Starting phenix.real_space_refine
on Wed Feb  4 07:20:18 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y1m_33566/02_2026/7y1m_33566.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y1m_33566/02_2026/7y1m_33566.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y1m_33566/02_2026/7y1m_33566.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y1m_33566/02_2026/7y1m_33566.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y1m_33566/02_2026/7y1m_33566.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y1m_33566/02_2026/7y1m_33566.cif"
  }
  resolution = 3.57
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.006 sd=   0.085
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      45      5.16       5
     C    5836      2.51       5
     N    1494      2.21       5
     O    1575      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8957
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8864
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1166, 8864
          Classifications: {'peptide': 1166}
          Incomplete info: {'truncation_to_alanine': 94}
          Link IDs: {'PTRANS': 35, 'TRANS': 1130}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 331
          Unresolved non-hydrogen angles: 411
          Unresolved non-hydrogen dihedrals: 258
          Unresolved non-hydrogen chiralities: 17
          Planarities with less than four sites: {'ARG:plan': 9, 'GLU:plan': 19, 'ASP:plan': 21, 'GLN:plan1': 4, 'ASN:plan1': 3, 'TYR:plan': 1, 'PHE:plan': 2}
          Unresolved non-hydrogen planarities: 227
    Chain: "A"
      Number of atoms: 93
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 93
          Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1, 'BJX': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
  Time building chain proxies: 2.28, per 1000 atoms: 0.25
  Number of scatterers: 8957
  At special positions: 0
  Unit cell: (70.89, 105.918, 130.104, 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      45     16.00
     P       5     15.00
     Mg      2     11.99
     O    1575      8.00
     N    1494      7.00
     C    5836      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.59
  Conformation dependent library (CDL) restraints added in 339.5 milliseconds
  

