Starting phenix.real_space_refine
on Thu Feb 13 21:01:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5yw7_6847/02_2025/5yw7_6847.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5yw7_6847/02_2025/5yw7_6847.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5yw7_6847/02_2025/5yw7_6847.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5yw7_6847/02_2025/5yw7_6847.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5yw7_6847/02_2025/5yw7_6847.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5yw7_6847/02_2025/5yw7_6847.cif"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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      49      5.16       5
     Cl      1      4.86       5
     C    5785      2.51       5
     N    1524      2.21       5
     O    1582      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 38 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8944
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 8880
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1140, 8880
          Classifications: {'peptide': 1140}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 37, 'TRANS': 1102}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 83
          Unresolved non-hydrogen angles: 106
          Unresolved non-hydrogen dihedrals: 73
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 69
    Chain: "B"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 64
          Unusual residues: {'AGS': 1, 'GBM': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.81, per 1000 atoms: 0.65
  Number of scatterers: 8944
  At special positions: 0
  Unit cell: (107.61, 78.07, 132.93, 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      49     16.00
     P       3     15.00
     O    1582      8.00
     N    1524      7.00
     C    5785      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.51
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2162

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 5 sheets defined
      69.4% alpha, 6.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.97
  Creating SS restraints...
    Processing helix  chain 'B' and resid 225 through 230
    Processing helix  chain 'B' and resid 232 through 243
      removed outlier: 4.250A  pdb=" N   PHE B 236 " --> pdb=" O   TRP B 232 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   LYS B 242 " --> pdb=" O   LYS B 238 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 275
      removed outlier: 3.616A  pdb=" N   ASN B 262 " --> pdb=" O   ARG B 258 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 329
      removed outlier: 6.309A  pdb=" N   ARG B 297 " --> pdb=" O   HIS B 293 " (cutoff:3.500A)
      removed outlier: 7.381A  pdb=" N   ARG B 298 " --> pdb=" O   ALA B 294 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   LEU B 299 " --> pdb=" O   PHE B 295 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ILE B 300 " --> pdb=" O   GLY B 296 " (cutoff:3.500A)
      Proline residue:  B 317  - end of helix
    Processing helix  chain 'B' and resid 355 through 402
      removed outlier: 3.630A  pdb=" N   MET B 400 " --> pdb=" O   TYR B 396 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   HIS B 401 " --> pdb=" O   ASN B 397 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   LEU B 402 " --> pdb=" O   LYS B 398 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 412 through 423
    Processing helix  chain 'B' and resid 423 through 457
      Proline residue:  B 436  - end of helix
      removed outlier: 3.536A  pdb=" N   TRP B 439 " --> pdb=" O   CYS B 435 " (cutoff:3.500A)
      Proline residue:  B 442  - end of helix
    Processing helix  chain 'B' and resid 457 through 503
      removed outlier: 3.732A  pdb=" N   LEU B 461 " --> pdb=" O   GLY B 457 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ILE B 462 " --> pdb=" O   VAL B 458 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ILE B 468 " --> pdb=" O   ALA B 464 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   ALA B 471 " --> pdb=" O   ILE B 467 " (cutoff:3.500A)
      Proline residue:  B 472  - end of helix
      removed outlier: 3.595A  pdb=" N   GLU B 501 " --> pdb=" O   LYS B 497 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   MET B 502 " --> pdb=" O   GLN B 498 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 505 through 512
      removed outlier: 4.018A  pdb=" N   TYR B 512 " --> pdb=" O   LEU B 508 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 514 through 560
      removed outlier: 3.655A  pdb=" N   ARG B 521 " --> pdb=" O   ILE B 517 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   LYS B 528 " --> pdb=" O   VAL B 524 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   ALA B 535 " --> pdb=" O   THR B 531 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   THR B 548 " --> pdb=" O   ILE B 544 " (cutoff:3.500A)
      Proline residue:  B 551  - end of helix
      removed outlier: 3.554A  pdb=" N   VAL B 555 " --> pdb=" O   PRO B 551 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 572 through 615
      removed outlier: 3.532A  pdb=" N   ALA B 576 " --> pdb=" O   SER B 572 " (cutoff:3.500A)
      Proline residue:  B 589  - end of helix
      removed outlier: 4.446A  pdb=" N   LEU B 592 " --> pdb=" O   THR B 588 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LEU B 593 " --> pdb=" O   PRO B 589 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   SER B 594 " --> pdb=" O   LEU B 590 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   SER B 595 " --> pdb=" O   PHE B 591 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 718 through 727
    Processing helix  chain 'B' and resid 783 through 790
    Processing helix  chain 'B' and resid 796 through 806
    Processing helix  chain 'B' and resid 808 through 815
      removed outlier: 3.579A  pdb=" N   LEU B 815 " --> pdb=" O   ASP B 811 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 831 through 846
      removed outlier: 3.543A  pdb=" N   GLN B 846 " --> pdb=" O   ARG B 842 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 861 through 872
    Processing helix  chain 'B' and resid 893 through 897
      removed outlier: 3.652A  pdb=" N   ALA B 897 " --> pdb=" O   LEU B 894 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 914 through 919
    Processing helix  chain 'B' and resid 997 through 1007
      removed outlier: 4.439A  pdb=" N   CYS B1001 " --> pdb=" O   PRO B 997 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1009 through 1039
