Starting phenix.real_space_refine
on Thu Feb 13 23:01:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vlr_32024/02_2025/7vlr_32024.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vlr_32024/02_2025/7vlr_32024.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vlr_32024/02_2025/7vlr_32024.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vlr_32024/02_2025/7vlr_32024.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vlr_32024/02_2025/7vlr_32024.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vlr_32024/02_2025/7vlr_32024.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.007 sd=   0.131
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       5      5.49       5
     Mg      2      5.21       5
     S      46      5.16       5
     C    5833      2.51       5
     N    1493      2.21       5
     O    1624      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9003
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8908
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1145, 8908
          Classifications: {'peptide': 1145}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 33, 'TRANS': 1111}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 100
          Unresolved non-hydrogen angles: 123
          Unresolved non-hydrogen dihedrals: 80
          Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6, 'GLU:plan': 8, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 83
    Chain: "A"
      Number of atoms: 95
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 95
          Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1, 'Y01': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
  Time building chain proxies: 5.70, per 1000 atoms: 0.63
  Number of scatterers: 9003
  At special positions: 0
  Unit cell: (72.27, 90.666, 135.342, 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      46     16.00
     P       5     15.00
     Mg      2     11.99
     O    1624      8.00
     N    1493      7.00
     C    5833      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.58
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2158

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 5 sheets defined
      72.2% alpha, 8.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 256 through 278
      removed outlier: 3.518A  pdb=" N   ASN A 260 " --> pdb=" O   ARG A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 327
      removed outlier: 5.870A  pdb=" N   ARG A 295 " --> pdb=" O   ARG A 291 " (cutoff:3.500A)
      Proline residue:  A 296  - end of helix
      removed outlier: 3.505A  pdb=" N   LEU A 309 " --> pdb=" O   TYR A 305 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   GLY A 314 " --> pdb=" O   LEU A 310 " (cutoff:3.500A)
      Proline residue:  A 315  - end of helix
    Processing helix  chain 'A' and resid 342 through 347
      removed outlier: 3.740A  pdb=" N   ASN A 347 " --> pdb=" O   GLU A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 395
    Processing helix  chain 'A' and resid 397 through 402
    Processing helix  chain 'A' and resid 406 through 416
      removed outlier: 3.562A  pdb=" N   VAL A 414 " --> pdb=" O   ILE A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 428
    Processing helix  chain 'A' and resid 429 through 450
      Proline residue:  A 435  - end of helix
    Processing helix  chain 'A' and resid 451 through 462
      removed outlier: 4.207A  pdb=" N   VAL A 455 " --> pdb=" O   SER A 451 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   GLY A 456 " --> pdb=" O   SER A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 505
      removed outlier: 5.915A  pdb=" N   LYS A 500 " --> pdb=" O   LEU A 496 " (cutoff:3.500A)
      removed outlier: 6.327A  pdb=" N   LEU A 501 " --> pdb=" O   LYS A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 507 through 559
      Proline residue:  A 544  - end of helix
    Processing helix  chain 'A' and resid 564 through 607
      Proline residue:  A 581  - end of helix
      removed outlier: 4.305A  pdb=" N   LEU A 584 " --> pdb=" O   THR A 580 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   SER A 586 " --> pdb=" O   LEU A 582 " (cutoff:3.500A)
      removed outlier: 5.020A  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 785 through 791
      removed outlier: 4.482A  pdb=" N   ASP A 789 " --> pdb=" O   SER A 785 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 809 through 824
    Processing helix  chain 'A' and resid 839 through 850
    Processing helix  chain 'A' and resid 853 through 858
    Processing helix  chain 'A' and resid 868 through 874
      removed outlier: 4.046A  pdb=" N   THR A 873 " --> pdb=" O   GLN A 870 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 891 through 899
    Processing helix  chain 'A' and resid 899 through 911
    Processing helix  chain 'A' and resid 976 through 984
    Processing helix  chain 'A' and resid 988 through 1016
    Processing helix  chain 'A' and resid 1029 through 1075
      removed outlier: 4.071A  pdb=" N   VAL A1053 " --> pdb=" O   THR A1049 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   GLU A1054 " --> pdb=" O   SER A1050 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU A1074 " --> pdb=" O   ASN A1070 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1076 through 1083
      removed outlier: 3.735A  pdb=" N   PHE A1080 " --> pdb=" O   PRO A1076 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1085 through 1102
      removed outlier: 4.151A  pdb=" N   ARG A1091 " --> pdb=" O   LEU A1087 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ASP A1095 " --> pdb=" O   ARG A1091 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   THR A1096 " --> pdb=" O   PHE A1092 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1102 through 1128
    Processing helix  chain 'A' and resid 1130 through 1176
      removed outlier: 3.741A  pdb=" N   ALA A1134 " --> pdb=" O   VAL A1130 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   ALA A1136 " --> pdb=" O   LEU A1132 " (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 1238
      removed outlier: 3.578A  pdb=" N   SER A1238 " --> pdb=" O   SER A1234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1240 through 1282
      removed outlier: 3.563A  pdb=" N   VAL A1244 " --> pdb=" O   ASN A1240 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   GLY A1245 " --> pdb=" O   SER A1241 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   THR A1255 " --> pdb=" O   ALA A1251 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   ASN A1256 " --> pdb=" O   LEU A1252 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ASN A1259 " --> pdb=" O   THR A1255 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   TRP A1260 " --> pdb=" O   ASN A1256 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   ALA A1274 " --> pdb=" O   VAL A1270 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   VAL A1275 " --> pdb=" O   GLN A1271 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   LEU A1282 " --> pdb=" O   VAL A1278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1347 through 1355
