Starting phenix.real_space_refine
on Sat Aug 23 03:13:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y1l_33565/08_2025/7y1l_33565.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y1l_33565/08_2025/7y1l_33565.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.73
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y1l_33565/08_2025/7y1l_33565.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y1l_33565/08_2025/7y1l_33565.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y1l_33565/08_2025/7y1l_33565.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y1l_33565/08_2025/7y1l_33565.map"
  }
  resolution = 3.73
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.063
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       6      5.49       5
     Mg      2      5.21       5
     S      36      5.16       5
     C    5816      2.51       5
     N    1516      2.21       5
     O    1579      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8955
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8858
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1189, 8858
          Classifications: {'peptide': 1189}
          Incomplete info: {'truncation_to_alanine': 152}
          Link IDs: {'PTRANS': 35, 'TRANS': 1153}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 541
          Unresolved non-hydrogen angles: 669
          Unresolved non-hydrogen dihedrals: 429
          Unresolved non-hydrogen chiralities: 30
          Planarities with less than four sites: {'PHE:plan': 2, 'ASP:plan': 28, 'GLU:plan': 29, 'ARG:plan': 8, 'ASN:plan1': 8, 'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 2}
          Unresolved non-hydrogen planarities: 341
    Chain: "A"
      Number of atoms: 97
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 97
          Unusual residues: {' MG': 2, 'ATP': 2, 'BJX': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
  Time building chain proxies: 2.60, per 1000 atoms: 0.29
  Number of scatterers: 8955
  At special positions: 0
  Unit cell: (76.728, 100.914, 133.44, 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      36     16.00
     P       6     15.00
     Mg      2     11.99
     O    1579      8.00
     N    1516      7.00
     C    5816      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: 1.06
  Conformation dependent library (CDL) restraints added in 384.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2246

