O   LEU C 470 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   GLU C 494 " --> pdb=" O   GLU C 490 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 505 through 512
      removed outlier: 3.703A  pdb=" N   TYR C 512 " --> pdb=" O   LEU C 508 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 515 through 564
      removed outlier: 4.277A  pdb=" N   THR C 525 " --> pdb=" O   ARG C 521 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   SER C 543 " --> pdb=" O   TYR C 539 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ILE C 544 " --> pdb=" O   THR C 540 " (cutoff:3.500A)
      Proline residue:  C 551  - end of helix
    Processing helix  chain 'C' and resid 572 through 615
      Proline residue:  C 589  - end of helix
      removed outlier: 3.972A  pdb=" N   LEU C 592 " --> pdb=" O   THR C 588 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   SER C 594 " --> pdb=" O   LEU C 590 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   SER C 595 " --> pdb=" O   PHE C 591 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 718 through 727
    Processing helix  chain 'C' and resid 785 through 790
    Processing helix  chain 'C' and resid 795 through 806
    Processing helix  chain 'C' and resid 808 through 815
      removed outlier: 3.870A  pdb=" N   LEU C 815 " --> pdb=" O   ASP C 811 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 831 through 846
      removed outlier: 3.698A  pdb=" N   GLN C 846 " --> pdb=" O   ARG C 842 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 862 through 879
    Processing helix  chain 'C' and resid 996 through 1009
      removed outlier: 3.602A  pdb=" N   GLY C1009 " --> pdb=" O   LEU C1005 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1009 through 1043
      removed outlier: 4.494A  pdb=" N   LEU C1015 " --> pdb=" O   LEU C1011 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1061 through 1107
      removed outlier: 3.906A  pdb=" N   LEU C1074 " --> pdb=" O   LEU C1070 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   GLU C1087 " --> pdb=" O   SER C1083 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1109 through 1116
      removed outlier: 4.033A  pdb=" N   PHE C1113 " --> pdb=" O   PRO C1109 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1117 through 1135
      removed outlier: 3.716A  pdb=" N   ILE C1121 " --> pdb=" O   PRO C1117 " (cutoff:3.500A)
      removed outlier: 4.733A  pdb=" N   ASP C1128 " --> pdb=" O   ARG C1124 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   HIS C1135 " --> pdb=" O   THR C1131 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1135 through 1161
      removed outlier: 4.000A  pdb=" N   LEU C1148 " --> pdb=" O   SER C1144 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1163 through 1210
      removed outlier: 3.744A  pdb=" N   ALA C1167 " --> pdb=" O   VAL C1163 " (cutoff:3.500A)
      Proline residue:  C1170  - end of helix
      removed outlier: 3.720A  pdb=" N   ASP C1188 " --> pdb=" O   VAL C1184 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   THR C1196 " --> pdb=" O   LEU C1192 " (cutoff:3.500A)
      Proline residue:  C1199  - end of helix
      removed outlier: 3.587A  pdb=" N   VAL C1208 " --> pdb=" O   PHE C1204 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   GLY C1210 " --> pdb=" O   GLU C1206 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1210 through 1218
      removed outlier: 3.769A  pdb=" N   ILE C1214 " --> pdb=" O   GLY C1210 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ARG C1218 " --> pdb=" O   ILE C1214 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1219 through 1273
      removed outlier: 3.927A  pdb=" N   PHE C1223 " --> pdb=" O   TYR C1219 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ALA C1237 " --> pdb=" O   SER C1233 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   HIS C1273 " --> pdb=" O   SER C1269 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1278 through 1292
      removed outlier: 3.522A  pdb=" N   GLY C1282 " --> pdb=" O   ALA C1278 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   TYR C1287 " --> pdb=" O   LEU C1283 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   MET C1290 " --> pdb=" O   THR C1286 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   SER C1292 " --> pdb=" O   ALA C1288 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1294 through 1320
      removed outlier: 3.806A  pdb=" N   ALA C1311 " --> pdb=" O   ILE C1307 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   VAL C1312 " --> pdb=" O   GLN C1308 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   ILE C1315 " --> pdb=" O   ALA C1311 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1385 through 1392
    Processing helix  chain 'C' and resid 1414 through 1419
    Processing helix  chain 'C' and resid 1435 through 1441
    Processing helix  chain 'C' and resid 1447 through 1458
      removed outlier: 3.596A  pdb=" N   LEU C1451 " --> pdb=" O   SER C1447 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1460 through 1465
    Processing helix  chain 'C' and resid 1484 through 1498
      removed outlier: 4.140A  pdb=" N   GLN C1488 " --> pdb=" O   GLN C1484 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1512 through 1531
    Processing helix  chain 'C' and resid 1539 through 1543
      removed outlier: 3.525A  pdb=" N   ILE C1543 " --> pdb=" O   VAL C1540 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1564 through 1570
      removed outlier: 4.193A  pdb=" N   SER C1568 " --> pdb=" O   GLU C1564 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1571 through 1578
    Processing sheet with id=AA1, first strand: chain 'C' and resid 338 through 340
      removed outlier: 4.227A  pdb=" N   THR C 338 " --> pdb=" O   PHE C 345 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 702 through 703
    Processing sheet with id=AA3, first strand: chain 'C' and resid 852 through 853
      removed outlier: 4.264A  pdb=" N   ILE C 901 " --> pdb=" O   MET C 710 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   VAL C 712 " --> pdb=" O   ILE C 901 " (cutoff:3.500A)
      removed outlier: 7.220A  pdb=" N   ALA C 902 " --> pdb=" O   GLN C 909 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 1366 through 1368
      removed outlier: 4.391A  pdb=" N   GLN C1346 " --> pdb=" O   ILE C1404 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ILE C1404 " --> pdb=" O   GLN C1346 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 1352 through 1353
    Processing sheet with id=AA6, first strand: chain 'C' and resid 1375 through 1376
    Processing sheet with id=AA7, first strand: chain 'C' and resid 1422 through 1424
      removed outlier: 6.898A  pdb=" N   SER C1423 " --> pdb=" O   ILE C1504 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'C' and resid 1549 through 1551

    698 hydrogen bonds defined for protein.
    2052 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.55

