Starting phenix.real_space_refine
on Thu Feb 13 19:30:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5ywd_6853/02_2025/5ywd_6853.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5ywd_6853/02_2025/5ywd_6853.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5ywd_6853/02_2025/5ywd_6853.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5ywd_6853/02_2025/5ywd_6853.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5ywd_6853/02_2025/5ywd_6853.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5ywd_6853/02_2025/5ywd_6853.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     Mg      2      5.21       5
     S      47      5.16       5
     C    5806      2.51       5
     N    1533      2.21       5
     O    1605      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 35 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8997
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 8941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1154, 8941
          Classifications: {'peptide': 1154}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'PTRANS': 36, 'TRANS': 1117}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 118
          Unresolved non-hydrogen angles: 145
          Unresolved non-hydrogen dihedrals: 100
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 5, 'ARG:plan': 5, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 78
    Chain: "B"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {' MG': 2, 'ADP': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 4.98, per 1000 atoms: 0.55
  Number of scatterers: 8997
  At special positions: 0
  Unit cell: (93.895, 78.07, 138.205, 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)
     S      47     16.00
     P       4     15.00
     Mg      2     11.99
     O    1605      8.00
     N    1533      7.00
     C    5806      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.34
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2184

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 5 sheets defined
      69.8% alpha, 6.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.92
  Creating SS restraints...
    Processing helix  chain 'B' and resid 223 through 230
      removed outlier: 3.501A  pdb=" N   LYS B 227 " --> pdb=" O   ASN B 223 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   GLY B 228 " --> pdb=" O   LEU B 224 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   THR B 229 " --> pdb=" O   LEU B 225 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 232 through 243
      removed outlier: 4.326A  pdb=" N   PHE B 236 " --> pdb=" O   TRP B 232 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   HIS B 241 " --> pdb=" O   ILE B 237 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   LYS B 242 " --> pdb=" O   LYS B 238 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 257
    Processing helix  chain 'B' and resid 258 through 276
    Processing helix  chain 'B' and resid 284 through 296
      removed outlier: 3.600A  pdb=" N   TRP B 288 " --> pdb=" O   ALA B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 296 through 329
      Proline residue:  B 317  - end of helix
    Processing helix  chain 'B' and resid 355 through 402
      removed outlier: 3.763A  pdb=" N   MET B 400 " --> pdb=" O   TYR B 396 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   HIS B 401 " --> pdb=" O   ASN B 397 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 403 through 409
      removed outlier: 3.759A  pdb=" N   MET B 409 " --> pdb=" O   SER B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 410 through 412
      No H-bonds generated for 'chain 'B' and resid 410 through 412'
    Processing helix  chain 'B' and resid 413 through 439
      Proline residue:  B 436  - end of helix
    Processing helix  chain 'B' and resid 440 through 457
      removed outlier: 4.388A  pdb=" N   TYR B 454 " --> pdb=" O   ILE B 450 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ILE B 455 " --> pdb=" O   LEU B 451 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 459 through 504
      removed outlier: 4.497A  pdb=" N   GLY B 463 " --> pdb=" O   SER B 459 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   ALA B 471 " --> pdb=" O   ILE B 467 " (cutoff:3.500A)
      Proline residue:  B 472  - end of helix
      removed outlier: 3.800A  pdb=" N   ALA B 484 " --> pdb=" O   LYS B 480 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   SER B 487 " --> pdb=" O   GLN B 483 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LYS B 497 " --> pdb=" O   ASN B 493 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 505 through 512
      removed outlier: 3.901A  pdb=" N   TYR B 512 " --> pdb=" O   LEU B 508 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 514 through 564
      removed outlier: 3.663A  pdb=" N   PHE B 518 " --> pdb=" O   TRP B 514 " (cutoff:3.500A)
      Proline residue:  B 551  - end of helix
      removed outlier: 3.505A  pdb=" N   SER B 564 " --> pdb=" O   VAL B 560 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 572 through 615
      removed outlier: 3.500A  pdb=" N   ALA B 576 " --> pdb=" O   SER B 572 " (cutoff:3.500A)
      Proline residue:  B 589  - end of helix
      removed outlier: 3.820A  pdb=" N   SER B 594 " --> pdb=" O   LEU B 590 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   SER B 595 " --> pdb=" O   PHE B 591 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   ARG B 598 " --> pdb=" O   SER B 594 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   SER B 599 " --> pdb=" O   SER B 595 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LYS B 602 " --> pdb=" O   ARG B 598 " (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 795 through 806
      removed outlier: 3.686A  pdb=" N   LYS B 800 " --> pdb=" O   LYS B 796 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 808 through 815
    Processing helix  chain 'B' and resid 824 through 828
      removed outlier: 3.767A  pdb=" N   ILE B 828 " --> pdb=" O   GLU B 825 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 831 through 846
      removed outlier: 3.660A  pdb=" N   ARG B 835 " --> pdb=" O   SER B 831 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   GLN B 836 " --> pdb=" O   GLY B 832 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 861 through 872
    Processing helix  chain 'B' and resid 893 through 897
    Processing helix  chain 'B' and resid 914 through 920
    Processing helix  chain 'B' and resid 1000 through 1009
      removed outlier: 3.505A  pdb=" N   TYR B1004 " --> pdb=" O   ALA B1000 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1011 through 1039
      removed outlier: 3.615A  pdb=" N   ASP B1039 " --> pdb=" O   ALA B1035 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1061 through 1107
      removed outlier: 3.576A  pdb=" N   SER B1073 " --> pdb=" O   THR B1069 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   ILE B1076 " --> pdb=" O   CYS B1072 " (cutoff:3.500A)
      removed outlier: 3.624A  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 1135
    Processing helix  chain 'B' and resid 1135 through 1161
    Processing helix  chain 'B' and resid 1163 through 1166
    Processing helix  chain 'B' and resid 1167 through 1210
      removed outlier: 4.156A  pdb=" N   LEU B1171 " --> pdb=" O   ALA B1167 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   VAL B1184 " --> pdb=" O   LYS B1180 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ALA B1185 " --> pdb=" O   TYR B1181 " (cutoff:3.500A)
      Proline residue:  B1199  - end of helix
    Processing helix  chain 'B' and resid 1210 through 1218
      removed outlier: 3.514A  pdb=" N   ILE B1214 " --> pdb=" O   GLY B1210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1219 through 1274
      removed outlier: 4.209A  pdb=" N   LEU B1272 " --> pdb=" O   ILE B1268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1278 through 1320
      removed outlier: 4.422A  pdb=" N   GLY B1282 " --> pdb=" O   ALA B1278 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   LEU B1283 " --> pdb=" O   GLY B1279 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   ASN B1293 " --> pdb=" O   LEU B1289 " (cutoff:3.500A)
      removed outlier: 4.803A  pdb=" N   ASN B1296 " --> pdb=" O   SER B1292 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   LYS B1320 " --> pdb=" O   HIS B1316 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1384 through 1393
    Processing helix  chain 'B' and resid 1414 through 1420
      removed outlier: 3.629A  pdb=" N   LEU B1418 " --> pdb=" O   PRO B1414 " (cutoff:3.500A)
    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
      removed outlier: 3.507A  pdb=" N   ALA B1466 " --> pdb=" O   LEU B1462 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1483 through 1499
      removed outlier: 3.984A  pdb=" N   LYS B1499 " --> pdb=" O   ALA B1495 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1513 through 1528
      removed outlier: 4.040A  pdb=" N   ILE B1519 " --> pdb=" O   ALA B1515 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1539 through 1546
      removed outlier: 3.641A  pdb=" N   ILE B1543 " --> pdb=" O   ARG B1539 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ALA B1546 " --> pdb=" O   THR B1542 " (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: 6.337A  pdb=" N   VAL B 851 " --> pdb=" O   VAL B 885 " (cutoff:3.500A)
      removed outlier: 7.635A  pdb=" N   VAL B 887 " --> pdb=" O   VAL B 851 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   LEU B 853 " --> pdb=" O   VAL B 887 " (cutoff:3.500A)
      removed outlier: 5.883A  pdb=" N   THR B 709 " --> pdb=" O   LEU B 886 " (cutoff:3.500A)
      removed outlier: 7.153A  pdb=" N   ILE B 900 " --> pdb=" O   GLU B 911 " (cutoff:3.500A)
      removed outlier: 5.043A  pdb=" N   GLU B 911 " --> pdb=" O   ILE B 900 " (cutoff:3.500A)
      removed outlier: 7.210A  pdb=" N   ALA B 902 " --> pdb=" O   GLN B 909 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 1362 through 1369
      removed outlier: 6.484A  pdb=" N   LYS B1363 " --> pdb=" O   SER B1351 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   SER B1351 " --> pdb=" O   LYS B1363 " (cutoff:3.500A)
      removed outlier: 5.277A  pdb=" N   VAL B1365 " --> pdb=" O   ASN B1349 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   LEU B1350 " --> pdb=" O   GLU B1400 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   GLU B1400 " --> pdb=" O   LEU B1350 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 1422 through 1425
      removed outlier: 6.491A  pdb=" N   SER B1423 " --> pdb=" O   ILE B1504 " (cutoff:3.500A)
      removed outlier: 7.793A  pdb=" N   ASP B1506 " --> pdb=" O   SER B1423 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   ILE B1425 " --> pdb=" O   ASP B1506 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   PHE B1503 " --> pdb=" O   VAL B1534 " (cutoff:3.500A)
      removed outlier: 8.046A  pdb=" N   ILE B1536 " --> pdb=" O   PHE B1503 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   MET B1505 " --> pdb=" O   ILE B1536 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   LYS B1374 " --> pdb=" O   LEU B1548 " (cutoff:3.500A)
      removed outlier: 8.358A  pdb=" N   MET B1550 " --> pdb=" O   LYS B1374 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   GLY B1376 " --> pdb=" O   MET B1550 " (cutoff:3.500A)
      removed outlier: 7.648A  pdb=" N   LEU B1552 " --> pdb=" O   GLY B1376 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   CYS B1378 " --> pdb=" O   LEU B1552 " (cutoff:3.500A)

