Starting phenix.real_space_refine
on Sat Aug 23 03:17:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5yw7_6847/08_2025/5yw7_6847.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5yw7_6847/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/5yw7_6847/08_2025/5yw7_6847.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5yw7_6847/08_2025/5yw7_6847.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/5yw7_6847/08_2025/5yw7_6847.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5yw7_6847/08_2025/5yw7_6847.map"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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, 'ARG:plan': 3, 'ASP:plan': 5, 'GLU:plan': 3, 'TRP:plan': 1}
          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: 1.69, per 1000 atoms: 0.19
  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: 0.75
  Conformation dependent library (CDL) restraints added in 309.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.23
  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: 1.03

  Time building geometry restraints manager: 1.00 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:             2.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.630
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.420
-------------------------------------------------------------------------------
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= 0.277
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.003   0.000   ARG B1494 
 TYR   0.014   0.001   TYR B 378 
 PHE   0.016   0.001   PHE B 305 
 TRP   0.010   0.001   TRP B1037 
 HIS   0.004   0.001   HIS B 584 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 ( 9114)
  covalent geometry    : angle       0.71015 (12369)
  hydrogen bonds       : bond        0.16066 (  574)
  hydrogen bonds       : angle       6.59212 ( 1695)

*********************** 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  : 0.194 
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: 0.8996 (mtpp) cc_final: 0.7907 (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: 0.8545 (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: 0.8203 (tpp80)
REVERT: B  320 ILE cc_start: 0.9508 (mt) cc_final: 0.9235 (mt)
REVERT: B  367 LEU cc_start: 0.9377 (pp) cc_final: 0.9161 (pp)
REVERT: B  374 GLN cc_start: 0.9396 (OUTLIER) cc_final: 0.9136 (mm-40)
REVERT: B  510 LYS cc_start: 0.9375 (mtpp) cc_final: 0.9054 (mtmt)
REVERT: B  581 SER cc_start: 0.9663 (m) cc_final: 0.9341 (p)
REVERT: B  590 LEU cc_start: 0.9261 (mt) cc_final: 0.8896 (tp)
REVERT: B  708 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8280 (tt)
REVERT: B  730 MET cc_start: 0.7235 (mtm) cc_final: 0.6738 (mtp)
REVERT: B  820 GLN cc_start: 0.9011 (mt0) cc_final: 0.8752 (mp10)
REVERT: B  869 MET cc_start: 0.9030 (tmm) cc_final: 0.8492 (tmm)
REVERT: B  886 LEU cc_start: 0.9249 (tt) cc_final: 0.8385 (tt)
REVERT: B 1064 TYR cc_start: 0.7769 (m-80) cc_final: 0.7375 (m-80)
REVERT: B 1078 LEU cc_start: 0.9037 (tp) cc_final: 0.8640 (tp)
REVERT: B 1104 ARG cc_start: 0.8368 (mmm-85) cc_final: 0.7933 (tpp80)
REVERT: B 1146 SER cc_start: 0.9252 (m) cc_final: 0.8715 (p)
REVERT: B 1190 GLN cc_start: 0.9228 (tp40) cc_final: 0.8865 (tt0)
REVERT: B 1206 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7939 (mt-10)
REVERT: B 1214 ILE cc_start: 0.9600 (mt) cc_final: 0.9296 (tp)
REVERT: B 1232 ASP cc_start: 0.8570 (t70) cc_final: 0.8351 (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: 0.8693 (m110)
REVERT: B 1305 MET cc_start: 0.8941 (tpt) cc_final: 0.8537 (tpt)
REVERT: B 1490 PHE cc_start: 0.9192 (m-80) cc_final: 0.8672 (m-80)
REVERT: B 1505 MET cc_start: 0.7959 (ttm) cc_final: 0.7382 (mmt)
REVERT: B 1550 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8294 (ttt)
REVERT: B 1551 VAL cc_start: 0.8720 (OUTLIER) cc_final: 0.8399 (p)
REVERT: B 1561 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.7942 (p0)
  outliers start: 63
  outliers final: 20
  residues processed: 374
  average time/residue: 0.0683
  time to fit residues: 35.3995
Evaluate side-chains
  225 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 199
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.0070
   chunk 113 optimal weight:    6.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:    8.9990
   overall best weight:    1.1402