  Time building geometry restraints manager: 2.78 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1543
        1.31 -     1.43: 2702
        1.43 -     1.56: 5567
        1.56 -     1.68: 7
        1.68 -     1.81: 53
  Bond restraints: 9872
  Sorted by residual:
  bond pdb=" O5  GBM C1601 "
       pdb=" S2  GBM C1601 "
    ideal  model  delta    sigma   weight residual
    1.448  1.648 -0.200 2.00e-02 2.50e+03 9.97e+01
  bond pdb=" O4  GBM C1601 "
       pdb=" S2  GBM C1601 "
    ideal  model  delta    sigma   weight residual
    1.453  1.647 -0.194 2.00e-02 2.50e+03 9.43e+01
  bond pdb=" C4  ATP C1602 "
       pdb=" C5  ATP C1602 "
    ideal  model  delta    sigma   weight residual
    1.388  1.467 -0.079 1.00e-02 1.00e+04 6.26e+01
  bond pdb=" C5  ATP C1602 "
       pdb=" C6  ATP C1602 "
    ideal  model  delta    sigma   weight residual
    1.409  1.475 -0.066 1.00e-02 1.00e+04 4.31e+01
  bond pdb=" C17 GBM C1601 "
       pdb=" N8  GBM C1601 "
    ideal  model  delta    sigma   weight residual
    1.340  1.443 -0.103 2.00e-02 2.50e+03 2.65e+01
  ... (remaining 9867 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.44: 13477
        4.44 -     8.88: 84
        8.88 -    13.32: 12
       13.32 -    17.76: 1
       17.76 -    22.20: 2
  Bond angle restraints: 13576
  Sorted by residual:
  angle pdb=" PB  ATP C1602 "
        pdb=" O3B ATP C1602 "
        pdb=" PG  ATP C1602 "
      ideal   model   delta    sigma   weight residual
     139.87  117.67   22.20 1.00e+00 1.00e+00 4.93e+02
  angle pdb=" PA  ATP C1602 "
        pdb=" O3A ATP C1602 "
        pdb=" PB  ATP C1602 "
      ideal   model   delta    sigma   weight residual
     136.83  117.58   19.25 1.00e+00 1.00e+00 3.70e+02
  angle pdb=" C5  ATP C1602 "
        pdb=" C4  ATP C1602 "
        pdb=" N3  ATP C1602 "
      ideal   model   delta    sigma   weight residual
     126.80  119.13    7.67 1.00e+00 1.00e+00 5.88e+01
  angle pdb=" C   LEU C 571 "
        pdb=" N   SER C 572 "
        pdb=" CA  SER C 572 "
      ideal   model   delta    sigma   weight residual
     121.70  134.37  -12.67 1.80e+00 3.09e-01 4.95e+01
  angle pdb=" N3  ATP C1602 "
        pdb=" C4  ATP C1602 "
        pdb=" N9  ATP C1602 "
      ideal   model   delta    sigma   weight residual
     127.04  135.10   -8.06 1.15e+00 7.59e-01 4.93e+01
  ... (remaining 13571 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.79: 5444
       16.79 -    33.58: 219
       33.58 -    50.37: 47
       50.37 -    67.16: 6
       67.16 -    83.95: 5
  Dihedral angle restraints: 5721
    sinusoidal: 1521
      harmonic: 4200
  Sorted by residual:
  dihedral pdb=" CA  LYS C 252 "
           pdb=" C   LYS C 252 "
           pdb=" N   LEU C 253 "
           pdb=" CA  LEU C 253 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  132.03   47.97     0      5.00e+00 4.00e-02 9.20e+01
  dihedral pdb=" CA  ILE C 996 "
           pdb=" C   ILE C 996 "
           pdb=" N   PRO C 997 "
           pdb=" CA  PRO C 997 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -137.86  -42.14     0      5.00e+00 4.00e-02 7.10e+01
  dihedral pdb=" CA  LYS C1562 "
           pdb=" C   LYS C1562 "
           pdb=" N   PRO C1563 "
           pdb=" CA  PRO C1563 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.85   28.15     0      5.00e+00 4.00e-02 3.17e+01
  ... (remaining 5718 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1144
       0.056 -    0.111: 416
       0.111 -    0.167: 75
       0.167 -    0.222: 7
       0.222 -    0.278: 4
  Chirality restraints: 1646
  Sorted by residual:
  chirality pdb=" CG  LEU C1248 "
            pdb=" CB  LEU C1248 "
            pdb=" CD1 LEU C1248 "
            pdb=" CD2 LEU C1248 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.31   -0.28 2.00e-01 2.50e+01 1.93e+00
  chirality pdb=" CA  LEU C 175 "
            pdb=" N   LEU C 175 "
            pdb=" C   LEU C 175 "
            pdb=" CB  LEU C 175 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.33e+00
  chirality pdb=" C1' ATP C1602 "
            pdb=" C2' ATP C1602 "
            pdb=" N9  ATP C1602 "
            pdb=" O4' ATP C1602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.41    2.64   -0.23 2.00e-01 2.50e+01 1.29e+00
  ... (remaining 1643 not shown)