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 6 sheets defined
      72.6% alpha, 8.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 216 through 228
    Processing helix  chain 'A' and resid 228 through 238
      removed outlier: 3.893A  pdb=" N   ASN A 232 " --> pdb=" O   TYR A 228 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   THR A 233 " --> pdb=" O   TRP A 229 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   LEU A 234 " --> pdb=" O   TRP A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 255
    Processing helix  chain 'A' and resid 256 through 274
      removed outlier: 3.813A  pdb=" N   LYS A 274 " --> pdb=" O   GLU A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 312
      removed outlier: 3.691A  pdb=" N   ALA A 288 " --> pdb=" O   SER A 284 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   ARG A 295 " --> pdb=" O   ARG A 291 " (cutoff:3.500A)
      Proline residue:  A 296  - end of helix
    Processing helix  chain 'A' and resid 312 through 324
      removed outlier: 3.910A  pdb=" N   LEU A 316 " --> pdb=" O   PHE A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 348
      removed outlier: 3.622A  pdb=" N   GLU A 346 " --> pdb=" O   GLU A 343 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   ALA A 348 " --> pdb=" O   LEU A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 395
    Processing helix  chain 'A' and resid 405 through 416
    Processing helix  chain 'A' and resid 416 through 450
      Proline residue:  A 429  - end of helix
      removed outlier: 3.942A  pdb=" N   TRP A 432 " --> pdb=" O   CYS A 428 " (cutoff:3.500A)
      Proline residue:  A 435  - end of helix
    Processing helix  chain 'A' and resid 452 through 462
      removed outlier: 4.420A  pdb=" N   GLY A 456 " --> pdb=" O   SER A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 497
      removed outlier: 3.533A  pdb=" N   ILE A 466 " --> pdb=" O   LEU A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 506
    Processing helix  chain 'A' and resid 507 through 558
      removed outlier: 3.647A  pdb=" N   THR A 528 " --> pdb=" O   SER A 524 " (cutoff:3.500A)
      Proline residue:  A 544  - end of helix
    Processing helix  chain 'A' and resid 564 through 607
      removed outlier: 4.442A  pdb=" N   THR A 580 " --> pdb=" O   HIS A 576 " (cutoff:3.500A)
      Proline residue:  A 581  - end of helix
      removed outlier: 4.178A  pdb=" N   SER A 586 " --> pdb=" O   LEU A 582 " (cutoff:3.500A)
      removed outlier: 4.789A  pdb=" N   THR A 587 " --> pdb=" O   PHE A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 706 through 715
    Processing helix  chain 'A' and resid 761 through 768
    Processing helix  chain 'A' and resid 773 through 784
    Processing helix  chain 'A' and resid 786 through 793
    Processing helix  chain 'A' and resid 809 through 824
    Processing helix  chain 'A' and resid 839 through 850
    Processing helix  chain 'A' and resid 852 through 859
      removed outlier: 3.581A  pdb=" N   ASP A 858 " --> pdb=" O   PHE A 854 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 891 through 899
    Processing helix  chain 'A' and resid 899 through 912
      removed outlier: 3.546A  pdb=" N   LYS A 907 " --> pdb=" O   TYR A 903 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 925 through 937
    Processing helix  chain 'A' and resid 974 through 986
      removed outlier: 3.810A  pdb=" N   GLY A 985 " --> pdb=" O   TYR A 981 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   GLY A 986 " --> pdb=" O   LEU A 982 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 986 through 1017
      removed outlier: 4.092A  pdb=" N   GLU A1017 " --> pdb=" O   THR A1013 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1028 through 1074
    Processing helix  chain 'A' and resid 1076 through 1083
      removed outlier: 4.050A  pdb=" N   PHE A1080 " --> pdb=" O   PRO A1076 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1084 through 1094
      removed outlier: 3.591A  pdb=" N   ILE A1088 " --> pdb=" O   PRO A1084 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   PHE A1092 " --> pdb=" O   ILE A1088 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1094 through 1102
    Processing helix  chain 'A' and resid 1102 through 1128
    Processing helix  chain 'A' and resid 1130 through 1176
      removed outlier: 4.419A  pdb=" N   ALA A1134 " --> pdb=" O   VAL A1130 " (cutoff:3.500A)
      Proline residue:  A1137  - end of helix
      Proline residue:  A1166  - end of helix
    Processing helix  chain 'A' and resid 1177 through 1185
    Processing helix  chain 'A' and resid 1186 through 1237
    Processing helix  chain 'A' and resid 1240 through 1282
      removed outlier: 4.062A  pdb=" N   THR A1255 " --> pdb=" O   ALA A1251 " (cutoff:3.500A)
      removed outlier: 4.545A  pdb=" N   ASN A1256 " --> pdb=" O   LEU A1252 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   TYR A1257 " --> pdb=" O   THR A1253 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   ASN A1259 " --> pdb=" O   THR A1255 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   TRP A1260 " --> pdb=" O   ASN A1256 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   VAL A1262 " --> pdb=" O   LEU A1258 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ALA A1274 " --> pdb=" O   VAL A1270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1301 through 1305
      removed outlier: 4.322A  pdb=" N   GLU A1305 " --> pdb=" O   TRP A1302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1347 through 1356
    Processing helix  chain 'A' and resid 1377 through 1384
    Processing helix  chain 'A' and resid 1399 through 1404
    Processing helix  chain 'A' and resid 1410 through 1421
    Processing helix  chain 'A' and resid 1423 through 1430
    Processing helix  chain 'A' and resid 1432 through 1435
    Processing helix  chain 'A' and resid 1439 through 1443
      removed outlier: 3.967A  pdb=" N   GLU A1443 " --> pdb=" O   GLU A1440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1446 through 1462
      removed outlier: 3.550A  pdb=" N   LYS A1462 " --> pdb=" O   ALA A1458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1476 through 1490
    Processing helix  chain 'A' and resid 1502 through 1507
      removed outlier: 3.896A  pdb=" N   ILE A1506 " --> pdb=" O   ARG A1502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1525 through 1533
    Processing helix  chain 'A' and resid 1535 through 1543
    Processing sheet with id=AA1, first strand: chain 'A' and resid 684 through 687
      removed outlier: 5.313A  pdb=" N   SER A 685 " --> pdb=" O   PHE A 675 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   PHE A 675 " --> pdb=" O   SER A 685 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 684 through 687
      removed outlier: 5.313A  pdb=" N   SER A 685 " --> pdb=" O   PHE A 675 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   PHE A 675 " --> pdb=" O   SER A 685 " (cutoff:3.500A)
      removed outlier: 5.890A  pdb=" N   VAL A 670 " --> pdb=" O   TYR A 726 " (cutoff:3.500A)
      removed outlier: 7.469A  pdb=" N   TYR A 726 " --> pdb=" O   VAL A 670 " (cutoff:3.500A)
      removed outlier: 5.964A  pdb=" N   ASN A 672 " --> pdb=" O   LYS A 724 " (cutoff:3.500A)
      removed outlier: 4.944A  pdb=" N   LYS A 724 " --> pdb=" O   ASN A 672 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 748 through 751
      removed outlier: 6.100A  pdb=" N   ALA A 749 " --> pdb=" O   PHE A 830 " (cutoff:3.500A)
      removed outlier: 7.390A  pdb=" N   ASP A 832 " --> pdb=" O   ALA A 749 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   ALA A 751 " --> pdb=" O   ASP A 832 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   VAL A 829 " --> pdb=" O   VAL A 863 " (cutoff:3.500A)
      removed outlier: 7.900A  pdb=" N   VAL A 865 " --> pdb=" O   VAL A 829 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   LEU A 831 " --> pdb=" O   VAL A 865 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   THR A 697 " --> pdb=" O   LEU A 864 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1325 through 1332
      removed outlier: 6.308A  pdb=" N   LYS A1326 " --> pdb=" O   CYS A1314 " (cutoff:3.500A)
      removed outlier: 6.002A  pdb=" N   CYS A1314 " --> pdb=" O   LYS A1326 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   VAL A1328 " --> pdb=" O   ASP A1312 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   LEU A1313 " --> pdb=" O   ASP A1363 " (cutoff:3.500A)
      removed outlier: 6.327A  pdb=" N   ASP A1363 " --> pdb=" O   LEU A1313 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   VAL A1315 " --> pdb=" O   ILE A1361 " (cutoff:3.500A)
      removed outlier: 7.024A  pdb=" N   ILE A1361 " --> pdb=" O   VAL A1315 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1465 through 1469
      removed outlier: 6.205A  pdb=" N   LYS A1337 " --> pdb=" O   LEU A1511 " (cutoff:3.500A)
      removed outlier: 7.706A  pdb=" N   ILE A1513 " --> pdb=" O   LYS A1337 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   GLY A1339 " --> pdb=" O   ILE A1513 " (cutoff:3.500A)
      removed outlier: 7.386A  pdb=" N   MET A1515 " --> pdb=" O   GLY A1339 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   CYS A1341 " --> pdb=" O   MET A1515 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLU A1522 " --> pdb=" O   VAL A1514 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   LYS A1516 " --> pdb=" O   ILE A1520 " (cutoff:3.500A)
      removed outlier: 5.227A  pdb=" N   ILE A1520 " --> pdb=" O   LYS A1516 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1397 through 1398

    654 hydrogen bonds defined for protein.
    1935 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.81