    607 hydrogen bonds defined for protein.
    1782 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.00

  Time building geometry restraints manager: 2.68 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2847
        1.34 -     1.46: 2105
        1.46 -     1.59: 4133
        1.59 -     1.71: 6
        1.71 -     1.83: 75
  Bond restraints: 9166
  Sorted by residual:
  bond pdb=" C   ILE B1136 "
       pdb=" N   PRO B1137 "
    ideal  model  delta    sigma   weight residual
    1.334  1.370 -0.036 2.34e-02 1.83e+03 2.36e+00
  bond pdb=" C   ARG B 297 "
       pdb=" O   ARG B 297 "
    ideal  model  delta    sigma   weight residual
    1.237  1.219  0.018 1.17e-02 7.31e+03 2.25e+00
  bond pdb=" CB  GLN B 369 "
       pdb=" CG  GLN B 369 "
    ideal  model  delta    sigma   weight residual
    1.520  1.476  0.044 3.00e-02 1.11e+03 2.20e+00
  bond pdb=" CB  PHE B 432 "
       pdb=" CG  PHE B 432 "
    ideal  model  delta    sigma   weight residual
    1.502  1.468  0.034 2.30e-02 1.89e+03 2.15e+00
  bond pdb=" CB  ASN B1293 "
       pdb=" CG  ASN B1293 "
    ideal  model  delta    sigma   weight residual
    1.516  1.480  0.036 2.50e-02 1.60e+03 2.12e+00
  ... (remaining 9161 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.42: 12276
        2.42 -     4.85: 131
        4.85 -     7.27: 26
        7.27 -     9.70: 10
        9.70 -    12.12: 4
  Bond angle restraints: 12447
  Sorted by residual:
  angle pdb=" N   GLY B 296 "
        pdb=" CA  GLY B 296 "
        pdb=" C   GLY B 296 "
      ideal   model   delta    sigma   weight residual
     110.77  122.89  -12.12 1.93e+00 2.68e-01 3.94e+01
  angle pdb=" N   ALA B 294 "
        pdb=" CA  ALA B 294 "
        pdb=" C   ALA B 294 "
      ideal   model   delta    sigma   weight residual
     111.07  116.41   -5.34 1.07e+00 8.73e-01 2.49e+01
  angle pdb=" O1B ADP B2501 "
        pdb=" PB  ADP B2501 "
        pdb=" O3B ADP B2501 "
      ideal   model   delta    sigma   weight residual
     119.90  109.75   10.15 3.00e+00 1.11e-01 1.14e+01
  angle pdb=" N   SER B 302 "
        pdb=" CA  SER B 302 "
        pdb=" C   SER B 302 "
      ideal   model   delta    sigma   weight residual
     111.28  107.64    3.64 1.09e+00 8.42e-01 1.11e+01
  angle pdb=" O2B ADP B2502 "
        pdb=" PB  ADP B2502 "
        pdb=" O3B ADP B2502 "
      ideal   model   delta    sigma   weight residual
     119.90  109.96    9.94 3.00e+00 1.11e-01 1.10e+01
  ... (remaining 12442 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.72: 5278
       28.72 -    57.43: 179
       57.43 -    86.15: 15
       86.15 -   114.86: 2
      114.86 -   143.58: 2
  Dihedral angle restraints: 5476
    sinusoidal: 2121
      harmonic: 3355
  Sorted by residual:
  dihedral pdb=" C5' ADP B2502 "
           pdb=" O5' ADP B2502 "
           pdb=" PA  ADP B2502 "
           pdb=" O2A ADP B2502 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   83.58 -143.58     1      2.00e+01 2.50e-03 4.33e+01
  dihedral pdb=" O1B ADP B2502 "
           pdb=" O3A ADP B2502 "
           pdb=" PB  ADP B2502 "
           pdb=" PA  ADP B2502 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -177.39  117.39     1      2.00e+01 2.50e-03 3.50e+01
  dihedral pdb=" CA  PHE B 566 "
           pdb=" C   PHE B 566 "
           pdb=" N   LYS B 567 "
           pdb=" CA  LYS B 567 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.80  -27.20     0      5.00e+00 4.00e-02 2.96e+01
  ... (remaining 5473 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 1041
       0.036 -    0.073: 332
       0.073 -    0.109: 100
       0.109 -    0.146: 27
       0.146 -    0.182: 2
  Chirality restraints: 1502
  Sorted by residual:
  chirality pdb=" CA  ALA B 294 "
            pdb=" N   ALA B 294 "
            pdb=" C   ALA B 294 "
            pdb=" CB  ALA B 294 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.30    0.18 2.00e-01 2.50e+01 8.30e-01
  chirality pdb=" CA  TYR B1294 "
            pdb=" N   TYR B1294 "
            pdb=" C   TYR B1294 "
            pdb=" CB  TYR B1294 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.95e-01
  chirality pdb=" CA  ILE B1504 "
            pdb=" N   ILE B1504 "
            pdb=" C   ILE B1504 "
            pdb=" CB  ILE B1504 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.95e-01
  ... (remaining 1499 not shown)