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2200

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 6 sheets defined
      72.9% alpha, 6.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 216 through 227
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 231 through 238
    Processing helix  chain 'A' and resid 252 through 255
    Processing helix  chain 'A' and resid 256 through 273
    Processing helix  chain 'A' and resid 284 through 312
      removed outlier: 6.440A  pdb=" N   ARG A 295 " --> pdb=" O   ARG A 291 " (cutoff:3.500A)
      Proline residue:  A 296  - end of helix
    Processing helix  chain 'A' and resid 312 through 324
      removed outlier: 3.962A  pdb=" N   LEU A 316 " --> pdb=" O   PHE A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 347
      removed outlier: 3.768A  pdb=" N   GLU A 346 " --> pdb=" O   GLU A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 394
    Processing helix  chain 'A' and resid 405 through 416
    Processing helix  chain 'A' and resid 416 through 428
    Processing helix  chain 'A' and resid 429 through 449
      Proline residue:  A 435  - end of helix
    Processing helix  chain 'A' and resid 452 through 462
      removed outlier: 4.198A  pdb=" N   GLY A 456 " --> pdb=" O   SER A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 497
      removed outlier: 3.757A  pdb=" N   ILE A 466 " --> pdb=" O   LEU A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 505
    Processing helix  chain 'A' and resid 507 through 559
      removed outlier: 3.510A  pdb=" N   THR A 518 " --> pdb=" O   SER A 514 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   THR A 528 " --> pdb=" O   SER A 524 " (cutoff:3.500A)
      Proline residue:  A 544  - end of helix
    Processing helix  chain 'A' and resid 564 through 607
      removed outlier: 4.330A  pdb=" N   THR A 580 " --> pdb=" O   HIS A 576 " (cutoff:3.500A)
      Proline residue:  A 581  - end of helix
      removed outlier: 4.422A  pdb=" N   SER A 586 " --> pdb=" O   LEU A 582 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   THR A 587 " --> pdb=" O   PHE A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 706 through 716
    Processing helix  chain 'A' and resid 761 through 768
    Processing helix  chain 'A' and resid 773 through 785
    Processing helix  chain 'A' and resid 786 through 793
    Processing helix  chain 'A' and resid 809 through 824
    Processing helix  chain 'A' and resid 839 through 850
    Processing helix  chain 'A' and resid 853 through 858
      removed outlier: 3.933A  pdb=" N   ASP A 858 " --> pdb=" O   PHE A 854 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 871 through 875
    Processing helix  chain 'A' and resid 891 through 899
    Processing helix  chain 'A' and resid 899 through 912
      removed outlier: 3.543A  pdb=" N   LEU A 909 " --> pdb=" O   HIS A 905 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ARG A 912 " --> pdb=" O   THR A 908 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 974 through 985
      removed outlier: 4.189A  pdb=" N   GLY A 985 " --> pdb=" O   TYR A 981 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 986 through 1017
      removed outlier: 4.050A  pdb=" N   GLU A1017 " --> pdb=" O   THR A1013 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1028 through 1074
    Processing helix  chain 'A' and resid 1076 through 1083
      removed outlier: 3.723A  pdb=" N   PHE A1080 " --> pdb=" O   PRO A1076 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1084 through 1102
      removed outlier: 3.664A  pdb=" N   ILE A1088 " --> pdb=" O   PRO A1084 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ASP A1095 " --> pdb=" O   ARG A1091 " (cutoff:3.500A)
      removed outlier: 4.458A  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: 4.160A  pdb=" N   ALA A1134 " --> pdb=" O   VAL A1130 " (cutoff:3.500A)
      Proline residue:  A1137  - end of helix
      removed outlier: 3.657A  pdb=" N   VAL A1140 " --> pdb=" O   ALA A1136 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   GLU A1158 " --> pdb=" O   LYS A1154 " (cutoff:3.500A)
      Proline residue:  A1166  - end of helix
    Processing helix  chain 'A' and resid 1177 through 1185
    Processing helix  chain 'A' and resid 1186 through 1237
    Processing helix  chain 'A' and resid 1240 through 1283
      removed outlier: 3.913A  pdb=" N   THR A1255 " --> pdb=" O   ALA A1251 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ASN A1256 " --> pdb=" O   LEU A1252 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   TYR A1257 " --> pdb=" O   THR A1253 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   ASN A1259 " --> pdb=" O   THR A1255 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   TRP A1260 " --> pdb=" O   ASN A1256 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   VAL A1262 " --> pdb=" O   LEU A1258 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ALA A1274 " --> pdb=" O   VAL A1270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1294 through 1298
    Processing helix  chain 'A' and resid 1301 through 1305
      removed outlier: 3.546A  pdb=" N   GLN A1304 " --> pdb=" O   HIS A1301 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   GLU A1305 " --> pdb=" O   TRP A1302 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1301 through 1305'
    Processing helix  chain 'A' and resid 1347 through 1357
      removed outlier: 3.761A  pdb=" N   LEU A1351 " --> pdb=" O   GLY A1347 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   SER A1352 " --> pdb=" O   LYS A1348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1377 through 1384
    Processing helix  chain 'A' and resid 1399 through 1404
    Processing helix  chain 'A' and resid 1410 through 1421
      removed outlier: 3.729A  pdb=" N   LEU A1414 " --> pdb=" O   THR A1410 " (cutoff:3.500A)
    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: 3.856A  pdb=" N   GLU A1443 " --> pdb=" O   GLU A1440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1446 through 1462
    Processing helix  chain 'A' and resid 1476 through 1490
    Processing helix  chain 'A' and resid 1502 through 1508
      removed outlier: 4.276A  pdb=" N   ILE A1506 " --> pdb=" O   ARG A1502 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   THR A1508 " --> pdb=" O   HIS A1504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1525 through 1530
    Processing helix  chain 'A' and resid 1536 through 1541
    Processing sheet with id=AA1, first strand: chain 'A' and resid 690 through 691
      removed outlier: 3.717A  pdb=" N   ILE A 668 " --> pdb=" O   ILE A 691 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   THR A 671 " --> pdb=" O   LYS A 724 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   LYS A 724 " --> pdb=" O   THR A 671 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 684 through 687
      removed outlier: 3.611A  pdb=" N   ASN A 686 " --> pdb=" O   GLY A 673 " (cutoff:3.500A)
      removed outlier: 6.272A  pdb=" N   GLY A 673 " --> pdb=" O   ASN A 686 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 748 through 751
      removed outlier: 6.184A  pdb=" N   ALA A 749 " --> pdb=" O   PHE A 830 " (cutoff:3.500A)
      removed outlier: 7.484A  pdb=" N   ASP A 832 " --> pdb=" O   ALA A 749 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   ALA A 751 " --> pdb=" O   ASP A 832 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   LEU A 696 " --> pdb=" O   TRP A 877 " (cutoff:3.500A)
      removed outlier: 7.781A  pdb=" N   ILE A 879 " --> pdb=" O   LEU A 696 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   MET A 698 " --> pdb=" O   ILE A 879 " (cutoff:3.500A)
      removed outlier: 7.604A  pdb=" N   MET A 881 " --> pdb=" O   MET A 698 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   VAL A 700 " --> pdb=" O   MET A 881 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1325 through 1332
      removed outlier: 5.923A  pdb=" N   LYS A1326 " --> pdb=" O   VAL A1315 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   VAL A1315 " --> pdb=" O   LYS A1326 " (cutoff:3.500A)
      removed outlier: 7.435A  pdb=" N   ALA A1330 " --> pdb=" O   HIS A1311 " (cutoff:3.500A)
      removed outlier: 5.363A  pdb=" N   HIS A1311 " --> pdb=" O   ALA A1330 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   ILE A1332 " --> pdb=" O   LYS A1309 " (cutoff:3.500A)
      removed outlier: 5.378A  pdb=" N   LYS A1309 " --> pdb=" O   ILE A1332 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   ILE A1308 " --> pdb=" O   ILE A1368 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   ILE A1368 " --> pdb=" O   ILE A1308 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   ILE A1310 " --> pdb=" O   ILE A1366 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   ILE A1366 " --> pdb=" O   ILE A1310 " (cutoff:3.500A)
      removed outlier: 7.250A  pdb=" N   ASP A1312 " --> pdb=" O   GLY A1364 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   GLY A1364 " --> pdb=" O   ASP A1312 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   CYS A1314 " --> pdb=" O   PHE A1362 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1386 through 1388
      removed outlier: 6.487A  pdb=" N   SER A1386 " --> pdb=" O   ILE A1467 " (cutoff:3.500A)
      removed outlier: 7.964A  pdb=" N   ASP A1469 " --> pdb=" O   SER A1386 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   ILE A1388 " --> pdb=" O   ASP A1469 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   LEU A1466 " --> pdb=" O   VAL A1497 " (cutoff:3.500A)
      removed outlier: 7.647A  pdb=" N   ILE A1499 " --> pdb=" O   LEU A1466 " (cutoff:3.500A)
      removed outlier: 6.321A  pdb=" N   MET A1468 " --> pdb=" O   ILE A1499 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LEU A1511 " --> pdb=" O   LYS A1337 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   CYS A1341 " --> pdb=" O   ILE A1513 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1397 through 1398

    631 hydrogen bonds defined for protein.
    1857 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.81