-------------------------------------------------------------------------------
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 485 GLN
B 846 GLN
B1134 GLN
** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1541 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.080783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.060941 restraints weight = 33189.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.062922 restraints weight = 19836.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.064294 restraints weight = 13589.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.065155 restraints weight = 10273.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.065844 restraints weight = 8492.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.3202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9114  Z= 0.194
  Angle     :  0.712  10.484  12369  Z= 0.362
  Chirality :  0.044   0.171   1492
  Planarity :  0.005   0.066   1516
  Dihedral  :  8.349 114.237   1255
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  4.02 %
    Favored  : 95.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.99 (0.24), residues: 1122
  helix:  0.16 (0.18), residues: 750
  sheet: -1.49 (0.53), residues: 79
  loop : -2.40 (0.32), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.023   0.001   ARG B1251 
 TYR   0.022   0.002   TYR B 512 
 PHE   0.020   0.002   PHE B 566 
 TRP   0.029   0.002   TRP B1247 
 HIS   0.004   0.001   HIS B1024 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 9114)
  covalent geometry    : angle       0.71223 (12369)
  hydrogen bonds       : bond        0.06997 (  574)
  hydrogen bonds       : angle       5.07537 ( 1695)

*********************** 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
  248 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 245
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  222 VAL cc_start: 0.8734 (m) cc_final: 0.8246 (p)
REVERT: B  227 LYS cc_start: 0.9084 (mtpp) cc_final: 0.8035 (tttt)
REVERT: B  253 LEU cc_start: 0.9027 (tp) cc_final: 0.8810 (tp)
REVERT: B  262 ASN cc_start: 0.8612 (m-40) cc_final: 0.8356 (m-40)
REVERT: B  306 ARG cc_start: 0.8923 (tpt90) cc_final: 0.8671 (tpp80)
REVERT: B  433 PHE cc_start: 0.8658 (m-10) cc_final: 0.8269 (m-80)
REVERT: B  581 SER cc_start: 0.9671 (m) cc_final: 0.9405 (p)
REVERT: B  602 LYS cc_start: 0.9238 (tptt) cc_final: 0.8878 (tptp)
REVERT: B  808 LEU cc_start: 0.9181 (tp) cc_final: 0.8915 (tp)
REVERT: B  869 MET cc_start: 0.8436 (tmm) cc_final: 0.7957 (tmm)
REVERT: B 1078 LEU cc_start: 0.9168 (tp) cc_final: 0.8965 (tp)
REVERT: B 1104 ARG cc_start: 0.8485 (mmm-85) cc_final: 0.8058 (tpp80)
REVERT: B 1128 ASP cc_start: 0.8396 (m-30) cc_final: 0.7666 (m-30)
REVERT: B 1148 LEU cc_start: 0.9190 (mm) cc_final: 0.8927 (mt)
REVERT: B 1290 MET cc_start: 0.8915 (ttm) cc_final: 0.8493 (tmm)
REVERT: B 1305 MET cc_start: 0.8518 (tpt) cc_final: 0.8277 (tpt)
REVERT: B 1431 LEU cc_start: 0.8957 (mt) cc_final: 0.8737 (pt)
REVERT: B 1490 PHE cc_start: 0.9133 (m-80) cc_final: 0.8793 (m-80)
  outliers start: 3
  outliers final: 0
  residues processed: 248
  average time/residue: 0.0602
  time to fit residues: 21.8172
Evaluate side-chains
  167 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 90 optimal weight:    0.0770
   chunk 60 optimal weight:    4.9990
   chunk 53 optimal weight:    7.9990
   chunk 112 optimal weight:    5.9990
   chunk 31 optimal weight:    0.8980
   chunk 47 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 107 optimal weight:    8.9990
   chunk 106 optimal weight:    0.1980
   chunk 96 optimal weight:    6.9990
   overall best weight:    0.6138

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.081926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.062037 restraints weight = 32774.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.064055 restraints weight = 19388.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.065454 restraints weight = 13218.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.066407 restraints weight = 9936.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.066940 restraints weight = 8086.239|
|-----------------------------------------------------------------------------|
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.3917

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= 0.155
  Angle     :  0.643   9.508  12369  Z= 0.320
  Chirality :  0.041   0.146   1492
  Planarity :  0.004   0.043   1516
  Dihedral  :  7.999 115.666   1255
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.14 (0.24), residues: 1122
  helix:  0.85 (0.19), residues: 754
  sheet: -1.38 (0.52), residues: 79
  loop : -2.16 (0.33), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B1251 
 TYR   0.033   0.002   TYR B 512 
 PHE   0.026   0.002   PHE B 295 
 TRP   0.020   0.002   TRP B 778 
 HIS   0.002   0.001   HIS B 896 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 9114)
  covalent geometry    : angle       0.64268 (12369)
  hydrogen bonds       : bond        0.06215 (  574)
  hydrogen bonds       : angle       4.62160 ( 1695)