  Planarity restraints: 1531
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 550 "   -0.032 5.00e-02 4.00e+02   4.82e-02 3.71e+00
        pdb=" N   PRO B 551 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO B 551 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 551 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 432 "    0.016 2.00e-02 2.50e+03   1.23e-02 2.64e+00
        pdb=" CG  PHE B 432 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 432 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 432 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 432 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 432 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 432 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 316 "    0.023 5.00e-02 4.00e+02   3.50e-02 1.97e+00
        pdb=" N   PRO B 317 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO B 317 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 317 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1528 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 66
        2.60 -     3.18: 7928
        3.18 -     3.75: 14223
        3.75 -     4.33: 18156
        4.33 -     4.90: 29979
  Nonbonded interactions: 70352
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN B 775 "
            pdb="MG    MG B2503 "
     model   vdw
     2.031 2.170
  nonbonded pdb=" O3B ADP B2501 "
            pdb="MG    MG B2503 "
     model   vdw
     2.091 2.170
  nonbonded pdb=" NE2 GLN B 775 "
            pdb="MG    MG B2503 "
     model   vdw
     2.132 2.250
  nonbonded pdb=" O   PRO B 769 "
            pdb=" OG1 THR B 848 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" NE2 HIS B 562 "
            pdb=" O   SER B 569 "
     model   vdw
     2.260 3.120
  ... (remaining 70347 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:             1.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.400
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7458
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      :  0.003   0.044   9166  Z= 0.225
  Angle     :  0.728  12.121  12447  Z= 0.374
  Chirality :  0.040   0.182   1502
  Planarity :  0.004   0.048   1531
  Dihedral  : 14.120 143.579   3292
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  6.20 %
    Allowed  :  8.57 %
    Favored  : 85.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.54 (0.22), residues: 1138
  helix: -0.15 (0.17), residues: 737
  sheet: -0.89 (0.57), residues: 86
  loop : -3.02 (0.28), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B1339 
 HIS   0.009   0.001   HIS B1024 
 PHE   0.027   0.002   PHE B 432 
 TYR   0.014   0.002   TYR B 512 
 ARG   0.009   0.001   ARG B 370 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  414 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 354
  time to evaluate  : 1.002 
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  226 SER cc_start: 0.9578 (t) cc_final: 0.9352 (p)
REVERT: B  243 LYS cc_start: 0.8947 (tttt) cc_final: 0.8609 (mptt)
REVERT: B  257 MET cc_start: 0.9155 (mmm) cc_final: 0.8705 (mmm)
REVERT: B  314 PHE cc_start: 0.5124 (m-10) cc_final: 0.3953 (m-80)
REVERT: B  370 ARG cc_start: 0.9219 (mmt-90) cc_final: 0.8622 (mmp80)
REVERT: B  376 SER cc_start: 0.9497 (t) cc_final: 0.9173 (p)
REVERT: B  429 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8303 (mtm)
REVERT: B  497 LYS cc_start: 0.7549 (mtmt) cc_final: 0.7329 (mtmt)
REVERT: B  512 TYR cc_start: 0.8729 (p90) cc_final: 0.8376 (p90)
REVERT: B  514 TRP cc_start: 0.8379 (m-10) cc_final: 0.7373 (m-10)
REVERT: B  523 GLU cc_start: 0.9064 (tp30) cc_final: 0.8790 (tm-30)
REVERT: B  529 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8512 (tm-30)
REVERT: B  530 MET cc_start: 0.9529 (tpp) cc_final: 0.9146 (tpp)
REVERT: B  547 ASN cc_start: 0.8279 (m-40) cc_final: 0.8011 (m110)
REVERT: B  574 SER cc_start: 0.7792 (OUTLIER) cc_final: 0.6675 (p)
REVERT: B  580 LEU cc_start: 0.8488 (tp) cc_final: 0.8165 (mt)
REVERT: B  581 SER cc_start: 0.9631 (m) cc_final: 0.9411 (p)
REVERT: B  685 PHE cc_start: 0.6642 (t80) cc_final: 0.5729 (t80)
REVERT: B  696 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.5257 (tp)
REVERT: B  778 TRP cc_start: 0.8903 (p-90) cc_final: 0.8542 (p-90)
REVERT: B  781 ASN cc_start: 0.8222 (t0) cc_final: 0.7890 (m-40)
REVERT: B  855 ASP cc_start: 0.8781 (t0) cc_final: 0.8325 (t0)
REVERT: B  861 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.7798 (p0)
REVERT: B  868 LEU cc_start: 0.9775 (tp) cc_final: 0.9468 (mm)
REVERT: B  891 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8137 (mt)
REVERT: B  892 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8239 (pt0)
REVERT: B  915 LYS cc_start: 0.9438 (mttt) cc_final: 0.9106 (tppt)
REVERT: B 1011 LEU cc_start: 0.8630 (tp) cc_final: 0.8407 (pt)
REVERT: B 1012 LEU cc_start: 0.9076 (mt) cc_final: 0.8771 (mp)
REVERT: B 1079 CYS cc_start: 0.9220 (t) cc_final: 0.8804 (p)
REVERT: B 1087 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8670 (mm-30)
REVERT: B 1092 LYS cc_start: 0.9187 (mttm) cc_final: 0.8643 (tptt)
REVERT: B 1096 ARG cc_start: 0.8680 (tpp80) cc_final: 0.8190 (tmt170)
REVERT: B 1114 GLU cc_start: 0.8751 (tt0) cc_final: 0.8402 (tm-30)
REVERT: B 1194 ASP cc_start: 0.9293 (t0) cc_final: 0.9086 (m-30)
REVERT: B 1202 SER cc_start: 0.9244 (m) cc_final: 0.8162 (p)
REVERT: B 1220 GLU cc_start: 0.9498 (mt-10) cc_final: 0.9185 (mp0)
REVERT: B 1222 ARG cc_start: 0.9217 (mmt-90) cc_final: 0.8453 (mmm160)
REVERT: B 1246 ARG cc_start: 0.8823 (mmt-90) cc_final: 0.8094 (mmm-85)
REVERT: B 1281 VAL cc_start: 0.9708 (t) cc_final: 0.9457 (p)
REVERT: B 1395 MET cc_start: 0.8874 (mmt) cc_final: 0.8494 (mmm)
REVERT: B 1425 ILE cc_start: 0.9213 (mt) cc_final: 0.8652 (mt)
REVERT: B 1505 MET cc_start: 0.8052 (ttm) cc_final: 0.7675 (mmt)
REVERT: B 1507 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8310 (mp0)
REVERT: B 1517 GLU cc_start: 0.9090 (tp30) cc_final: 0.8852 (tp30)
REVERT: B 1536 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8269 (mp)
REVERT: B 1552 LEU cc_start: 0.9618 (mt) cc_final: 0.9220 (tp)
  outliers start: 60
  outliers final: 20
  residues processed: 389
  average time/residue: 0.2238
  time to fit residues: 119.3886
Evaluate side-chains
  250 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 223
  time to evaluate  : 1.024 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    3.9990
   chunk 87 optimal weight:    8.9990
   chunk 48 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 58 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 90 optimal weight:    8.9990
   chunk 34 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9990
   chunk 104 optimal weight:    7.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
B 374 GLN
B 419 ASN
** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 562 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1203 HIS
B1301 ASN
B1308 GLN
B1348 GLN
B1481 ASN
B1484 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.092327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.073908 restraints weight = 28983.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.076189 restraints weight = 19015.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.077855 restraints weight = 13788.379|
|-----------------------------------------------------------------------------|
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.3663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   9166  Z= 0.350
  Angle     :  0.769   9.418  12447  Z= 0.383
  Chirality :  0.045   0.227   1502
  Planarity :  0.005   0.044   1531
  Dihedral  :  7.576 140.755   1251
  Min Nonbonded Distance : 1.917