  Time building geometry restraints manager: 0.78 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1371
        1.31 -     1.43: 2421
        1.43 -     1.56: 5262
        1.56 -     1.68: 16
        1.68 -     1.81: 72
  Bond restraints: 9142
  Sorted by residual:
  bond pdb=" C16 BJX A1604 "
       pdb=" N1  BJX A1604 "
    ideal  model  delta    sigma   weight residual
    1.344  1.449 -0.105 2.00e-02 2.50e+03 2.73e+01
  bond pdb=" CA  GLN A 323 "
       pdb=" C   GLN A 323 "
    ideal  model  delta    sigma   weight residual
    1.524  1.588 -0.064 1.27e-02 6.20e+03 2.58e+01
  bond pdb=" CA  ILE A 321 "
       pdb=" C   ILE A 321 "
    ideal  model  delta    sigma   weight residual
    1.524  1.575 -0.051 1.22e-02 6.72e+03 1.76e+01
  bond pdb=" CA  GLY A 320 "
       pdb=" C   GLY A 320 "
    ideal  model  delta    sigma   weight residual
    1.516  1.559 -0.043 1.09e-02 8.42e+03 1.54e+01
  bond pdb=" CA  VAL A 322 "
       pdb=" C   VAL A 322 "
    ideal  model  delta    sigma   weight residual
    1.523  1.573 -0.049 1.27e-02 6.20e+03 1.50e+01
  ... (remaining 9137 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 12242
        1.56 -     3.12: 141
        3.12 -     4.68: 46
        4.68 -     6.24: 16
        6.24 -     7.81: 5
  Bond angle restraints: 12450
  Sorted by residual:
  angle pdb=" C   ILE A 321 "
        pdb=" CA  ILE A 321 "
        pdb=" CB  ILE A 321 "
      ideal   model   delta    sigma   weight residual
     111.97  105.44    6.53 1.28e+00 6.10e-01 2.60e+01
  angle pdb=" C   VAL A 322 "
        pdb=" CA  VAL A 322 "
        pdb=" CB  VAL A 322 "
      ideal   model   delta    sigma   weight residual
     112.14  105.83    6.31 1.35e+00 5.49e-01 2.18e+01
  angle pdb=" N   VAL A 322 "
        pdb=" CA  VAL A 322 "
        pdb=" CB  VAL A 322 "
      ideal   model   delta    sigma   weight residual
     110.54  115.92   -5.38 1.36e+00 5.41e-01 1.56e+01
  angle pdb=" N   GLN A 323 "
        pdb=" CA  GLN A 323 "
        pdb=" CB  GLN A 323 "
      ideal   model   delta    sigma   weight residual
     110.01  115.58   -5.57 1.45e+00 4.76e-01 1.48e+01
  angle pdb=" N   ILE A 321 "
        pdb=" CA  ILE A 321 "
        pdb=" CB  ILE A 321 "
      ideal   model   delta    sigma   weight residual
     110.55  114.76   -4.21 1.17e+00 7.31e-01 1.29e+01
  ... (remaining 12445 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.81: 5313
       31.81 -    63.61: 81
       63.61 -    95.42: 11
       95.42 -   127.23: 3
      127.23 -   159.03: 3
  Dihedral angle restraints: 5411
    sinusoidal: 2017
      harmonic: 3394
  Sorted by residual:
  dihedral pdb=" O1B ADP A1605 "
           pdb=" O3A ADP A1605 "
           pdb=" PB  ADP A1605 "
           pdb=" PA  ADP A1605 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  158.34  141.66     1      2.00e+01 2.50e-03 4.28e+01
  dihedral pdb=" O2A ADP A1605 "
           pdb=" O3A ADP A1605 "
           pdb=" PA  ADP A1605 "
           pdb=" PB  ADP A1605 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   49.28 -109.28     1      2.00e+01 2.50e-03 3.19e+01
  dihedral pdb=" C5' ADP A1605 "
           pdb=" O5' ADP A1605 "
           pdb=" PA  ADP A1605 "
           pdb=" O2A ADP A1605 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   47.81 -107.80     1      2.00e+01 2.50e-03 3.13e+01
  ... (remaining 5408 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 1365
       0.065 -    0.129: 128
       0.129 -    0.194: 6
       0.194 -    0.258: 2
       0.258 -    0.323: 3
  Chirality restraints: 1504
  Sorted by residual:
  chirality pdb=" CA  ILE A 321 "
            pdb=" N   ILE A 321 "
            pdb=" C   ILE A 321 "
            pdb=" CB  ILE A 321 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.76   -0.32 2.00e-01 2.50e+01 2.60e+00
  chirality pdb=" C2' ATP A1603 "
            pdb=" C1' ATP A1603 "
            pdb=" C3' ATP A1603 "
            pdb=" O2' ATP A1603 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.97    0.29 2.00e-01 2.50e+01 2.16e+00
  chirality pdb=" C3' ATP A1603 "
            pdb=" C2' ATP A1603 "
            pdb=" C4' ATP A1603 "
            pdb=" O3' ATP A1603 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.92    0.28 2.00e-01 2.50e+01 1.98e+00
  ... (remaining 1501 not shown)

  Planarity restraints: 1513
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 580 "    0.035 5.00e-02 4.00e+02   5.29e-02 4.48e+00
        pdb=" N   PRO A 581 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO A 581 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 581 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 752 "   -0.007 2.00e-02 2.50e+03   1.31e-02 1.72e+00
        pdb=" C   ALA A 752 "    0.023 2.00e-02 2.50e+03
        pdb=" O   ALA A 752 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   GLN A 753 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 505 "    0.006 2.00e-02 2.50e+03   1.30e-02 1.68e+00
        pdb=" C   TYR A 505 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   TYR A 505 "    0.008 2.00e-02 2.50e+03
        pdb=" N   ALA A 506 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1510 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1662
        2.77 -     3.30: 9507
        3.30 -     3.83: 14884
        3.83 -     4.37: 16655
        4.37 -     4.90: 29806
  Nonbonded interactions: 72514
  Sorted by model distance:
  nonbonded pdb="MG    MG A1602 "
            pdb=" O1G ATP A1603 "
     model   vdw
     2.234 2.170
  nonbonded pdb=" N   GLU A 889 "
            pdb=" OE1 GLU A 889 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" OG  SER A1349 "
            pdb=" O1A ADP A1605 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" OE1 GLN A 753 "
            pdb="MG    MG A1602 "
     model   vdw
     2.284 2.170
  nonbonded pdb=" NH1 ARG A1400 "
            pdb=" OD1 ASP A1435 "
     model   vdw
     2.288 3.120
  ... (remaining 72509 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.990
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
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   0.105   9142  Z= 0.208
  Angle     :  0.526   7.805  12450  Z= 0.279
  Chirality :  0.040   0.323   1504
  Planarity :  0.003   0.053   1513
  Dihedral  : 12.727 159.034   3211
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  2.74 %
    Favored  : 96.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.52 (0.25), residues: 1150
  helix:  2.26 (0.19), residues: 790
  sheet:  0.77 (0.62), residues: 73
  loop :  0.32 (0.36), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1461 
 TYR   0.011   0.001   TYR A 505 
 PHE   0.011   0.001   PHE A1149 
 TRP   0.007   0.001   TRP A1214 
 HIS   0.004   0.001   HIS A1065 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 9142)
  covalent geometry    : angle       0.52636 (12450)
  hydrogen bonds       : bond        0.12350 (  631)
  hydrogen bonds       : angle       5.19950 ( 1857)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 143
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
REVERT: A  225 LYS cc_start: 0.8145 (mtmt) cc_final: 0.7415 (tptt)
REVERT: A  284 SER cc_start: 0.8518 (t) cc_final: 0.8231 (m)
REVERT: A  351 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7900 (mp)
REVERT: A  405 MET cc_start: 0.7217 (mmm) cc_final: 0.6848 (mmt)
REVERT: A  687 ILE cc_start: 0.7740 (mt) cc_final: 0.7534 (mt)
REVERT: A  698 MET cc_start: 0.8240 (mtm) cc_final: 0.8028 (mtp)
REVERT: A  993 MET cc_start: 0.7777 (ttm) cc_final: 0.7556 (ttm)
REVERT: A 1083 THR cc_start: 0.9034 (m) cc_final: 0.8528 (p)
REVERT: A 1333 LYS cc_start: 0.8363 (mtmm) cc_final: 0.7955 (tmtt)
REVERT: A 1445 PHE cc_start: 0.8392 (m-80) cc_final: 0.8150 (m-80)
  outliers start: 3
  outliers final: 0
  residues processed: 146
  average time/residue: 0.0989
  time to fit residues: 20.2981
Evaluate side-chains
  104 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  351 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:   20.0000
   chunk 113 optimal weight:    5.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.0870
   chunk 51 optimal weight:    7.9990
   chunk 100 optimal weight:    0.9990
   overall best weight:    0.9962