      removed outlier: 3.950A  pdb=" N   PHE A1355 " --> pdb=" O   LEU A1351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1377 through 1384
      removed outlier: 3.523A  pdb=" N   ARG A1384 " --> pdb=" O   THR A1380 " (cutoff:3.500A)
    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: 3.618A  pdb=" N   GLU A1443 " --> pdb=" O   GLU A1440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1446 through 1462
      removed outlier: 4.218A  pdb=" N   ARG A1461 " --> pdb=" O   ARG A1457 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   LYS A1462 " --> pdb=" O   ALA A1458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1476 through 1491
      removed outlier: 3.729A  pdb=" N   ILE A1482 " --> pdb=" O   ALA A1478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1502 through 1507
      removed outlier: 4.086A  pdb=" N   ILE A1506 " --> pdb=" O   ARG A1502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1525 through 1532
    Processing helix  chain 'A' and resid 1535 through 1545
    Processing sheet with id=AA1, first strand: chain 'A' and resid 682 through 692
      removed outlier: 6.919A  pdb=" N   PHE A 675 " --> pdb=" O   THR A 683 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   SER A 685 " --> pdb=" O   GLY A 673 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   GLY A 673 " --> pdb=" O   SER A 685 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   ILE A 687 " --> pdb=" O   THR A 671 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   THR A 671 " --> pdb=" O   ILE A 687 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   ILE A 689 " --> pdb=" O   LYS A 669 " (cutoff:3.500A)
      removed outlier: 4.794A  pdb=" N   LYS A 669 " --> pdb=" O   ILE A 689 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ILE A 691 " --> pdb=" O   ALA A 667 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   GLY A 673 " --> pdb=" O   GLU A 722 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   GLU A 722 " --> pdb=" O   GLY A 673 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   PHE A 675 " --> pdb=" O   THR A 720 " (cutoff:3.500A)
      removed outlier: 7.179A  pdb=" N   THR A 720 " --> pdb=" O   PHE A 675 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 748 through 751
      removed outlier: 6.592A  pdb=" N   VAL A 829 " --> pdb=" O   VAL A 863 " (cutoff:3.500A)
      removed outlier: 7.779A  pdb=" N   VAL A 865 " --> pdb=" O   VAL A 829 " (cutoff:3.500A)
      removed outlier: 7.311A  pdb=" N   LEU A 831 " --> pdb=" O   VAL A 865 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   THR A 697 " --> pdb=" O   LEU A 864 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   ILE A 878 " --> pdb=" O   GLU A 889 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   GLU A 889 " --> pdb=" O   ILE A 878 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   ALA A 880 " --> pdb=" O   LEU A 887 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1328 through 1332
      removed outlier: 5.367A  pdb=" N   VAL A1328 " --> pdb=" O   ASP A1312 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   LEU A1313 " --> pdb=" O   ASP A1363 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   ASP A1363 " --> pdb=" O   LEU A1313 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   VAL A1315 " --> pdb=" O   ILE A1361 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   ILE A1361 " --> pdb=" O   VAL A1315 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1386 through 1388
      removed outlier: 6.890A  pdb=" N   SER A1386 " --> pdb=" O   ILE A1467 " (cutoff:3.500A)
      removed outlier: 7.727A  pdb=" N   ASP A1469 " --> pdb=" O   SER A1386 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   ILE A1388 " --> pdb=" O   ASP A1469 " (cutoff:3.500A)
      removed outlier: 6.182A  pdb=" N   LEU A1466 " --> pdb=" O   VAL A1497 " (cutoff:3.500A)
      removed outlier: 7.268A  pdb=" N   ILE A1499 " --> pdb=" O   LEU A1466 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   MET A1468 " --> pdb=" O   ILE A1499 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   VAL A1338 " --> pdb=" O   THR A1498 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   LYS A1337 " --> pdb=" O   LEU A1511 " (cutoff:3.500A)
      removed outlier: 8.065A  pdb=" N   ILE A1513 " --> pdb=" O   LYS A1337 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   GLY A1339 " --> pdb=" O   ILE A1513 " (cutoff:3.500A)
      removed outlier: 7.629A  pdb=" N   MET A1515 " --> pdb=" O   GLY A1339 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   CYS A1341 " --> pdb=" O   MET A1515 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   VAL A1512 " --> pdb=" O   TYR A1523 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   TYR A1523 " --> pdb=" O   VAL A1512 " (cutoff:3.500A)
      removed outlier: 7.086A  pdb=" N   VAL A1514 " --> pdb=" O   LEU A1521 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1397 through 1398

    626 hydrogen bonds defined for protein.
    1845 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.71

  Time building geometry restraints manager: 2.82 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1844
        1.33 -     1.45: 2044
        1.45 -     1.57: 5217
        1.57 -     1.70: 6
        1.70 -     1.82: 74
  Bond restraints: 9185
  Sorted by residual:
  bond pdb=" CAY Y01 A1601 "
       pdb=" OAW Y01 A1601 "
    ideal  model  delta    sigma   weight residual
    1.332  1.461 -0.129 2.00e-02 2.50e+03 4.14e+01
  bond pdb=" CAX Y01 A1601 "
       pdb=" OAH Y01 A1601 "
    ideal  model  delta    sigma   weight residual
    1.248  1.330 -0.082 2.00e-02 2.50e+03 1.67e+01
  bond pdb=" CA  PHE A1281 "
       pdb=" C   PHE A1281 "
    ideal  model  delta    sigma   weight residual
    1.522  1.485  0.037 1.41e-02 5.03e+03 6.75e+00
  bond pdb=" CA  VAL A1278 "
       pdb=" CB  VAL A1278 "
    ideal  model  delta    sigma   weight residual
    1.540  1.511  0.029 1.25e-02 6.40e+03 5.47e+00
  bond pdb=" CA  SER A1280 "
       pdb=" C   SER A1280 "
    ideal  model  delta    sigma   weight residual
    1.523  1.496  0.027 1.30e-02 5.92e+03 4.42e+00
  ... (remaining 9180 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.81: 12260
        1.81 -     3.62: 184
        3.62 -     5.43: 33
        5.43 -     7.23: 9
        7.23 -     9.04: 4
  Bond angle restraints: 12490
  Sorted by residual:
  angle pdb=" C5' ATP A1605 "
        pdb=" C4' ATP A1605 "
        pdb=" O4' ATP A1605 "
      ideal   model   delta    sigma   weight residual
     109.53  103.39    6.14 1.44e+00 4.84e-01 1.82e+01
  angle pdb=" N9  ATP A1605 "