Molprobity Statistics.
  All-atom Clashscore : 13.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  4.86 %
    Favored  : 94.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.24), residues: 1138
  helix:  0.96 (0.18), residues: 739
  sheet: -0.42 (0.55), residues: 86
  loop : -2.48 (0.33), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B1339 
 HIS   0.008   0.001   HIS B 562 
 PHE   0.040   0.003   PHE B1240 
 TYR   0.016   0.002   TYR B 230 
 ARG   0.010   0.001   ARG B 370 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 255
  time to evaluate  : 1.019 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  243 LYS cc_start: 0.8891 (tttt) cc_final: 0.8679 (mptt)
REVERT: B  305 PHE cc_start: 0.9097 (m-10) cc_final: 0.8754 (m-80)
REVERT: B  314 PHE cc_start: 0.8149 (m-10) cc_final: 0.7928 (m-80)
REVERT: B  419 ASN cc_start: 0.8833 (m-40) cc_final: 0.8484 (m110)
REVERT: B  502 MET cc_start: 0.9542 (ttt) cc_final: 0.9272 (ttt)
REVERT: B  512 TYR cc_start: 0.8431 (p90) cc_final: 0.7553 (p90)
REVERT: B  581 SER cc_start: 0.9669 (m) cc_final: 0.9469 (p)
REVERT: B  719 LYS cc_start: 0.9360 (mtmt) cc_final: 0.8993 (mttm)
REVERT: B  791 GLU cc_start: 0.8244 (mp0) cc_final: 0.7629 (mp0)
REVERT: B  802 VAL cc_start: 0.9668 (t) cc_final: 0.9199 (t)
REVERT: B  855 ASP cc_start: 0.8681 (t0) cc_final: 0.8058 (t0)
REVERT: B  868 LEU cc_start: 0.9667 (tp) cc_final: 0.9445 (mm)
REVERT: B  869 MET cc_start: 0.8445 (tpp) cc_final: 0.8009 (tpp)
REVERT: B  876 LEU cc_start: 0.9394 (tp) cc_final: 0.8867 (tp)
REVERT: B  903 MET cc_start: 0.8914 (mmp) cc_final: 0.8689 (mmm)
REVERT: B 1012 LEU cc_start: 0.9246 (mt) cc_final: 0.8905 (mp)
REVERT: B 1079 CYS cc_start: 0.9122 (t) cc_final: 0.8858 (p)
REVERT: B 1092 LYS cc_start: 0.9391 (mttm) cc_final: 0.8895 (tptt)
REVERT: B 1202 SER cc_start: 0.9244 (m) cc_final: 0.8301 (p)
REVERT: B 1427 GLN cc_start: 0.9114 (pp30) cc_final: 0.8667 (pp30)
REVERT: B 1517 GLU cc_start: 0.8852 (tp30) cc_final: 0.8431 (tp30)
REVERT: B 1552 LEU cc_start: 0.9336 (mt) cc_final: 0.9129 (tp)
  outliers start: 3
  outliers final: 0
  residues processed: 256
  average time/residue: 0.1932
  time to fit residues: 70.9384
Evaluate side-chains
  189 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 90 optimal weight:    8.9990
   chunk 77 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 96 optimal weight:    0.7980
   chunk 21 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9990
   chunk 69 optimal weight:    0.6980
   chunk 4 optimal weight:    0.0770
   chunk 20 optimal weight:    2.9990
   overall best weight:    0.6540

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

Flipped N/Q/H residues before XYZ refinement:
** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 474 GLN
** B 562 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 846 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.094551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.075894 restraints weight = 28865.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.078392 restraints weight = 18419.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.080211 restraints weight = 13061.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.4440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9166  Z= 0.203
  Angle     :  0.686  10.634  12447  Z= 0.331
  Chirality :  0.042   0.184   1502
  Planarity :  0.004   0.075   1531
  Dihedral  :  7.047 143.509   1251
  Min Nonbonded Distance : 1.909

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  3.93 %
    Favored  : 95.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.25), residues: 1138
  helix:  1.59 (0.19), residues: 731
  sheet: -0.04 (0.57), residues: 86
  loop : -1.94 (0.34), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 514 
 HIS   0.006   0.001   HIS B1024 
 PHE   0.024   0.002   PHE B 433 
 TYR   0.014   0.001   TYR B 454 
 ARG   0.005   0.001   ARG B 370 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 262
  time to evaluate  : 1.043 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  219 GLN cc_start: 0.7913 (tm-30) cc_final: 0.7437 (tm-30)
REVERT: B  305 PHE cc_start: 0.9014 (m-10) cc_final: 0.8586 (m-80)
REVERT: B  314 PHE cc_start: 0.8210 (m-10) cc_final: 0.7965 (m-80)
REVERT: B  502 MET cc_start: 0.9475 (ttt) cc_final: 0.9235 (ttt)
REVERT: B  512 TYR cc_start: 0.8414 (p90) cc_final: 0.7352 (p90)
REVERT: B  514 TRP cc_start: 0.8277 (m-10) cc_final: 0.6971 (m-10)
REVERT: B  530 MET cc_start: 0.9388 (tpp) cc_final: 0.9120 (tpp)
REVERT: B  547 ASN cc_start: 0.8211 (m-40) cc_final: 0.7998 (m110)
REVERT: B  562 HIS cc_start: 0.8382 (t70) cc_final: 0.8146 (t70)
REVERT: B  615 SER cc_start: 0.9152 (t) cc_final: 0.8949 (p)
REVERT: B  719 LYS cc_start: 0.9376 (mtmt) cc_final: 0.8952 (mttm)
REVERT: B  801 MET cc_start: 0.8689 (tmm) cc_final: 0.8459 (tmm)
REVERT: B  802 VAL cc_start: 0.9719 (t) cc_final: 0.9428 (t)
REVERT: B  855 ASP cc_start: 0.8592 (t0) cc_final: 0.7957 (t0)
REVERT: B  869 MET cc_start: 0.8444 (tpp) cc_final: 0.8010 (tpp)
REVERT: B  903 MET cc_start: 0.9008 (mmp) cc_final: 0.8751 (mmm)
REVERT: B 1005 LEU cc_start: 0.8451 (mt) cc_final: 0.8222 (pp)
REVERT: B 1012 LEU cc_start: 0.9134 (mt) cc_final: 0.8895 (mp)
REVERT: B 1079 CYS cc_start: 0.9109 (t) cc_final: 0.8858 (p)
REVERT: B 1092 LYS cc_start: 0.9304 (mttm) cc_final: 0.8869 (tptt)
REVERT: B 1202 SER cc_start: 0.9210 (m) cc_final: 0.7934 (p)
REVERT: B 1428 ASP cc_start: 0.8839 (t0) cc_final: 0.8135 (p0)
REVERT: B 1507 GLU cc_start: 0.9086 (pt0) cc_final: 0.8703 (pt0)
REVERT: B 1517 GLU cc_start: 0.8810 (tp30) cc_final: 0.8446 (tp30)
  outliers start: 4
  outliers final: 1
  residues processed: 263
  average time/residue: 0.1951
  time to fit residues: 74.7569
Evaluate side-chains
  197 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 196
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 80 optimal weight:    0.6980
   chunk 99 optimal weight:    5.9990
   chunk 44 optimal weight:    0.0070
   chunk 76 optimal weight:    0.9990
   chunk 87 optimal weight:    4.9990
   chunk 55 optimal weight:    0.8980
   chunk 88 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 69 optimal weight:    0.8980
   chunk 103 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0870
   overall best weight:    0.5176