  Time building geometry restraints manager: 1.31 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1360
        1.31 -     1.43: 2411
        1.43 -     1.56: 5277
        1.56 -     1.68: 31
        1.68 -     1.81: 58
  Bond restraints: 9137
  Sorted by residual:
  bond pdb=" C16 BJX A1605 "
       pdb=" N1  BJX A1605 "
    ideal  model  delta    sigma   weight residual
    1.344  1.453 -0.109 2.00e-02 2.50e+03 2.99e+01
  bond pdb=" CA  MET A 231 "
       pdb=" C   MET A 231 "
    ideal  model  delta    sigma   weight residual
    1.522  1.588 -0.065 1.36e-02 5.41e+03 2.30e+01
  bond pdb=" CA  ARG A1542 "
       pdb=" C   ARG A1542 "
    ideal  model  delta    sigma   weight residual
    1.523  1.584 -0.061 1.30e-02 5.92e+03 2.20e+01
  bond pdb=" CA  ASN A 232 "
       pdb=" CB  ASN A 232 "
    ideal  model  delta    sigma   weight residual
    1.528  1.599 -0.070 1.56e-02 4.11e+03 2.02e+01
  bond pdb=" CA  VAL A1541 "
       pdb=" C   VAL A1541 "
    ideal  model  delta    sigma   weight residual
    1.524  1.579 -0.055 1.22e-02 6.72e+03 2.00e+01
  ... (remaining 9132 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 12211
        1.55 -     3.10: 169
        3.10 -     4.65: 51
        4.65 -     6.20: 25
        6.20 -     7.75: 10
  Bond angle restraints: 12466
  Sorted by residual:
  angle pdb=" C   ILE A 321 "
        pdb=" CA  ILE A 321 "
        pdb=" CB  ILE A 321 "
      ideal   model   delta    sigma   weight residual
     111.97  104.22    7.75 1.28e+00 6.10e-01 3.66e+01
  angle pdb=" C   VAL A 322 "
        pdb=" CA  VAL A 322 "
        pdb=" CB  VAL A 322 "
      ideal   model   delta    sigma   weight residual
     112.14  105.00    7.14 1.35e+00 5.49e-01 2.79e+01
  angle pdb=" N   TRP A 229 "
        pdb=" CA  TRP A 229 "
        pdb=" CB  TRP A 229 "
      ideal   model   delta    sigma   weight residual
     110.12  117.70   -7.58 1.47e+00 4.63e-01 2.66e+01
  angle pdb=" O   ILE A 318 "
        pdb=" C   ILE A 318 "
        pdb=" N   SER A 319 "
      ideal   model   delta    sigma   weight residual
     121.87  126.38   -4.51 9.70e-01 1.06e+00 2.16e+01
  angle pdb=" N   ILE A 321 "
        pdb=" CA  ILE A 321 "
        pdb=" CB  ILE A 321 "
      ideal   model   delta    sigma   weight residual
     110.55  115.94   -5.39 1.17e+00 7.31e-01 2.12e+01
  ... (remaining 12461 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.03: 5302
       31.03 -    62.06: 101
       62.06 -    93.10: 9
       93.10 -   124.13: 0
      124.13 -   155.16: 1
  Dihedral angle restraints: 5413
    sinusoidal: 1950
      harmonic: 3463
  Sorted by residual:
  dihedral pdb=" O   BJX A1605 "
           pdb=" C16 BJX A1605 "
           pdb=" C17 BJX A1605 "
           pdb=" C18 BJX A1605 "
      ideal   model   delta sinusoidal    sigma   weight residual
      10.31 -144.85  155.16     1      3.00e+01 1.11e-03 2.03e+01
  dihedral pdb=" CA  GLN A 323 "
           pdb=" C   GLN A 323 "
           pdb=" N   ARG A 324 "
           pdb=" CA  ARG A 324 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.87   21.13     0      5.00e+00 4.00e-02 1.79e+01
  dihedral pdb=" CA  ASP A1100 "
           pdb=" C   ASP A1100 "
           pdb=" N   GLN A1101 "
           pdb=" CA  GLN A1101 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.50  -16.50     0      5.00e+00 4.00e-02 1.09e+01
  ... (remaining 5410 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 1371
       0.064 -    0.129: 129
       0.129 -    0.193: 10
       0.193 -    0.257: 1
       0.257 -    0.322: 8
  Chirality restraints: 1519
  Sorted by residual:
  chirality pdb=" CA  ILE A 321 "
            pdb=" N   ILE A 321 "
            pdb=" C   ILE A 321 "
            pdb=" CB  ILE A 321 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.75   -0.32 2.00e-01 2.50e+01 2.59e+00
  chirality pdb=" CA  VAL A1541 "
            pdb=" N   VAL A1541 "
            pdb=" C   VAL A1541 "
            pdb=" CB  VAL A1541 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.74   -0.30 2.00e-01 2.50e+01 2.22e+00
  chirality pdb=" C2' ATP A1603 "
            pdb=" C1' ATP A1603 "
            pdb=" C3' ATP A1603 "
            pdb=" O2' ATP A1603 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.97    0.29 2.00e-01 2.50e+01 2.14e+00
  ... (remaining 1516 not shown)