*********************** 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
  230 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  227 LYS cc_start: 0.9121 (mtpp) cc_final: 0.8155 (tttt)
REVERT: B  233 MET cc_start: 0.9082 (mmm) cc_final: 0.8613 (mmm)
REVERT: B  319 CYS cc_start: 0.9049 (m) cc_final: 0.8555 (t)
REVERT: B  420 LEU cc_start: 0.9089 (mt) cc_final: 0.8882 (mt)
REVERT: B  581 SER cc_start: 0.9691 (m) cc_final: 0.9443 (p)
REVERT: B  583 PHE cc_start: 0.9168 (m-10) cc_final: 0.8915 (m-10)
REVERT: B  602 LYS cc_start: 0.9192 (tptt) cc_final: 0.8842 (tptp)
REVERT: B  808 LEU cc_start: 0.9105 (tp) cc_final: 0.8697 (tp)
REVERT: B  838 ILE cc_start: 0.9811 (mt) cc_final: 0.9597 (tp)
REVERT: B  869 MET cc_start: 0.8062 (tmm) cc_final: 0.7849 (tmm)
REVERT: B 1078 LEU cc_start: 0.9191 (tp) cc_final: 0.8931 (tp)
REVERT: B 1104 ARG cc_start: 0.8530 (mmm-85) cc_final: 0.8042 (tpp80)
REVERT: B 1128 ASP cc_start: 0.8386 (m-30) cc_final: 0.7699 (m-30)
REVERT: B 1148 LEU cc_start: 0.9191 (mm) cc_final: 0.8952 (mt)
REVERT: B 1246 ARG cc_start: 0.9527 (mmp80) cc_final: 0.9135 (mmp80)
REVERT: B 1290 MET cc_start: 0.8837 (ttm) cc_final: 0.8395 (ttp)
REVERT: B 1300 ARG cc_start: 0.8749 (ttm170) cc_final: 0.8507 (mtp180)
REVERT: B 1305 MET cc_start: 0.8563 (tpt) cc_final: 0.8311 (tpt)
REVERT: B 1431 LEU cc_start: 0.9003 (mt) cc_final: 0.8613 (pt)
REVERT: B 1490 PHE cc_start: 0.9129 (m-80) cc_final: 0.8718 (m-80)
REVERT: B 1505 MET cc_start: 0.7810 (ttt) cc_final: 0.7584 (mmt)
REVERT: B 1550 MET cc_start: 0.8651 (mtm) cc_final: 0.8155 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 230
  average time/residue: 0.0620
  time to fit residues: 21.0048
Evaluate side-chains
  173 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 90 optimal weight:    5.9990
   chunk 38 optimal weight:    8.9990
   chunk 103 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 113 optimal weight:    3.9990
   chunk 98 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 107 optimal weight:    6.9990
   chunk 108 optimal weight:    0.6980
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1134 GLN
B1135 HIS
** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1439 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.079607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.060526 restraints weight = 33528.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.062440 restraints weight = 20018.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.063708 restraints weight = 13660.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.064578 restraints weight = 10358.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.065155 restraints weight = 8492.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.4511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   9114  Z= 0.204
  Angle     :  0.693  11.398  12369  Z= 0.350
  Chirality :  0.042   0.142   1492
  Planarity :  0.004   0.040   1516
  Dihedral  :  7.806 113.246   1255
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.05 (0.24), residues: 1122
  helix:  0.89 (0.18), residues: 765
  sheet: -0.95 (0.54), residues: 72
  loop : -1.98 (0.34), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B1215 
 TYR   0.013   0.002   TYR B 512 
 PHE   0.031   0.002   PHE B1223 
 TRP   0.014   0.002   TRP B1247 
 HIS   0.004   0.001   HIS B1273 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 9114)
  covalent geometry    : angle       0.69281 (12369)
  hydrogen bonds       : bond        0.05826 (  574)
  hydrogen bonds       : angle       4.61058 ( 1695)

*********************** 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
  208 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 0.336 
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: 0.9068 (mtpp) cc_final: 0.8127 (tttt)
REVERT: B  319 CYS cc_start: 0.9032 (m) cc_final: 0.8567 (t)
REVERT: B  503 LEU cc_start: 0.9238 (mm) cc_final: 0.8839 (tp)
REVERT: B  509 LEU cc_start: 0.9493 (mt) cc_final: 0.9198 (mt)
REVERT: B  581 SER cc_start: 0.9705 (m) cc_final: 0.9415 (p)
REVERT: B  583 PHE cc_start: 0.9177 (m-10) cc_final: 0.8934 (m-10)
REVERT: B  602 LYS cc_start: 0.9220 (tptt) cc_final: 0.8922 (tptp)
REVERT: B  808 LEU cc_start: 0.9004 (tp) cc_final: 0.8532 (tp)
REVERT: B 1078 LEU cc_start: 0.9278 (tp) cc_final: 0.9036 (tp)
REVERT: B 1104 ARG cc_start: 0.8650 (mmm-85) cc_final: 0.8197 (tpp80)
REVERT: B 1128 ASP cc_start: 0.8644 (m-30) cc_final: 0.8013 (m-30)
REVERT: B 1246 ARG cc_start: 0.9601 (mmp80) cc_final: 0.9063 (mmp80)
REVERT: B 1300 ARG cc_start: 0.8687 (ttm170) cc_final: 0.8424 (mtp180)
REVERT: B 1305 MET cc_start: 0.8537 (tpt) cc_final: 0.8273 (tpt)
REVERT: B 1490 PHE cc_start: 0.9103 (m-80) cc_final: 0.8899 (m-80)
REVERT: B 1505 MET cc_start: 0.8240 (ttt) cc_final: 0.7744 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 208
  average time/residue: 0.0653
  time to fit residues: 19.8702
Evaluate side-chains
  147 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 15 optimal weight:    0.5980
   chunk 64 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 3 optimal weight:    0.3980
   chunk 58 optimal weight:    5.9990
   chunk 79 optimal weight:    0.6980
   chunk 106 optimal weight:    4.9990
   chunk 85 optimal weight:    0.0870
   chunk 2 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.5558