      removed outlier: 3.532A  pdb=" N   LEU B1013 " --> pdb=" O   GLY B1009 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   SER B1014 " --> pdb=" O   ILE B1010 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   LEU B1015 " --> pdb=" O   LEU B1011 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   SER B1019 " --> pdb=" O   LEU B1015 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   ASP B1031 " --> pdb=" O   LEU B1027 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS B1036 " --> pdb=" O   TYR B1032 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   ASP B1039 " --> pdb=" O   ALA B1035 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1061 through 1107
      removed outlier: 3.541A  pdb=" N   LEU B1107 " --> pdb=" O   ASN B1103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1109 through 1116
    Processing helix  chain 'B' and resid 1117 through 1127
      removed outlier: 3.828A  pdb=" N   ILE B1121 " --> pdb=" O   PRO B1117 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   PHE B1125 " --> pdb=" O   ILE B1121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1127 through 1161
      Proline residue:  B1137  - end of helix
      removed outlier: 3.576A  pdb=" N   THR B1161 " --> pdb=" O   ILE B1157 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1161 through 1210
      removed outlier: 3.588A  pdb=" N   LEU B1165 " --> pdb=" O   THR B1161 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   VAL B1166 " --> pdb=" O   PRO B1162 " (cutoff:3.500A)
      Proline residue:  B1170  - end of helix
      removed outlier: 3.539A  pdb=" N   PHE B1177 " --> pdb=" O   VAL B1173 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   TYR B1181 " --> pdb=" O   PHE B1177 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   PHE B1182 " --> pdb=" O   ILE B1178 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   ALA B1185 " --> pdb=" O   TYR B1181 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   ASP B1188 " --> pdb=" O   VAL B1184 " (cutoff:3.500A)
      Proline residue:  B1199  - end of helix
      removed outlier: 3.525A  pdb=" N   GLY B1210 " --> pdb=" O   GLU B1206 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1210 through 1218
    Processing helix  chain 'B' and resid 1219 through 1271
      removed outlier: 3.724A  pdb=" N   ALA B1237 " --> pdb=" O   SER B1233 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   THR B1242 " --> pdb=" O   SER B1238 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   VAL B1260 " --> pdb=" O   GLY B1256 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   SER B1269 " --> pdb=" O   ALA B1265 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1277 through 1289
      removed outlier: 4.573A  pdb=" N   VAL B1281 " --> pdb=" O   SER B1277 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   GLY B1282 " --> pdb=" O   ALA B1278 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   LEU B1283 " --> pdb=" O   GLY B1279 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1290 through 1320
      removed outlier: 3.639A  pdb=" N   TYR B1294 " --> pdb=" O   MET B1290 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   ARG B1314 " --> pdb=" O   GLY B1310 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   ILE B1315 " --> pdb=" O   ALA B1311 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   HIS B1316 " --> pdb=" O   VAL B1312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1384 through 1393
    Processing helix  chain 'B' and resid 1414 through 1420
    Processing helix  chain 'B' and resid 1435 through 1441
    Processing helix  chain 'B' and resid 1447 through 1458
    Processing helix  chain 'B' and resid 1460 through 1466
    Processing helix  chain 'B' and resid 1483 through 1499
      removed outlier: 3.855A  pdb=" N   LYS B1499 " --> pdb=" O   ALA B1495 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1513 through 1528
      removed outlier: 4.097A  pdb=" N   ILE B1519 " --> pdb=" O   ALA B1515 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1539 through 1546
      removed outlier: 3.674A  pdb=" N   ILE B1543 " --> pdb=" O   ARG B1539 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ALA B1546 " --> pdb=" O   THR B1542 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1562 through 1570
      removed outlier: 4.306A  pdb=" N   SER B1568 " --> pdb=" O   GLU B1564 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   LYS B1570 " --> pdb=" O   LEU B1566 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 701 through 703
    Processing sheet with id=AA2, first strand: chain 'B' and resid 685 through 686
    Processing sheet with id=AA3, first strand: chain 'B' and resid 771 through 773
      removed outlier: 6.709A  pdb=" N   ALA B 771 " --> pdb=" O   PHE B 852 " (cutoff:3.500A)
      removed outlier: 8.226A  pdb=" N   ASP B 854 " --> pdb=" O   ALA B 771 " (cutoff:3.500A)
      removed outlier: 7.493A  pdb=" N   ALA B 773 " --> pdb=" O   ASP B 854 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   VAL B 851 " --> pdb=" O   VAL B 885 " (cutoff:3.500A)
      removed outlier: 7.678A  pdb=" N   VAL B 887 " --> pdb=" O   VAL B 851 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   LEU B 853 " --> pdb=" O   VAL B 887 " (cutoff:3.500A)
      removed outlier: 7.110A  pdb=" N   ILE B 900 " --> pdb=" O   GLU B 911 " (cutoff:3.500A)
      removed outlier: 4.972A  pdb=" N   GLU B 911 " --> pdb=" O   ILE B 900 " (cutoff:3.500A)
      removed outlier: 7.324A  pdb=" N   ALA B 902 " --> pdb=" O   GLN B 909 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 1365 through 1369
      removed outlier: 7.090A  pdb=" N   ALA B1367 " --> pdb=" O   GLN B1348 " (cutoff:3.500A)
      removed outlier: 4.860A  pdb=" N   GLN B1348 " --> pdb=" O   ALA B1367 " (cutoff:3.500A)
      removed outlier: 7.288A  pdb=" N   ILE B1369 " --> pdb=" O   GLN B1346 " (cutoff:3.500A)
      removed outlier: 5.530A  pdb=" N   GLN B1346 " --> pdb=" O   ILE B1369 " (cutoff:3.500A)
      removed outlier: 5.206A  pdb=" N   ILE B1347 " --> pdb=" O   ILE B1404 " (cutoff:3.500A)
      removed outlier: 7.111A  pdb=" N   ILE B1404 " --> pdb=" O   ILE B1347 " (cutoff:3.500A)
      removed outlier: 5.648A  pdb=" N   ASN B1349 " --> pdb=" O   ARG B1402 " (cutoff:3.500A)
      removed outlier: 4.659A  pdb=" N   ARG B1402 " --> pdb=" O   ASN B1349 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   MET B1398 " --> pdb=" O   ARG B1353 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 1423 through 1425
      removed outlier: 6.594A  pdb=" N   SER B1423 " --> pdb=" O   ILE B1504 " (cutoff:3.500A)
      removed outlier: 7.601A  pdb=" N   ASP B1506 " --> pdb=" O   SER B1423 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   ILE B1425 " --> pdb=" O   ASP B1506 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   PHE B1503 " --> pdb=" O   VAL B1534 " (cutoff:3.500A)
      removed outlier: 8.255A  pdb=" N   ILE B1536 " --> pdb=" O   PHE B1503 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   MET B1505 " --> pdb=" O   ILE B1536 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   MET B1550 " --> pdb=" O   GLY B1376 " (cutoff:3.500A)