  Planarity restraints: 1519
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 227 "    0.020 2.00e-02 2.50e+03   4.11e-02 1.69e+01
        pdb=" C   THR A 227 "   -0.071 2.00e-02 2.50e+03
        pdb=" O   THR A 227 "    0.027 2.00e-02 2.50e+03
        pdb=" N   TYR A 228 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 229 "    0.032 2.00e-02 2.50e+03   2.00e-02 1.00e+01
        pdb=" CG  TRP A 229 "   -0.053 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 229 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 229 "    0.005 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 229 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 229 "    0.007 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 229 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 229 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 229 "   -0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 229 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 580 "   -0.035 5.00e-02 4.00e+02   5.36e-02 4.59e+00
        pdb=" N   PRO A 581 "    0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO A 581 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 581 "   -0.030 5.00e-02 4.00e+02
  ... (remaining 1516 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1124
        2.74 -     3.28: 10067
        3.28 -     3.82: 15369
        3.82 -     4.36: 16713
        4.36 -     4.90: 29355
  Nonbonded interactions: 72628
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN A 753 "
            pdb="MG    MG A1602 "
     model   vdw
     2.202 2.170
  nonbonded pdb=" OD2 ASP A1008 "
            pdb=" OH  TYR A1250 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" ND2 ASN A 430 "
            pdb=" O   BJX A1605 "
     model   vdw
     2.212 3.120
  nonbonded pdb=" OD1 ASN A 232 "
            pdb=" NE1 TRP A1214 "
     model   vdw
     2.216 3.120
  nonbonded pdb="MG    MG A1601 "
            pdb=" O3B ATP A1604 "
     model   vdw
     2.220 2.170
  ... (remaining 72623 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:             3.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     11.630
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
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      :  0.005   0.109   9137  Z= 0.290
  Angle     :  0.587   7.748  12466  Z= 0.344
  Chirality :  0.043   0.322   1519
  Planarity :  0.004   0.068   1519
  Dihedral  : 12.439 155.161   3167
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  4.45 %
    Favored  : 94.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.57 (0.25), residues: 1173
  helix:  2.33 (0.18), residues: 794
  sheet:  1.23 (0.67), residues: 68
  loop :  0.20 (0.37), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1218 
 TYR   0.026   0.001   TYR A 228 
 PHE   0.014   0.001   PHE A1149 
 TRP   0.053   0.001   TRP A 229 
 HIS   0.005   0.001   HIS A1504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 ( 9137)
  covalent geometry    : angle       0.58722 (12466)
  hydrogen bonds       : bond        0.13021 (  652)
  hydrogen bonds       : angle       5.81291 ( 1935)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 169
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
REVERT: A  228 TYR cc_start: 0.9049 (m-80) cc_final: 0.8114 (m-80)
REVERT: A  434 MET cc_start: 0.8460 (tpp) cc_final: 0.7850 (mmm)
REVERT: A  523 LEU cc_start: 0.9038 (mm) cc_final: 0.8570 (pp)
REVERT: A  786 LEU cc_start: 0.9339 (tp) cc_final: 0.9097 (tp)
REVERT: A  814 GLN cc_start: 0.8797 (pt0) cc_final: 0.8182 (tt0)
REVERT: A 1044 PHE cc_start: 0.8345 (t80) cc_final: 0.8078 (t80)
REVERT: A 1091 ARG cc_start: 0.8267 (mmt-90) cc_final: 0.8035 (mmt180)
REVERT: A 1367 VAL cc_start: 0.6280 (t) cc_final: 0.6010 (t)
REVERT: A 1426 MET cc_start: 0.9063 (mmm) cc_final: 0.8845 (tpp)
  outliers start: 9
  outliers final: 3
  residues processed: 176
  average time/residue: 0.0720
  time to fit residues: 19.5407
Evaluate side-chains
  128 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 125
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue 1160 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 108 optimal weight:    0.0570
   chunk 49 optimal weight:    8.9990
   chunk 97 optimal weight:    7.9990
   chunk 113 optimal weight:    5.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.0770
   chunk 51 optimal weight:    1.9990
   chunk 117 optimal weight:    9.9990
   overall best weight:    0.5258

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

Flipped N/Q/H residues before XYZ refinement:
A 576 HIS
A 867 HIS
A1186 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.118077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.091342 restraints weight = 21363.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.090679 restraints weight = 11619.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.091765 restraints weight = 9111.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.093144 restraints weight = 6363.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.093222 restraints weight = 5454.102|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
moved from start:          0.1511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9137  Z= 0.133
  Angle     :  0.571   7.728  12466  Z= 0.283
  Chirality :  0.040   0.175   1519
  Planarity :  0.003   0.041   1519
  Dihedral  :  9.699 124.105   1359
  Min Nonbonded Distance : 1.981

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 10.73 %
    Favored  : 87.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.87 (0.25), residues: 1173
  helix:  2.57 (0.18), residues: 805
  sheet:  0.85 (0.64), residues: 68
  loop :  0.30 (0.37), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 970 
 TYR   0.011   0.001   TYR A1331 
 PHE   0.016   0.001   PHE A 569 
 TRP   0.012   0.001   TRP A 230 
 HIS   0.006   0.001   HIS A1504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 9137)
  covalent geometry    : angle       0.57072 (12466)
  hydrogen bonds       : bond        0.04692 (  652)
  hydrogen bonds       : angle       4.57034 ( 1935)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 160
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
REVERT: A  228 TYR cc_start: 0.9013 (m-80) cc_final: 0.8144 (m-80)
REVERT: A  434 MET cc_start: 0.8526 (tpp) cc_final: 0.8012 (mmm)
REVERT: A  814 GLN cc_start: 0.8793 (pt0) cc_final: 0.8374 (tt0)
REVERT: A  822 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8954 (mm)
REVERT: A  975 TRP cc_start: 0.8656 (m100) cc_final: 0.8139 (m100)
REVERT: A 1044 PHE cc_start: 0.8511 (t80) cc_final: 0.8133 (t80)
REVERT: A 1091 ARG cc_start: 0.8152 (mmt-90) cc_final: 0.7908 (mmt180)
REVERT: A 1123 MET cc_start: 0.8606 (tpp) cc_final: 0.8403 (tpp)
  outliers start: 12
  outliers final: 5
  residues processed: 167
  average time/residue: 0.0713
  time to fit residues: 18.4427
Evaluate side-chains
  136 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 130
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  509 HIS
Chi-restraints excluded: chain A residue  822 LEU
Chi-restraints excluded: chain A residue 1128 THR
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1160 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0670
   chunk 99 optimal weight:   10.0000
   chunk 49 optimal weight:    0.8980
   chunk 51 optimal weight:    7.9990
   chunk 43 optimal weight:    8.9990
   chunk 59 optimal weight:    3.9990
   chunk 93 optimal weight:    0.0670
   chunk 85 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9990
   chunk 107 optimal weight:    2.9990
   overall best weight:    0.5258

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.118651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.092080 restraints weight = 21493.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.091220 restraints weight = 11352.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.092244 restraints weight = 9112.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.093214 restraints weight = 6370.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.093420 restraints weight = 5531.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.1918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9137  Z= 0.127
  Angle     :  0.555   7.455  12466  Z= 0.271
  Chirality :  0.040   0.232   1519
  Planarity :  0.003   0.047   1519
  Dihedral  :  9.262 128.115   1357
  Min Nonbonded Distance : 2.004