  Planarity restraints: 1752
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C 420 "   -0.017 2.00e-02 2.50e+03   3.33e-02 1.11e+01
        pdb=" C   LEU C 420 "    0.058 2.00e-02 2.50e+03
        pdb=" O   LEU C 420 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   VAL C 421 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET C 441 "    0.043 5.00e-02 4.00e+02   6.50e-02 6.76e+00
        pdb=" N   PRO C 442 "   -0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO C 442 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO C 442 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C1037 "    0.023 2.00e-02 2.50e+03   1.62e-02 6.53e+00
        pdb=" CG  TRP C1037 "   -0.044 2.00e-02 2.50e+03
        pdb=" CD1 TRP C1037 "    0.011 2.00e-02 2.50e+03
        pdb=" CD2 TRP C1037 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP C1037 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP C1037 "    0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP C1037 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C1037 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C1037 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP C1037 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1749 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2259
        2.78 -     3.31: 9152
        3.31 -     3.84: 15453
        3.84 -     4.37: 16243
        4.37 -     4.90: 28403
  Nonbonded interactions: 71510
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C 123 "
            pdb=" O   LEU C 135 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" OD2 ASP C1128 "
            pdb=" NH1 ARG C1314 "
     model   vdw
     2.271 3.120
  nonbonded pdb=" O   GLU C 791 "
            pdb=" OH  TYR C1219 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" OG1 THR C 338 "
            pdb=" O   PHE C 345 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" O   THR C 789 "
            pdb=" OG  SER C 792 "
     model   vdw
     2.308 3.040
  ... (remaining 71505 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:             0.470
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     25.190
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5080
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      :  0.008   0.200   9872  Z= 0.558
  Angle     :  1.063  22.204  13576  Z= 0.612
  Chirality :  0.058   0.278   1646
  Planarity :  0.008   0.065   1752
  Dihedral  : 11.133  83.951   2988
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.98 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 2.04 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.29 (0.17), residues: 1429
  helix: -2.33 (0.12), residues: 915
  sheet: -3.78 (0.52), residues: 60
  loop : -3.46 (0.26), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.003   TRP C1037 
 HIS   0.012   0.002   HIS C1098 
 PHE   0.040   0.003   PHE C 432 
 TYR   0.033   0.003   TYR C 179 
 ARG   0.014   0.002   ARG C1145 

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

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

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 0.968 
Fit side-chains
   revert: symmetry clash
REVERT: C  112 MET cc_start: 0.6739 (mtm) cc_final: 0.6412 (mtp)
REVERT: C  301 LEU cc_start: 0.6998 (tp) cc_final: 0.6398 (tt)
REVERT: C  393 THR cc_start: 0.5310 (m) cc_final: 0.5049 (t)
REVERT: C 1163 VAL cc_start: 0.6894 (t) cc_final: 0.6651 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 223
  average time/residue: 0.2306
  time to fit residues: 71.4998
Evaluate side-chains
  143 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 1.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 120 optimal weight:   50.0000
   chunk 108 optimal weight:    0.9980
   chunk 60 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 73 optimal weight:   50.0000
   chunk 57 optimal weight:    6.9990
   chunk 112 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9990
   chunk 68 optimal weight:    0.0070
   chunk 83 optimal weight:   50.0000
   chunk 129 optimal weight:   50.0000
   overall best weight:    1.4002

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

Flipped N/Q/H residues before XYZ refinement:
C 160 HIS
C 219 GLN
C 374 GLN
C 397 ASN
C 707 GLN
C 896 HIS
** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.134661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.113217 restraints weight = 17728.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.115908 restraints weight = 8323.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.117634 restraints weight = 4851.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6013
moved from start:          0.2875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9872  Z= 0.212
  Angle     :  0.698   9.082  13576  Z= 0.362
  Chirality :  0.044   0.243   1646
  Planarity :  0.006   0.062   1752
  Dihedral  :  6.890  73.229   1561
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 12.25 %
    Favored  : 83.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 2.04 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.86 (0.21), residues: 1429
  helix: -0.14 (0.16), residues: 924
  sheet: -3.56 (0.53), residues: 64
  loop : -3.16 (0.27), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C  65 
 HIS   0.005   0.001   HIS C 867 
 PHE   0.022   0.002   PHE C 432 
 TYR   0.032   0.002   TYR C 123 
 ARG   0.007   0.001   ARG C 826 

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

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

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 174
  time to evaluate  : 1.078 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 28
  outliers final: 11
  residues processed: 191
  average time/residue: 0.1990
  time to fit residues: 56.0454
Evaluate side-chains
  155 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 144
  time to evaluate  : 1.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue  264 GLN
Chi-restraints excluded: chain C residue  319 CYS
Chi-restraints excluded: chain C residue  456 LEU
Chi-restraints excluded: chain C residue  531 THR
Chi-restraints excluded: chain C residue  542 ILE
Chi-restraints excluded: chain C residue 1028 VAL
Chi-restraints excluded: chain C residue 1192 LEU
Chi-restraints excluded: chain C residue 1213 THR
Chi-restraints excluded: chain C residue 1242 THR
Chi-restraints excluded: chain C residue 1272 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 61 optimal weight:    9.9990
   chunk 132 optimal weight:    1.9990
   chunk 113 optimal weight:    0.5980
   chunk 32 optimal weight:    6.9990
   chunk 49 optimal weight:    6.9990
   chunk 131 optimal weight:    2.9990
   chunk 33 optimal weight:    8.9990
   chunk 70 optimal weight:   20.0000
   chunk 47 optimal weight:    0.8980
   chunk 79 optimal weight:   20.0000
   chunk 40 optimal weight:   10.0000
   overall best weight:    2.6986

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

Flipped N/Q/H residues before XYZ refinement:
** C  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  72 ASN
C 105 HIS
C 125 HIS
C 262 ASN
** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1224 GLN
C1245 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.137429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.113000 restraints weight = 18411.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.115876 restraints weight = 8596.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.117824 restraints weight = 5050.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7116
moved from start:          0.6008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   9872  Z= 0.288
  Angle     :  0.764  14.950  13576  Z= 0.391
  Chirality :  0.048   0.257   1646
  Planarity :  0.005   0.052   1752
  Dihedral  :  6.838  71.996   1561
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 17.00 %
    Favored  : 77.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 2.04 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.94 (0.22), residues: 1429
  helix:  0.61 (0.17), residues: 926
  sheet: -3.32 (0.54), residues: 64
  loop : -2.91 (0.28), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP C  65 
 HIS   0.013   0.002   HIS C  36 
 PHE   0.028   0.003   PHE C 314 
 TYR   0.025   0.002   TYR C1064 
 ARG   0.009   0.001   ARG C1246 