        pdb=" C1' ATP A1605 "
        pdb=" O4' ATP A1605 "
      ideal   model   delta    sigma   weight residual
     108.36  103.86    4.50 1.26e+00 6.30e-01 1.28e+01
  angle pdb=" O2A ATP A1605 "
        pdb=" PA  ATP A1605 "
        pdb=" O5' ATP A1605 "
      ideal   model   delta    sigma   weight residual
     108.07  117.11   -9.04 2.65e+00 1.42e-01 1.16e+01
  angle pdb=" C3' ATP A1605 "
        pdb=" C4' ATP A1605 "
        pdb=" C5' ATP A1605 "
      ideal   model   delta    sigma   weight residual
     115.19  109.26    5.93 1.76e+00 3.23e-01 1.14e+01
  angle pdb=" C   LEU A1282 "
        pdb=" N   THR A1283 "
        pdb=" CA  THR A1283 "
      ideal   model   delta    sigma   weight residual
     122.06  115.89    6.17 1.86e+00 2.89e-01 1.10e+01
  ... (remaining 12485 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.66: 5348
       27.66 -    55.33: 150
       55.33 -    82.99: 17
       82.99 -   110.65: 1
      110.65 -   138.31: 1
  Dihedral angle restraints: 5517
    sinusoidal: 2185
      harmonic: 3332
  Sorted by residual:
  dihedral pdb=" O2A ADP A1602 "
           pdb=" O3A ADP A1602 "
           pdb=" PA  ADP A1602 "
           pdb=" PB  ADP A1602 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   78.31 -138.31     1      2.00e+01 2.50e-03 4.19e+01
  dihedral pdb=" O1B ADP A1602 "
           pdb=" O3A ADP A1602 "
           pdb=" PB  ADP A1602 "
           pdb=" PA  ADP A1602 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   17.53  -77.53     1      2.00e+01 2.50e-03 1.88e+01
  dihedral pdb=" CA  ILE A 416 "
           pdb=" C   ILE A 416 "
           pdb=" N   GLU A 417 "
           pdb=" CA  GLU A 417 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.08  -17.92     0      5.00e+00 4.00e-02 1.28e+01
  ... (remaining 5514 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 1300
       0.061 -    0.121: 168
       0.121 -    0.182: 20
       0.182 -    0.242: 3
       0.242 -    0.303: 3
  Chirality restraints: 1494
  Sorted by residual:
  chirality pdb=" C4' ATP A1605 "
            pdb=" C3' ATP A1605 "
            pdb=" C5' ATP A1605 "
            pdb=" O4' ATP A1605 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.80    0.30 2.00e-01 2.50e+01 2.30e+00
  chirality pdb=" CA  PHE A1281 "
            pdb=" N   PHE A1281 "
            pdb=" C   PHE A1281 "
            pdb=" CB  PHE A1281 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.96e+00
  chirality pdb=" CBB Y01 A1601 "
            pdb=" CAC Y01 A1601 "
            pdb=" CAO Y01 A1601 "
            pdb=" CBE Y01 A1601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.58    2.33    0.24 2.00e-01 2.50e+01 1.50e+00
  ... (remaining 1491 not shown)

  Planarity restraints: 1527
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 851 "   -0.011 2.00e-02 2.50e+03   2.22e-02 4.94e+00
        pdb=" C   ILE A 851 "    0.038 2.00e-02 2.50e+03
        pdb=" O   ILE A 851 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   LEU A 852 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 848 "   -0.009 2.00e-02 2.50e+03   1.88e-02 3.54e+00
        pdb=" C   GLN A 848 "    0.033 2.00e-02 2.50e+03
        pdb=" O   GLN A 848 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   GLU A 849 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 543 "   -0.025 5.00e-02 4.00e+02   3.73e-02 2.23e+00
        pdb=" N   PRO A 544 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A 544 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 544 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1524 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 32
        2.62 -     3.19: 8467
        3.19 -     3.76: 14100
        3.76 -     4.33: 19747
        4.33 -     4.90: 32483
  Nonbonded interactions: 74829
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN A 753 "
            pdb="MG    MG A1603 "
     model   vdw
     2.052 2.170
  nonbonded pdb=" OG  SER A 708 "
            pdb="MG    MG A1603 "
     model   vdw
     2.072 2.170
  nonbonded pdb=" O1B ADP A1602 "
            pdb="MG    MG A1604 "
     model   vdw
     2.121 2.170
  nonbonded pdb=" NZ  LYS A 503 "
            pdb=" OE2 GLU A 508 "
     model   vdw
     2.352 3.120
  nonbonded pdb=" OE2 GLU A 717 "
            pdb=" NH2 ARG A1182 "
     model   vdw
     2.356 3.120
  ... (remaining 74824 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.070
  Set scattering table:                    0.070
  Process input model:                     24.630
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.129   9185  Z= 0.239
  Angle     :  0.607   9.042  12490  Z= 0.316
  Chirality :  0.044   0.303   1494
  Planarity :  0.004   0.037   1527
  Dihedral  : 12.838 138.314   3359
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  :  3.96 %
    Favored  : 95.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.25), residues: 1133
  helix:  1.66 (0.19), residues: 747
  sheet: -0.21 (0.61), residues: 60
  loop : -0.31 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 423 
 HIS   0.003   0.001   HIS A1065 
 PHE   0.006   0.001   PHE A 424 
 TYR   0.007   0.001   TYR A1523 
 ARG   0.002   0.000   ARG A1413 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 232
  time to evaluate  : 1.051 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  289 MET cc_start: 0.9174 (mtm) cc_final: 0.8761 (mtp)
REVERT: A  539 MET cc_start: 0.8834 (mmt) cc_final: 0.8436 (mmm)
REVERT: A  718 MET cc_start: 0.8589 (ptt) cc_final: 0.8231 (ptp)
REVERT: A  792 LEU cc_start: 0.8963 (mt) cc_final: 0.8653 (tt)
REVERT: A  833 ASP cc_start: 0.8146 (t0) cc_final: 0.7568 (t70)
REVERT: A  849 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7751 (mt-10)
REVERT: A 1047 LEU cc_start: 0.8667 (tp) cc_final: 0.8324 (tp)
REVERT: A 1192 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7374 (mp10)
REVERT: A 1205 TYR cc_start: 0.7453 (t80) cc_final: 0.7238 (t80)
REVERT: A 1259 ASN cc_start: 0.8189 (t0) cc_final: 0.7980 (t0)
REVERT: A 1470 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6468 (mt-10)
REVERT: A 1502 ARG cc_start: 0.7294 (mtm110) cc_final: 0.6704 (ttp80)
  outliers start: 9
  outliers final: 2
  residues processed: 238
  average time/residue: 0.2441
  time to fit residues: 77.4426
Evaluate side-chains
  113 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 110
  time to evaluate  : 1.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  387 MET
Chi-restraints excluded: chain A residue 1192 GLN
Chi-restraints excluded: chain A residue 1379 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.9980
   chunk 86 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 29 optimal weight:    5.9990
   chunk 58 optimal weight:    4.9990
   chunk 46 optimal weight:    3.9990
   chunk 89 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 54 optimal weight:    6.9990