-------------------------------------------------------------------------------
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 = 0.3409 r_free = 0.3409 target = 0.082144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.063099 restraints weight = 32583.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.065077 restraints weight = 19387.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.066450 restraints weight = 13292.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.067352 restraints weight = 10001.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.067995 restraints weight = 8162.429|
|-----------------------------------------------------------------------------|
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.4890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9114  Z= 0.138
  Angle     :  0.639   9.864  12369  Z= 0.316
  Chirality :  0.041   0.163   1492
  Planarity :  0.004   0.045   1516
  Dihedral  :  7.609 113.584   1255
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.35 (0.25), residues: 1122
  helix:  1.11 (0.18), residues: 761
  sheet: -1.01 (0.54), residues: 79
  loop : -1.74 (0.36), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B1419 
 TYR   0.013   0.001   TYR B1254 
 PHE   0.030   0.002   PHE B 432 
 TRP   0.014   0.001   TRP B1247 
 HIS   0.003   0.000   HIS B1024 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 9114)
  covalent geometry    : angle       0.63900 (12369)
  hydrogen bonds       : bond        0.05497 (  574)
  hydrogen bonds       : angle       4.41022 ( 1695)

*********************** 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
  224 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  227 LYS cc_start: 0.9113 (mtpp) cc_final: 0.8059 (tttt)
REVERT: B  257 MET cc_start: 0.7705 (ptp) cc_final: 0.7096 (ptp)
REVERT: B  319 CYS cc_start: 0.8989 (m) cc_final: 0.8623 (t)
REVERT: B  361 LEU cc_start: 0.9566 (mm) cc_final: 0.9048 (tp)
REVERT: B  394 LYS cc_start: 0.9174 (tppp) cc_final: 0.8881 (tppp)
REVERT: B  509 LEU cc_start: 0.9395 (mt) cc_final: 0.9140 (mt)
REVERT: B  530 MET cc_start: 0.9047 (mmt) cc_final: 0.8763 (mmt)
REVERT: B  583 PHE cc_start: 0.9111 (m-10) cc_final: 0.8848 (m-10)
REVERT: B  602 LYS cc_start: 0.9145 (tptt) cc_final: 0.8819 (tptp)
REVERT: B  808 LEU cc_start: 0.8954 (tp) cc_final: 0.8550 (tp)
REVERT: B 1078 LEU cc_start: 0.9253 (tp) cc_final: 0.8989 (tp)
REVERT: B 1091 LEU cc_start: 0.9049 (tt) cc_final: 0.8800 (tt)
REVERT: B 1104 ARG cc_start: 0.8481 (mmm-85) cc_final: 0.8018 (tpp80)
REVERT: B 1124 ARG cc_start: 0.8598 (mmp80) cc_final: 0.8121 (mmp80)
REVERT: B 1128 ASP cc_start: 0.8392 (m-30) cc_final: 0.7318 (m-30)
REVERT: B 1134 GLN cc_start: 0.8414 (mm-40) cc_final: 0.8065 (mm-40)
REVERT: B 1246 ARG cc_start: 0.9483 (mmp80) cc_final: 0.9108 (mmp80)
REVERT: B 1290 MET cc_start: 0.8462 (ttt) cc_final: 0.8230 (ttm)
REVERT: B 1305 MET cc_start: 0.8487 (tpt) cc_final: 0.8230 (tpt)
REVERT: B 1505 MET cc_start: 0.7869 (ttt) cc_final: 0.7515 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 224
  average time/residue: 0.0582
  time to fit residues: 19.2948
Evaluate side-chains
  154 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 105 optimal weight:    6.9990
   chunk 106 optimal weight:    5.9990
   chunk 113 optimal weight:    1.9990
   chunk 46 optimal weight:    4.9990
   chunk 86 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 49 optimal weight:    0.2980
   chunk 101 optimal weight:    5.9990
   chunk 17 optimal weight:    0.6980
   chunk 79 optimal weight:    0.7980
   overall best weight:    0.9182