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

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

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 201
  time to evaluate  : 0.990 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  162 ILE cc_start: 0.8006 (mm) cc_final: 0.7637 (mm)
REVERT: C  452 LEU cc_start: 0.8323 (tp) cc_final: 0.8109 (tp)
REVERT: C 1030 ILE cc_start: 0.7833 (tp) cc_final: 0.7579 (tt)
REVERT: C 1191 GLN cc_start: 0.6743 (OUTLIER) cc_final: 0.6449 (mp10)
  outliers start: 36
  outliers final: 23
  residues processed: 221
  average time/residue: 0.1874
  time to fit residues: 61.1452
Evaluate side-chains
  194 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 170
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue  121 VAL
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  299 LEU
Chi-restraints excluded: chain C residue  304 THR
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain C residue  397 ASN
Chi-restraints excluded: chain C residue  404 THR
Chi-restraints excluded: chain C residue  434 LEU
Chi-restraints excluded: chain C residue  440 THR
Chi-restraints excluded: chain C residue  456 LEU
Chi-restraints excluded: chain C residue  587 VAL
Chi-restraints excluded: chain C residue  593 LEU
Chi-restraints excluded: chain C residue 1028 VAL
Chi-restraints excluded: chain C residue 1154 LEU
Chi-restraints excluded: chain C residue 1173 VAL
Chi-restraints excluded: chain C residue 1191 GLN
Chi-restraints excluded: chain C residue 1242 THR
Chi-restraints excluded: chain C residue 1245 ASN
Chi-restraints excluded: chain C residue 1253 GLU
Chi-restraints excluded: chain C residue 1272 LEU
Chi-restraints excluded: chain C residue 1276 LEU
Chi-restraints excluded: chain C residue 1283 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 55 optimal weight:   10.0000
   chunk 91 optimal weight:    6.9990
   chunk 127 optimal weight:    0.7980
   chunk 138 optimal weight:   50.0000
   chunk 65 optimal weight:    3.9990
   chunk 102 optimal weight:    9.9990
   chunk 134 optimal weight:    0.2980
   chunk 142 optimal weight:   40.0000
   chunk 33 optimal weight:    0.9990
   chunk 67 optimal weight:   40.0000
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
** C  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1197 GLN
C1203 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.137334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.112788 restraints weight = 18300.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.115585 restraints weight = 8664.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.117485 restraints weight = 5174.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7216
moved from start:          0.6623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9872  Z= 0.192
  Angle     :  0.603   8.936  13576  Z= 0.311
  Chirality :  0.042   0.212   1646
  Planarity :  0.004   0.054   1752
  Dihedral  :  6.269  68.585   1561
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 21.04 %
    Favored  : 73.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 2.04 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.23), residues: 1429
  helix:  1.22 (0.17), residues: 923
  sheet: -3.18 (0.55), residues: 64
  loop : -2.58 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  65 
 HIS   0.004   0.001   HIS C1024 
 PHE   0.019   0.001   PHE C1182 
 TYR   0.052   0.002   TYR C 142 
 ARG   0.006   0.001   ARG C 289 

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

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

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 175
  time to evaluate  : 1.028 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  434 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8317 (mm)
REVERT: C  452 LEU cc_start: 0.8384 (tp) cc_final: 0.8158 (tp)
REVERT: C  531 THR cc_start: 0.7534 (OUTLIER) cc_final: 0.7324 (p)
REVERT: C 1030 ILE cc_start: 0.7749 (tp) cc_final: 0.7502 (pt)
REVERT: C 1238 SER cc_start: 0.9295 (t) cc_final: 0.9080 (t)
  outliers start: 39
  outliers final: 20
  residues processed: 195
  average time/residue: 0.1830
  time to fit residues: 53.1794
Evaluate side-chains
  185 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 163
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  153 LYS
Chi-restraints excluded: chain C residue  241 HIS
Chi-restraints excluded: chain C residue  304 THR
Chi-restraints excluded: chain C residue  319 CYS
Chi-restraints excluded: chain C residue  357 VAL
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain C residue  404 THR
Chi-restraints excluded: chain C residue  434 LEU
Chi-restraints excluded: chain C residue  454 TYR
Chi-restraints excluded: chain C residue  456 LEU
Chi-restraints excluded: chain C residue  531 THR
Chi-restraints excluded: chain C residue  770 VAL
Chi-restraints excluded: chain C residue 1028 VAL
Chi-restraints excluded: chain C residue 1096 ARG
Chi-restraints excluded: chain C residue 1154 LEU
Chi-restraints excluded: chain C residue 1165 LEU
Chi-restraints excluded: chain C residue 1192 LEU
Chi-restraints excluded: chain C residue 1201 VAL
Chi-restraints excluded: chain C residue 1253 GLU
Chi-restraints excluded: chain C residue 1283 LEU
Chi-restraints excluded: chain C residue 1291 VAL
Chi-restraints excluded: chain C residue 1298 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 63 optimal weight:   30.0000
   chunk 20 optimal weight:    4.9990
   chunk 30 optimal weight:    8.9990
   chunk 71 optimal weight:   20.0000
   chunk 33 optimal weight:    9.9990
   chunk 110 optimal weight:    9.9990
   chunk 70 optimal weight:   20.0000
   chunk 135 optimal weight:   50.0000
   chunk 87 optimal weight:   10.0000
   chunk 128 optimal weight:   40.0000
   chunk 66 optimal weight:   40.0000
   overall best weight:    8.7992

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

Flipped N/Q/H residues before XYZ refinement:
C  71 HIS
** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 397 ASN
C 437 ASN
** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1301 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.126715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.101044 restraints weight = 19273.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.103382 restraints weight = 9911.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.104974 restraints weight = 6338.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.9642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.116   9872  Z= 0.535
  Angle     :  0.907  10.814  13576  Z= 0.475
  Chirality :  0.054   0.258   1646
  Planarity :  0.006   0.056   1752
  Dihedral  :  7.545  69.695   1561
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.26 %
    Favored  : 91.74 %
  Rotamer:
    Outliers :  9.65 %
    Allowed  : 16.43 %
    Favored  : 73.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 2.04 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.24 (0.21), residues: 1429
  helix:  0.30 (0.16), residues: 920
  sheet: -3.68 (0.59), residues: 52
  loop : -2.77 (0.27), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP C1037 
 HIS   0.007   0.002   HIS C  36 
 PHE   0.027   0.003   PHE C 577 
 TYR   0.032   0.004   TYR C1254 
 ARG   0.008   0.001   ARG C 193 