   chunk 66 optimal weight:    2.9990
   chunk 103 optimal weight:    5.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 367 GLN
A 437 GLN
A 576 HIS
A 841 HIS
A 911 ASN
A1402 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.114312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.089942 restraints weight = 14665.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.3073 rms_B_bonded: 2.55
r_work: 0.2936 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.2910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   9185  Z= 0.358
  Angle     :  0.642   9.553  12490  Z= 0.322
  Chirality :  0.044   0.173   1494
  Planarity :  0.004   0.040   1527
  Dihedral  :  8.509 134.997   1343
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 11.47 %
    Favored  : 85.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.26 (0.25), residues: 1133
  helix:  2.15 (0.18), residues: 757
  sheet:  0.72 (0.63), residues: 69
  loop :  0.11 (0.36), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 980 
 HIS   0.004   0.001   HIS A1102 
 PHE   0.015   0.002   PHE A 293 
 TYR   0.014   0.002   TYR A1523 
 ARG   0.004   0.001   ARG A1112 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 107
  time to evaluate  : 1.030 
Fit side-chains
REVERT: A  289 MET cc_start: 0.9248 (mtm) cc_final: 0.8986 (mtp)
REVERT: A  422 MET cc_start: 0.7844 (ttp) cc_final: 0.7601 (ttm)
REVERT: A  440 MET cc_start: 0.8563 (mmm) cc_final: 0.7994 (mtm)
REVERT: A  487 GLU cc_start: 0.8414 (tt0) cc_final: 0.8139 (tp30)
REVERT: A  748 VAL cc_start: 0.8936 (OUTLIER) cc_final: 0.8731 (m)
REVERT: A  833 ASP cc_start: 0.8453 (t0) cc_final: 0.7716 (t70)
REVERT: A  849 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7522 (mt-10)
REVERT: A  993 MET cc_start: 0.8522 (ttp) cc_final: 0.8251 (ttp)
REVERT: A 1192 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7269 (mp10)
REVERT: A 1319 ASN cc_start: 0.7700 (m-40) cc_final: 0.7270 (m-40)
REVERT: A 1502 ARG cc_start: 0.6974 (mtm110) cc_final: 0.6524 (ttp80)
  outliers start: 26
  outliers final: 16
  residues processed: 127
  average time/residue: 0.2239
  time to fit residues: 40.2424
Evaluate side-chains
  100 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 82
  time to evaluate  : 1.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  387 MET
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  806 ILE
Chi-restraints excluded: chain A residue  843 SER
Chi-restraints excluded: chain A residue  895 ILE
Chi-restraints excluded: chain A residue 1052 THR
Chi-restraints excluded: chain A residue 1121 ILE
Chi-restraints excluded: chain A residue 1162 SER
Chi-restraints excluded: chain A residue 1192 GLN
Chi-restraints excluded: chain A residue 1226 ILE
Chi-restraints excluded: chain A residue 1254 ILE
Chi-restraints excluded: chain A residue 1315 VAL
Chi-restraints excluded: chain A residue 1379 HIS
Chi-restraints excluded: chain A residue 1482 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 69 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 103 optimal weight:    0.0470
   chunk 47 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9980
   chunk 78 optimal weight:    0.6980
   chunk 87 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   overall best weight:    0.6278

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

Flipped N/Q/H residues before XYZ refinement:
A 509 HIS
A1090 ASN
A1264 ASN
A1311 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.118104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.094636 restraints weight = 14681.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3146 rms_B_bonded: 2.49
r_work: 0.3009 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.3353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9185  Z= 0.167
  Angle     :  0.509   8.056  12490  Z= 0.258
  Chirality :  0.039   0.199   1494
  Planarity :  0.003   0.048   1527
  Dihedral  :  8.265 130.847   1343
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 12.93 %
    Favored  : 84.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.73 (0.25), residues: 1133
  helix:  2.57 (0.18), residues: 762
  sheet:  0.67 (0.60), residues: 75
  loop :  0.10 (0.37), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 980 
 HIS   0.003   0.001   HIS A1065 
 PHE   0.014   0.001   PHE A 356 
 TYR   0.009   0.001   TYR A1523 
 ARG   0.002   0.000   ARG A1263 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 119
  time to evaluate  : 1.036 
Fit side-chains
   revert: symmetry clash
REVERT: A  278 HIS cc_start: 0.5850 (m170) cc_final: 0.5570 (m170)
REVERT: A  289 MET cc_start: 0.9221 (mtm) cc_final: 0.8944 (mtp)
REVERT: A  422 MET cc_start: 0.7736 (ttp) cc_final: 0.7530 (ttm)
REVERT: A  440 MET cc_start: 0.8523 (mmm) cc_final: 0.8036 (mtm)
REVERT: A  487 GLU cc_start: 0.8349 (tt0) cc_final: 0.8099 (tp30)
REVERT: A  849 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7436 (mt-10)
REVERT: A 1055 TRP cc_start: 0.8538 (t-100) cc_final: 0.8116 (t-100)
REVERT: A 1159 LEU cc_start: 0.8622 (tp) cc_final: 0.8415 (tp)
REVERT: A 1192 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7078 (mp10)
REVERT: A 1194 MET cc_start: 0.9058 (tmm) cc_final: 0.8340 (tmm)
REVERT: A 1248 LEU cc_start: 0.8776 (mm) cc_final: 0.8390 (mm)
REVERT: A 1281 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.7405 (t80)
REVERT: A 1289 TYR cc_start: 0.8427 (m-80) cc_final: 0.8200 (m-80)
REVERT: A 1381 LEU cc_start: 0.8592 (tp) cc_final: 0.8387 (tt)
REVERT: A 1502 ARG cc_start: 0.6957 (mtm110) cc_final: 0.6518 (ttp80)
REVERT: A 1517 ARG cc_start: 0.8591 (mtm180) cc_final: 0.8332 (mtm180)
  outliers start: 22
  outliers final: 10
  residues processed: 135
  average time/residue: 0.2017
  time to fit residues: 39.2162
Evaluate side-chains
  106 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  387 MET
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  806 ILE
Chi-restraints excluded: chain A residue 1052 THR
Chi-restraints excluded: chain A residue 1192 GLN
Chi-restraints excluded: chain A residue 1216 GLU
Chi-restraints excluded: chain A residue 1281 PHE
Chi-restraints excluded: chain A residue 1315 VAL
Chi-restraints excluded: chain A residue 1379 HIS
Chi-restraints excluded: chain A residue 1408 LYS
Chi-restraints excluded: chain A residue 1430 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 57 optimal weight:    6.9990
   chunk 70 optimal weight:    2.9990
   chunk 107 optimal weight:    5.9990
   chunk 95 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 47 optimal weight:    0.7980
   chunk 42 optimal weight:    3.9990
   chunk 106 optimal weight:    3.9990
   overall best weight:    1.3386

-------------------------------------------------------------------------------