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

Flipped N/Q/H residues before XYZ refinement:
** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 814 GLN
A1028 GLN
A1402 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.150816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.117482 restraints weight = 12976.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.117061 restraints weight = 9004.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.118058 restraints weight = 6736.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.118164 restraints weight = 5313.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.119294 restraints weight = 5031.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.1271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9142  Z= 0.160
  Angle     :  0.611  10.221  12450  Z= 0.294
  Chirality :  0.041   0.170   1504
  Planarity :  0.004   0.047   1513
  Dihedral  : 10.729 141.036   1302
  Min Nonbonded Distance : 1.877

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  8.22 %
    Favored  : 90.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.63 (0.25), residues: 1150
  helix:  2.28 (0.18), residues: 801
  sheet:  0.66 (0.60), residues: 68
  loop :  0.52 (0.37), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1357 
 TYR   0.015   0.001   TYR A 505 
 PHE   0.015   0.001   PHE A 552 
 TRP   0.009   0.001   TRP A1214 
 HIS   0.005   0.001   HIS A1001 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 9142)
  covalent geometry    : angle       0.61143 (12450)
  hydrogen bonds       : bond        0.04802 (  631)
  hydrogen bonds       : angle       4.26294 ( 1857)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 116
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
REVERT: A  225 LYS cc_start: 0.8139 (mtmt) cc_final: 0.7383 (tptt)
REVERT: A  284 SER cc_start: 0.8672 (t) cc_final: 0.8384 (m)
REVERT: A  405 MET cc_start: 0.7020 (mmm) cc_final: 0.6723 (mmt)
REVERT: A 1083 THR cc_start: 0.8915 (m) cc_final: 0.8568 (p)
REVERT: A 1123 MET cc_start: 0.8434 (tpp) cc_final: 0.7755 (tpp)
REVERT: A 1333 LYS cc_start: 0.8289 (mtmm) cc_final: 0.8008 (tmtt)
REVERT: A 1334 PRO cc_start: 0.7746 (Cg_endo) cc_final: 0.6533 (Cg_exo)
REVERT: A 1445 PHE cc_start: 0.8426 (m-80) cc_final: 0.8199 (m-80)
  outliers start: 13
  outliers final: 8
  residues processed: 125
  average time/residue: 0.0879
  time to fit residues: 15.8021
Evaluate side-chains
  109 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  432 TRP
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  761 THR
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue 1072 ILE
Chi-restraints excluded: chain A residue 1355 PHE
Chi-restraints excluded: chain A residue 1403 LEU
Chi-restraints excluded: chain A residue 1437 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 99 optimal weight:    1.9990
   chunk 49 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 43 optimal weight:    5.9990
   chunk 59 optimal weight:    7.9990
   chunk 93 optimal weight:   10.0000
   chunk 12 optimal weight:    2.9990
   chunk 85 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 107 optimal weight:    1.9990
   chunk 108 optimal weight:    0.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.148505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.115293 restraints weight = 12943.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.114371 restraints weight = 9284.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.115068 restraints weight = 7415.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.115429 restraints weight = 6097.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.115798 restraints weight = 5502.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.1572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   9142  Z= 0.193
  Angle     :  0.603   7.437  12450  Z= 0.291
  Chirality :  0.041   0.170   1504
  Planarity :  0.004   0.046   1513
  Dihedral  : 10.412 141.812   1300
  Min Nonbonded Distance : 1.894