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.081275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.062307 restraints weight = 32810.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.064321 restraints weight = 19400.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.065647 restraints weight = 13130.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.066627 restraints weight = 9911.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.067209 restraints weight = 7999.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.5201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9114  Z= 0.149
  Angle     :  0.633   7.629  12369  Z= 0.319
  Chirality :  0.041   0.164   1492
  Planarity :  0.004   0.043   1516
  Dihedral  :  7.463 111.392   1255
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.48 (0.25), residues: 1122
  helix:  1.21 (0.18), residues: 757
  sheet: -0.62 (0.58), residues: 74
  loop : -1.77 (0.35), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B1419 
 TYR   0.016   0.001   TYR B 512 
 PHE   0.034   0.002   PHE B1393 
 TRP   0.011   0.001   TRP B 514 
 HIS   0.003   0.001   HIS B1024 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 9114)
  covalent geometry    : angle       0.63307 (12369)
  hydrogen bonds       : bond        0.05246 (  574)
  hydrogen bonds       : angle       4.36797 ( 1695)

*********************** 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
  210 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  227 LYS cc_start: 0.9064 (mtpp) cc_final: 0.8035 (tttt)
REVERT: B  263 TYR cc_start: 0.8755 (t80) cc_final: 0.8539 (t80)
REVERT: B  319 CYS cc_start: 0.9052 (m) cc_final: 0.8633 (t)
REVERT: B  361 LEU cc_start: 0.9624 (mm) cc_final: 0.9143 (tp)
REVERT: B  394 LYS cc_start: 0.9193 (tppp) cc_final: 0.8938 (tppp)
REVERT: B  509 LEU cc_start: 0.9377 (mt) cc_final: 0.9075 (mt)
REVERT: B  512 TYR cc_start: 0.7606 (p90) cc_final: 0.6336 (p90)
REVERT: B  530 MET cc_start: 0.9083 (mmt) cc_final: 0.8753 (mmt)
REVERT: B  536 PHE cc_start: 0.8809 (t80) cc_final: 0.8570 (t80)
REVERT: B  583 PHE cc_start: 0.9190 (m-10) cc_final: 0.8947 (m-10)
REVERT: B  602 LYS cc_start: 0.9183 (tptt) cc_final: 0.8940 (tptm)
REVERT: B  808 LEU cc_start: 0.8910 (tp) cc_final: 0.8506 (tp)
REVERT: B  900 ILE cc_start: 0.8889 (mm) cc_final: 0.8576 (pt)
REVERT: B 1078 LEU cc_start: 0.9250 (tp) cc_final: 0.8995 (tt)
REVERT: B 1091 LEU cc_start: 0.8987 (tt) cc_final: 0.8776 (tt)
REVERT: B 1104 ARG cc_start: 0.8498 (mmm-85) cc_final: 0.8036 (tpp80)
REVERT: B 1124 ARG cc_start: 0.8610 (mmp80) cc_final: 0.8166 (mmp80)
REVERT: B 1128 ASP cc_start: 0.8383 (m-30) cc_final: 0.7496 (m-30)
REVERT: B 1134 GLN cc_start: 0.8434 (mm-40) cc_final: 0.8116 (mm-40)
REVERT: B 1229 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8381 (tm-30)
REVERT: B 1246 ARG cc_start: 0.9500 (mmp80) cc_final: 0.9049 (mmp80)
REVERT: B 1295 LEU cc_start: 0.9362 (mt) cc_final: 0.9154 (mm)
REVERT: B 1300 ARG cc_start: 0.8613 (ttm170) cc_final: 0.8363 (mtp180)
REVERT: B 1305 MET cc_start: 0.8543 (tpt) cc_final: 0.8273 (tpt)
REVERT: B 1377 ILE cc_start: 0.9490 (mm) cc_final: 0.9173 (mp)
REVERT: B 1490 PHE cc_start: 0.8894 (m-80) cc_final: 0.8468 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 210
  average time/residue: 0.0601
  time to fit residues: 18.5796
Evaluate side-chains
  159 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 51 optimal weight:    6.9990
   chunk 65 optimal weight:    0.8980
   chunk 81 optimal weight:    0.5980
   chunk 12 optimal weight:    2.9990
   chunk 32 optimal weight:    0.3980
   chunk 79 optimal weight:    0.7980
   chunk 73 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 102 optimal weight:    0.2980
   chunk 64 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   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
** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1521 GLN
B1569 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.082406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.063258 restraints weight = 33210.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.065256 restraints weight = 19804.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.066616 restraints weight = 13468.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.067539 restraints weight = 10090.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.068121 restraints weight = 8166.466|
|-----------------------------------------------------------------------------|
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.5424