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 = 0.3457 r_free = 0.3457 target = 0.115478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.091738 restraints weight = 14811.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.3099 rms_B_bonded: 2.48
r_work: 0.2962 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.3711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9185  Z= 0.238
  Angle     :  0.537   9.158  12490  Z= 0.267
  Chirality :  0.041   0.196   1494
  Planarity :  0.003   0.050   1527
  Dihedral  :  8.131 134.885   1343
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 14.08 %
    Favored  : 83.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.67 (0.25), residues: 1133
  helix:  2.49 (0.19), residues: 764
  sheet:  0.74 (0.61), residues: 75
  loop :  0.13 (0.37), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1055 
 HIS   0.004   0.001   HIS A1065 
 PHE   0.011   0.001   PHE A1190 
 TYR   0.013   0.001   TYR A1205 
 ARG   0.002   0.000   ARG A 381 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 99
  time to evaluate  : 1.005 
Fit side-chains
REVERT: A  289 MET cc_start: 0.9278 (mtm) cc_final: 0.8996 (mtp)
REVERT: A  422 MET cc_start: 0.7823 (ttp) cc_final: 0.7595 (ttm)
REVERT: A  434 MET cc_start: 0.8726 (mtp) cc_final: 0.8402 (mtt)
REVERT: A  440 MET cc_start: 0.8594 (mmm) cc_final: 0.8137 (mtm)
REVERT: A  487 GLU cc_start: 0.8400 (tt0) cc_final: 0.8112 (tp30)
REVERT: A  698 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8503 (mtp)
REVERT: A  843 SER cc_start: 0.9309 (OUTLIER) cc_final: 0.8955 (p)
REVERT: A  993 MET cc_start: 0.8046 (ttp) cc_final: 0.7845 (ttp)
REVERT: A 1055 TRP cc_start: 0.8559 (t-100) cc_final: 0.8307 (t-100)
REVERT: A 1192 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7225 (mp10)
REVERT: A 1216 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7797 (mt-10)
REVERT: A 1248 LEU cc_start: 0.8761 (mm) cc_final: 0.8290 (mm)
REVERT: A 1502 ARG cc_start: 0.6999 (mtm110) cc_final: 0.6579 (ttp80)
REVERT: A 1517 ARG cc_start: 0.8566 (mtm180) cc_final: 0.8300 (mtm180)
  outliers start: 25
  outliers final: 16
  residues processed: 117
  average time/residue: 0.1978
  time to fit residues: 33.2280
Evaluate side-chains
  106 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 86
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  572 LEU
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  698 MET
Chi-restraints excluded: chain A residue  700 VAL
Chi-restraints excluded: chain A residue  806 ILE
Chi-restraints excluded: chain A residue  843 SER
Chi-restraints excluded: chain A residue  895 ILE
Chi-restraints excluded: chain A residue  989 LEU
Chi-restraints excluded: chain A residue 1052 THR
Chi-restraints excluded: chain A residue 1162 SER
Chi-restraints excluded: chain A residue 1192 GLN
Chi-restraints excluded: chain A residue 1205 TYR
Chi-restraints excluded: chain A residue 1216 GLU
Chi-restraints excluded: chain A residue 1280 SER
Chi-restraints excluded: chain A residue 1315 VAL
Chi-restraints excluded: chain A residue 1379 HIS
Chi-restraints excluded: chain A residue 1430 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 102 optimal weight:    5.9990
   chunk 73 optimal weight:    4.9990
   chunk 25 optimal weight:    0.8980
   chunk 77 optimal weight:    0.5980
   chunk 45 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9990
   chunk 92 optimal weight:    0.5980
   chunk 38 optimal weight:    6.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A 702 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.116144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.092315 restraints weight = 14703.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.3124 rms_B_bonded: 2.51
r_work: 0.2984 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.3941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9185  Z= 0.200
  Angle     :  0.517  10.511  12490  Z= 0.259
  Chirality :  0.040   0.196   1494
  Planarity :  0.004   0.073   1527
  Dihedral  :  7.817 136.693   1340
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 15.54 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.72 (0.25), residues: 1133
  helix:  2.52 (0.18), residues: 764
  sheet:  0.90 (0.61), residues: 75
  loop :  0.15 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1055 
 HIS   0.004   0.001   HIS A1065 
 PHE   0.011   0.001   PHE A1149 
 TYR   0.012   0.001   TYR A1523 
 ARG   0.006   0.000   ARG A1542 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.967 
Fit side-chains
REVERT: A  289 MET cc_start: 0.9310 (mtm) cc_final: 0.9042 (mtp)
REVERT: A  422 MET cc_start: 0.7764 (ttp) cc_final: 0.7524 (ttm)
REVERT: A  440 MET cc_start: 0.8623 (mmm) cc_final: 0.8278 (ttm)
REVERT: A  487 GLU cc_start: 0.8365 (tt0) cc_final: 0.8144 (tp30)
REVERT: A  590 ARG cc_start: 0.7919 (ttm-80) cc_final: 0.7687 (ttp80)
REVERT: A  698 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8483 (mtp)
REVERT: A  843 SER cc_start: 0.9331 (OUTLIER) cc_final: 0.9015 (p)
REVERT: A  983 THR cc_start: 0.8710 (m) cc_final: 0.8428 (p)
REVERT: A 1055 TRP cc_start: 0.8558 (t-100) cc_final: 0.8346 (t-100)
REVERT: A 1192 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7177 (mp10)
REVERT: A 1194 MET cc_start: 0.9132 (tmm) cc_final: 0.8291 (tmm)
REVERT: A 1216 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7858 (mt-10)
REVERT: A 1248 LEU cc_start: 0.8754 (mm) cc_final: 0.8336 (mm)
REVERT: A 1281 PHE cc_start: 0.7896 (OUTLIER) cc_final: 0.7434 (t80)
REVERT: A 1398 SER cc_start: 0.8880 (m) cc_final: 0.8415 (t)
REVERT: A 1502 ARG cc_start: 0.6944 (mtm110) cc_final: 0.6578 (ttp80)
REVERT: A 1517 ARG cc_start: 0.8612 (mtm180) cc_final: 0.8337 (mtm180)
  outliers start: 21
  outliers final: 13
  residues processed: 119
  average time/residue: 0.2047
  time to fit residues: 34.6785
Evaluate side-chains
  104 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 86
  time to evaluate  : 1.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  698 MET
Chi-restraints excluded: chain A residue  700 VAL
Chi-restraints excluded: chain A residue  806 ILE
Chi-restraints excluded: chain A residue  843 SER
Chi-restraints excluded: chain A residue  895 ILE
Chi-restraints excluded: chain A residue 1007 ILE
Chi-restraints excluded: chain A residue 1162 SER
Chi-restraints excluded: chain A residue 1192 GLN
Chi-restraints excluded: chain A residue 1216 GLU
Chi-restraints excluded: chain A residue 1281 PHE
Chi-restraints excluded: chain A residue 1315 VAL
Chi-restraints excluded: chain A residue 1379 HIS
Chi-restraints excluded: chain A residue 1430 LEU
Chi-restraints excluded: chain A residue 1474 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 97 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 54 optimal weight:    3.9990
   chunk 91 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0770
   chunk 52 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 17 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.7940