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  :  9.54 %
    Favored  : 88.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.52 (0.24), residues: 1150
  helix:  2.21 (0.18), residues: 800
  sheet:  0.68 (0.60), residues: 69
  loop :  0.43 (0.36), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 820 
 TYR   0.018   0.001   TYR A 228 
 PHE   0.017   0.001   PHE A 552 
 TRP   0.010   0.001   TRP A1214 
 HIS   0.006   0.001   HIS A1065 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 9142)
  covalent geometry    : angle       0.60322 (12450)
  hydrogen bonds       : bond        0.04769 (  631)
  hydrogen bonds       : angle       4.18735 ( 1857)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
REVERT: A  225 LYS cc_start: 0.8161 (mtmt) cc_final: 0.7382 (tptt)
REVERT: A  239 HIS cc_start: 0.8370 (OUTLIER) cc_final: 0.7652 (m90)
REVERT: A  284 SER cc_start: 0.8731 (t) cc_final: 0.8363 (m)
REVERT: A  405 MET cc_start: 0.7069 (mmm) cc_final: 0.6784 (mmt)
REVERT: A 1083 THR cc_start: 0.8812 (m) cc_final: 0.8517 (p)
REVERT: A 1123 MET cc_start: 0.8508 (tpp) cc_final: 0.7758 (tpp)
REVERT: A 1289 TYR cc_start: 0.7730 (m-80) cc_final: 0.7397 (m-80)
REVERT: A 1333 LYS cc_start: 0.8288 (mtmm) cc_final: 0.8032 (tmtt)
REVERT: A 1334 PRO cc_start: 0.7688 (Cg_endo) cc_final: 0.6693 (Cg_exo)
  outliers start: 19
  outliers final: 13
  residues processed: 123
  average time/residue: 0.0933
  time to fit residues: 16.7201
Evaluate side-chains
  115 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 HIS
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  432 TRP
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  761 THR
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue 1072 ILE
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1162 SER
Chi-restraints excluded: chain A residue 1355 PHE
Chi-restraints excluded: chain A residue 1399 ILE
Chi-restraints excluded: chain A residue 1403 LEU
Chi-restraints excluded: chain A residue 1437 THR
Chi-restraints excluded: chain A residue 1483 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 85 optimal weight:    0.9980
   chunk 100 optimal weight:   20.0000
   chunk 105 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 79 optimal weight:    0.6980
   chunk 84 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 493 ASN
** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.146456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.115610 restraints weight = 13229.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.115328 restraints weight = 12943.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.116563 restraints weight = 11080.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.116726 restraints weight = 8185.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.117082 restraints weight = 6884.203|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.1827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9142  Z= 0.135
  Angle     :  0.558   7.779  12450  Z= 0.266
  Chirality :  0.040   0.170   1504
  Planarity :  0.004   0.044   1513
  Dihedral  : 10.039 131.482   1300
  Min Nonbonded Distance : 1.911