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= 0.138
  Angle     :  0.639   7.760  12369  Z= 0.318
  Chirality :  0.042   0.186   1492
  Planarity :  0.004   0.050   1516
  Dihedral  :  7.397 111.660   1255
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.50 (0.25), residues: 1122
  helix:  1.20 (0.18), residues: 759
  sheet: -0.56 (0.58), residues: 72
  loop : -1.71 (0.35), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B1419 
 TYR   0.048   0.002   TYR B 512 
 PHE   0.021   0.002   PHE B1204 
 TRP   0.019   0.001   TRP B 514 
 HIS   0.003   0.000   HIS B1024 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 9114)
  covalent geometry    : angle       0.63882 (12369)
  hydrogen bonds       : bond        0.05172 (  574)
  hydrogen bonds       : angle       4.35154 ( 1695)

*********************** 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  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  227 LYS cc_start: 0.9051 (mtpp) cc_final: 0.7991 (tttt)
REVERT: B  319 CYS cc_start: 0.9002 (m) cc_final: 0.8480 (t)
REVERT: B  323 ILE cc_start: 0.9362 (mm) cc_final: 0.9099 (mm)
REVERT: B  361 LEU cc_start: 0.9586 (mm) cc_final: 0.9116 (tp)
REVERT: B  509 LEU cc_start: 0.9462 (mt) cc_final: 0.9243 (mt)
REVERT: B  530 MET cc_start: 0.9061 (mmt) cc_final: 0.8760 (mmt)
REVERT: B  583 PHE cc_start: 0.9140 (m-10) cc_final: 0.8867 (m-10)
REVERT: B  602 LYS cc_start: 0.9144 (tptt) cc_final: 0.8881 (tptm)
REVERT: B  900 ILE cc_start: 0.8866 (mm) cc_final: 0.8564 (pt)
REVERT: B 1078 LEU cc_start: 0.9303 (tp) cc_final: 0.8991 (tt)
REVERT: B 1091 LEU cc_start: 0.8950 (tt) cc_final: 0.8733 (tt)
REVERT: B 1104 ARG cc_start: 0.8434 (mmm-85) cc_final: 0.7975 (tpp80)
REVERT: B 1124 ARG cc_start: 0.8563 (mmp80) cc_final: 0.8119 (mmp80)
REVERT: B 1128 ASP cc_start: 0.8270 (m-30) cc_final: 0.7264 (m-30)
REVERT: B 1229 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8370 (tm-30)
REVERT: B 1246 ARG cc_start: 0.9492 (mmp80) cc_final: 0.9065 (mmp80)
REVERT: B 1305 MET cc_start: 0.8556 (tpt) cc_final: 0.8303 (tpt)
REVERT: B 1377 ILE cc_start: 0.9497 (mm) cc_final: 0.9262 (mp)
REVERT: B 1395 MET cc_start: 0.9083 (mmm) cc_final: 0.8870 (mmm)
REVERT: B 1431 LEU cc_start: 0.9188 (mt) cc_final: 0.8800 (mm)
REVERT: B 1490 PHE cc_start: 0.8914 (m-80) cc_final: 0.8507 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 214
  average time/residue: 0.0759
  time to fit residues: 24.0865
Evaluate side-chains
  156 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 104 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 87 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9990
   chunk 90 optimal weight:    0.0570
   chunk 15 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.6900

-------------------------------------------------------------------------------
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 = 0.3402 r_free = 0.3402 target = 0.082132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.063153 restraints weight = 32807.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.065137 restraints weight = 19845.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.066490 restraints weight = 13602.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.067427 restraints weight = 10217.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.068023 restraints weight = 8273.614|
|-----------------------------------------------------------------------------|
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.5653

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= 0.144
  Angle     :  0.637   7.883  12369  Z= 0.320
  Chirality :  0.041   0.170   1492
  Planarity :  0.004   0.076   1516
  Dihedral  :  7.371 113.412   1255
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.25), residues: 1122
  helix:  1.18 (0.18), residues: 763
  sheet: -0.52 (0.57), residues: 72
  loop : -1.62 (0.35), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B1419 
 TYR   0.027   0.002   TYR B 512 
 PHE   0.024   0.002   PHE B 295 
 TRP   0.019   0.001   TRP B 514 
 HIS   0.003   0.001   HIS B1024 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 9114)
  covalent geometry    : angle       0.63679 (12369)
  hydrogen bonds       : bond        0.05041 (  574)
  hydrogen bonds       : angle       4.31971 ( 1695)