-------------------------------------------------------------------------------
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 = 0.3480 r_free = 0.3480 target = 0.117199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.093447 restraints weight = 14708.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 2.51
r_work: 0.3002 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.4146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9185  Z= 0.175
  Angle     :  0.512  11.662  12490  Z= 0.251
  Chirality :  0.039   0.194   1494
  Planarity :  0.003   0.052   1527
  Dihedral  :  7.555 138.228   1340
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 16.58 %
    Favored  : 81.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.80 (0.25), residues: 1133
  helix:  2.58 (0.18), residues: 764
  sheet:  0.96 (0.60), residues: 75
  loop :  0.17 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1055 
 HIS   0.004   0.001   HIS A1001 
 PHE   0.013   0.001   PHE A 552 
 TYR   0.010   0.001   TYR A1523 
 ARG   0.004   0.000   ARG A1542 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 90
  time to evaluate  : 0.945 
Fit side-chains
REVERT: A  289 MET cc_start: 0.9311 (mtm) cc_final: 0.9028 (mtp)
REVERT: A  422 MET cc_start: 0.7701 (ttp) cc_final: 0.7440 (ttm)
REVERT: A  440 MET cc_start: 0.8607 (mmm) cc_final: 0.8296 (ttm)
REVERT: A  487 GLU cc_start: 0.8368 (tt0) cc_final: 0.8150 (tp30)
REVERT: A  590 ARG cc_start: 0.7910 (ttm-80) cc_final: 0.7696 (ttp80)
REVERT: A  698 MET cc_start: 0.8783 (mtm) cc_final: 0.8468 (mtp)
REVERT: A  843 SER cc_start: 0.9333 (OUTLIER) cc_final: 0.9048 (p)
REVERT: A  983 THR cc_start: 0.8795 (m) cc_final: 0.8562 (p)
REVERT: A 1192 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7152 (mp10)
REVERT: A 1194 MET cc_start: 0.9130 (tmm) cc_final: 0.8250 (tmm)
REVERT: A 1216 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7904 (mt-10)
REVERT: A 1248 LEU cc_start: 0.8738 (mm) cc_final: 0.8349 (mm)
REVERT: A 1281 PHE cc_start: 0.7771 (OUTLIER) cc_final: 0.7447 (t80)
REVERT: A 1398 SER cc_start: 0.8837 (m) cc_final: 0.8402 (t)
REVERT: A 1502 ARG cc_start: 0.6949 (mtm110) cc_final: 0.6411 (ttp80)
REVERT: A 1517 ARG cc_start: 0.8599 (mtm180) cc_final: 0.8316 (mtm180)
  outliers start: 20
  outliers final: 16
  residues processed: 107
  average time/residue: 0.2062
  time to fit residues: 31.8527
Evaluate side-chains
  105 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 85
  time to evaluate  : 0.994 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  387 MET
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  700 VAL
Chi-restraints excluded: chain A residue  806 ILE
Chi-restraints excluded: chain A residue  843 SER
Chi-restraints excluded: chain A residue  989 LEU
Chi-restraints excluded: chain A residue  990 LEU
Chi-restraints excluded: chain A residue 1007 ILE
Chi-restraints excluded: chain A residue 1192 GLN
Chi-restraints excluded: chain A residue 1205 TYR
Chi-restraints excluded: chain A residue 1216 GLU
Chi-restraints excluded: chain A residue 1281 PHE
Chi-restraints excluded: chain A residue 1315 VAL
Chi-restraints excluded: chain A residue 1379 HIS
Chi-restraints excluded: chain A residue 1430 LEU
Chi-restraints excluded: chain A residue 1474 SER
Chi-restraints excluded: chain A residue 1514 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 85 optimal weight:    4.9990
   chunk 61 optimal weight:    0.8980
   chunk 1 optimal weight:    0.8980
   chunk 106 optimal weight:    3.9990
   chunk 84 optimal weight:    7.9990
   chunk 108 optimal weight:    1.9990
   chunk 113 optimal weight:    4.9990
   chunk 112 optimal weight:    8.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
A1090 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.115691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.091899 restraints weight = 14845.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 2.52
r_work: 0.2978 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.4254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9185  Z= 0.210
  Angle     :  0.523  11.050  12490  Z= 0.258
  Chirality :  0.040   0.198   1494
  Planarity :  0.003   0.053   1527
  Dihedral  :  7.540 142.772   1340
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 16.79 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.78 (0.25), residues: 1133
  helix:  2.53 (0.18), residues: 764
  sheet:  1.26 (0.63), residues: 69
  loop :  0.18 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A1055 
 HIS   0.004   0.001   HIS A1001 
 PHE   0.012   0.001   PHE A1149 
 TYR   0.016   0.001   TYR A1009 
 ARG   0.004   0.000   ARG A1263 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 86
  time to evaluate  : 0.979 
Fit side-chains
REVERT: A  289 MET cc_start: 0.9324 (mtm) cc_final: 0.9050 (mtp)
REVERT: A  422 MET cc_start: 0.7734 (ttp) cc_final: 0.7457 (ttm)
REVERT: A  440 MET cc_start: 0.8635 (mmm) cc_final: 0.8291 (ttm)
REVERT: A  487 GLU cc_start: 0.8397 (tt0) cc_final: 0.8138 (tp30)
REVERT: A  549 LEU cc_start: 0.8169 (tt) cc_final: 0.7943 (tp)
REVERT: A  590 ARG cc_start: 0.7925 (ttm-80) cc_final: 0.7668 (ttp80)
REVERT: A  698 MET cc_start: 0.8836 (mtm) cc_final: 0.8502 (mtp)
REVERT: A  843 SER cc_start: 0.9320 (OUTLIER) cc_final: 0.9052 (p)
REVERT: A  983 THR cc_start: 0.8798 (m) cc_final: 0.8582 (p)
REVERT: A 1192 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7396 (mp10)
REVERT: A 1215 LEU cc_start: 0.8350 (tp) cc_final: 0.7900 (tt)
REVERT: A 1216 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7965 (mt-10)
REVERT: A 1248 LEU cc_start: 0.8713 (mm) cc_final: 0.8304 (mm)
REVERT: A 1281 PHE cc_start: 0.7801 (OUTLIER) cc_final: 0.7419 (t80)
REVERT: A 1398 SER cc_start: 0.8883 (m) cc_final: 0.8425 (t)
REVERT: A 1414 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8224 (mt)
REVERT: A 1502 ARG cc_start: 0.7003 (mtm110) cc_final: 0.6481 (ttp80)
REVERT: A 1517 ARG cc_start: 0.8608 (mtm180) cc_final: 0.8341 (mtm180)
  outliers start: 25
  outliers final: 18
  residues processed: 108
  average time/residue: 0.1849
  time to fit residues: 29.5062
Evaluate side-chains
  105 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 82
  time to evaluate  : 1.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  387 MET
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  700 VAL
Chi-restraints excluded: chain A residue  806 ILE
Chi-restraints excluded: chain A residue  843 SER
Chi-restraints excluded: chain A residue  895 ILE
Chi-restraints excluded: chain A residue  990 LEU
Chi-restraints excluded: chain A residue 1007 ILE
Chi-restraints excluded: chain A residue 1192 GLN
Chi-restraints excluded: chain A residue 1205 TYR
Chi-restraints excluded: chain A residue 1216 GLU
Chi-restraints excluded: chain A residue 1253 THR
Chi-restraints excluded: chain A residue 1280 SER