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 11.07 %
    Favored  : 86.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.67 (0.24), residues: 1150
  helix:  2.36 (0.18), residues: 803
  sheet:  0.62 (0.59), residues: 71
  loop :  0.40 (0.37), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 774 
 TYR   0.015   0.001   TYR A 228 
 PHE   0.013   0.001   PHE A 552 
 TRP   0.007   0.001   TRP A1214 
 HIS   0.004   0.001   HIS A1065 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 9142)
  covalent geometry    : angle       0.55772 (12450)
  hydrogen bonds       : bond        0.04380 (  631)
  hydrogen bonds       : angle       4.00451 ( 1857)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  225 LYS cc_start: 0.8026 (mtmt) cc_final: 0.7175 (tptt)
REVERT: A  239 HIS cc_start: 0.8297 (OUTLIER) cc_final: 0.7458 (m90)
REVERT: A  284 SER cc_start: 0.8718 (t) cc_final: 0.8378 (m)
REVERT: A  405 MET cc_start: 0.7088 (mmm) cc_final: 0.6805 (mmt)
REVERT: A  707 LYS cc_start: 0.8000 (ptpp) cc_final: 0.7770 (mtmm)
REVERT: A  910 MET cc_start: 0.7062 (mpp) cc_final: 0.5548 (ttt)
REVERT: A 1083 THR cc_start: 0.8829 (m) cc_final: 0.8542 (p)
REVERT: A 1123 MET cc_start: 0.8543 (tpp) cc_final: 0.7913 (tpp)
REVERT: A 1128 THR cc_start: 0.8901 (m) cc_final: 0.8240 (p)
REVERT: A 1322 LYS cc_start: 0.8672 (ttpt) cc_final: 0.8058 (tptt)
REVERT: A 1333 LYS cc_start: 0.8228 (mtmm) cc_final: 0.8017 (tmtt)
REVERT: A 1334 PRO cc_start: 0.7619 (Cg_endo) cc_final: 0.6604 (Cg_exo)
  outliers start: 19
  outliers final: 13
  residues processed: 125
  average time/residue: 0.0905
  time to fit residues: 16.2684
Evaluate side-chains
  117 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 HIS
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  432 TRP
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  524 SER
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue 1072 ILE
Chi-restraints excluded: chain A residue 1219 THR
Chi-restraints excluded: chain A residue 1355 PHE
Chi-restraints excluded: chain A residue 1399 ILE
Chi-restraints excluded: chain A residue 1403 LEU
Chi-restraints excluded: chain A residue 1437 THR
Chi-restraints excluded: chain A residue 1512 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 100 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 99 optimal weight:    7.9990
   chunk 29 optimal weight:    0.7980
   chunk 60 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 115 optimal weight:    8.9990
   chunk 75 optimal weight:    4.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.146975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.115732 restraints weight = 13071.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.114214 restraints weight = 14641.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.115298 restraints weight = 12684.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.117135 restraints weight = 8885.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.116998 restraints weight = 7956.142|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.2001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9142  Z= 0.132
  Angle     :  0.540   8.102  12450  Z= 0.257
  Chirality :  0.039   0.165   1504
  Planarity :  0.003   0.043   1513
  Dihedral  :  9.807 129.329   1300
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 11.40 %
    Favored  : 86.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.79 (0.25), residues: 1150
  helix:  2.45 (0.18), residues: 800
  sheet:  0.79 (0.59), residues: 71
  loop :  0.41 (0.37), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1357 
 TYR   0.015   0.001   TYR A 228 
 PHE   0.013   0.001   PHE A 552 
 TRP   0.007   0.001   TRP A 906 
 HIS   0.005   0.001   HIS A1065 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 9142)
  covalent geometry    : angle       0.54029 (12450)
  hydrogen bonds       : bond        0.04228 (  631)
  hydrogen bonds       : angle       3.87778 ( 1857)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  225 LYS cc_start: 0.8059 (mtmt) cc_final: 0.7218 (tptt)
REVERT: A  239 HIS cc_start: 0.8242 (OUTLIER) cc_final: 0.7331 (m90)
REVERT: A  284 SER cc_start: 0.8763 (t) cc_final: 0.8384 (m)
REVERT: A  405 MET cc_start: 0.7031 (mmm) cc_final: 0.6753 (mmt)
REVERT: A  707 LYS cc_start: 0.8057 (ptpp) cc_final: 0.7794 (mtmm)
REVERT: A 1123 MET cc_start: 0.8512 (tpp) cc_final: 0.7894 (tpp)
REVERT: A 1128 THR cc_start: 0.8789 (m) cc_final: 0.8215 (p)
REVERT: A 1322 LYS cc_start: 0.8692 (ttpt) cc_final: 0.8057 (tptt)
REVERT: A 1334 PRO cc_start: 0.7559 (Cg_endo) cc_final: 0.6502 (Cg_exo)
  outliers start: 19
  outliers final: 14
  residues processed: 125
  average time/residue: 0.1007
  time to fit residues: 17.7567
Evaluate side-chains
  114 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 HIS
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  432 TRP
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  524 SER
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue 1072 ILE
Chi-restraints excluded: chain A residue 1146 GLN
Chi-restraints excluded: chain A residue 1219 THR
Chi-restraints excluded: chain A residue 1399 ILE
Chi-restraints excluded: chain A residue 1403 LEU
Chi-restraints excluded: chain A residue 1437 THR
Chi-restraints excluded: chain A residue 1483 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 82 optimal weight:    0.9980
   chunk 102 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   chunk 70 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 107 optimal weight:    0.9990
   chunk 85 optimal weight:    2.9990
   chunk 37 optimal weight:    7.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.150883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.118322 restraints weight = 12888.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.117410 restraints weight = 10159.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.118210 restraints weight = 7646.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.118373 restraints weight = 6199.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.119997 restraints weight = 5577.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.2156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9142  Z= 0.135
  Angle     :  0.559   8.294  12450  Z= 0.266
  Chirality :  0.039   0.172   1504
  Planarity :  0.003   0.043   1513
  Dihedral  :  9.679 128.382   1300
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 12.39 %