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

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

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 180
  time to evaluate  : 1.171 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   80 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8547 (tp)
REVERT: C  153 LYS cc_start: 0.9482 (OUTLIER) cc_final: 0.9129 (tttt)
REVERT: C  158 TYR cc_start: 0.7342 (t80) cc_final: 0.6840 (t80)
REVERT: C  167 LEU cc_start: 0.8577 (tp) cc_final: 0.8163 (tp)
REVERT: C  227 LYS cc_start: 0.9375 (mttt) cc_final: 0.9027 (mtmm)
REVERT: C  266 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8565 (tt)
REVERT: C  308 LEU cc_start: 0.9127 (tp) cc_final: 0.8896 (mt)
REVERT: C  314 PHE cc_start: 0.7852 (OUTLIER) cc_final: 0.7360 (m-10)
REVERT: C  444 GLN cc_start: 0.7876 (tp-100) cc_final: 0.7469 (tt0)
REVERT: C  483 GLN cc_start: 0.8597 (tt0) cc_final: 0.8136 (tm-30)
REVERT: C  528 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7578 (mtpt)
REVERT: C  574 SER cc_start: 0.8024 (p) cc_final: 0.7770 (p)
REVERT: C 1030 ILE cc_start: 0.8596 (tp) cc_final: 0.8348 (mm)
REVERT: C 1091 LEU cc_start: 0.8709 (tp) cc_final: 0.8302 (tt)
REVERT: C 1191 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7473 (mm110)
REVERT: C 1194 ASP cc_start: 0.7842 (t0) cc_final: 0.7635 (t0)
REVERT: C 1229 GLU cc_start: 0.8267 (tp30) cc_final: 0.8054 (tm-30)
  outliers start: 67
  outliers final: 38
  residues processed: 220
  average time/residue: 0.1995
  time to fit residues: 62.9562
Evaluate side-chains
  195 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 151
  time to evaluate  : 1.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue   73 LEU
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue   80 ILE
Chi-restraints excluded: chain C residue  140 LEU
Chi-restraints excluded: chain C residue  151 THR
Chi-restraints excluded: chain C residue  153 LYS
Chi-restraints excluded: chain C residue  187 VAL
Chi-restraints excluded: chain C residue  189 VAL
Chi-restraints excluded: chain C residue  241 HIS
Chi-restraints excluded: chain C residue  266 LEU
Chi-restraints excluded: chain C residue  300 ILE
Chi-restraints excluded: chain C residue  304 THR
Chi-restraints excluded: chain C residue  314 PHE
Chi-restraints excluded: chain C residue  320 ILE
Chi-restraints excluded: chain C residue  383 THR
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain C residue  391 ILE
Chi-restraints excluded: chain C residue  404 THR
Chi-restraints excluded: chain C residue  440 THR
Chi-restraints excluded: chain C residue  443 VAL
Chi-restraints excluded: chain C residue  454 TYR
Chi-restraints excluded: chain C residue  456 LEU
Chi-restraints excluded: chain C residue  466 VAL
Chi-restraints excluded: chain C residue  528 LYS
Chi-restraints excluded: chain C residue  588 THR
Chi-restraints excluded: chain C residue  770 VAL
Chi-restraints excluded: chain C residue 1028 VAL
Chi-restraints excluded: chain C residue 1096 ARG
Chi-restraints excluded: chain C residue 1136 ILE
Chi-restraints excluded: chain C residue 1158 SER
Chi-restraints excluded: chain C residue 1160 VAL
Chi-restraints excluded: chain C residue 1165 LEU
Chi-restraints excluded: chain C residue 1173 VAL
Chi-restraints excluded: chain C residue 1191 GLN
Chi-restraints excluded: chain C residue 1201 VAL
Chi-restraints excluded: chain C residue 1212 THR
Chi-restraints excluded: chain C residue 1213 THR
Chi-restraints excluded: chain C residue 1231 THR
Chi-restraints excluded: chain C residue 1250 VAL
Chi-restraints excluded: chain C residue 1259 VAL
Chi-restraints excluded: chain C residue 1272 LEU
Chi-restraints excluded: chain C residue 1291 VAL
Chi-restraints excluded: chain C residue 1298 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 30 optimal weight:    4.9990
   chunk 57 optimal weight:    0.8980
   chunk 115 optimal weight:    6.9990
   chunk 33 optimal weight:    0.3980
   chunk 10 optimal weight:    2.9990
   chunk 104 optimal weight:    2.9990
   chunk 47 optimal weight:    8.9990
   chunk 82 optimal weight:    7.9990
   chunk 76 optimal weight:    0.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
C 125 HIS
C 397 ASN
** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 437 ASN
C 491 HIS
** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.133162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.107673 restraints weight = 18718.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.110349 restraints weight = 9185.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.112136 restraints weight = 5617.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.9815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9872  Z= 0.188
  Angle     :  0.650   9.115  13576  Z= 0.329
  Chirality :  0.044   0.275   1646
  Planarity :  0.005   0.059   1752
  Dihedral  :  6.600  66.285   1561
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 26.22 %
    Favored  : 69.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.23), residues: 1429
  helix:  1.15 (0.17), residues: 931
  sheet: -3.34 (0.57), residues: 65
  loop : -2.46 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP C 899 
 HIS   0.011   0.001   HIS C 125 
 PHE   0.031   0.001   PHE C1164 
 TYR   0.044   0.002   TYR C 142 
 ARG   0.014   0.001   ARG C 289 