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 13.58 %
    Favored  : 84.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.86 (0.25), residues: 1173
  helix:  2.59 (0.18), residues: 802
  sheet:  0.88 (0.63), residues: 68
  loop :  0.26 (0.36), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 363 
 TYR   0.013   0.001   TYR A1205 
 PHE   0.018   0.001   PHE A1362 
 TRP   0.015   0.001   TRP A1302 
 HIS   0.007   0.001   HIS A1504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 9137)
  covalent geometry    : angle       0.55482 (12466)
  hydrogen bonds       : bond        0.04465 (  652)
  hydrogen bonds       : angle       4.41038 ( 1935)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 143
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
REVERT: A  228 TYR cc_start: 0.9033 (m-80) cc_final: 0.8211 (m-80)
REVERT: A  434 MET cc_start: 0.8506 (tpp) cc_final: 0.7978 (mmm)
REVERT: A  502 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8513 (mp)
REVERT: A  517 GLU cc_start: 0.8804 (tp30) cc_final: 0.8237 (tp30)
REVERT: A  814 GLN cc_start: 0.8812 (pt0) cc_final: 0.8395 (tt0)
REVERT: A  822 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9015 (mm)
REVERT: A 1044 PHE cc_start: 0.8492 (t80) cc_final: 0.8132 (t80)
REVERT: A 1111 THR cc_start: 0.9171 (p) cc_final: 0.8908 (t)
REVERT: A 1302 TRP cc_start: 0.8163 (t60) cc_final: 0.7758 (t60)
  outliers start: 16
  outliers final: 10
  residues processed: 151
  average time/residue: 0.0732
  time to fit residues: 17.1565
Evaluate side-chains
  142 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 130
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  509 HIS
Chi-restraints excluded: chain A residue  822 LEU
Chi-restraints excluded: chain A residue  886 VAL
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1159 LEU
Chi-restraints excluded: chain A residue 1248 LEU
Chi-restraints excluded: chain A residue 1258 LEU
Chi-restraints excluded: chain A residue 1259 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 100 optimal weight:   10.0000
   chunk 53 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9990
   chunk 70 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9990
   chunk 67 optimal weight:    0.0270
   chunk 85 optimal weight:    0.8980
   chunk 117 optimal weight:    6.9990
   chunk 105 optimal weight:   20.0000
   chunk 27 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.7844

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

Flipped N/Q/H residues before XYZ refinement:
A 576 HIS
A1379 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.117529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.089446 restraints weight = 21811.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.088306 restraints weight = 11930.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.089411 restraints weight = 9618.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.090845 restraints weight = 6706.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.090892 restraints weight = 5811.905|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.2211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9137  Z= 0.125
  Angle     :  0.535   8.829  12466  Z= 0.264
  Chirality :  0.039   0.181   1519
  Planarity :  0.003   0.046   1519
  Dihedral  :  8.912 130.807   1355
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 15.07 %
    Favored  : 82.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.81 (0.25), residues: 1173
  helix:  2.56 (0.18), residues: 800
  sheet:  0.89 (0.61), residues: 68
  loop :  0.21 (0.35), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1382 
 TYR   0.011   0.001   TYR A1205 
 PHE   0.017   0.001   PHE A 988 
 TRP   0.009   0.001   TRP A1302 
 HIS   0.007   0.001   HIS A1504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 9137)
  covalent geometry    : angle       0.53495 (12466)
  hydrogen bonds       : bond        0.04326 (  652)
  hydrogen bonds       : angle       4.27244 ( 1935)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 142
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
REVERT: A  228 TYR cc_start: 0.9041 (m-80) cc_final: 0.8241 (m-80)
REVERT: A  243 ILE cc_start: 0.9161 (mm) cc_final: 0.8878 (mp)
REVERT: A  434 MET cc_start: 0.8493 (tpp) cc_final: 0.7880 (mmm)
REVERT: A  517 GLU cc_start: 0.8773 (tp30) cc_final: 0.8114 (tp30)
REVERT: A  523 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8550 (pp)
REVERT: A  814 GLN cc_start: 0.8814 (pt0) cc_final: 0.8424 (tt0)
REVERT: A  822 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9079 (mm)
REVERT: A 1044 PHE cc_start: 0.8525 (t80) cc_final: 0.8121 (t80)
REVERT: A 1155 ASP cc_start: 0.8380 (t0) cc_final: 0.8111 (t0)
  outliers start: 19
  outliers final: 12
  residues processed: 152
  average time/residue: 0.0626
  time to fit residues: 15.6112
Evaluate side-chains
  141 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 127
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  509 HIS
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  718 MET
Chi-restraints excluded: chain A residue  822 LEU
Chi-restraints excluded: chain A residue 1115 LEU
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1159 LEU
Chi-restraints excluded: chain A residue 1258 LEU
Chi-restraints excluded: chain A residue 1259 ASN
Chi-restraints excluded: chain A residue 1361 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 116 optimal weight:    9.9990
   chunk 89 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   chunk 113 optimal weight:    0.8980
   chunk 92 optimal weight:    2.9990
   chunk 74 optimal weight:    0.5980
   chunk 100 optimal weight:    0.0870
   chunk 34 optimal weight:    2.9990
   chunk 27 optimal weight:    7.9990
   chunk 99 optimal weight:    9.9990
   overall best weight:    0.7158