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

Flipped N/Q/H residues before XYZ refinement:
** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 562 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.095659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.077031 restraints weight = 28209.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.079537 restraints weight = 18057.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.081341 restraints weight = 12785.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.4912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9166  Z= 0.178
  Angle     :  0.679  11.090  12447  Z= 0.325
  Chirality :  0.042   0.164   1502
  Planarity :  0.004   0.068   1531
  Dihedral  :  6.720 138.332   1251
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  3.31 %
    Favored  : 96.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.25), residues: 1138
  helix:  1.73 (0.19), residues: 737
  sheet:  0.14 (0.57), residues: 86
  loop : -1.93 (0.33), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 688 
 HIS   0.006   0.001   HIS B1024 
 PHE   0.015   0.001   PHE B1240 
 TYR   0.014   0.001   TYR B 454 
 ARG   0.008   0.000   ARG B 526 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 244
  time to evaluate  : 1.054 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  219 GLN cc_start: 0.8003 (tm-30) cc_final: 0.7554 (tm-30)
REVERT: B  305 PHE cc_start: 0.8970 (m-10) cc_final: 0.8757 (m-80)
REVERT: B  314 PHE cc_start: 0.8244 (m-10) cc_final: 0.7751 (m-80)
REVERT: B  383 THR cc_start: 0.9716 (m) cc_final: 0.9439 (p)
REVERT: B  387 LEU cc_start: 0.9607 (tp) cc_final: 0.9343 (tp)
REVERT: B  502 MET cc_start: 0.9469 (ttt) cc_final: 0.8419 (tmm)
REVERT: B  512 TYR cc_start: 0.8327 (p90) cc_final: 0.7197 (p90)
REVERT: B  514 TRP cc_start: 0.8325 (m-10) cc_final: 0.6997 (m-10)
REVERT: B  547 ASN cc_start: 0.8246 (m-40) cc_final: 0.8038 (m110)
REVERT: B  719 LYS cc_start: 0.9319 (mtmt) cc_final: 0.8964 (mttp)
REVERT: B  802 VAL cc_start: 0.9731 (t) cc_final: 0.9416 (t)
REVERT: B  855 ASP cc_start: 0.8536 (t0) cc_final: 0.7944 (t0)
REVERT: B  869 MET cc_start: 0.8580 (tpp) cc_final: 0.7403 (tpp)
REVERT: B 1012 LEU cc_start: 0.9178 (mt) cc_final: 0.8924 (mp)
REVERT: B 1079 CYS cc_start: 0.9131 (t) cc_final: 0.8849 (p)
REVERT: B 1092 LYS cc_start: 0.9260 (mttm) cc_final: 0.8850 (tptt)
REVERT: B 1202 SER cc_start: 0.9010 (m) cc_final: 0.8121 (p)
REVERT: B 1206 GLU cc_start: 0.8430 (pm20) cc_final: 0.7982 (mp0)
REVERT: B 1249 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7877 (mt-10)
REVERT: B 1428 ASP cc_start: 0.8892 (t0) cc_final: 0.8150 (p0)
REVERT: B 1507 GLU cc_start: 0.9062 (pt0) cc_final: 0.8799 (pt0)
REVERT: B 1517 GLU cc_start: 0.8753 (tp30) cc_final: 0.8433 (tp30)
REVERT: B 1552 LEU cc_start: 0.9452 (mt) cc_final: 0.9036 (tp)
  outliers start: 2
  outliers final: 0
  residues processed: 245
  average time/residue: 0.1722
  time to fit residues: 62.6143
Evaluate side-chains
  186 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.980 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 38 optimal weight:    9.9990
   chunk 99 optimal weight:    0.8980
   chunk 68 optimal weight:    7.9990
   chunk 100 optimal weight:    0.4980
   chunk 14 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 75 optimal weight:    6.9990
   chunk 56 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 889 HIS
B1234 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.094942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.076179 restraints weight = 28772.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.078681 restraints weight = 18488.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.080485 restraints weight = 13120.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.5284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9166  Z= 0.199
  Angle     :  0.670  11.216  12447  Z= 0.321
  Chirality :  0.042   0.188   1502
  Planarity :  0.004   0.050   1531
  Dihedral  :  6.405 130.527   1251
  Min Nonbonded Distance : 1.914

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  2.69 %
    Favored  : 97.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.25), residues: 1138
  helix:  1.88 (0.19), residues: 730
  sheet:  0.35 (0.57), residues: 86
  loop : -1.67 (0.33), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 288 
 HIS   0.006   0.001   HIS B1024 
 PHE   0.016   0.001   PHE B 433 
 TYR   0.033   0.002   TYR B 893 
 ARG   0.003   0.000   ARG B 526 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 227
  time to evaluate  : 1.028 
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  219 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7529 (tm-30)
REVERT: B  233 MET cc_start: 0.8684 (mmp) cc_final: 0.8427 (tpp)
REVERT: B  270 PHE cc_start: 0.8667 (m-80) cc_final: 0.8449 (m-80)
REVERT: B  305 PHE cc_start: 0.9107 (m-10) cc_final: 0.8748 (m-80)
REVERT: B  314 PHE cc_start: 0.8128 (m-10) cc_final: 0.7833 (m-80)
REVERT: B  383 THR cc_start: 0.9681 (m) cc_final: 0.9467 (p)
REVERT: B  387 LEU cc_start: 0.9681 (tp) cc_final: 0.9451 (tp)
REVERT: B  433 PHE cc_start: 0.8850 (m-10) cc_final: 0.8506 (m-80)
REVERT: B  451 LEU cc_start: 0.9440 (tp) cc_final: 0.9215 (pp)
REVERT: B  502 MET cc_start: 0.9460 (ttt) cc_final: 0.8128 (tmm)
REVERT: B  512 TYR cc_start: 0.8334 (p90) cc_final: 0.7220 (p90)
REVERT: B  719 LYS cc_start: 0.9430 (mtmt) cc_final: 0.9074 (mttp)
REVERT: B  802 VAL cc_start: 0.9769 (t) cc_final: 0.9547 (p)
REVERT: B  855 ASP cc_start: 0.8583 (t0) cc_final: 0.8004 (t0)
REVERT: B  869 MET cc_start: 0.8546 (tpp) cc_final: 0.7605 (tpp)
REVERT: B  903 MET cc_start: 0.8807 (mmm) cc_final: 0.8459 (mmm)
REVERT: B 1005 LEU cc_start: 0.8487 (mt) cc_final: 0.8277 (pp)
REVERT: B 1012 LEU cc_start: 0.9237 (mt) cc_final: 0.9006 (mp)
REVERT: B 1079 CYS cc_start: 0.9184 (t) cc_final: 0.8870 (p)
REVERT: B 1092 LYS cc_start: 0.9229 (mttm) cc_final: 0.8819 (tptt)
REVERT: B 1110 MET cc_start: 0.8218 (mmm) cc_final: 0.7936 (mmm)
REVERT: B 1206 GLU cc_start: 0.8434 (pm20) cc_final: 0.8106 (pm20)
REVERT: B 1249 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7921 (mt-10)
REVERT: B 1395 MET cc_start: 0.8717 (tpt) cc_final: 0.8507 (tpt)
REVERT: B 1503 PHE cc_start: 0.8356 (m-10) cc_final: 0.8101 (m-10)
REVERT: B 1505 MET cc_start: 0.8347 (mmt) cc_final: 0.8109 (mmp)
REVERT: B 1507 GLU cc_start: 0.9032 (pt0) cc_final: 0.8810 (pt0)
REVERT: B 1517 GLU cc_start: 0.8711 (tp30) cc_final: 0.8362 (tp30)
REVERT: B 1552 LEU cc_start: 0.9573 (mt) cc_final: 0.9107 (tp)
  outliers start: 2
  outliers final: 0
  residues processed: 228
  average time/residue: 0.1672
  time to fit residues: 56.9131
Evaluate side-chains
  184 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 38 optimal weight:   10.0000
   chunk 1 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   chunk 4 optimal weight:    0.6980
   chunk 57 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 96 optimal weight:    3.9990
   chunk 108 optimal weight:    5.9990
   chunk 61 optimal weight:    7.9990
   chunk 85 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   overall best weight:    2.7388