    574 hydrogen bonds defined for protein.
    1695 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: 3.41

  Time building geometry restraints manager: 2.85 seconds

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

  Histogram of bond lengths:
        1.21 -     1.38: 3342
        1.38 -     1.56: 5688
        1.56 -     1.73: 8
        1.73 -     1.90: 75
        1.90 -     2.08: 1
  Bond restraints: 9114
  Sorted by residual:
  bond pdb=" C4  AGS B2002 "
       pdb=" C5  AGS B2002 "
    ideal  model  delta    sigma   weight residual
    1.386  1.470 -0.084 1.00e-02 1.00e+04 7.11e+01
  bond pdb=" C18 GBM B2001 "
       pdb=" S2  GBM B2001 "
    ideal  model  delta    sigma   weight residual
    1.765  1.604  0.161 2.00e-02 2.50e+03 6.52e+01
  bond pdb=" C5  AGS B2002 "
       pdb=" C6  AGS B2002 "
    ideal  model  delta    sigma   weight residual
    1.409  1.482 -0.073 1.00e-02 1.00e+04 5.39e+01
  bond pdb=" PG  AGS B2002 "
       pdb=" S1G AGS B2002 "
    ideal  model  delta    sigma   weight residual
    1.949  2.075 -0.126 2.00e-02 2.50e+03 3.97e+01
  bond pdb=" C8  AGS B2002 "
       pdb=" N7  AGS B2002 "
    ideal  model  delta    sigma   weight residual
    1.311  1.357 -0.046 1.00e-02 1.00e+04 2.09e+01
  ... (remaining 9109 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.40: 12179
        2.40 -     4.79: 151
        4.79 -     7.19: 29
        7.19 -     9.58: 7
        9.58 -    11.98: 3
  Bond angle restraints: 12369
  Sorted by residual:
  angle pdb=" C5  AGS B2002 "
        pdb=" C4  AGS B2002 "
        pdb=" N3  AGS B2002 "
      ideal   model   delta    sigma   weight residual
     126.80  118.59    8.21 7.41e-01 1.82e+00 1.23e+02
  angle pdb=" C4  AGS B2002 "
        pdb=" C5  AGS B2002 "
        pdb=" N7  AGS B2002 "
      ideal   model   delta    sigma   weight residual
     110.73  106.71    4.02 4.52e-01 4.89e+00 7.91e+01
  angle pdb=" C5  AGS B2002 "
        pdb=" N7  AGS B2002 "
        pdb=" C8  AGS B2002 "
      ideal   model   delta    sigma   weight residual
     103.67  107.37   -3.70 4.26e-01 5.51e+00 7.52e+01
  angle pdb=" N3  AGS B2002 "
        pdb=" C4  AGS B2002 "
        pdb=" N9  AGS B2002 "
      ideal   model   delta    sigma   weight residual
     127.16  135.21   -8.05 1.06e+00 8.92e-01 5.78e+01
  angle pdb=" C   SER B 532 "
        pdb=" N   LEU B 533 "
        pdb=" CA  LEU B 533 "
      ideal   model   delta    sigma   weight residual
     120.28  130.85  -10.57 1.44e+00 4.82e-01 5.39e+01
  ... (remaining 12364 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.76: 5216
       24.76 -    49.52: 212
       49.52 -    74.28: 33
       74.28 -    99.05: 4
       99.05 -   123.81: 2
  Dihedral angle restraints: 5467
    sinusoidal: 2147
      harmonic: 3320
  Sorted by residual:
  dihedral pdb=" CA  PHE B 295 "
           pdb=" C   PHE B 295 "
           pdb=" N   GLY B 296 "
           pdb=" CA  GLY B 296 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.49   25.51     0      5.00e+00 4.00e-02 2.60e+01
  dihedral pdb=" N   SER B1501 "
           pdb=" C   SER B1501 "
           pdb=" CA  SER B1501 "
           pdb=" CB  SER B1501 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  133.62  -10.82     0      2.50e+00 1.60e-01 1.87e+01
  dihedral pdb=" CA  GLY B 296 "
           pdb=" C   GLY B 296 "
           pdb=" N   ARG B 297 "
           pdb=" CA  ARG B 297 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.77  -21.23     0      5.00e+00 4.00e-02 1.80e+01
  ... (remaining 5464 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 1378
       0.075 -    0.149: 98
       0.149 -    0.224: 10
       0.224 -    0.299: 4
       0.299 -    0.373: 2
  Chirality restraints: 1492
  Sorted by residual:
  chirality pdb=" CA  LYS B1444 "
            pdb=" N   LYS B1444 "
            pdb=" C   LYS B1444 "
            pdb=" CB  LYS B1444 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.48e+00
  chirality pdb=" CA  SER B1501 "
            pdb=" N   SER B1501 "
            pdb=" C   SER B1501 "
            pdb=" CB  SER B1501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.08e+00
  chirality pdb=" CA  ASP B1133 "
            pdb=" N   ASP B1133 "
            pdb=" C   ASP B1133 "
            pdb=" CB  ASP B1133 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.08e+00
  ... (remaining 1489 not shown)

  Planarity restraints: 1516
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C25 GBM B2001 "   -0.321 2.00e-02 2.50e+03   2.73e-01 9.29e+02
        pdb=" C26 GBM B2001 "    0.077 2.00e-02 2.50e+03
        pdb=" C27 GBM B2001 "   -0.172 2.00e-02 2.50e+03
        pdb=" N10 GBM B2001 "    0.478 2.00e-02 2.50e+03
        pdb=" O6  GBM B2001 "   -0.062 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C11 GBM B2001 "    0.081 2.00e-02 2.50e+03   7.61e-02 8.68e+01
        pdb=" C17 GBM B2001 "   -0.037 2.00e-02 2.50e+03
        pdb=" N8  GBM B2001 "   -0.039 2.00e-02 2.50e+03
        pdb=" N9  GBM B2001 "   -0.130 2.00e-02 2.50e+03
        pdb=" O3  GBM B2001 "    0.047 2.00e-02 2.50e+03
        pdb=" S2  GBM B2001 "    0.079 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B1128 "    0.019 2.00e-02 2.50e+03   3.85e-02 1.48e+01
        pdb=" C   ASP B1128 "   -0.067 2.00e-02 2.50e+03
        pdb=" O   ASP B1128 "    0.025 2.00e-02 2.50e+03
        pdb=" N   CYS B1129 "    0.023 2.00e-02 2.50e+03
  ... (remaining 1513 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1778
        2.78 -     3.31: 9102
        3.31 -     3.84: 14871
        3.84 -     4.37: 16363
        4.37 -     4.90: 28009
  Nonbonded interactions: 70123
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B1031 "
            pdb=" OH  TYR B1287 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" CB  TYR B 512 "
            pdb=" NH2 ARG B1498 "
     model   vdw
     2.269 3.520
  nonbonded pdb=" O   SER B1126 "
            pdb=" ND2 ASN B1130 "
     model   vdw
     2.275 3.120
  nonbonded pdb=" O   GLN B 846 "
            pdb=" NH2 ARG B 882 "
     model   vdw
     2.308 3.120
  nonbonded pdb=" O   THR B 783 "
            pdb=" ND2 ASN B 787 "
     model   vdw
     2.309 3.120
  ... (remaining 70118 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             2.830
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.480
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  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:3.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
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      :  0.004   0.161   9114  Z= 0.293
  Angle     :  0.710  11.976  12369  Z= 0.444
  Chirality :  0.046   0.373   1492
  Planarity :  0.008   0.273   1516
  Dihedral  : 13.432 123.808   3305
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 14.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  6.49 %
    Allowed  :  8.97 %
    Favored  : 84.54 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.58 (0.22), residues: 1122
  helix: -1.14 (0.17), residues: 750
  sheet: -1.78 (0.54), residues: 79
  loop : -2.81 (0.31), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B1037 
 HIS   0.004   0.001   HIS B 584 
 PHE   0.016   0.001   PHE B 305 
 TYR   0.014   0.001   TYR B 378 
 ARG   0.003   0.000   ARG B1494 