*********************** 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
  209 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 209
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  227 LYS cc_start: 0.8997 (mtpp) cc_final: 0.7971 (tttt)
REVERT: B  319 CYS cc_start: 0.8984 (m) cc_final: 0.8457 (t)
REVERT: B  323 ILE cc_start: 0.9370 (mm) cc_final: 0.9100 (mm)
REVERT: B  361 LEU cc_start: 0.9596 (mm) cc_final: 0.9126 (tp)
REVERT: B  394 LYS cc_start: 0.9095 (tppp) cc_final: 0.8853 (tppp)
REVERT: B  509 LEU cc_start: 0.9414 (mt) cc_final: 0.9141 (mt)
REVERT: B  530 MET cc_start: 0.9054 (mmt) cc_final: 0.8745 (mmt)
REVERT: B  602 LYS cc_start: 0.9141 (tptt) cc_final: 0.8711 (tppt)
REVERT: B  808 LEU cc_start: 0.8963 (tp) cc_final: 0.8559 (tp)
REVERT: B  900 ILE cc_start: 0.8866 (mm) cc_final: 0.8562 (pt)
REVERT: B 1078 LEU cc_start: 0.9347 (tp) cc_final: 0.9060 (tt)
REVERT: B 1091 LEU cc_start: 0.8940 (tt) cc_final: 0.8722 (tt)
REVERT: B 1104 ARG cc_start: 0.8447 (mmm-85) cc_final: 0.7976 (tpp80)
REVERT: B 1124 ARG cc_start: 0.8553 (mmp80) cc_final: 0.8138 (mmp80)
REVERT: B 1128 ASP cc_start: 0.8273 (m-30) cc_final: 0.7470 (m-30)
REVERT: B 1229 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8397 (tm-30)
REVERT: B 1246 ARG cc_start: 0.9512 (mmp80) cc_final: 0.9040 (mmp80)
REVERT: B 1305 MET cc_start: 0.8547 (tpt) cc_final: 0.8336 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 209
  average time/residue: 0.0716
  time to fit residues: 22.5637
Evaluate side-chains
  154 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 30 optimal weight:    0.6980
   chunk 60 optimal weight:    2.9990
   chunk 92 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0470
   chunk 50 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 91 optimal weight:    0.4980
   overall best weight:    0.6480

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.082391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.063270 restraints weight = 33193.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.065284 restraints weight = 20035.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.066621 restraints weight = 13647.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.067552 restraints weight = 10310.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.068115 restraints weight = 8388.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.5837

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= 0.137
  Angle     :  0.647   8.009  12369  Z= 0.319
  Chirality :  0.041   0.170   1492
  Planarity :  0.004   0.067   1516
  Dihedral  :  7.341 114.678   1255
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.54 (0.25), residues: 1122
  helix:  1.21 (0.18), residues: 761
  sheet: -0.43 (0.58), residues: 72
  loop : -1.65 (0.35), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B1419 
 TYR   0.034   0.001   TYR B 512 
 PHE   0.018   0.002   PHE B 295 
 TRP   0.014   0.001   TRP B 688 
 HIS   0.003   0.000   HIS B1024 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 9114)
  covalent geometry    : angle       0.64685 (12369)
  hydrogen bonds       : bond        0.04966 (  574)
  hydrogen bonds       : angle       4.29508 ( 1695)

*********************** 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
  206 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  227 LYS cc_start: 0.8975 (mtpp) cc_final: 0.7944 (tttt)
REVERT: B  319 CYS cc_start: 0.8952 (m) cc_final: 0.8513 (t)
REVERT: B  323 ILE cc_start: 0.9327 (mm) cc_final: 0.9059 (mm)
REVERT: B  394 LYS cc_start: 0.9102 (tppp) cc_final: 0.8860 (tppp)
REVERT: B  509 LEU cc_start: 0.9406 (mt) cc_final: 0.9105 (mt)
REVERT: B  530 MET cc_start: 0.9038 (mmt) cc_final: 0.8724 (mmt)
REVERT: B  602 LYS cc_start: 0.9117 (tptt) cc_final: 0.8764 (tptp)
REVERT: B  808 LEU cc_start: 0.9018 (tp) cc_final: 0.8634 (tp)
REVERT: B  900 ILE cc_start: 0.8883 (mm) cc_final: 0.8573 (pt)
REVERT: B 1091 LEU cc_start: 0.8929 (tt) cc_final: 0.8720 (tt)
REVERT: B 1104 ARG cc_start: 0.8455 (mmm-85) cc_final: 0.7965 (tpp80)
REVERT: B 1124 ARG cc_start: 0.8558 (mmp80) cc_final: 0.8122 (mmp80)
REVERT: B 1128 ASP cc_start: 0.8230 (m-30) cc_final: 0.7474 (m-30)
REVERT: B 1229 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8338 (tm-30)
REVERT: B 1246 ARG cc_start: 0.9510 (mmp80) cc_final: 0.9065 (mmp80)
REVERT: B 1258 CYS cc_start: 0.8944 (t) cc_final: 0.8742 (t)
REVERT: B 1305 MET cc_start: 0.8564 (tpt) cc_final: 0.8319 (tpt)
REVERT: B 1395 MET cc_start: 0.9042 (mmm) cc_final: 0.8775 (mmm)
REVERT: B 1431 LEU cc_start: 0.9194 (mt) cc_final: 0.8891 (mm)
REVERT: B 1490 PHE cc_start: 0.8776 (m-80) cc_final: 0.8314 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 206
  average time/residue: 0.0760
  time to fit residues: 23.5725
Evaluate side-chains
  147 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 92 optimal weight:    0.2980
   chunk 38 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 18 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 107 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 74 optimal weight:    0.5980
   chunk 109 optimal weight:   10.0000
   chunk 11 optimal weight:    0.6980
   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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.082517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.063114 restraints weight = 33233.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.065130 restraints weight = 19850.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.066511 restraints weight = 13562.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.067471 restraints weight = 10171.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.068131 restraints weight = 8233.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.5951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9114  Z= 0.137
  Angle     :  0.645   7.781  12369  Z= 0.320
  Chirality :  0.041   0.160   1492
  Planarity :  0.004   0.063   1516
  Dihedral  :  7.270 115.558   1255
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.25), residues: 1122
  helix:  1.28 (0.18), residues: 753
  sheet: -0.33 (0.59), residues: 72
  loop : -1.54 (0.34), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 306 
 TYR   0.012   0.001   TYR B1004 
 PHE   0.020   0.002   PHE B 363 
 TRP   0.013   0.001   TRP B 514 
 HIS   0.003   0.000   HIS B1024 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 9114)
  covalent geometry    : angle       0.64525 (12369)
  hydrogen bonds       : bond        0.04926 (  574)
  hydrogen bonds       : angle       4.26336 ( 1695)