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

Flipped N/Q/H residues before XYZ refinement:
A 576 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.117917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.089896 restraints weight = 21819.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.088872 restraints weight = 12508.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.089714 restraints weight = 10154.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.091421 restraints weight = 7085.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.091294 restraints weight = 5477.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.2438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9137  Z= 0.122
  Angle     :  0.525   9.609  12466  Z= 0.262
  Chirality :  0.039   0.190   1519
  Planarity :  0.003   0.044   1519
  Dihedral  :  8.676 132.298   1355
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 15.53 %
    Favored  : 82.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.78 (0.24), residues: 1173
  helix:  2.54 (0.18), residues: 796
  sheet:  0.99 (0.60), residues: 68
  loop :  0.19 (0.35), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1382 
 TYR   0.008   0.001   TYR A1331 
 PHE   0.019   0.001   PHE A 988 
 TRP   0.018   0.001   TRP A1302 
 HIS   0.007   0.001   HIS A1504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 9137)
  covalent geometry    : angle       0.52479 (12466)
  hydrogen bonds       : bond        0.04244 (  652)
  hydrogen bonds       : angle       4.21770 ( 1935)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 139
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
REVERT: A  228 TYR cc_start: 0.9031 (m-80) cc_final: 0.8260 (m-80)
REVERT: A  434 MET cc_start: 0.8484 (tpp) cc_final: 0.8050 (mmm)
REVERT: A  517 GLU cc_start: 0.8760 (tp30) cc_final: 0.8105 (tp30)
REVERT: A  523 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8553 (pp)
REVERT: A  814 GLN cc_start: 0.8815 (pt0) cc_final: 0.8377 (tt0)
REVERT: A  822 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9092 (mm)
REVERT: A 1044 PHE cc_start: 0.8533 (t80) cc_final: 0.8136 (t80)
REVERT: A 1215 LEU cc_start: 0.8351 (tp) cc_final: 0.7953 (tt)
REVERT: A 1302 TRP cc_start: 0.8289 (t60) cc_final: 0.7800 (t60)
  outliers start: 20
  outliers final: 12
  residues processed: 151
  average time/residue: 0.0634
  time to fit residues: 15.6047
Evaluate side-chains
  137 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 123
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  509 HIS
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  715 LEU
Chi-restraints excluded: chain A residue  718 MET
Chi-restraints excluded: chain A residue  822 LEU
Chi-restraints excluded: chain A residue 1115 LEU
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1159 LEU
Chi-restraints excluded: chain A residue 1179 THR
Chi-restraints excluded: chain A residue 1226 ILE
Chi-restraints excluded: chain A residue 1258 LEU
Chi-restraints excluded: chain A residue 1259 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 87 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   chunk 26 optimal weight:    8.9990
   chunk 60 optimal weight:    6.9990
   chunk 71 optimal weight:    6.9990
   chunk 57 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9990
   chunk 82 optimal weight:    0.8980
   chunk 117 optimal weight:    4.9990
   chunk 102 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    1.5386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.116705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.089345 restraints weight = 21584.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.087146 restraints weight = 12323.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.088369 restraints weight = 9560.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.089841 restraints weight = 6616.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.089821 restraints weight = 5782.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.2422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   9137  Z= 0.165
  Angle     :  0.560  10.028  12466  Z= 0.278
  Chirality :  0.040   0.202   1519
  Planarity :  0.003   0.045   1519
  Dihedral  :  8.707 138.219   1355
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 16.78 %
    Favored  : 80.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.70 (0.24), residues: 1173
  helix:  2.48 (0.18), residues: 797
  sheet:  1.02 (0.60), residues: 68
  loop :  0.13 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1382 
 TYR   0.008   0.001   TYR A 228 
 PHE   0.021   0.001   PHE A 988 
 TRP   0.010   0.001   TRP A1302 
 HIS   0.007   0.001   HIS A1504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 9137)
  covalent geometry    : angle       0.56036 (12466)
  hydrogen bonds       : bond        0.04393 (  652)
  hydrogen bonds       : angle       4.22937 ( 1935)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 133
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
REVERT: A  228 TYR cc_start: 0.9092 (m-80) cc_final: 0.8271 (m-80)
REVERT: A  434 MET cc_start: 0.8588 (tpp) cc_final: 0.7995 (mmm)
REVERT: A  517 GLU cc_start: 0.8812 (tp30) cc_final: 0.8132 (tp30)
REVERT: A  523 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8550 (pp)
REVERT: A  814 GLN cc_start: 0.8817 (pt0) cc_final: 0.8393 (tt0)
REVERT: A  822 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9136 (mm)
REVERT: A 1044 PHE cc_start: 0.8545 (t80) cc_final: 0.8149 (t80)
  outliers start: 23
  outliers final: 18
  residues processed: 147
  average time/residue: 0.0639
  time to fit residues: 15.4248
Evaluate side-chains
  144 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 124
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  509 HIS
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  715 LEU
Chi-restraints excluded: chain A residue  718 MET
Chi-restraints excluded: chain A residue  822 LEU
Chi-restraints excluded: chain A residue  971 THR
Chi-restraints excluded: chain A residue 1115 LEU
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1159 LEU
Chi-restraints excluded: chain A residue 1179 THR
Chi-restraints excluded: chain A residue 1187 GLU
Chi-restraints excluded: chain A residue 1226 ILE
Chi-restraints excluded: chain A residue 1248 LEU
Chi-restraints excluded: chain A residue 1258 LEU
Chi-restraints excluded: chain A residue 1259 ASN
Chi-restraints excluded: chain A residue 1361 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 14 optimal weight:    0.5980
   chunk 64 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 106 optimal weight:    8.9990
   chunk 41 optimal weight:    8.9990
   chunk 95 optimal weight:   20.0000
   chunk 59 optimal weight:   10.0000
   chunk 19 optimal weight:    0.6980
   chunk 110 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
A 576 HIS
A1444 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.116233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.089381 restraints weight = 21834.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.087261 restraints weight = 11908.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.088423 restraints weight = 9178.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.089890 restraints weight = 6349.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.089866 restraints weight = 5431.256|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.2496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   9137  Z= 0.157
  Angle     :  0.557  11.006  12466  Z= 0.276
  Chirality :  0.040   0.204   1519
  Planarity :  0.003   0.044   1519
  Dihedral  :  8.712 139.329   1355
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 17.58 %
    Favored  : 79.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.66 (0.24), residues: 1173
  helix:  2.45 (0.18), residues: 797
  sheet:  1.15 (0.59), residues: 68
  loop :  0.09 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1382 
 TYR   0.013   0.001   TYR A1205 
 PHE   0.031   0.001   PHE A 988 
 TRP   0.017   0.001   TRP A1302 
 HIS   0.007   0.001   HIS A1504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 9137)
  covalent geometry    : angle       0.55724 (12466)
  hydrogen bonds       : bond        0.04408 (  652)
  hydrogen bonds       : angle       4.21815 ( 1935)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 131
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
REVERT: A  228 TYR cc_start: 0.9071 (m-80) cc_final: 0.8247 (m-80)
REVERT: A  434 MET cc_start: 0.8603 (tpp) cc_final: 0.8012 (mmm)
REVERT: A  517 GLU cc_start: 0.8824 (tp30) cc_final: 0.8144 (tp30)
REVERT: A  523 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8553 (pp)
REVERT: A  814 GLN cc_start: 0.8795 (pt0) cc_final: 0.8361 (tt0)
REVERT: A  822 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9141 (mm)
REVERT: A 1044 PHE cc_start: 0.8532 (t80) cc_final: 0.8130 (t80)
REVERT: A 1302 TRP cc_start: 0.8390 (t60) cc_final: 0.7945 (t60)
  outliers start: 23
  outliers final: 18
  residues processed: 146
  average time/residue: 0.0621
  time to fit residues: 14.9266
Evaluate side-chains
  143 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 123
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  509 HIS
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  715 LEU
Chi-restraints excluded: chain A residue  718 MET
Chi-restraints excluded: chain A residue  822 LEU
Chi-restraints excluded: chain A residue  971 THR
Chi-restraints excluded: chain A residue 1115 LEU
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1159 LEU
Chi-restraints excluded: chain A residue 1179 THR
Chi-restraints excluded: chain A residue 1187 GLU
Chi-restraints excluded: chain A residue 1226 ILE
Chi-restraints excluded: chain A residue 1258 LEU
Chi-restraints excluded: chain A residue 1259 ASN
Chi-restraints excluded: chain A residue 1361 ILE
Chi-restraints excluded: chain A residue 1444 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 0 optimal weight:    9.9990
   chunk 17 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 77 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    5.9990
   chunk 60 optimal weight:    8.9990
   chunk 82 optimal weight:    0.7980
   chunk 65 optimal weight:    0.5980
   chunk 74 optimal weight:    0.0770
   overall best weight:    0.8540