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  400 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 337
  time to evaluate  : 1.072 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  227 LYS cc_start: 0.8996 (mtpp) cc_final: 0.7908 (tttt)
REVERT: B  233 MET cc_start: 0.9511 (mmm) cc_final: 0.9075 (mmm)
REVERT: B  263 TYR cc_start: 0.9117 (t80) cc_final: 0.8846 (t80)
REVERT: B  270 PHE cc_start: 0.8821 (t80) cc_final: 0.8547 (t80)
REVERT: B  299 LEU cc_start: 0.9230 (tp) cc_final: 0.8882 (tt)
REVERT: B  306 ARG cc_start: 0.8570 (tpt90) cc_final: 0.8201 (tpp80)
REVERT: B  320 ILE cc_start: 0.9508 (mt) cc_final: 0.9237 (mt)
REVERT: B  367 LEU cc_start: 0.9377 (pp) cc_final: 0.9160 (pp)
REVERT: B  374 GLN cc_start: 0.9396 (OUTLIER) cc_final: 0.9137 (mm-40)
REVERT: B  510 LYS cc_start: 0.9375 (mtpp) cc_final: 0.9057 (mtmt)
REVERT: B  581 SER cc_start: 0.9663 (m) cc_final: 0.9339 (p)
REVERT: B  590 LEU cc_start: 0.9261 (mt) cc_final: 0.8880 (tp)
REVERT: B  708 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8277 (tt)
REVERT: B  730 MET cc_start: 0.7235 (mtm) cc_final: 0.6721 (mtp)
REVERT: B  820 GLN cc_start: 0.9011 (mt0) cc_final: 0.8750 (mp10)
REVERT: B  869 MET cc_start: 0.9030 (tmm) cc_final: 0.8488 (tmm)
REVERT: B  886 LEU cc_start: 0.9249 (tt) cc_final: 0.8387 (tt)
REVERT: B 1078 LEU cc_start: 0.9037 (tp) cc_final: 0.8637 (tp)
REVERT: B 1146 SER cc_start: 0.9252 (m) cc_final: 0.8719 (p)
REVERT: B 1190 GLN cc_start: 0.9228 (tp40) cc_final: 0.8863 (tt0)
REVERT: B 1206 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7936 (mt-10)
REVERT: B 1214 ILE cc_start: 0.9600 (mt) cc_final: 0.9295 (tp)
REVERT: B 1232 ASP cc_start: 0.8570 (t70) cc_final: 0.8350 (t70)
REVERT: B 1246 ARG cc_start: 0.9469 (OUTLIER) cc_final: 0.9247 (mmp80)
REVERT: B 1301 ASN cc_start: 0.8902 (m110) cc_final: 0.8694 (m110)
REVERT: B 1305 MET cc_start: 0.8941 (tpt) cc_final: 0.8537 (tpt)
REVERT: B 1398 MET cc_start: 0.4986 (mmm) cc_final: 0.4592 (mpp)
REVERT: B 1490 PHE cc_start: 0.9192 (m-80) cc_final: 0.8674 (m-80)
REVERT: B 1505 MET cc_start: 0.7959 (ttm) cc_final: 0.7393 (mmt)
REVERT: B 1550 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8475 (mtp)
REVERT: B 1551 VAL cc_start: 0.8720 (OUTLIER) cc_final: 0.8465 (p)
REVERT: B 1561 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.7954 (p0)
  outliers start: 63
  outliers final: 20
  residues processed: 374
  average time/residue: 0.2175
  time to fit residues: 110.9937
Evaluate side-chains
  223 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 197
  time to evaluate  : 1.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    4.9990
   chunk 86 optimal weight:    0.9980
   chunk 47 optimal weight:    0.4980
   chunk 29 optimal weight:    3.9990
   chunk 58 optimal weight:    6.9990
   chunk 46 optimal weight:    2.9990
   chunk 89 optimal weight:    0.0070
   chunk 34 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9990
   chunk 66 optimal weight:    4.9990
   chunk 103 optimal weight:    0.9990
   overall best weight:    0.6600

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

Flipped N/Q/H residues before XYZ refinement:
B 262 ASN
B 416 GLN
B 846 GLN
B1134 GLN
** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1541 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.081665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.062131 restraints weight = 32413.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.064132 restraints weight = 19165.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.065502 restraints weight = 13092.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.3268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   9114  Z= 0.224
  Angle     :  0.700  10.973  12369  Z= 0.351
  Chirality :  0.043   0.171   1492
  Planarity :  0.005   0.057   1516
  Dihedral  :  8.278 113.749   1255
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  4.12 %
    Favored  : 95.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.93 (0.24), residues: 1122
  helix:  0.21 (0.18), residues: 750
  sheet: -1.44 (0.54), residues: 79
  loop : -2.39 (0.32), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B1247 
 HIS   0.004   0.001   HIS B1135 
 PHE   0.023   0.002   PHE B1240 
 TYR   0.028   0.002   TYR B1064 
 ARG   0.008   0.001   ARG B1498 

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 251
  time to evaluate  : 1.045 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  222 VAL cc_start: 0.8745 (m) cc_final: 0.8413 (p)
REVERT: B  227 LYS cc_start: 0.9069 (mtpp) cc_final: 0.8068 (tttt)
REVERT: B  233 MET cc_start: 0.8882 (mmm) cc_final: 0.8490 (mmm)
REVERT: B  306 ARG cc_start: 0.8894 (tpt90) cc_final: 0.8684 (tpp80)
REVERT: B  420 LEU cc_start: 0.9085 (mt) cc_final: 0.8867 (mt)
REVERT: B  429 MET cc_start: 0.8672 (ttp) cc_final: 0.8402 (ttp)
REVERT: B  433 PHE cc_start: 0.8572 (m-10) cc_final: 0.8310 (m-80)
REVERT: B  581 SER cc_start: 0.9693 (m) cc_final: 0.9423 (p)
REVERT: B  602 LYS cc_start: 0.9211 (tptt) cc_final: 0.8851 (tptp)
REVERT: B  808 LEU cc_start: 0.9212 (tp) cc_final: 0.8935 (tp)
REVERT: B  869 MET cc_start: 0.8432 (tmm) cc_final: 0.7929 (tmm)
REVERT: B 1078 LEU cc_start: 0.9155 (tp) cc_final: 0.8936 (tp)
REVERT: B 1128 ASP cc_start: 0.8380 (m-30) cc_final: 0.7674 (m-30)
REVERT: B 1290 MET cc_start: 0.8967 (ttm) cc_final: 0.8617 (ttp)
REVERT: B 1305 MET cc_start: 0.8528 (tpt) cc_final: 0.8312 (tpt)
REVERT: B 1440 LEU cc_start: 0.9305 (mt) cc_final: 0.9090 (mt)
REVERT: B 1460 LEU cc_start: 0.7705 (mt) cc_final: 0.7299 (mt)
REVERT: B 1490 PHE cc_start: 0.9135 (m-80) cc_final: 0.8899 (m-80)
REVERT: B 1566 LEU cc_start: 0.5838 (OUTLIER) cc_final: 0.5607 (pt)
  outliers start: 3
  outliers final: 0
  residues processed: 253
  average time/residue: 0.1798
  time to fit residues: 66.2799
Evaluate side-chains
  178 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 177
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 86 optimal weight:    2.9990
   chunk 90 optimal weight:    0.8980
   chunk 76 optimal weight:    3.9990
   chunk 95 optimal weight:    0.7980
   chunk 68 optimal weight:    0.4980
   chunk 81 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 104 optimal weight:    0.4980
   chunk 74 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B 262 ASN
B 781 ASN
B1134 GLN
B1135 HIS
** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1301 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.082374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.062779 restraints weight = 32751.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.064736 restraints weight = 19558.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.066070 restraints weight = 13423.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.4014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9114  Z= 0.197
  Angle     :  0.643   8.716  12369  Z= 0.322
  Chirality :  0.041   0.144   1492
  Planarity :  0.004   0.043   1516
  Dihedral  :  7.964 116.111   1255
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  4.23 %
    Favored  : 95.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.25), residues: 1122
  helix:  0.90 (0.19), residues: 760
  sheet: -1.28 (0.53), residues: 79
  loop : -2.13 (0.34), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B 514 
 HIS   0.003   0.001   HIS B 896 
 PHE   0.027   0.002   PHE B 295 
 TYR   0.042   0.002   TYR B 512 
 ARG   0.003   0.000   ARG B1498 