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

Flipped N/Q/H residues before XYZ refinement:
B 262 ASN
** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.087477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.069807 restraints weight = 30425.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.072040 restraints weight = 19635.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.073674 restraints weight = 14101.034|
|-----------------------------------------------------------------------------|
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.5901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.085   9166  Z= 0.429
  Angle     :  0.842  10.824  12447  Z= 0.423
  Chirality :  0.047   0.225   1502
  Planarity :  0.005   0.053   1531
  Dihedral  :  6.960 122.665   1251
  Min Nonbonded Distance : 1.900

Molprobity Statistics.
  All-atom Clashscore : 18.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.72 %
    Favored  : 96.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.25), residues: 1138
  helix:  1.17 (0.18), residues: 742
  sheet:  0.23 (0.61), residues: 78
  loop : -1.86 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP B 232 
 HIS   0.008   0.002   HIS B1316 
 PHE   0.029   0.003   PHE B1240 
 TYR   0.018   0.002   TYR B 893 
 ARG   0.006   0.001   ARG B1246 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 215
  time to evaluate  : 1.051 
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  219 GLN cc_start: 0.8102 (tm-30) cc_final: 0.7743 (tm-30)
REVERT: B  305 PHE cc_start: 0.9267 (m-10) cc_final: 0.8872 (m-80)
REVERT: B  314 PHE cc_start: 0.8155 (m-10) cc_final: 0.7890 (m-80)
REVERT: B  378 TYR cc_start: 0.9201 (t80) cc_final: 0.8409 (t80)
REVERT: B  383 THR cc_start: 0.9713 (m) cc_final: 0.9511 (p)
REVERT: B  502 MET cc_start: 0.9419 (ttt) cc_final: 0.8238 (tmm)
REVERT: B  506 MET cc_start: 0.8473 (tpp) cc_final: 0.8209 (tpt)
REVERT: B  512 TYR cc_start: 0.8696 (p90) cc_final: 0.7449 (p90)
REVERT: B  710 MET cc_start: 0.8567 (mmp) cc_final: 0.8122 (mmp)
REVERT: B  717 CYS cc_start: 0.7592 (m) cc_final: 0.7297 (m)
REVERT: B  719 LYS cc_start: 0.9588 (mtmt) cc_final: 0.9152 (mttp)
REVERT: B  855 ASP cc_start: 0.8776 (t0) cc_final: 0.8231 (t0)
REVERT: B  886 LEU cc_start: 0.9408 (tt) cc_final: 0.9073 (tt)
REVERT: B  903 MET cc_start: 0.8522 (mmm) cc_final: 0.8299 (mmm)
REVERT: B 1005 LEU cc_start: 0.8581 (mt) cc_final: 0.8293 (pp)
REVERT: B 1012 LEU cc_start: 0.9327 (mt) cc_final: 0.9098 (mp)
REVERT: B 1079 CYS cc_start: 0.9235 (t) cc_final: 0.8909 (p)
REVERT: B 1092 LYS cc_start: 0.9390 (mttm) cc_final: 0.9125 (mmtm)
REVERT: B 1206 GLU cc_start: 0.8532 (pm20) cc_final: 0.8219 (pm20)
REVERT: B 1229 GLU cc_start: 0.9027 (tm-30) cc_final: 0.8818 (tm-30)
REVERT: B 1427 GLN cc_start: 0.8966 (pp30) cc_final: 0.8747 (pp30)
REVERT: B 1517 GLU cc_start: 0.8792 (tp30) cc_final: 0.8421 (tp30)
REVERT: B 1550 MET cc_start: 0.8674 (ptp) cc_final: 0.8469 (ptp)
REVERT: B 1560 PHE cc_start: 0.7628 (m-80) cc_final: 0.7325 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 216
  average time/residue: 0.1663
  time to fit residues: 54.0532
Evaluate side-chains
  178 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 177
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 48 optimal weight:    0.8980
   chunk 91 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9980
   chunk 79 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 89 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   chunk 112 optimal weight:    3.9990
   chunk 99 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
B 406 ASN
** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 547 ASN
** B 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 892 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.091710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.073456 restraints weight = 29141.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.075861 restraints weight = 18542.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.077592 restraints weight = 13163.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.6072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9166  Z= 0.199
  Angle     :  0.723  11.632  12447  Z= 0.346
  Chirality :  0.043   0.183   1502
  Planarity :  0.004   0.052   1531
  Dihedral  :  6.355 110.907   1251
  Min Nonbonded Distance : 1.900