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.117829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.090817 restraints weight = 21632.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.088628 restraints weight = 12179.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.089759 restraints weight = 9395.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.091571 restraints weight = 6578.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.091483 restraints weight = 5415.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8416
moved from start:          0.2613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9137  Z= 0.129
  Angle     :  0.553  11.421  12466  Z= 0.270
  Chirality :  0.039   0.201   1519
  Planarity :  0.003   0.039   1519
  Dihedral  :  8.637 138.757   1355
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 18.26 %
    Favored  : 79.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.66 (0.24), residues: 1173
  helix:  2.45 (0.18), residues: 797
  sheet:  1.24 (0.59), residues: 68
  loop :  0.07 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1382 
 TYR   0.019   0.001   TYR A1205 
 PHE   0.032   0.001   PHE A 988 
 TRP   0.014   0.001   TRP A 906 
 HIS   0.007   0.001   HIS A1504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 9137)
  covalent geometry    : angle       0.55322 (12466)
  hydrogen bonds       : bond        0.04296 (  652)
  hydrogen bonds       : angle       4.17211 ( 1935)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 131
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
REVERT: A  228 TYR cc_start: 0.9018 (m-80) cc_final: 0.8272 (m-80)
REVERT: A  434 MET cc_start: 0.8558 (tpp) cc_final: 0.8132 (mmm)
REVERT: A  517 GLU cc_start: 0.8801 (tp30) cc_final: 0.8117 (tp30)
REVERT: A  523 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8547 (pp)
REVERT: A  814 GLN cc_start: 0.8812 (pt0) cc_final: 0.8385 (tt0)
REVERT: A  822 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9130 (mm)
REVERT: A 1044 PHE cc_start: 0.8529 (t80) cc_final: 0.8146 (t80)
REVERT: A 1302 TRP cc_start: 0.8358 (t60) cc_final: 0.7988 (t60)
  outliers start: 20
  outliers final: 15
  residues processed: 145
  average time/residue: 0.0642
  time to fit residues: 15.1726
Evaluate side-chains
  140 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 123
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  509 HIS
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  715 LEU
Chi-restraints excluded: chain A residue  718 MET
Chi-restraints excluded: chain A residue  822 LEU
Chi-restraints excluded: chain A residue  971 THR
Chi-restraints excluded: chain A residue 1115 LEU
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1159 LEU
Chi-restraints excluded: chain A residue 1179 THR
Chi-restraints excluded: chain A residue 1187 GLU
Chi-restraints excluded: chain A residue 1258 LEU
Chi-restraints excluded: chain A residue 1259 ASN
Chi-restraints excluded: chain A residue 1361 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 53 optimal weight:    9.9990
   chunk 19 optimal weight:    0.0670
   chunk 28 optimal weight:    5.9990
   chunk 11 optimal weight:    0.1980
   chunk 95 optimal weight:   20.0000
   chunk 37 optimal weight:    6.9990
   chunk 78 optimal weight:    4.9990
   chunk 69 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   overall best weight:    0.9720