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 224
  time to evaluate  : 1.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  227 LYS cc_start: 0.9110 (mtpp) cc_final: 0.8125 (tttt)
REVERT: B  233 MET cc_start: 0.8977 (mmm) cc_final: 0.8592 (mmm)
REVERT: B  319 CYS cc_start: 0.9121 (m) cc_final: 0.8685 (t)
REVERT: B  420 LEU cc_start: 0.9080 (mt) cc_final: 0.8840 (mt)
REVERT: B  503 LEU cc_start: 0.9176 (mm) cc_final: 0.8582 (tp)
REVERT: B  581 SER cc_start: 0.9670 (m) cc_final: 0.9421 (p)
REVERT: B  583 PHE cc_start: 0.9176 (m-10) cc_final: 0.8919 (m-10)
REVERT: B  590 LEU cc_start: 0.9258 (mt) cc_final: 0.9045 (mt)
REVERT: B  602 LYS cc_start: 0.9190 (tptt) cc_final: 0.8869 (tptp)
REVERT: B  869 MET cc_start: 0.7973 (tmm) cc_final: 0.7754 (tmm)
REVERT: B 1078 LEU cc_start: 0.9236 (tp) cc_final: 0.8990 (tp)
REVERT: B 1128 ASP cc_start: 0.8394 (m-30) cc_final: 0.7764 (m-30)
REVERT: B 1290 MET cc_start: 0.8822 (ttm) cc_final: 0.8533 (ttp)
REVERT: B 1305 MET cc_start: 0.8567 (tpt) cc_final: 0.8302 (tpt)
REVERT: B 1490 PHE cc_start: 0.9153 (m-80) cc_final: 0.8713 (m-80)
REVERT: B 1505 MET cc_start: 0.7752 (ttt) cc_final: 0.7541 (mmp)
  outliers start: 3
  outliers final: 0
  residues processed: 225
  average time/residue: 0.1919
  time to fit residues: 63.9739
Evaluate side-chains
  170 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 31 optimal weight:    5.9990
   chunk 83 optimal weight:    0.7980
   chunk 36 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 82 optimal weight:    0.5980
   chunk 42 optimal weight:    0.0070
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.5998

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

Flipped N/Q/H residues before XYZ refinement:
B 262 ASN
B1134 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.082621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.063210 restraints weight = 32076.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.065276 restraints weight = 19124.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.066655 restraints weight = 12905.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.4500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9114  Z= 0.187
  Angle     :  0.635   8.776  12369  Z= 0.314
  Chirality :  0.041   0.143   1492
  Planarity :  0.004   0.043   1516
  Dihedral  :  7.692 116.599   1255
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.25), residues: 1122
  helix:  1.15 (0.19), residues: 754
  sheet: -1.12 (0.56), residues: 79
  loop : -1.90 (0.34), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 514 
 HIS   0.002   0.001   HIS B1024 
 PHE   0.027   0.002   PHE B 433 
 TYR   0.021   0.001   TYR B 512 
 ARG   0.019   0.001   ARG B1251 

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 0.961 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  227 LYS cc_start: 0.9105 (mtpp) cc_final: 0.8127 (tttt)
REVERT: B  233 MET cc_start: 0.8926 (mmm) cc_final: 0.8455 (mmm)
REVERT: B  319 CYS cc_start: 0.9098 (m) cc_final: 0.8674 (t)
REVERT: B  361 LEU cc_start: 0.9602 (mm) cc_final: 0.9084 (tp)
REVERT: B  368 LEU cc_start: 0.9089 (tp) cc_final: 0.8872 (tp)
REVERT: B  420 LEU cc_start: 0.8998 (mt) cc_final: 0.8765 (mt)
REVERT: B  581 SER cc_start: 0.9665 (m) cc_final: 0.9382 (p)
REVERT: B  583 PHE cc_start: 0.9167 (m-10) cc_final: 0.8881 (m-10)
REVERT: B  602 LYS cc_start: 0.9165 (tptt) cc_final: 0.8858 (tptp)
REVERT: B  808 LEU cc_start: 0.9212 (tp) cc_final: 0.8754 (tp)
REVERT: B 1078 LEU cc_start: 0.9253 (tp) cc_final: 0.8985 (tp)
REVERT: B 1128 ASP cc_start: 0.8432 (m-30) cc_final: 0.7752 (m-30)
REVERT: B 1246 ARG cc_start: 0.9456 (mmp80) cc_final: 0.9042 (mmp80)
REVERT: B 1258 CYS cc_start: 0.9050 (t) cc_final: 0.8848 (t)
REVERT: B 1305 MET cc_start: 0.8583 (tpt) cc_final: 0.8334 (tpt)
REVERT: B 1490 PHE cc_start: 0.9151 (m-80) cc_final: 0.8751 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 223
  average time/residue: 0.1669
  time to fit residues: 54.8535
Evaluate side-chains
  160 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 1.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0470
   chunk 73 optimal weight:    2.9990
   chunk 1 optimal weight:    0.1980
   chunk 81 optimal weight:    0.9990
   chunk 108 optimal weight:    5.9990
   chunk 39 optimal weight:    4.9990
   chunk 85 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.5878

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

Flipped N/Q/H residues before XYZ refinement:
B 262 ASN
B1134 GLN
** B1296 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 = 0.3432 r_free = 0.3432 target = 0.083087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.063954 restraints weight = 32037.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.065919 restraints weight = 19165.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.067183 restraints weight = 13129.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.4808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9114  Z= 0.183
  Angle     :  0.624   8.423  12369  Z= 0.309
  Chirality :  0.041   0.143   1492
  Planarity :  0.004   0.050   1516
  Dihedral  :  7.552 117.848   1255
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.25), residues: 1122
  helix:  1.22 (0.19), residues: 756
  sheet: -1.00 (0.55), residues: 79
  loop : -1.85 (0.34), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B1037 
 HIS   0.002   0.000   HIS B1024 
 PHE   0.029   0.002   PHE B1223 
 TYR   0.019   0.001   TYR B 512 
 ARG   0.006   0.000   ARG B1419 