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

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

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 172
  time to evaluate  : 1.089 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   32 ASN cc_start: 0.8146 (m110) cc_final: 0.7900 (m-40)
REVERT: C   88 GLU cc_start: 0.7304 (tp30) cc_final: 0.7008 (tp30)
REVERT: C  153 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.8930 (tttt)
REVERT: C  158 TYR cc_start: 0.7152 (t80) cc_final: 0.6654 (t80)
REVERT: C  227 LYS cc_start: 0.9347 (mttt) cc_final: 0.8963 (mtmm)
REVERT: C  483 GLN cc_start: 0.8437 (tt0) cc_final: 0.8103 (tm-30)
REVERT: C  574 SER cc_start: 0.7538 (p) cc_final: 0.7169 (p)
REVERT: C 1038 THR cc_start: 0.8061 (t) cc_final: 0.7823 (t)
REVERT: C 1091 LEU cc_start: 0.8652 (tp) cc_final: 0.8280 (tt)
REVERT: C 1230 TYR cc_start: 0.8779 (m-80) cc_final: 0.8445 (m-80)
REVERT: C 1305 MET cc_start: 0.7993 (tmm) cc_final: 0.7714 (tpp)
  outliers start: 32
  outliers final: 16
  residues processed: 191
  average time/residue: 0.1985
  time to fit residues: 55.7827
Evaluate side-chains
  173 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 156
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue  125 HIS
Chi-restraints excluded: chain C residue  153 LYS
Chi-restraints excluded: chain C residue  190 ILE
Chi-restraints excluded: chain C residue  241 HIS
Chi-restraints excluded: chain C residue  299 LEU
Chi-restraints excluded: chain C residue  343 VAL
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain C residue  404 THR
Chi-restraints excluded: chain C residue  454 TYR
Chi-restraints excluded: chain C residue  546 MET
Chi-restraints excluded: chain C residue  770 VAL
Chi-restraints excluded: chain C residue 1096 ARG
Chi-restraints excluded: chain C residue 1157 ILE
Chi-restraints excluded: chain C residue 1158 SER
Chi-restraints excluded: chain C residue 1165 LEU
Chi-restraints excluded: chain C residue 1219 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 20 optimal weight:    7.9990
   chunk 106 optimal weight:    5.9990
   chunk 115 optimal weight:    6.9990
   chunk 5 optimal weight:   20.0000
   chunk 127 optimal weight:   50.0000
   chunk 97 optimal weight:    8.9990
   chunk 3 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 136 optimal weight:   40.0000
   chunk 58 optimal weight:    1.9990
   chunk 70 optimal weight:   20.0000
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
C 219 GLN
C 293 HIS
C 491 HIS
C 547 ASN
** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.128154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.102243 restraints weight = 19363.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.104767 restraints weight = 9726.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.106425 restraints weight = 6064.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          1.0266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   9872  Z= 0.316
  Angle     :  0.705   9.501  13576  Z= 0.364
  Chirality :  0.047   0.248   1646
  Planarity :  0.005   0.058   1752
  Dihedral  :  6.704  68.574   1561
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  6.05 %
    Allowed  : 26.95 %
    Favored  : 67.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 2.04 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.23), residues: 1429
  helix:  1.21 (0.17), residues: 931
  sheet: -3.46 (0.63), residues: 51
  loop : -2.47 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP C 899 
 HIS   0.029   0.002   HIS C 125 
 PHE   0.029   0.002   PHE C1164 
 TYR   0.047   0.002   TYR C 142 
 ARG   0.013   0.001   ARG C 289 

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

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

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 148
  time to evaluate  : 1.015 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   73 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7985 (tt)
REVERT: C   80 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8427 (tp)
REVERT: C   88 GLU cc_start: 0.7622 (tp30) cc_final: 0.7062 (tp30)
REVERT: C  153 LYS cc_start: 0.9445 (OUTLIER) cc_final: 0.9016 (tttt)
REVERT: C  158 TYR cc_start: 0.7346 (t80) cc_final: 0.6763 (t80)
REVERT: C  227 LYS cc_start: 0.9439 (mttt) cc_final: 0.9038 (mtmm)
REVERT: C  483 GLN cc_start: 0.8495 (tt0) cc_final: 0.8190 (tm-30)
REVERT: C  574 SER cc_start: 0.7871 (p) cc_final: 0.7555 (p)
REVERT: C 1066 MET cc_start: 0.7045 (ppp) cc_final: 0.6841 (ppp)
REVERT: C 1091 LEU cc_start: 0.8778 (tp) cc_final: 0.8290 (tt)
REVERT: C 1229 GLU cc_start: 0.8218 (tp30) cc_final: 0.8016 (tm-30)
  outliers start: 42
  outliers final: 30
  residues processed: 169
  average time/residue: 0.1895
  time to fit residues: 47.3751
Evaluate side-chains
  172 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 139
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue   73 LEU
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue   80 ILE
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain C residue  140 LEU
Chi-restraints excluded: chain C residue  151 THR
Chi-restraints excluded: chain C residue  153 LYS
Chi-restraints excluded: chain C residue  190 ILE
Chi-restraints excluded: chain C residue  299 LEU
Chi-restraints excluded: chain C residue  302 SER
Chi-restraints excluded: chain C residue  320 ILE
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain C residue  440 THR
Chi-restraints excluded: chain C residue  454 TYR
Chi-restraints excluded: chain C residue  490 GLU
Chi-restraints excluded: chain C residue  491 HIS
Chi-restraints excluded: chain C residue  546 MET
Chi-restraints excluded: chain C residue  587 VAL
Chi-restraints excluded: chain C residue  606 SER
Chi-restraints excluded: chain C residue  770 VAL
Chi-restraints excluded: chain C residue 1096 ARG
Chi-restraints excluded: chain C residue 1136 ILE
Chi-restraints excluded: chain C residue 1157 ILE
Chi-restraints excluded: chain C residue 1158 SER
Chi-restraints excluded: chain C residue 1163 VAL
Chi-restraints excluded: chain C residue 1165 LEU
Chi-restraints excluded: chain C residue 1201 VAL
Chi-restraints excluded: chain C residue 1212 THR
Chi-restraints excluded: chain C residue 1213 THR
Chi-restraints excluded: chain C residue 1219 TYR
Chi-restraints excluded: chain C residue 1272 LEU
Chi-restraints excluded: chain C residue 1315 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 50 optimal weight:   20.0000
   chunk 49 optimal weight:   20.0000
   chunk 141 optimal weight:   50.0000
   chunk 12 optimal weight:    2.9990
   chunk 130 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 35 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9990
   chunk 140 optimal weight:    4.9990
   chunk 66 optimal weight:    5.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
C 125 HIS
C 293 HIS
** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 491 HIS
** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.131276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.105614 restraints weight = 19160.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.108289 restraints weight = 9463.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.110060 restraints weight = 5813.022|
|-----------------------------------------------------------------------------|
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          1.0414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   9872  Z= 0.195
  Angle     :  0.628   9.181  13576  Z= 0.320
  Chirality :  0.043   0.224   1646
  Planarity :  0.005   0.057   1752
  Dihedral  :  6.389  65.834   1561
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 28.10 %
    Favored  : 67.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 2.04 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.23), residues: 1429
  helix:  1.51 (0.17), residues: 932
  sheet: -3.42 (0.63), residues: 51
  loop : -2.21 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 232 
 HIS   0.013   0.001   HIS C 293 
 PHE   0.032   0.001   PHE C1164 
 TYR   0.040   0.002   TYR C 142 
 ARG   0.007   0.001   ARG C 289 