Chi-restraints excluded: chain A residue 1281 PHE
Chi-restraints excluded: chain A residue 1315 VAL
Chi-restraints excluded: chain A residue 1379 HIS
Chi-restraints excluded: chain A residue 1414 LEU
Chi-restraints excluded: chain A residue 1430 LEU
Chi-restraints excluded: chain A residue 1474 SER
Chi-restraints excluded: chain A residue 1514 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 16 optimal weight:    0.7980
   chunk 106 optimal weight:    4.9990
   chunk 8 optimal weight:   10.0000
   chunk 39 optimal weight:    1.9990
   chunk 103 optimal weight:    3.9990
   chunk 76 optimal weight:    0.7980
   chunk 47 optimal weight:    0.4980
   chunk 83 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A1090 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.117648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.093824 restraints weight = 14816.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 2.51
r_work: 0.3008 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.4375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9185  Z= 0.162
  Angle     :  0.497  10.492  12490  Z= 0.245
  Chirality :  0.039   0.195   1494
  Planarity :  0.003   0.054   1527
  Dihedral  :  7.405 142.171   1340
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 17.31 %
    Favored  : 80.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.91 (0.25), residues: 1133
  helix:  2.65 (0.19), residues: 764
  sheet:  1.33 (0.63), residues: 68
  loop :  0.17 (0.35), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 423 
 HIS   0.003   0.000   HIS A1065 
 PHE   0.011   0.001   PHE A1149 
 TYR   0.016   0.001   TYR A1009 
 ARG   0.004   0.000   ARG A1263 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 93
  time to evaluate  : 0.956 
Fit side-chains
REVERT: A  289 MET cc_start: 0.9297 (mtm) cc_final: 0.9027 (mtp)
REVERT: A  422 MET cc_start: 0.7644 (ttp) cc_final: 0.7367 (ttm)
REVERT: A  440 MET cc_start: 0.8647 (mmm) cc_final: 0.8280 (ttm)
REVERT: A  487 GLU cc_start: 0.8381 (tt0) cc_final: 0.8133 (tp30)
REVERT: A  549 LEU cc_start: 0.8139 (tt) cc_final: 0.7929 (tp)
REVERT: A  698 MET cc_start: 0.8783 (mtm) cc_final: 0.8464 (mtp)
REVERT: A  797 ASP cc_start: 0.8739 (OUTLIER) cc_final: 0.8497 (t70)
REVERT: A  806 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8335 (pt)
REVERT: A  843 SER cc_start: 0.9310 (OUTLIER) cc_final: 0.9063 (p)
REVERT: A  983 THR cc_start: 0.8793 (m) cc_final: 0.8575 (p)
REVERT: A 1192 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7204 (mp10)
REVERT: A 1215 LEU cc_start: 0.8323 (tp) cc_final: 0.7890 (tt)
REVERT: A 1216 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7897 (mt-10)
REVERT: A 1248 LEU cc_start: 0.8713 (mm) cc_final: 0.8335 (mm)
REVERT: A 1281 PHE cc_start: 0.7804 (OUTLIER) cc_final: 0.7429 (t80)
REVERT: A 1398 SER cc_start: 0.8810 (m) cc_final: 0.8377 (t)
REVERT: A 1440 GLU cc_start: 0.7953 (tt0) cc_final: 0.7474 (pm20)
REVERT: A 1502 ARG cc_start: 0.6965 (mtm110) cc_final: 0.6538 (ttp-110)
REVERT: A 1517 ARG cc_start: 0.8580 (mtm180) cc_final: 0.8315 (mtm180)
  outliers start: 23
  outliers final: 15
  residues processed: 113
  average time/residue: 0.1997
  time to fit residues: 32.4121
Evaluate side-chains
  106 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 85
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  387 MET
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  700 VAL
Chi-restraints excluded: chain A residue  797 ASP
Chi-restraints excluded: chain A residue  806 ILE
Chi-restraints excluded: chain A residue  843 SER
Chi-restraints excluded: chain A residue  990 LEU
Chi-restraints excluded: chain A residue 1007 ILE
Chi-restraints excluded: chain A residue 1192 GLN
Chi-restraints excluded: chain A residue 1205 TYR
Chi-restraints excluded: chain A residue 1216 GLU
Chi-restraints excluded: chain A residue 1253 THR
Chi-restraints excluded: chain A residue 1281 PHE
Chi-restraints excluded: chain A residue 1315 VAL
Chi-restraints excluded: chain A residue 1379 HIS
Chi-restraints excluded: chain A residue 1430 LEU
Chi-restraints excluded: chain A residue 1474 SER
Chi-restraints excluded: chain A residue 1514 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 4 optimal weight:    0.4980
   chunk 54 optimal weight:    0.8980
   chunk 41 optimal weight:   10.0000
   chunk 82 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 7 optimal weight:    7.9990
   chunk 76 optimal weight:    0.9980
   chunk 111 optimal weight:    5.9990
   chunk 106 optimal weight:    0.9990
   chunk 96 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A1090 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.117239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.093542 restraints weight = 14762.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 2.51
r_work: 0.3001 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.4453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9185  Z= 0.174
  Angle     :  0.509  11.862  12490  Z= 0.248
  Chirality :  0.039   0.194   1494
  Planarity :  0.003   0.055   1527
  Dihedral  :  7.375 142.035   1340
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 17.21 %
    Favored  : 80.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.96 (0.25), residues: 1133
  helix:  2.67 (0.18), residues: 765
  sheet:  1.39 (0.63), residues: 68
  loop :  0.20 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 423 
 HIS   0.004   0.001   HIS A1065 
 PHE   0.011   0.001   PHE A1149 
 TYR   0.016   0.001   TYR A1009 
 ARG   0.004   0.000   ARG A1263 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 91
  time to evaluate  : 0.988 
Fit side-chains
REVERT: A  289 MET cc_start: 0.9314 (mtm) cc_final: 0.9026 (mtp)
REVERT: A  422 MET cc_start: 0.7660 (ttp) cc_final: 0.7370 (ttm)
REVERT: A  440 MET cc_start: 0.8626 (mmm) cc_final: 0.8276 (ttm)
REVERT: A  487 GLU cc_start: 0.8385 (tt0) cc_final: 0.8141 (tp30)
REVERT: A  549 LEU cc_start: 0.8167 (tt) cc_final: 0.7942 (tp)
REVERT: A  698 MET cc_start: 0.8794 (mtm) cc_final: 0.8477 (mtp)
REVERT: A  797 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8540 (t70)
REVERT: A  806 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8252 (pt)
REVERT: A  843 SER cc_start: 0.9302 (OUTLIER) cc_final: 0.9066 (p)
REVERT: A 1192 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.7239 (mp10)
REVERT: A 1215 LEU cc_start: 0.8375 (tp) cc_final: 0.7916 (tt)
REVERT: A 1216 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7902 (mt-10)
REVERT: A 1248 LEU cc_start: 0.8711 (mm) cc_final: 0.8333 (mm)
REVERT: A 1281 PHE cc_start: 0.7752 (OUTLIER) cc_final: 0.7440 (t80)
REVERT: A 1398 SER cc_start: 0.8831 (m) cc_final: 0.8396 (t)
REVERT: A 1414 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8186 (mt)
REVERT: A 1440 GLU cc_start: 0.7938 (tt0) cc_final: 0.7489 (pm20)