    Favored  : 85.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.78 (0.25), residues: 1150
  helix:  2.44 (0.18), residues: 800
  sheet:  0.75 (0.60), residues: 71
  loop :  0.42 (0.37), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 774 
 TYR   0.011   0.001   TYR A 228 
 PHE   0.013   0.001   PHE A 552 
 TRP   0.007   0.001   TRP A1214 
 HIS   0.005   0.001   HIS A1065 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 9142)
  covalent geometry    : angle       0.55927 (12450)
  hydrogen bonds       : bond        0.04208 (  631)
  hydrogen bonds       : angle       3.86306 ( 1857)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 107
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  225 LYS cc_start: 0.8143 (mtmt) cc_final: 0.7438 (tttp)
REVERT: A  239 HIS cc_start: 0.8065 (OUTLIER) cc_final: 0.7141 (m90)
REVERT: A  284 SER cc_start: 0.8746 (t) cc_final: 0.8291 (m)
REVERT: A  405 MET cc_start: 0.6856 (mmm) cc_final: 0.6559 (mmt)
REVERT: A  520 MET cc_start: 0.7371 (OUTLIER) cc_final: 0.7002 (mtp)
REVERT: A  910 MET cc_start: 0.6646 (mpp) cc_final: 0.5388 (ttt)
REVERT: A 1091 ARG cc_start: 0.7304 (mmp80) cc_final: 0.7085 (mtp85)
REVERT: A 1123 MET cc_start: 0.8357 (tpp) cc_final: 0.7728 (tpp)
REVERT: A 1128 THR cc_start: 0.8669 (m) cc_final: 0.8163 (p)
REVERT: A 1322 LYS cc_start: 0.8689 (ttpt) cc_final: 0.8068 (tptt)
REVERT: A 1376 LEU cc_start: 0.8527 (mt) cc_final: 0.8225 (mt)
REVERT: A 1445 PHE cc_start: 0.8344 (m-80) cc_final: 0.8051 (m-80)
REVERT: A 1468 MET cc_start: 0.7446 (mtt) cc_final: 0.7207 (mtt)
  outliers start: 19
  outliers final: 15
  residues processed: 122
  average time/residue: 0.0950
  time to fit residues: 16.5791
Evaluate side-chains
  115 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 HIS
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  432 TRP
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  520 MET
Chi-restraints excluded: chain A residue  524 SER
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue 1072 ILE
Chi-restraints excluded: chain A residue 1146 GLN
Chi-restraints excluded: chain A residue 1162 SER
Chi-restraints excluded: chain A residue 1219 THR
Chi-restraints excluded: chain A residue 1399 ILE
Chi-restraints excluded: chain A residue 1403 LEU
Chi-restraints excluded: chain A residue 1437 THR
Chi-restraints excluded: chain A residue 1512 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:   20.0000
   chunk 88 optimal weight:    0.9980
   chunk 76 optimal weight:    0.8980
   chunk 112 optimal weight:    8.9990
   chunk 114 optimal weight:   10.0000
   chunk 73 optimal weight:    0.6980
   chunk 85 optimal weight:    0.6980
   chunk 113 optimal weight:    6.9990
   chunk 81 optimal weight:    1.9990
   chunk 106 optimal weight:   10.0000
   chunk 17 optimal weight:    3.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 493 ASN
A 686 ASN
** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.150381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.117982 restraints weight = 13022.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.117071 restraints weight = 10115.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.118100 restraints weight = 8368.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.118841 restraints weight = 6327.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.118954 restraints weight = 5198.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.2232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9142  Z= 0.147
  Angle     :  0.573   8.375  12450  Z= 0.270
  Chirality :  0.039   0.165   1504
  Planarity :  0.003   0.043   1513
  Dihedral  :  9.573 129.470   1300
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 12.39 %
    Favored  : 85.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.77 (0.25), residues: 1150
  helix:  2.40 (0.18), residues: 804
  sheet:  0.84 (0.65), residues: 62
  loop :  0.49 (0.37), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 774 
 TYR   0.014   0.001   TYR A 228 
 PHE   0.014   0.001   PHE A 552 
 TRP   0.008   0.001   TRP A1214 
 HIS   0.005   0.001   HIS A1065 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 9142)
  covalent geometry    : angle       0.57257 (12450)
  hydrogen bonds       : bond        0.04230 (  631)
  hydrogen bonds       : angle       3.85774 ( 1857)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  225 LYS cc_start: 0.8129 (mtmt) cc_final: 0.7492 (tttp)
REVERT: A  239 HIS cc_start: 0.8164 (OUTLIER) cc_final: 0.7276 (m90)
REVERT: A  284 SER cc_start: 0.8777 (t) cc_final: 0.8321 (m)
REVERT: A  405 MET cc_start: 0.6892 (mmm) cc_final: 0.6596 (mmt)
REVERT: A  520 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.7032 (mtp)
REVERT: A  910 MET cc_start: 0.6695 (mpp) cc_final: 0.5481 (ttt)
REVERT: A 1091 ARG cc_start: 0.7360 (mmp80) cc_final: 0.7135 (mtp85)
REVERT: A 1123 MET cc_start: 0.8395 (tpp) cc_final: 0.7737 (tpp)
REVERT: A 1128 THR cc_start: 0.8667 (m) cc_final: 0.8161 (p)
REVERT: A 1322 LYS cc_start: 0.8685 (ttpt) cc_final: 0.8078 (tptt)
REVERT: A 1445 PHE cc_start: 0.8352 (m-80) cc_final: 0.8062 (m-80)
REVERT: A 1468 MET cc_start: 0.7329 (mtt) cc_final: 0.7088 (mtt)
  outliers start: 21
  outliers final: 17
  residues processed: 120
  average time/residue: 0.0893
  time to fit residues: 15.5202
Evaluate side-chains
  117 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 HIS
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  432 TRP
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  493 ASN
Chi-restraints excluded: chain A residue  520 MET
Chi-restraints excluded: chain A residue  524 SER
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  761 THR
Chi-restraints excluded: chain A residue 1072 ILE
Chi-restraints excluded: chain A residue 1146 GLN
Chi-restraints excluded: chain A residue 1162 SER
Chi-restraints excluded: chain A residue 1219 THR
Chi-restraints excluded: chain A residue 1399 ILE
Chi-restraints excluded: chain A residue 1403 LEU
Chi-restraints excluded: chain A residue 1437 THR
Chi-restraints excluded: chain A residue 1512 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   chunk 71 optimal weight:    0.8980
   chunk 76 optimal weight:    1.9990
   chunk 115 optimal weight:    8.9990
   chunk 97 optimal weight:   20.0000
   chunk 50 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0270
   chunk 42 optimal weight:    0.7980
   overall best weight:    0.7440