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

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

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 159
  time to evaluate  : 1.044 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   80 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8310 (tp)
REVERT: C   88 GLU cc_start: 0.7417 (tp30) cc_final: 0.6980 (tp30)
REVERT: C  158 TYR cc_start: 0.7250 (t80) cc_final: 0.6689 (t80)
REVERT: C  227 LYS cc_start: 0.9400 (mttt) cc_final: 0.9022 (mtmm)
REVERT: C  483 GLN cc_start: 0.8458 (tt0) cc_final: 0.8189 (tm-30)
REVERT: C  574 SER cc_start: 0.7604 (p) cc_final: 0.7198 (p)
REVERT: C 1038 THR cc_start: 0.8040 (t) cc_final: 0.7829 (t)
REVERT: C 1091 LEU cc_start: 0.8763 (tp) cc_final: 0.8301 (tt)
REVERT: C 1230 TYR cc_start: 0.8800 (m-80) cc_final: 0.8554 (m-80)
  outliers start: 34
  outliers final: 22
  residues processed: 177
  average time/residue: 0.1925
  time to fit residues: 49.9663
Evaluate side-chains
  171 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 148
  time to evaluate  : 1.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue   73 LEU
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue   80 ILE
Chi-restraints excluded: chain C residue  153 LYS
Chi-restraints excluded: chain C residue  190 ILE
Chi-restraints excluded: chain C residue  299 LEU
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain C residue  412 MET
Chi-restraints excluded: chain C residue  491 HIS
Chi-restraints excluded: chain C residue  587 VAL
Chi-restraints excluded: chain C residue  606 SER
Chi-restraints excluded: chain C residue  770 VAL
Chi-restraints excluded: chain C residue 1096 ARG
Chi-restraints excluded: chain C residue 1136 ILE
Chi-restraints excluded: chain C residue 1165 LEU
Chi-restraints excluded: chain C residue 1201 VAL
Chi-restraints excluded: chain C residue 1213 THR
Chi-restraints excluded: chain C residue 1219 TYR
Chi-restraints excluded: chain C residue 1259 VAL
Chi-restraints excluded: chain C residue 1306 GLU
Chi-restraints excluded: chain C residue 1307 ILE
Chi-restraints excluded: chain C residue 1315 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 97 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   chunk 28 optimal weight:    0.0040
   chunk 126 optimal weight:   50.0000
   chunk 53 optimal weight:    9.9990
   chunk 52 optimal weight:    8.9990
   chunk 95 optimal weight:    0.6980
   chunk 54 optimal weight:    7.9990
   chunk 124 optimal weight:   50.0000
   chunk 82 optimal weight:   40.0000
   overall best weight:    2.3398

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

Flipped N/Q/H residues before XYZ refinement:
** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 293 HIS
** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 491 HIS
** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1245 ASN ** 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 = 0.3798 r_free = 0.3798 target = 0.130214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.104690 restraints weight = 18836.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.107343 restraints weight = 9323.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.109082 restraints weight = 5739.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          1.0599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9872  Z= 0.205
  Angle     :  0.639  10.346  13576  Z= 0.324
  Chirality :  0.043   0.153   1646
  Planarity :  0.005   0.057   1752
  Dihedral  :  6.284  67.693   1561
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 28.10 %
    Favored  : 66.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 2.04 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.23), residues: 1429
  helix:  1.67 (0.17), residues: 932
  sheet: -3.45 (0.64), residues: 51
  loop : -2.17 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 899 
 HIS   0.017   0.002   HIS C 491 
 PHE   0.030   0.001   PHE C1164 
 TYR   0.049   0.002   TYR C 142 
 ARG   0.011   0.001   ARG C 289 

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

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

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 145
  time to evaluate  : 0.977 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   80 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8325 (tp)
REVERT: C   88 GLU cc_start: 0.7458 (tp30) cc_final: 0.6970 (tp30)
REVERT: C  158 TYR cc_start: 0.7299 (t80) cc_final: 0.6720 (t80)
REVERT: C  227 LYS cc_start: 0.9422 (mttt) cc_final: 0.9002 (mtmm)
REVERT: C  257 MET cc_start: 0.8741 (mpp) cc_final: 0.8335 (mtt)
REVERT: C  483 GLN cc_start: 0.8465 (tt0) cc_final: 0.8209 (tm-30)
REVERT: C  574 SER cc_start: 0.7654 (p) cc_final: 0.7248 (p)
REVERT: C 1038 THR cc_start: 0.8089 (t) cc_final: 0.7879 (t)
REVERT: C 1091 LEU cc_start: 0.8773 (tp) cc_final: 0.8332 (tt)
REVERT: C 1230 TYR cc_start: 0.8826 (m-80) cc_final: 0.8539 (m-80)
REVERT: C 1305 MET cc_start: 0.8072 (tmm) cc_final: 0.7732 (tpp)
  outliers start: 35
  outliers final: 29
  residues processed: 162
  average time/residue: 0.1852
  time to fit residues: 45.0837
Evaluate side-chains
  171 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 141
  time to evaluate  : 1.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue   73 LEU
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue   80 ILE
Chi-restraints excluded: chain C residue  140 LEU
Chi-restraints excluded: chain C residue  153 LYS
Chi-restraints excluded: chain C residue  187 VAL
Chi-restraints excluded: chain C residue  190 ILE
Chi-restraints excluded: chain C residue  218 LEU
Chi-restraints excluded: chain C residue  241 HIS
Chi-restraints excluded: chain C residue  299 LEU
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain C residue  456 LEU
Chi-restraints excluded: chain C residue  491 HIS
Chi-restraints excluded: chain C residue  587 VAL
Chi-restraints excluded: chain C residue  606 SER
Chi-restraints excluded: chain C residue  770 VAL
Chi-restraints excluded: chain C residue 1096 ARG
Chi-restraints excluded: chain C residue 1136 ILE
Chi-restraints excluded: chain C residue 1157 ILE
Chi-restraints excluded: chain C residue 1158 SER
Chi-restraints excluded: chain C residue 1165 LEU
Chi-restraints excluded: chain C residue 1201 VAL
Chi-restraints excluded: chain C residue 1213 THR
Chi-restraints excluded: chain C residue 1219 TYR
Chi-restraints excluded: chain C residue 1259 VAL
Chi-restraints excluded: chain C residue 1283 LEU
Chi-restraints excluded: chain C residue 1306 GLU
Chi-restraints excluded: chain C residue 1307 ILE
Chi-restraints excluded: chain C residue 1315 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 120 optimal weight:    1.9990
   chunk 139 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9990
   chunk 111 optimal weight:    1.9990
   chunk 93 optimal weight:   10.0000
   chunk 19 optimal weight:    6.9990
   chunk 11 optimal weight:    1.9990
   chunk 101 optimal weight:    6.9990
   chunk 5 optimal weight:   30.0000
   chunk 76 optimal weight:    0.0980
   overall best weight:    1.4188