REVERT: A 1502 ARG cc_start: 0.6974 (mtm110) cc_final: 0.6554 (ttp-110)
REVERT: A 1517 ARG cc_start: 0.8559 (mtm180) cc_final: 0.8301 (mtm180)
  outliers start: 22
  outliers final: 15
  residues processed: 111
  average time/residue: 0.1873
  time to fit residues: 30.7728
Evaluate side-chains
  106 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 84
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  387 MET
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  700 VAL
Chi-restraints excluded: chain A residue  797 ASP
Chi-restraints excluded: chain A residue  806 ILE
Chi-restraints excluded: chain A residue  843 SER
Chi-restraints excluded: chain A residue 1007 ILE
Chi-restraints excluded: chain A residue 1121 ILE
Chi-restraints excluded: chain A residue 1192 GLN
Chi-restraints excluded: chain A residue 1205 TYR
Chi-restraints excluded: chain A residue 1216 GLU
Chi-restraints excluded: chain A residue 1253 THR
Chi-restraints excluded: chain A residue 1281 PHE
Chi-restraints excluded: chain A residue 1315 VAL
Chi-restraints excluded: chain A residue 1379 HIS
Chi-restraints excluded: chain A residue 1414 LEU
Chi-restraints excluded: chain A residue 1430 LEU
Chi-restraints excluded: chain A residue 1474 SER
Chi-restraints excluded: chain A residue 1514 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 82 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0770
   chunk 52 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   chunk 95 optimal weight:    1.9990
   chunk 86 optimal weight:    0.8980
   chunk 22 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 56 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.7542

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

Flipped N/Q/H residues before XYZ refinement:
A1090 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.117728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.093922 restraints weight = 14853.461|
|-----------------------------------------------------------------------------|
r_work (start): 0.3139 rms_B_bonded: 2.53
r_work: 0.3000 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.4528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9185  Z= 0.168
  Angle     :  0.503  11.079  12490  Z= 0.247
  Chirality :  0.039   0.187   1494
  Planarity :  0.003   0.055   1527
  Dihedral  :  7.334 141.006   1340
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 17.62 %
    Favored  : 79.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.96 (0.25), residues: 1133
  helix:  2.67 (0.18), residues: 764
  sheet:  1.47 (0.63), residues: 68
  loop :  0.19 (0.35), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 423 
 HIS   0.004   0.001   HIS A1065 
 PHE   0.011   0.001   PHE A1149 
 TYR   0.017   0.001   TYR A1009 
 ARG   0.004   0.000   ARG A1263 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 90
  time to evaluate  : 0.961 
Fit side-chains
REVERT: A  289 MET cc_start: 0.9270 (mtm) cc_final: 0.9013 (mtp)
REVERT: A  422 MET cc_start: 0.7606 (ttp) cc_final: 0.7316 (ttm)
REVERT: A  440 MET cc_start: 0.8544 (mmm) cc_final: 0.8203 (ttm)
REVERT: A  487 GLU cc_start: 0.8397 (tt0) cc_final: 0.8146 (tp30)
REVERT: A  549 LEU cc_start: 0.8166 (tt) cc_final: 0.7943 (tp)
REVERT: A  698 MET cc_start: 0.8943 (mtm) cc_final: 0.8600 (mtp)
REVERT: A  797 ASP cc_start: 0.8740 (OUTLIER) cc_final: 0.8539 (t70)
REVERT: A  806 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8323 (pt)
REVERT: A  843 SER cc_start: 0.9294 (OUTLIER) cc_final: 0.9071 (p)
REVERT: A 1192 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7209 (mp10)
REVERT: A 1215 LEU cc_start: 0.8355 (tp) cc_final: 0.7898 (tt)
REVERT: A 1216 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7945 (mt-10)
REVERT: A 1248 LEU cc_start: 0.8686 (mm) cc_final: 0.8257 (mm)
REVERT: A 1281 PHE cc_start: 0.7592 (OUTLIER) cc_final: 0.7358 (t80)
REVERT: A 1398 SER cc_start: 0.8812 (m) cc_final: 0.8379 (t)
REVERT: A 1414 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8166 (mt)
REVERT: A 1440 GLU cc_start: 0.7909 (tt0) cc_final: 0.7471 (pm20)
REVERT: A 1502 ARG cc_start: 0.6972 (mtm110) cc_final: 0.6602 (ttp-110)
REVERT: A 1517 ARG cc_start: 0.8558 (mtm180) cc_final: 0.8219 (mtm180)
  outliers start: 24
  outliers final: 16
  residues processed: 111
  average time/residue: 0.1949
  time to fit residues: 31.7482
Evaluate side-chains
  109 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 86
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  387 MET
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  700 VAL
Chi-restraints excluded: chain A residue  797 ASP
Chi-restraints excluded: chain A residue  806 ILE
Chi-restraints excluded: chain A residue  843 SER
Chi-restraints excluded: chain A residue 1007 ILE
Chi-restraints excluded: chain A residue 1121 ILE
Chi-restraints excluded: chain A residue 1162 SER
Chi-restraints excluded: chain A residue 1192 GLN
Chi-restraints excluded: chain A residue 1205 TYR
Chi-restraints excluded: chain A residue 1216 GLU
Chi-restraints excluded: chain A residue 1253 THR
Chi-restraints excluded: chain A residue 1281 PHE
Chi-restraints excluded: chain A residue 1315 VAL
Chi-restraints excluded: chain A residue 1379 HIS
Chi-restraints excluded: chain A residue 1414 LEU
Chi-restraints excluded: chain A residue 1430 LEU
Chi-restraints excluded: chain A residue 1474 SER
Chi-restraints excluded: chain A residue 1514 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 107 optimal weight:    4.9990
   chunk 98 optimal weight:    3.9990
   chunk 27 optimal weight:    0.4980
   chunk 17 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 62 optimal weight:    4.9990
   chunk 105 optimal weight:    1.9990
   chunk 103 optimal weight:    8.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A1090 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.117745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.093918 restraints weight = 14770.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3140 rms_B_bonded: 2.52
r_work: 0.3000 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.4586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9185  Z= 0.170
  Angle     :  0.509  11.797  12490  Z= 0.249
  Chirality :  0.039   0.198   1494
  Planarity :  0.003   0.055   1527
  Dihedral  :  7.308 140.067   1340
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 17.62 %
    Favored  : 79.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.97 (0.25), residues: 1133
  helix:  2.68 (0.18), residues: 764
  sheet:  1.56 (0.63), residues: 68
  loop :  0.18 (0.36), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 423 
 HIS   0.004   0.001   HIS A1065 
 PHE   0.010   0.001   PHE A1149 
 TYR   0.016   0.001   TYR A1009 
 ARG   0.004   0.000   ARG A1263 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3386.73 seconds
wall clock time: 61 minutes 17.67 seconds (3677.67 seconds total)