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.25), residues: 1138
  helix:  1.57 (0.19), residues: 748
  sheet:  0.21 (0.58), residues: 86
  loop : -1.73 (0.35), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 778 
 HIS   0.005   0.001   HIS B1024 
 PHE   0.021   0.002   PHE B1204 
 TYR   0.010   0.001   TYR B 512 
 ARG   0.003   0.000   ARG B1353 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 0.993 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  219 GLN cc_start: 0.7859 (tm-30) cc_final: 0.7435 (tm-30)
REVERT: B  233 MET cc_start: 0.8807 (mmp) cc_final: 0.8268 (mmm)
REVERT: B  305 PHE cc_start: 0.9204 (m-10) cc_final: 0.8815 (m-80)
REVERT: B  314 PHE cc_start: 0.8163 (m-10) cc_final: 0.7889 (m-80)
REVERT: B  378 TYR cc_start: 0.9131 (t80) cc_final: 0.8544 (t80)
REVERT: B  383 THR cc_start: 0.9702 (m) cc_final: 0.9502 (p)
REVERT: B  433 PHE cc_start: 0.8831 (m-10) cc_final: 0.8436 (m-80)
REVERT: B  502 MET cc_start: 0.9387 (ttt) cc_final: 0.8203 (tmm)
REVERT: B  512 TYR cc_start: 0.8744 (p90) cc_final: 0.7548 (p90)
REVERT: B  710 MET cc_start: 0.8571 (mmp) cc_final: 0.8307 (mmp)
REVERT: B  719 LYS cc_start: 0.9495 (mtmt) cc_final: 0.9075 (mttp)
REVERT: B  855 ASP cc_start: 0.8597 (t0) cc_final: 0.8032 (t0)
REVERT: B  868 LEU cc_start: 0.9638 (tp) cc_final: 0.9403 (mm)
REVERT: B  900 ILE cc_start: 0.9229 (mp) cc_final: 0.9011 (mp)
REVERT: B  903 MET cc_start: 0.8615 (mmm) cc_final: 0.8326 (mmm)
REVERT: B 1005 LEU cc_start: 0.8482 (mt) cc_final: 0.8221 (pp)
REVERT: B 1012 LEU cc_start: 0.9312 (mt) cc_final: 0.9096 (mp)
REVERT: B 1079 CYS cc_start: 0.9178 (t) cc_final: 0.8909 (p)
REVERT: B 1092 LYS cc_start: 0.9326 (mttm) cc_final: 0.9003 (mmtm)
REVERT: B 1110 MET cc_start: 0.8376 (mmm) cc_final: 0.8121 (mmm)
REVERT: B 1206 GLU cc_start: 0.8480 (pm20) cc_final: 0.8192 (pm20)
REVERT: B 1249 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7832 (mt-10)
REVERT: B 1427 GLN cc_start: 0.9015 (pp30) cc_final: 0.8737 (pp30)
REVERT: B 1507 GLU cc_start: 0.8995 (pt0) cc_final: 0.8787 (pt0)
REVERT: B 1517 GLU cc_start: 0.8693 (tp30) cc_final: 0.8356 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 220
  average time/residue: 0.1633
  time to fit residues: 54.1549
Evaluate side-chains
  183 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 82 optimal weight:    0.5980
   chunk 99 optimal weight:    0.9980
   chunk 40 optimal weight:    5.9990
   chunk 17 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 105 optimal weight:    0.8980
   chunk 49 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
B 406 ASN
** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 485 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.092376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.073898 restraints weight = 29926.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.076326 restraints weight = 19209.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.078071 restraints weight = 13697.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.6331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9166  Z= 0.201
  Angle     :  0.713  11.818  12447  Z= 0.342
  Chirality :  0.043   0.164   1502
  Planarity :  0.004   0.051   1531
  Dihedral  :  6.068  97.788   1251
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 12.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.25), residues: 1138
  helix:  1.69 (0.19), residues: 736
  sheet:  0.17 (0.57), residues: 86
  loop : -1.58 (0.35), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 778 
 HIS   0.004   0.001   HIS B1024 
 PHE   0.014   0.002   PHE B 321 
 TYR   0.011   0.001   TYR B 893 
 ARG   0.005   0.000   ARG B 370 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 1.025 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  219 GLN cc_start: 0.7880 (tm-30) cc_final: 0.7502 (tm-30)
REVERT: B  305 PHE cc_start: 0.9216 (m-10) cc_final: 0.8806 (m-80)
REVERT: B  314 PHE cc_start: 0.8061 (m-10) cc_final: 0.7806 (m-80)
REVERT: B  378 TYR cc_start: 0.9077 (t80) cc_final: 0.8633 (t80)
REVERT: B  429 MET cc_start: 0.8050 (mtt) cc_final: 0.7637 (mtt)
REVERT: B  433 PHE cc_start: 0.8861 (m-10) cc_final: 0.8431 (m-80)
REVERT: B  502 MET cc_start: 0.9351 (ttt) cc_final: 0.8168 (tmm)
REVERT: B  506 MET cc_start: 0.8207 (tpp) cc_final: 0.7963 (tpt)
REVERT: B  512 TYR cc_start: 0.8567 (p90) cc_final: 0.7437 (p90)
REVERT: B  562 HIS cc_start: 0.8049 (t70) cc_final: 0.7824 (t70)
REVERT: B  710 MET cc_start: 0.8583 (mmp) cc_final: 0.8184 (mmp)
REVERT: B  719 LYS cc_start: 0.9515 (mtmt) cc_final: 0.9125 (mttp)
REVERT: B  855 ASP cc_start: 0.8544 (t0) cc_final: 0.8004 (t0)
REVERT: B  886 LEU cc_start: 0.9442 (tt) cc_final: 0.9209 (tt)
REVERT: B  903 MET cc_start: 0.8592 (mmm) cc_final: 0.8302 (mmm)
REVERT: B 1005 LEU cc_start: 0.8472 (mt) cc_final: 0.8205 (pp)
REVERT: B 1012 LEU cc_start: 0.9322 (mt) cc_final: 0.9070 (mp)
REVERT: B 1079 CYS cc_start: 0.9335 (t) cc_final: 0.8929 (p)
REVERT: B 1092 LYS cc_start: 0.9315 (mttm) cc_final: 0.9041 (mmtm)
REVERT: B 1206 GLU cc_start: 0.8436 (pm20) cc_final: 0.8094 (mp0)
REVERT: B 1427 GLN cc_start: 0.8983 (pp30) cc_final: 0.8717 (pp30)
REVERT: B 1503 PHE cc_start: 0.8063 (m-10) cc_final: 0.7767 (m-10)
REVERT: B 1505 MET cc_start: 0.8248 (mmt) cc_final: 0.7667 (mtp)
REVERT: B 1507 GLU cc_start: 0.8973 (pt0) cc_final: 0.8656 (pp20)
REVERT: B 1517 GLU cc_start: 0.8696 (tp30) cc_final: 0.8357 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 217
  average time/residue: 0.1614
  time to fit residues: 52.7670
Evaluate side-chains
  178 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 113 optimal weight:    2.9990
   chunk 110 optimal weight:    1.9990
   chunk 111 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 79 optimal weight:    3.9990
   chunk 96 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
B 406 ASN
** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 498 GLN
** B 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1179 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.090697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.072649 restraints weight = 30383.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.075009 restraints weight = 19392.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.076759 restraints weight = 13819.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.6536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9166  Z= 0.256
  Angle     :  0.746  11.624  12447  Z= 0.364
  Chirality :  0.044   0.177   1502
  Planarity :  0.004   0.054   1531
  Dihedral  :  6.094  90.716   1251
  Min Nonbonded Distance : 1.886