********************** 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
  199 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.368 
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: 0.8951 (mtpp) cc_final: 0.7943 (tttt)
REVERT: B  319 CYS cc_start: 0.8952 (m) cc_final: 0.8503 (t)
REVERT: B  323 ILE cc_start: 0.9350 (mm) cc_final: 0.9064 (mm)
REVERT: B  509 LEU cc_start: 0.9382 (mt) cc_final: 0.9094 (mt)
REVERT: B  530 MET cc_start: 0.9038 (mmt) cc_final: 0.8728 (mmt)
REVERT: B  602 LYS cc_start: 0.9136 (tptt) cc_final: 0.8792 (tptp)
REVERT: B  900 ILE cc_start: 0.8900 (mm) cc_final: 0.8582 (pt)
REVERT: B 1091 LEU cc_start: 0.8906 (tt) cc_final: 0.8700 (tt)
REVERT: B 1104 ARG cc_start: 0.8423 (mmm-85) cc_final: 0.7946 (tpp80)
REVERT: B 1124 ARG cc_start: 0.8558 (mmp80) cc_final: 0.8129 (mmp80)
REVERT: B 1128 ASP cc_start: 0.8243 (m-30) cc_final: 0.7488 (m-30)
REVERT: B 1146 SER cc_start: 0.9280 (m) cc_final: 0.8843 (p)
REVERT: B 1229 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8350 (tm-30)
REVERT: B 1246 ARG cc_start: 0.9492 (mmp80) cc_final: 0.9051 (mmp80)
REVERT: B 1258 CYS cc_start: 0.8990 (t) cc_final: 0.8730 (t)
REVERT: B 1395 MET cc_start: 0.9114 (mmm) cc_final: 0.8846 (mmm)
REVERT: B 1431 LEU cc_start: 0.9150 (mt) cc_final: 0.8874 (mm)
REVERT: B 1490 PHE cc_start: 0.8773 (m-80) cc_final: 0.8303 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 199
  average time/residue: 0.0751
  time to fit residues: 22.6187
Evaluate side-chains
  151 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 110 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   chunk 54 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   chunk 98 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   chunk 46 optimal weight:    0.7980
   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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.082076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.063019 restraints weight = 32918.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.065052 restraints weight = 19545.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.066402 restraints weight = 13219.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.067322 restraints weight = 9906.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.067956 restraints weight = 8010.533|
|-----------------------------------------------------------------------------|
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.6125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9114  Z= 0.139
  Angle     :  0.653   8.223  12369  Z= 0.323
  Chirality :  0.042   0.186   1492
  Planarity :  0.004   0.059   1516
  Dihedral  :  7.259 116.418   1255
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.25), residues: 1122
  helix:  1.25 (0.19), residues: 752
  sheet: -0.23 (0.59), residues: 72
  loop : -1.49 (0.34), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 306 
 TYR   0.033   0.001   TYR B 512 
 PHE   0.016   0.002   PHE B1240 
 TRP   0.013   0.001   TRP B 688 
 HIS   0.003   0.001   HIS B1024 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 9114)
  covalent geometry    : angle       0.65349 (12369)
  hydrogen bonds       : bond        0.04871 (  574)
  hydrogen bonds       : angle       4.26449 ( 1695)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1348.88 seconds
wall clock time: 24 minutes 6.27 seconds (1446.27 seconds total)