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

Flipped N/Q/H residues before XYZ refinement:
A 362 GLN
A 576 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.117685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.090642 restraints weight = 21572.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.088518 restraints weight = 12113.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.089670 restraints weight = 9612.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.091075 restraints weight = 6555.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.091113 restraints weight = 5653.966|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.2703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9137  Z= 0.132
  Angle     :  0.557  11.541  12466  Z= 0.271
  Chirality :  0.039   0.205   1519
  Planarity :  0.003   0.035   1519
  Dihedral  :  8.579 139.138   1355
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 18.49 %
    Favored  : 79.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.68 (0.24), residues: 1173
  helix:  2.48 (0.18), residues: 797
  sheet:  1.23 (0.59), residues: 68
  loop :  0.02 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1382 
 TYR   0.025   0.001   TYR A1205 
 PHE   0.036   0.001   PHE A 988 
 TRP   0.014   0.001   TRP A 906 
 HIS   0.008   0.001   HIS A1504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 9137)
  covalent geometry    : angle       0.55695 (12466)
  hydrogen bonds       : bond        0.04272 (  652)
  hydrogen bonds       : angle       4.15259 ( 1935)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 125
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
REVERT: A  228 TYR cc_start: 0.9036 (m-80) cc_final: 0.8211 (m-80)
REVERT: A  362 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8391 (tm-30)
REVERT: A  434 MET cc_start: 0.8614 (tpp) cc_final: 0.8137 (mmm)
REVERT: A  517 GLU cc_start: 0.8809 (tp30) cc_final: 0.8124 (tp30)
REVERT: A  523 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8539 (pp)
REVERT: A  814 GLN cc_start: 0.8823 (pt0) cc_final: 0.8396 (tt0)
REVERT: A  822 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9155 (mm)
REVERT: A 1044 PHE cc_start: 0.8523 (t80) cc_final: 0.8148 (t80)
REVERT: A 1302 TRP cc_start: 0.8360 (t60) cc_final: 0.8032 (t60)
  outliers start: 19
  outliers final: 15
  residues processed: 138
  average time/residue: 0.0618
  time to fit residues: 14.1021
Evaluate side-chains
  138 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 120
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  362 GLN
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  509 HIS
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  715 LEU
Chi-restraints excluded: chain A residue  718 MET
Chi-restraints excluded: chain A residue  822 LEU
Chi-restraints excluded: chain A residue  971 THR
Chi-restraints excluded: chain A residue 1115 LEU
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1159 LEU
Chi-restraints excluded: chain A residue 1179 THR
Chi-restraints excluded: chain A residue 1187 GLU
Chi-restraints excluded: chain A residue 1258 LEU
Chi-restraints excluded: chain A residue 1259 ASN
Chi-restraints excluded: chain A residue 1361 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9990
   chunk 100 optimal weight:    6.9990
   chunk 31 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9980
   chunk 60 optimal weight:   10.0000
   chunk 82 optimal weight:    4.9990
   chunk 110 optimal weight:    8.9990
   chunk 49 optimal weight:   10.0000
   chunk 71 optimal weight:    5.9990
   chunk 21 optimal weight:    0.0970
   overall best weight:    1.5582

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

Flipped N/Q/H residues before XYZ refinement:
A 362 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.116557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.089381 restraints weight = 21500.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.087239 restraints weight = 12219.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.088426 restraints weight = 9564.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.089912 restraints weight = 6554.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.089923 restraints weight = 5633.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.2685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   9137  Z= 0.164
  Angle     :  0.577  11.725  12466  Z= 0.283
  Chirality :  0.040   0.212   1519
  Planarity :  0.003   0.034   1519
  Dihedral  :  8.611 141.862   1355
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 19.06 %
    Favored  : 78.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.62 (0.24), residues: 1173
  helix:  2.43 (0.18), residues: 797
  sheet:  1.20 (0.60), residues: 68
  loop :  0.02 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1382 
 TYR   0.025   0.001   TYR A1205 
 PHE   0.036   0.001   PHE A 988 
 TRP   0.014   0.001   TRP A 906 
 HIS   0.007   0.001   HIS A1504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 9137)
  covalent geometry    : angle       0.57696 (12466)
  hydrogen bonds       : bond        0.04379 (  652)
  hydrogen bonds       : angle       4.20420 ( 1935)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 119
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
REVERT: A  228 TYR cc_start: 0.9073 (m-80) cc_final: 0.8280 (m-80)
REVERT: A  362 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8403 (tm-30)
REVERT: A  434 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8020 (mmm)
REVERT: A  517 GLU cc_start: 0.8812 (tp30) cc_final: 0.8122 (tp30)
REVERT: A  523 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8556 (pp)
REVERT: A  814 GLN cc_start: 0.8794 (pt0) cc_final: 0.8378 (tt0)
REVERT: A  822 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9158 (mm)
REVERT: A 1044 PHE cc_start: 0.8537 (t80) cc_final: 0.8161 (t80)
REVERT: A 1302 TRP cc_start: 0.8380 (t60) cc_final: 0.8059 (t60)
  outliers start: 19
  outliers final: 15
  residues processed: 132
  average time/residue: 0.0588
  time to fit residues: 12.8835
Evaluate side-chains
  135 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 116
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  362 GLN
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  434 MET
Chi-restraints excluded: chain A residue  509 HIS
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  715 LEU
Chi-restraints excluded: chain A residue  718 MET
Chi-restraints excluded: chain A residue  822 LEU
Chi-restraints excluded: chain A residue  971 THR
Chi-restraints excluded: chain A residue 1115 LEU
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1159 LEU
Chi-restraints excluded: chain A residue 1179 THR
Chi-restraints excluded: chain A residue 1187 GLU
Chi-restraints excluded: chain A residue 1258 LEU
Chi-restraints excluded: chain A residue 1259 ASN
Chi-restraints excluded: chain A residue 1361 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 111 optimal weight:    9.9990
   chunk 21 optimal weight:    0.0970
   chunk 81 optimal weight:    0.6980
   chunk 80 optimal weight:    0.9980
   chunk 79 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   chunk 115 optimal weight:    6.9990
   chunk 78 optimal weight:    5.9990
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
A 362 GLN
A 576 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.117127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.089411 restraints weight = 21369.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.088492 restraints weight = 11755.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.089497 restraints weight = 9889.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.090288 restraints weight = 6758.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.090624 restraints weight = 5940.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.2788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9137  Z= 0.123
  Angle     :  0.565  12.308  12466  Z= 0.275
  Chirality :  0.039   0.202   1519
  Planarity :  0.003   0.035   1519
  Dihedral  :  8.538 140.599   1355
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 19.18 %
    Favored  : 78.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.63 (0.24), residues: 1173
  helix:  2.43 (0.18), residues: 797
  sheet:  1.27 (0.59), residues: 68
  loop :  0.02 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 363 
 TYR   0.023   0.001   TYR A1205 
 PHE   0.035   0.001   PHE A 988 
 TRP   0.012   0.001   TRP A 906 
 HIS   0.007   0.001   HIS A1504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 9137)
  covalent geometry    : angle       0.56520 (12466)
  hydrogen bonds       : bond        0.04246 (  652)
  hydrogen bonds       : angle       4.15104 ( 1935)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1412.69 seconds
wall clock time: 25 minutes 19.24 seconds (1519.24 seconds total)