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 0.987 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  227 LYS cc_start: 0.9104 (mtpp) cc_final: 0.8093 (tttt)
REVERT: B  233 MET cc_start: 0.8906 (mmm) cc_final: 0.8440 (mmm)
REVERT: B  319 CYS cc_start: 0.9066 (m) cc_final: 0.8643 (t)
REVERT: B  361 LEU cc_start: 0.9582 (mm) cc_final: 0.9062 (tp)
REVERT: B  368 LEU cc_start: 0.9086 (tp) cc_final: 0.8882 (tp)
REVERT: B  420 LEU cc_start: 0.8964 (mt) cc_final: 0.8700 (mt)
REVERT: B  512 TYR cc_start: 0.7783 (p90) cc_final: 0.7248 (p90)
REVERT: B  530 MET cc_start: 0.9023 (mmt) cc_final: 0.8686 (mmt)
REVERT: B  583 PHE cc_start: 0.9124 (m-10) cc_final: 0.8827 (m-10)
REVERT: B  602 LYS cc_start: 0.9149 (tptt) cc_final: 0.8735 (tppt)
REVERT: B  710 MET cc_start: 0.8552 (mmm) cc_final: 0.8340 (tpp)
REVERT: B  808 LEU cc_start: 0.9101 (tp) cc_final: 0.8711 (tp)
REVERT: B 1078 LEU cc_start: 0.9288 (tp) cc_final: 0.9044 (tp)
REVERT: B 1124 ARG cc_start: 0.8574 (mmp80) cc_final: 0.8104 (mmp80)
REVERT: B 1128 ASP cc_start: 0.8378 (m-30) cc_final: 0.7461 (m-30)
REVERT: B 1246 ARG cc_start: 0.9314 (mmp80) cc_final: 0.9018 (mmp80)
REVERT: B 1305 MET cc_start: 0.8547 (tpt) cc_final: 0.8321 (tpt)
REVERT: B 1490 PHE cc_start: 0.9138 (m-80) cc_final: 0.8713 (m-80)
REVERT: B 1504 ILE cc_start: 0.8949 (pt) cc_final: 0.8520 (pt)
REVERT: B 1505 MET cc_start: 0.6788 (mmp) cc_final: 0.5994 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 216
  average time/residue: 0.1700
  time to fit residues: 53.7414
Evaluate side-chains
  155 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.992 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 38 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   chunk 92 optimal weight:    0.1980
   chunk 53 optimal weight:    4.9990
   chunk 60 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 43 optimal weight:    0.4980
   chunk 77 optimal weight:    0.7980
   chunk 103 optimal weight:    5.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B 262 ASN
** B1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.083517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.064506 restraints weight = 32073.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.066459 restraints weight = 19259.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.067811 restraints weight = 13235.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.5123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9114  Z= 0.187
  Angle     :  0.625   8.415  12369  Z= 0.308
  Chirality :  0.040   0.149   1492
  Planarity :  0.004   0.043   1516
  Dihedral  :  7.453 118.262   1255
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.25), residues: 1122
  helix:  1.28 (0.19), residues: 753
  sheet: -0.98 (0.55), residues: 79
  loop : -1.78 (0.34), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 514 
 HIS   0.006   0.001   HIS B 889 
 PHE   0.022   0.002   PHE B 295 
 TYR   0.021   0.001   TYR B 893 
 ARG   0.005   0.000   ARG B1251 

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 222
  time to evaluate  : 0.980 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  227 LYS cc_start: 0.9033 (mtpp) cc_final: 0.7962 (tttt)
REVERT: B  233 MET cc_start: 0.8964 (mmm) cc_final: 0.8438 (mmm)
REVERT: B  257 MET cc_start: 0.7641 (ptp) cc_final: 0.6329 (ptp)
REVERT: B  319 CYS cc_start: 0.9066 (m) cc_final: 0.8605 (t)
REVERT: B  361 LEU cc_start: 0.9568 (mm) cc_final: 0.9126 (tp)
REVERT: B  368 LEU cc_start: 0.9071 (tp) cc_final: 0.8857 (tp)
REVERT: B  400 MET cc_start: 0.7717 (mmm) cc_final: 0.7466 (mmt)
REVERT: B  420 LEU cc_start: 0.8893 (mt) cc_final: 0.8624 (mt)
REVERT: B  512 TYR cc_start: 0.7670 (p90) cc_final: 0.6727 (p90)
REVERT: B  530 MET cc_start: 0.9039 (mmt) cc_final: 0.8782 (mmt)
REVERT: B  583 PHE cc_start: 0.9096 (m-10) cc_final: 0.8869 (m-10)
REVERT: B  602 LYS cc_start: 0.9128 (tptt) cc_final: 0.8718 (tppt)
REVERT: B  710 MET cc_start: 0.8585 (mmm) cc_final: 0.8384 (tpp)
REVERT: B  808 LEU cc_start: 0.9085 (tp) cc_final: 0.8716 (tp)
REVERT: B 1066 MET cc_start: 0.7452 (mmm) cc_final: 0.7087 (mmm)
REVERT: B 1078 LEU cc_start: 0.9274 (tp) cc_final: 0.9023 (tp)
REVERT: B 1124 ARG cc_start: 0.8539 (mmp80) cc_final: 0.8089 (mmp80)
REVERT: B 1128 ASP cc_start: 0.8373 (m-30) cc_final: 0.7352 (m-30)
REVERT: B 1246 ARG cc_start: 0.9452 (mmp80) cc_final: 0.8990 (mmp80)
REVERT: B 1305 MET cc_start: 0.8520 (tpt) cc_final: 0.8234 (tpt)
REVERT: B 1424 ILE cc_start: 0.9084 (tp) cc_final: 0.8860 (tp)
REVERT: B 1490 PHE cc_start: 0.9136 (m-80) cc_final: 0.8708 (m-80)
REVERT: B 1505 MET cc_start: 0.6776 (mmp) cc_final: 0.6224 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 222
  average time/residue: 0.1744
  time to fit residues: 56.7421
Evaluate side-chains
  157 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 1.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 50 optimal weight:    0.5980
   chunk 37 optimal weight:    8.9990
   chunk 6 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 110 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 68 optimal weight:    0.0170
   chunk 51 optimal weight:    0.4980
   chunk 14 optimal weight:    1.9990
   chunk 81 optimal weight:    0.6980
   overall best weight:    0.5218

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

Flipped N/Q/H residues before XYZ refinement:
B 262 ASN
** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.083446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.064031 restraints weight = 32569.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.066030 restraints weight = 19649.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.067269 restraints weight = 13487.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.5365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9114  Z= 0.174
  Angle     :  0.632   8.379  12369  Z= 0.308
  Chirality :  0.041   0.168   1492
  Planarity :  0.004   0.053   1516
  Dihedral  :  7.287 118.755   1255
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.25), residues: 1122
  helix:  1.35 (0.19), residues: 754
  sheet: -0.96 (0.56), residues: 79
  loop : -1.65 (0.34), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B1247 
 HIS   0.005   0.001   HIS B 889 
 PHE   0.022   0.001   PHE B 433 
 TYR   0.011   0.001   TYR B1004 
 ARG   0.008   0.000   ARG B1419 