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

Flipped N/Q/H residues before XYZ refinement:
A 399 ASN
** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1311 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.151264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.118728 restraints weight = 12914.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.118107 restraints weight = 9813.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.119284 restraints weight = 7012.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.119527 restraints weight = 5951.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.119805 restraints weight = 5291.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.2311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9142  Z= 0.130
  Angle     :  0.587  12.683  12450  Z= 0.275
  Chirality :  0.039   0.230   1504
  Planarity :  0.003   0.042   1513
  Dihedral  :  9.468 126.598   1300
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 12.50 %
    Favored  : 85.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.81 (0.25), residues: 1150
  helix:  2.44 (0.18), residues: 804
  sheet:  0.83 (0.65), residues: 62
  loop :  0.45 (0.37), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 774 
 TYR   0.014   0.001   TYR A 505 
 PHE   0.012   0.001   PHE A 552 
 TRP   0.007   0.001   TRP A1214 
 HIS   0.004   0.001   HIS A1065 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 9142)
  covalent geometry    : angle       0.58701 (12450)
  hydrogen bonds       : bond        0.04133 (  631)
  hydrogen bonds       : angle       3.80436 ( 1857)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  225 LYS cc_start: 0.8108 (mtmt) cc_final: 0.7438 (tttp)
REVERT: A  239 HIS cc_start: 0.8045 (OUTLIER) cc_final: 0.7110 (m90)
REVERT: A  284 SER cc_start: 0.8776 (t) cc_final: 0.8314 (m)
REVERT: A  405 MET cc_start: 0.6864 (mmm) cc_final: 0.6571 (mmt)
REVERT: A  520 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.7011 (mtp)
REVERT: A  910 MET cc_start: 0.6691 (mpp) cc_final: 0.5526 (ttt)
REVERT: A 1091 ARG cc_start: 0.7369 (mmp80) cc_final: 0.7154 (mtp85)
REVERT: A 1123 MET cc_start: 0.8343 (tpp) cc_final: 0.7683 (tpp)
REVERT: A 1128 THR cc_start: 0.8618 (OUTLIER) cc_final: 0.8188 (p)
REVERT: A 1322 LYS cc_start: 0.8689 (ttpt) cc_final: 0.8067 (tptt)
  outliers start: 20
  outliers final: 16
  residues processed: 118
  average time/residue: 0.0887
  time to fit residues: 15.2520
Evaluate side-chains
  118 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 HIS
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  317 CYS
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  432 TRP
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  520 MET
Chi-restraints excluded: chain A residue  524 SER
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  761 THR
Chi-restraints excluded: chain A residue 1072 ILE
Chi-restraints excluded: chain A residue 1128 THR
Chi-restraints excluded: chain A residue 1146 GLN
Chi-restraints excluded: chain A residue 1219 THR
Chi-restraints excluded: chain A residue 1399 ILE
Chi-restraints excluded: chain A residue 1403 LEU
Chi-restraints excluded: chain A residue 1437 THR
Chi-restraints excluded: chain A residue 1483 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 48 optimal weight:    0.6980
   chunk 59 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9980
   chunk 97 optimal weight:   20.0000
   chunk 0 optimal weight:    6.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 493 ASN
** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.151408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.119025 restraints weight = 12943.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.118104 restraints weight = 9859.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.119578 restraints weight = 7717.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.119993 restraints weight = 5907.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.120077 restraints weight = 4962.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.2399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9142  Z= 0.134
  Angle     :  0.571  11.551  12450  Z= 0.268
  Chirality :  0.039   0.181   1504
  Planarity :  0.004   0.042   1513
  Dihedral  :  9.316 126.661   1300
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 12.83 %
    Favored  : 84.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.80 (0.25), residues: 1150
  helix:  2.44 (0.18), residues: 802
  sheet:  0.84 (0.66), residues: 61
  loop :  0.44 (0.37), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A1461 
 TYR   0.015   0.001   TYR A 505 
 PHE   0.027   0.001   PHE A1445 
 TRP   0.008   0.001   TRP A 906 
 HIS   0.004   0.001   HIS A1065 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 9142)
  covalent geometry    : angle       0.57130 (12450)
  hydrogen bonds       : bond        0.04107 (  631)
  hydrogen bonds       : angle       3.79219 ( 1857)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  225 LYS cc_start: 0.8082 (mtmt) cc_final: 0.7371 (tttp)
REVERT: A  239 HIS cc_start: 0.7977 (OUTLIER) cc_final: 0.6996 (m90)
REVERT: A  284 SER cc_start: 0.8763 (t) cc_final: 0.8293 (m)
REVERT: A  405 MET cc_start: 0.6918 (mmm) cc_final: 0.6620 (mmt)
REVERT: A  520 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.7001 (mtp)
REVERT: A  910 MET cc_start: 0.6729 (mpp) cc_final: 0.5600 (ttt)
REVERT: A 1123 MET cc_start: 0.8365 (tpp) cc_final: 0.7711 (tpp)
REVERT: A 1128 THR cc_start: 0.8609 (OUTLIER) cc_final: 0.8184 (p)
REVERT: A 1322 LYS cc_start: 0.8682 (ttpt) cc_final: 0.8053 (tptt)
  outliers start: 20
  outliers final: 16
  residues processed: 116
  average time/residue: 0.0914
  time to fit residues: 15.4134
Evaluate side-chains
  117 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 HIS
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  317 CYS
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  432 TRP
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  493 ASN
Chi-restraints excluded: chain A residue  520 MET
Chi-restraints excluded: chain A residue  524 SER
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  761 THR
Chi-restraints excluded: chain A residue 1072 ILE
Chi-restraints excluded: chain A residue 1128 THR
Chi-restraints excluded: chain A residue 1146 GLN
Chi-restraints excluded: chain A residue 1162 SER
Chi-restraints excluded: chain A residue 1219 THR
Chi-restraints excluded: chain A residue 1437 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 83 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 71 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 24 optimal weight:    5.9990
   chunk 11 optimal weight:    0.6980
   chunk 88 optimal weight:    0.8980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 493 ASN
** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.151582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.119020 restraints weight = 12877.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.118395 restraints weight = 9632.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.119008 restraints weight = 7184.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.119434 restraints weight = 5982.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.119546 restraints weight = 5566.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.2453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9142  Z= 0.135
  Angle     :  0.593  11.360  12450  Z= 0.275
  Chirality :  0.039   0.175   1504
  Planarity :  0.004   0.091   1513
  Dihedral  :  9.250 126.002   1300
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 12.72 %
    Favored  : 84.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.79 (0.25), residues: 1150
  helix:  2.45 (0.18), residues: 802
  sheet:  0.81 (0.67), residues: 60
  loop :  0.41 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A1091 
 TYR   0.013   0.001   TYR A 505 
 PHE   0.031   0.001   PHE A1445 
 TRP   0.007   0.001   TRP A1214 
 HIS   0.004   0.001   HIS A1001 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 9142)
  covalent geometry    : angle       0.59267 (12450)
  hydrogen bonds       : bond        0.04120 (  631)
  hydrogen bonds       : angle       3.77993 ( 1857)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 102
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
REVERT: A  225 LYS cc_start: 0.8089 (mtmt) cc_final: 0.7421 (tttp)
REVERT: A  239 HIS cc_start: 0.7971 (OUTLIER) cc_final: 0.7017 (m90)
REVERT: A  284 SER cc_start: 0.8761 (t) cc_final: 0.8294 (m)
REVERT: A  405 MET cc_start: 0.6992 (mmm) cc_final: 0.6702 (mmt)
REVERT: A  520 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.7000 (mtp)
REVERT: A  910 MET cc_start: 0.6691 (mpp) cc_final: 0.5594 (ttt)
REVERT: A 1123 MET cc_start: 0.8342 (tpp) cc_final: 0.7687 (tpp)
REVERT: A 1128 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8194 (p)
REVERT: A 1322 LYS cc_start: 0.8661 (ttpt) cc_final: 0.8033 (tptt)
REVERT: A 1376 LEU cc_start: 0.8557 (mt) cc_final: 0.8197 (mt)
  outliers start: 21
  outliers final: 16
  residues processed: 117
  average time/residue: 0.0890
  time to fit residues: 15.1251
Evaluate side-chains
  115 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 HIS
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  317 CYS
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  432 TRP
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  493 ASN
Chi-restraints excluded: chain A residue  520 MET
Chi-restraints excluded: chain A residue  524 SER
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  761 THR
Chi-restraints excluded: chain A residue 1072 ILE
Chi-restraints excluded: chain A residue 1128 THR
Chi-restraints excluded: chain A residue 1146 GLN
Chi-restraints excluded: chain A residue 1162 SER
Chi-restraints excluded: chain A residue 1219 THR
Chi-restraints excluded: chain A residue 1483 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 51 optimal weight:    0.0870
   chunk 62 optimal weight:    0.7980
   chunk 44 optimal weight:    0.0870
   chunk 53 optimal weight:    7.9990
   chunk 29 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    0.5536

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

Flipped N/Q/H residues before XYZ refinement:
** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.152571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.118807 restraints weight = 12883.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.119155 restraints weight = 8580.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.120096 restraints weight = 6308.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.120482 restraints weight = 5027.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.120586 restraints weight = 4757.264|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.2513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9142  Z= 0.121
  Angle     :  0.573  11.271  12450  Z= 0.270
  Chirality :  0.039   0.182   1504
  Planarity :  0.004   0.061   1513
  Dihedral  :  9.190 124.086   1300
  Min Nonbonded Distance : 1.981

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 13.38 %
    Favored  : 84.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.82 (0.25), residues: 1150
  helix:  2.47 (0.18), residues: 802
  sheet:  0.69 (0.67), residues: 60
  loop :  0.43 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1091 
 TYR   0.022   0.001   TYR A 903 
 PHE   0.027   0.001   PHE A1445 
 TRP   0.009   0.001   TRP A 906 
 HIS   0.003   0.001   HIS A1001 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 9142)
  covalent geometry    : angle       0.57265 (12450)
  hydrogen bonds       : bond        0.04048 (  631)
  hydrogen bonds       : angle       3.76624 ( 1857)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1448.17 seconds
wall clock time: 25 minutes 55.52 seconds (1555.52 seconds total)