Molprobity Statistics.
  All-atom Clashscore : 14.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.83 %
    Favored  : 99.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.25), residues: 1138
  helix:  1.48 (0.18), residues: 748
  sheet:  0.10 (0.57), residues: 86
  loop : -1.75 (0.35), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 778 
 HIS   0.005   0.001   HIS B1024 
 PHE   0.015   0.002   PHE B 321 
 TYR   0.011   0.001   TYR B 512 
 ARG   0.004   0.000   ARG B 370 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 1.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  219 GLN cc_start: 0.7972 (tm-30) cc_final: 0.7605 (tm-30)
REVERT: B  233 MET cc_start: 0.8788 (mmp) cc_final: 0.8196 (mmm)
REVERT: B  305 PHE cc_start: 0.9253 (m-10) cc_final: 0.8859 (m-80)
REVERT: B  314 PHE cc_start: 0.8032 (m-10) cc_final: 0.7781 (m-80)
REVERT: B  378 TYR cc_start: 0.9123 (t80) cc_final: 0.8551 (t80)
REVERT: B  451 LEU cc_start: 0.9548 (tp) cc_final: 0.9327 (pp)
REVERT: B  502 MET cc_start: 0.9350 (ttt) cc_final: 0.8284 (tmm)
REVERT: B  509 LEU cc_start: 0.9488 (tt) cc_final: 0.9023 (tp)
REVERT: B  512 TYR cc_start: 0.8629 (p90) cc_final: 0.7458 (p90)
REVERT: B  710 MET cc_start: 0.8583 (mmp) cc_final: 0.8168 (mmp)
REVERT: B  719 LYS cc_start: 0.9541 (mtmt) cc_final: 0.9182 (mttp)
REVERT: B  855 ASP cc_start: 0.8624 (t0) cc_final: 0.8065 (t0)
REVERT: B  869 MET cc_start: 0.8521 (tpp) cc_final: 0.8263 (tpp)
REVERT: B  876 LEU cc_start: 0.9207 (tt) cc_final: 0.8801 (mm)
REVERT: B  886 LEU cc_start: 0.9483 (tt) cc_final: 0.9182 (tt)
REVERT: B  903 MET cc_start: 0.8527 (mmm) cc_final: 0.8227 (mmm)
REVERT: B 1005 LEU cc_start: 0.8472 (mt) cc_final: 0.8200 (pp)
REVERT: B 1079 CYS cc_start: 0.9358 (t) cc_final: 0.8958 (p)
REVERT: B 1092 LYS cc_start: 0.9332 (mttm) cc_final: 0.9003 (mmtm)
REVERT: B 1206 GLU cc_start: 0.8464 (pm20) cc_final: 0.8076 (mp0)
REVERT: B 1305 MET cc_start: 0.8643 (tmm) cc_final: 0.8366 (tmm)
REVERT: B 1505 MET cc_start: 0.8299 (mmt) cc_final: 0.7798 (mtp)
REVERT: B 1507 GLU cc_start: 0.8968 (pt0) cc_final: 0.8682 (pp20)
REVERT: B 1517 GLU cc_start: 0.8631 (tp30) cc_final: 0.8314 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 215
  average time/residue: 0.1652
  time to fit residues: 54.0076
Evaluate side-chains
  171 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 1.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 85 optimal weight:    0.4980
   chunk 65 optimal weight:    0.7980
   chunk 107 optimal weight:    0.8980
   chunk 81 optimal weight:    0.5980
   chunk 26 optimal weight:    0.5980
   chunk 87 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9990
   chunk 56 optimal weight:    0.0670
   chunk 102 optimal weight:    0.9990
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.4718

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

Flipped N/Q/H residues before XYZ refinement:
** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 775 GLN
B1316 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.093899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.075267 restraints weight = 29275.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.077733 restraints weight = 18813.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.079516 restraints weight = 13383.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.6708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9166  Z= 0.185
  Angle     :  0.737  11.942  12447  Z= 0.357
  Chirality :  0.044   0.282   1502
  Planarity :  0.004   0.053   1531
  Dihedral  :  5.831  85.719   1251
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.25), residues: 1138
  helix:  1.50 (0.19), residues: 747
  sheet: -0.10 (0.54), residues: 93
  loop : -1.57 (0.36), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 778 
 HIS   0.005   0.001   HIS B1024 
 PHE   0.024   0.002   PHE B 217 
 TYR   0.015   0.001   TYR B 377 
 ARG   0.004   0.000   ARG B1487 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 0.950 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  219 GLN cc_start: 0.7884 (tm-30) cc_final: 0.7561 (tm-30)
REVERT: B  305 PHE cc_start: 0.9187 (m-10) cc_final: 0.8757 (m-80)
REVERT: B  314 PHE cc_start: 0.8061 (m-10) cc_final: 0.7778 (m-80)
REVERT: B  378 TYR cc_start: 0.9091 (t80) cc_final: 0.8684 (t80)
REVERT: B  402 LEU cc_start: 0.9548 (tt) cc_final: 0.9345 (tt)
REVERT: B  433 PHE cc_start: 0.8843 (m-10) cc_final: 0.8465 (m-80)
REVERT: B  451 LEU cc_start: 0.9541 (tp) cc_final: 0.9327 (pp)
REVERT: B  502 MET cc_start: 0.9291 (ttt) cc_final: 0.8193 (tmm)
REVERT: B  506 MET cc_start: 0.8292 (tpp) cc_final: 0.8077 (tpt)
REVERT: B  508 LEU cc_start: 0.9467 (tt) cc_final: 0.9260 (tp)
REVERT: B  512 TYR cc_start: 0.8540 (p90) cc_final: 0.7559 (p90)
REVERT: B  518 PHE cc_start: 0.8235 (m-80) cc_final: 0.7961 (m-80)
REVERT: B  710 MET cc_start: 0.8587 (mmp) cc_final: 0.8163 (mmp)
REVERT: B  719 LYS cc_start: 0.9400 (mtmt) cc_final: 0.9149 (mttp)
REVERT: B  729 GLU cc_start: 0.8318 (tm-30) cc_final: 0.8085 (tt0)
REVERT: B  855 ASP cc_start: 0.8467 (t0) cc_final: 0.8015 (t0)
REVERT: B  868 LEU cc_start: 0.9655 (tp) cc_final: 0.9449 (mm)
REVERT: B  869 MET cc_start: 0.8595 (tpp) cc_final: 0.7209 (tpp)
REVERT: B  903 MET cc_start: 0.8641 (mmm) cc_final: 0.8363 (mmm)
REVERT: B 1079 CYS cc_start: 0.9356 (t) cc_final: 0.8939 (p)
REVERT: B 1092 LYS cc_start: 0.9303 (mttm) cc_final: 0.9011 (mmtm)
REVERT: B 1206 GLU cc_start: 0.8402 (pm20) cc_final: 0.8032 (mp0)
REVERT: B 1255 ILE cc_start: 0.9295 (mm) cc_final: 0.9077 (mm)
REVERT: B 1294 TYR cc_start: 0.8694 (m-80) cc_final: 0.8446 (m-80)
REVERT: B 1305 MET cc_start: 0.8609 (tmm) cc_final: 0.8347 (tmm)
REVERT: B 1427 GLN cc_start: 0.8832 (pp30) cc_final: 0.8623 (pp30)
REVERT: B 1503 PHE cc_start: 0.8102 (m-10) cc_final: 0.7677 (m-10)
REVERT: B 1505 MET cc_start: 0.8260 (mmt) cc_final: 0.7770 (mtp)
REVERT: B 1507 GLU cc_start: 0.8940 (pt0) cc_final: 0.8655 (pp20)
REVERT: B 1517 GLU cc_start: 0.8656 (tp30) cc_final: 0.8324 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 217
  average time/residue: 0.1750
  time to fit residues: 55.6463
Evaluate side-chains
  171 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 1.006 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 72 optimal weight:    0.9980
   chunk 2 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 22 optimal weight:    7.9990
   chunk 38 optimal weight:    9.9990
   chunk 80 optimal weight:    0.8980
   chunk 105 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 95 optimal weight:    8.9990
   chunk 109 optimal weight:    3.9990
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
B 406 ASN
** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.091374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.073549 restraints weight = 29691.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.075962 restraints weight = 18938.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.077632 restraints weight = 13418.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.6855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9166  Z= 0.242
  Angle     :  0.754  11.979  12447  Z= 0.369
  Chirality :  0.045   0.183   1502
  Planarity :  0.004   0.054   1531
  Dihedral  :  5.913  85.215   1251
  Min Nonbonded Distance : 1.879

Molprobity Statistics.
  All-atom Clashscore : 12.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.25), residues: 1138
  helix:  1.41 (0.18), residues: 748
  sheet: -0.14 (0.54), residues: 93
  loop : -1.63 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 778 
 HIS   0.009   0.001   HIS B1316 
 PHE   0.020   0.002   PHE B 217 
 TYR   0.008   0.001   TYR B1354 
 ARG   0.004   0.000   ARG B 495 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2824.86 seconds
wall clock time: 51 minutes 19.35 seconds (3079.35 seconds total)