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 0.998 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  233 MET cc_start: 0.8954 (mmm) cc_final: 0.8432 (mmm)
REVERT: B  319 CYS cc_start: 0.9024 (m) cc_final: 0.8506 (t)
REVERT: B  323 ILE cc_start: 0.9319 (mm) cc_final: 0.9066 (mm)
REVERT: B  361 LEU cc_start: 0.9530 (mm) cc_final: 0.8994 (tt)
REVERT: B  400 MET cc_start: 0.7810 (mmm) cc_final: 0.7501 (mmt)
REVERT: B  420 LEU cc_start: 0.8807 (mt) cc_final: 0.8589 (mt)
REVERT: B  509 LEU cc_start: 0.9160 (mt) cc_final: 0.8950 (mt)
REVERT: B  512 TYR cc_start: 0.7626 (p90) cc_final: 0.6232 (p90)
REVERT: B  530 MET cc_start: 0.9017 (mmt) cc_final: 0.8753 (mmt)
REVERT: B  583 PHE cc_start: 0.9066 (m-10) cc_final: 0.8857 (m-10)
REVERT: B  602 LYS cc_start: 0.9113 (tptt) cc_final: 0.8721 (tppt)
REVERT: B  808 LEU cc_start: 0.9109 (tp) cc_final: 0.8745 (tp)
REVERT: B  869 MET cc_start: 0.8703 (tpp) cc_final: 0.8367 (tpp)
REVERT: B 1066 MET cc_start: 0.7471 (mmm) cc_final: 0.7081 (mmm)
REVERT: B 1078 LEU cc_start: 0.9242 (tp) cc_final: 0.8960 (tp)
REVERT: B 1091 LEU cc_start: 0.8903 (tt) cc_final: 0.8699 (tt)
REVERT: B 1110 MET cc_start: 0.8507 (tpt) cc_final: 0.8243 (mmm)
REVERT: B 1124 ARG cc_start: 0.8511 (mmp80) cc_final: 0.8068 (mmp80)
REVERT: B 1128 ASP cc_start: 0.8320 (m-30) cc_final: 0.7390 (m-30)
REVERT: B 1246 ARG cc_start: 0.9368 (mmp80) cc_final: 0.9054 (mmp80)
REVERT: B 1395 MET cc_start: 0.9076 (mmm) cc_final: 0.8801 (mmm)
REVERT: B 1490 PHE cc_start: 0.9121 (m-80) cc_final: 0.8719 (m-80)
REVERT: B 1505 MET cc_start: 0.6770 (mmp) cc_final: 0.6226 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 214
  average time/residue: 0.1839
  time to fit residues: 56.9720
Evaluate side-chains
  155 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 110 optimal weight:    0.9990
   chunk 36 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 78 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 82 optimal weight:    0.9990
   chunk 89 optimal weight:    0.0050
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.7394

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

Flipped N/Q/H residues before XYZ refinement:
B 262 ASN
B1134 GLN
** B1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1296 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 = 0.3427 r_free = 0.3427 target = 0.083022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.063747 restraints weight = 32919.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.065711 restraints weight = 19849.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.067041 restraints weight = 13621.744|
|-----------------------------------------------------------------------------|
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.5543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9114  Z= 0.186
  Angle     :  0.636   8.286  12369  Z= 0.311
  Chirality :  0.041   0.169   1492
  Planarity :  0.004   0.054   1516
  Dihedral  :  7.269 117.897   1255
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.25), residues: 1122
  helix:  1.34 (0.18), residues: 755
  sheet: -1.02 (0.56), residues: 79
  loop : -1.57 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B1247 
 HIS   0.004   0.001   HIS B 889 
 PHE   0.021   0.001   PHE B 433 
 TYR   0.011   0.001   TYR B 512 
 ARG   0.006   0.000   ARG B 306 

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 0.801 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  233 MET cc_start: 0.9057 (mmm) cc_final: 0.8550 (mmm)
REVERT: B  319 CYS cc_start: 0.9044 (m) cc_final: 0.8515 (t)
REVERT: B  323 ILE cc_start: 0.9366 (mm) cc_final: 0.9088 (mm)
REVERT: B  361 LEU cc_start: 0.9545 (mm) cc_final: 0.9057 (tp)
REVERT: B  420 LEU cc_start: 0.8785 (mt) cc_final: 0.8566 (mt)
REVERT: B  509 LEU cc_start: 0.9102 (mt) cc_final: 0.8883 (mt)
REVERT: B  512 TYR cc_start: 0.7429 (p90) cc_final: 0.5916 (p90)
REVERT: B  530 MET cc_start: 0.9026 (mmt) cc_final: 0.8775 (mmt)
REVERT: B  583 PHE cc_start: 0.9085 (m-10) cc_final: 0.8866 (m-10)
REVERT: B  730 MET cc_start: 0.6563 (mtp) cc_final: 0.6299 (mtp)
REVERT: B  808 LEU cc_start: 0.9081 (tp) cc_final: 0.8679 (tp)
REVERT: B 1078 LEU cc_start: 0.9280 (tp) cc_final: 0.9074 (tt)
REVERT: B 1124 ARG cc_start: 0.8535 (mmp80) cc_final: 0.8107 (mmp80)
REVERT: B 1128 ASP cc_start: 0.8351 (m-30) cc_final: 0.7399 (m-30)
REVERT: B 1229 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8443 (tm-30)
REVERT: B 1246 ARG cc_start: 0.9499 (mmp80) cc_final: 0.9055 (mmp80)
REVERT: B 1258 CYS cc_start: 0.8982 (t) cc_final: 0.8763 (t)
REVERT: B 1290 MET cc_start: 0.8658 (ttt) cc_final: 0.8380 (ttm)
REVERT: B 1424 ILE cc_start: 0.9047 (tp) cc_final: 0.8747 (tp)
REVERT: B 1490 PHE cc_start: 0.9128 (m-80) cc_final: 0.8899 (m-80)
REVERT: B 1504 ILE cc_start: 0.8632 (pt) cc_final: 0.8331 (pt)
REVERT: B 1505 MET cc_start: 0.6707 (mmp) cc_final: 0.6344 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 203
  average time/residue: 0.1577
  time to fit residues: 48.2272
Evaluate side-chains
  146 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 1.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 110 optimal weight:    6.9990
   chunk 109 optimal weight:    8.9990
   chunk 26 optimal weight:    0.9980
   chunk 83 optimal weight:    0.6980
   chunk 45 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 69 optimal weight:    0.3980
   chunk 78 optimal weight:    0.5980
   chunk 111 optimal weight:    5.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 262 ASN
** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.083241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.063964 restraints weight = 32820.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.065878 restraints weight = 20039.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.067216 restraints weight = 13951.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.5718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9114  Z= 0.186
  Angle     :  0.652   8.306  12369  Z= 0.322
  Chirality :  0.041   0.185   1492
  Planarity :  0.004   0.047   1516
  Dihedral  :  7.190 117.477   1255
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.25), residues: 1122
  helix:  1.34 (0.19), residues: 752
  sheet: -1.10 (0.56), residues: 79
  loop : -1.44 (0.35), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B1247 
 HIS   0.004   0.001   HIS B 889 
 PHE   0.025   0.002   PHE B 295 
 TYR   0.011   0.001   TYR B1004 
 ARG   0.005   0.000   ARG B1419 