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

Flipped N/Q/H residues before XYZ refinement:
C 125 HIS
C 293 HIS
** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 491 HIS
** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.131484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.106249 restraints weight = 18952.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.108974 restraints weight = 9232.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.110769 restraints weight = 5604.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          1.0690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9872  Z= 0.176
  Angle     :  0.632  10.619  13576  Z= 0.317
  Chirality :  0.043   0.149   1646
  Planarity :  0.004   0.057   1752
  Dihedral  :  6.149  69.248   1561
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 28.39 %
    Favored  : 66.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 2.04 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.24), residues: 1429
  helix:  1.83 (0.17), residues: 934
  sheet: -3.41 (0.64), residues: 51
  loop : -2.13 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 232 
 HIS   0.013   0.002   HIS C 293 
 PHE   0.030   0.001   PHE C1164 
 TYR   0.045   0.002   TYR C 142 
 ARG   0.012   0.001   ARG C 289 

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

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

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 146
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   80 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8264 (tp)
REVERT: C   88 GLU cc_start: 0.7345 (tp30) cc_final: 0.6894 (tp30)
REVERT: C  158 TYR cc_start: 0.7302 (t80) cc_final: 0.6717 (t80)
REVERT: C  227 LYS cc_start: 0.9410 (mttt) cc_final: 0.8952 (mtmm)
REVERT: C  483 GLN cc_start: 0.8514 (tt0) cc_final: 0.8237 (tm-30)
REVERT: C  574 SER cc_start: 0.7598 (p) cc_final: 0.7164 (p)
REVERT: C 1038 THR cc_start: 0.8078 (t) cc_final: 0.7854 (t)
REVERT: C 1091 LEU cc_start: 0.8760 (tp) cc_final: 0.8331 (tt)
REVERT: C 1230 TYR cc_start: 0.8820 (m-80) cc_final: 0.8535 (m-80)
REVERT: C 1305 MET cc_start: 0.8023 (tmm) cc_final: 0.7675 (tpp)
  outliers start: 33
  outliers final: 27
  residues processed: 162
  average time/residue: 0.1903
  time to fit residues: 46.0636
Evaluate side-chains
  172 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 144
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue   73 LEU
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue   80 ILE
Chi-restraints excluded: chain C residue  125 HIS
Chi-restraints excluded: chain C residue  153 LYS
Chi-restraints excluded: chain C residue  187 VAL
Chi-restraints excluded: chain C residue  190 ILE
Chi-restraints excluded: chain C residue  218 LEU
Chi-restraints excluded: chain C residue  241 HIS
Chi-restraints excluded: chain C residue  299 LEU
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain C residue  456 LEU
Chi-restraints excluded: chain C residue  490 GLU
Chi-restraints excluded: chain C residue  587 VAL
Chi-restraints excluded: chain C residue  606 SER
Chi-restraints excluded: chain C residue  770 VAL
Chi-restraints excluded: chain C residue 1096 ARG
Chi-restraints excluded: chain C residue 1136 ILE
Chi-restraints excluded: chain C residue 1157 ILE
Chi-restraints excluded: chain C residue 1158 SER
Chi-restraints excluded: chain C residue 1165 LEU
Chi-restraints excluded: chain C residue 1201 VAL
Chi-restraints excluded: chain C residue 1259 VAL
Chi-restraints excluded: chain C residue 1281 VAL
Chi-restraints excluded: chain C residue 1283 LEU
Chi-restraints excluded: chain C residue 1306 GLU
Chi-restraints excluded: chain C residue 1315 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 121 optimal weight:   20.0000
   chunk 40 optimal weight:    7.9990
   chunk 18 optimal weight:    0.9990
   chunk 11 optimal weight:    6.9990
   chunk 57 optimal weight:    2.9990
   chunk 116 optimal weight:   40.0000
   chunk 13 optimal weight:    2.9990
   chunk 127 optimal weight:    0.4980
   chunk 16 optimal weight:   10.0000
   chunk 44 optimal weight:    4.9990
   chunk 118 optimal weight:   20.0000
   overall best weight:    2.4988

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

Flipped N/Q/H residues before XYZ refinement:
C 125 HIS
C 293 HIS
** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 491 HIS
** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.130477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.105230 restraints weight = 18787.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.107908 restraints weight = 9280.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.109630 restraints weight = 5687.533|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          1.0830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9872  Z= 0.207
  Angle     :  0.634  10.506  13576  Z= 0.320
  Chirality :  0.044   0.183   1646
  Planarity :  0.004   0.057   1752
  Dihedral  :  6.120  71.396   1561
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 28.67 %
    Favored  : 66.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 2.04 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.23), residues: 1429
  helix:  1.87 (0.17), residues: 940
  sheet: -3.47 (0.64), residues: 51
  loop : -2.24 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 899 
 HIS   0.019   0.002   HIS C 125 
 PHE   0.028   0.001   PHE C1164 
 TYR   0.043   0.002   TYR C 142 
 ARG   0.007   0.001   ARG C  74 

===============================================================================
Job complete
usr+sys time: 2899.47 seconds
wall clock time: 52 minutes 30.03 seconds (3150.03 seconds total)