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 1.097 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  233 MET cc_start: 0.9093 (mmm) cc_final: 0.8555 (mmm)
REVERT: B  319 CYS cc_start: 0.9048 (m) cc_final: 0.8575 (t)
REVERT: B  323 ILE cc_start: 0.9354 (mm) cc_final: 0.9077 (mm)
REVERT: B  509 LEU cc_start: 0.9107 (mt) cc_final: 0.8838 (mt)
REVERT: B  512 TYR cc_start: 0.7386 (p90) cc_final: 0.6224 (p90)
REVERT: B  530 MET cc_start: 0.9034 (mmt) cc_final: 0.8769 (mmt)
REVERT: B  602 LYS cc_start: 0.9073 (tptt) cc_final: 0.8679 (tppt)
REVERT: B  730 MET cc_start: 0.6631 (mtp) cc_final: 0.6376 (mtp)
REVERT: B  808 LEU cc_start: 0.9114 (tp) cc_final: 0.8707 (tp)
REVERT: B  869 MET cc_start: 0.8689 (tpp) cc_final: 0.8447 (tpt)
REVERT: B 1078 LEU cc_start: 0.9278 (tp) cc_final: 0.9049 (tt)
REVERT: B 1124 ARG cc_start: 0.8498 (mmp80) cc_final: 0.8073 (mmp80)
REVERT: B 1128 ASP cc_start: 0.8289 (m-30) cc_final: 0.7374 (m-30)
REVERT: B 1146 SER cc_start: 0.9280 (m) cc_final: 0.8810 (p)
REVERT: B 1229 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8408 (tm-30)
REVERT: B 1246 ARG cc_start: 0.9465 (mmp80) cc_final: 0.9061 (mmp80)
REVERT: B 1290 MET cc_start: 0.8684 (ttt) cc_final: 0.8429 (ttm)
REVERT: B 1424 ILE cc_start: 0.9098 (tp) cc_final: 0.8805 (tp)
REVERT: B 1490 PHE cc_start: 0.9133 (m-80) cc_final: 0.8914 (m-80)
REVERT: B 1504 ILE cc_start: 0.8741 (pt) cc_final: 0.8398 (pt)
REVERT: B 1505 MET cc_start: 0.6907 (mmp) cc_final: 0.6437 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 200
  average time/residue: 0.1614
  time to fit residues: 49.0895
Evaluate side-chains
  148 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 1.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 87 optimal weight:    1.9990
   chunk 83 optimal weight:    0.7980
   chunk 44 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 75 optimal weight:    0.5980
   chunk 113 optimal weight:    0.3980
   chunk 112 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 31 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 262 ASN
** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.082862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.063902 restraints weight = 32818.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.065826 restraints weight = 20004.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.067058 restraints weight = 13852.509|
|-----------------------------------------------------------------------------|
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.5882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9114  Z= 0.199
  Angle     :  0.663   8.429  12369  Z= 0.328
  Chirality :  0.041   0.165   1492
  Planarity :  0.004   0.045   1516
  Dihedral  :  7.155 117.094   1255
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.25), residues: 1122
  helix:  1.37 (0.19), residues: 751
  sheet: -1.07 (0.56), residues: 79
  loop : -1.41 (0.35), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B1247 
 HIS   0.004   0.001   HIS B 889 
 PHE   0.031   0.002   PHE B 433 
 TYR   0.030   0.001   TYR B1254 
 ARG   0.005   0.000   ARG B1419 

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 1.028 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  233 MET cc_start: 0.9098 (mmm) cc_final: 0.8563 (mmm)
REVERT: B  319 CYS cc_start: 0.9027 (m) cc_final: 0.8581 (t)
REVERT: B  323 ILE cc_start: 0.9336 (mm) cc_final: 0.9058 (mm)
REVERT: B  429 MET cc_start: 0.8657 (tmm) cc_final: 0.8258 (tmm)
REVERT: B  509 LEU cc_start: 0.9123 (mt) cc_final: 0.8892 (mt)
REVERT: B  530 MET cc_start: 0.9025 (mmt) cc_final: 0.8765 (mmt)
REVERT: B  710 MET cc_start: 0.8240 (tpt) cc_final: 0.7696 (mmm)
REVERT: B  730 MET cc_start: 0.6805 (mtp) cc_final: 0.6557 (mtt)
REVERT: B  808 LEU cc_start: 0.9098 (tp) cc_final: 0.8702 (tp)
REVERT: B  869 MET cc_start: 0.8733 (tpp) cc_final: 0.8470 (tpt)
REVERT: B  909 GLN cc_start: 0.8536 (tt0) cc_final: 0.8202 (tm-30)
REVERT: B 1078 LEU cc_start: 0.9274 (tp) cc_final: 0.9027 (tp)
REVERT: B 1124 ARG cc_start: 0.8512 (mmp80) cc_final: 0.8093 (mmp80)
REVERT: B 1128 ASP cc_start: 0.8303 (m-30) cc_final: 0.7351 (m-30)
REVERT: B 1146 SER cc_start: 0.9291 (m) cc_final: 0.8872 (p)
REVERT: B 1229 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8359 (tm-30)
REVERT: B 1246 ARG cc_start: 0.9469 (mmp80) cc_final: 0.9055 (mmp80)
REVERT: B 1258 CYS cc_start: 0.8948 (t) cc_final: 0.8741 (t)
REVERT: B 1424 ILE cc_start: 0.9150 (tp) cc_final: 0.8900 (tp)
REVERT: B 1504 ILE cc_start: 0.8786 (pt) cc_final: 0.8402 (pt)
REVERT: B 1505 MET cc_start: 0.6897 (mmp) cc_final: 0.6512 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 204
  average time/residue: 0.1658
  time to fit residues: 49.9094
Evaluate side-chains
  149 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 88 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 110 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 9 optimal weight:    0.1980
   chunk 75 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 99 optimal weight:    0.7980
   chunk 79 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B 262 ASN
** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.082960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.063877 restraints weight = 32432.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.065843 restraints weight = 19780.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.067136 restraints weight = 13586.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.6011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9114  Z= 0.183
  Angle     :  0.661   9.729  12369  Z= 0.321
  Chirality :  0.042   0.179   1492
  Planarity :  0.004   0.045   1516
  Dihedral  :  7.014 117.520   1255
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.75 (0.25), residues: 1122
  helix:  1.36 (0.19), residues: 758
  sheet: -0.98 (0.56), residues: 79
  loop : -1.36 (0.37), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B1247 
 HIS   0.003   0.001   HIS B1024 
 PHE   0.045   0.002   PHE B 433 
 TYR   0.021   0.001   TYR B 512 
 ARG   0.006   0.000   ARG B1419 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2722.31 seconds
wall clock time: 49 minutes 44.96 seconds (2984.96 seconds total)