Starting phenix.real_space_refine
on Thu Feb 13 22:13:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y1m_33566/02_2025/7y1m_33566.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y1m_33566/02_2025/7y1m_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_2025/7y1m_33566.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y1m_33566/02_2025/7y1m_33566.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y1m_33566/02_2025/7y1m_33566.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y1m_33566/02_2025/7y1m_33566.cif"
  }
  resolution = 3.57
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.006 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 21, 'PHE:plan': 2, 'GLU:plan': 19, 'ARG:plan': 9}
          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: 5.75, per 1000 atoms: 0.64
  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: 2.43
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 1.00
  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: 3.54

  Time building geometry restraints manager: 2.80 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:             1.880
  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:          0.310
  Check model and map are aligned:         0.070
  Set scattering table:                    0.070
  Process input model:                     24.090
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.460
-------------------------------------------------------------------------------
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= 0.222
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.52 (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
 TRP   0.007   0.001   TRP A1214 
 HIS   0.004   0.001   HIS A1065 
 PHE   0.011   0.001   PHE A1149 
 TYR   0.011   0.001   TYR A 505 
 ARG   0.002   0.000   ARG A1461 

*********************** 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  : 1.071 
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: 0.8230 (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: 0.7741 (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: 0.9035 (m) cc_final: 0.8528 (p)
REVERT: A 1333 LYS cc_start: 0.8364 (mtmm) cc_final: 0.7955 (tmtt)
REVERT: A 1445 PHE cc_start: 0.8392 (m-80) cc_final: 0.8149 (m-80)
  outliers start: 3
  outliers final: 0
  residues processed: 146
  average time/residue: 0.2178
  time to fit residues: 44.6822
Evaluate side-chains
  105 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
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 97 optimal weight:   20.0000
   chunk 87 optimal weight:    0.9990
   chunk 48 optimal weight:    0.0470
   chunk 30 optimal weight:    0.5980
   chunk 59 optimal weight:    5.9990
   chunk 46 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 55 optimal weight:    5.9990
   chunk 67 optimal weight:    0.6980
   chunk 105 optimal weight:    4.9990
   overall best weight:    0.8682

-------------------------------------------------------------------------------
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
A1504 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.151228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.119191 restraints weight = 12803.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.118767 restraints weight = 10972.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.119361 restraints weight = 7658.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.1173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9142  Z= 0.229
  Angle     :  0.596  10.086  12450  Z= 0.288
  Chirality :  0.040   0.174   1504
  Planarity :  0.004   0.047   1513
  Dihedral  : 10.901 141.998   1302
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  :  8.33 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.69 (0.25), residues: 1150
  helix:  2.33 (0.18), residues: 801
  sheet:  0.70 (0.60), residues: 68
  loop :  0.52 (0.37), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1214 
 HIS   0.005   0.001   HIS A1001 
 PHE   0.014   0.001   PHE A 552 
 TYR   0.016   0.001   TYR A 505 
 ARG   0.004   0.000   ARG A1357 

*********************** 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
  128 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 116
  time to evaluate  : 0.968 
Fit side-chains
   revert: symmetry clash
REVERT: A  225 LYS cc_start: 0.8142 (mtmt) cc_final: 0.7455 (tptt)
REVERT: A  284 SER cc_start: 0.8681 (t) cc_final: 0.8371 (m)
REVERT: A  405 MET cc_start: 0.7012 (mmm) cc_final: 0.6697 (mmt)
REVERT: A 1083 THR cc_start: 0.8867 (m) cc_final: 0.8537 (p)
REVERT: A 1123 MET cc_start: 0.8373 (tpp) cc_final: 0.7632 (tpp)
REVERT: A 1334 PRO cc_start: 0.7573 (Cg_endo) cc_final: 0.6367 (Cg_exo)
  outliers start: 12
  outliers final: 7
  residues processed: 123
  average time/residue: 0.2052
  time to fit residues: 36.5922
Evaluate side-chains
  108 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  865 VAL
Chi-restraints excluded: chain A residue 1072 ILE
Chi-restraints excluded: chain A residue 1355 PHE
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 69 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 64 optimal weight:    0.5980
   chunk 101 optimal weight:    7.9990
   chunk 50 optimal weight:    0.9980
   chunk 38 optimal weight:    7.9990
   chunk 76 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 98 optimal weight:    0.9980
   chunk 104 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   overall best weight:    1.1182

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1402 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.150257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.118310 restraints weight = 13068.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.117428 restraints weight = 9770.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.118077 restraints weight = 8186.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.1565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9142  Z= 0.241
  Angle     :  0.586   8.994  12450  Z= 0.281
  Chirality :  0.040   0.170   1504
  Planarity :  0.004   0.045   1513
  Dihedral  : 10.383 137.825   1300
  Min Nonbonded Distance : 1.898

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  :  9.54 %
    Favored  : 88.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.65 (0.24), residues: 1150
  helix:  2.35 (0.18), residues: 796
  sheet:  0.64 (0.61), residues: 69
  loop :  0.43 (0.36), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1214 
 HIS   0.005   0.001   HIS A1001 
 PHE   0.015   0.001   PHE A 552 
 TYR   0.017   0.001   TYR A 903 
 ARG   0.003   0.000   ARG A1357 

*********************** 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
  127 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 0.955 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  225 LYS cc_start: 0.8161 (mtmt) cc_final: 0.7412 (tptt)
REVERT: A  239 HIS cc_start: 0.8313 (OUTLIER) cc_final: 0.7663 (m90)
REVERT: A  284 SER cc_start: 0.8718 (t) cc_final: 0.8330 (m)
REVERT: A  405 MET cc_start: 0.7009 (mmm) cc_final: 0.6716 (mmt)
REVERT: A 1083 THR cc_start: 0.8760 (m) cc_final: 0.8470 (p)
REVERT: A 1123 MET cc_start: 0.8369 (tpp) cc_final: 0.7685 (tpp)
REVERT: A 1289 TYR cc_start: 0.7677 (m-80) cc_final: 0.7340 (m-80)
  outliers start: 16
  outliers final: 13
  residues processed: 121
  average time/residue: 0.2240
  time to fit residues: 38.9224
Evaluate side-chains
  116 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
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  910 MET
Chi-restraints excluded: chain A residue 1072 ILE
Chi-restraints excluded: chain A residue 1089 LEU
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 46 optimal weight:    0.8980
   chunk 66 optimal weight:    2.9990
   chunk 72 optimal weight:    0.7980
   chunk 36 optimal weight:    0.0980
   chunk 73 optimal weight:    1.9990
   chunk 92 optimal weight:   20.0000
   chunk 105 optimal weight:    3.9990
   chunk 15 optimal weight:    0.6980
   chunk 109 optimal weight:    8.9990
   chunk 100 optimal weight:    0.9980
   chunk 98 optimal weight:    0.8980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 ** 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 = 0.3780 r_free = 0.3780 target = 0.147461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.117342 restraints weight = 12971.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.116581 restraints weight = 13541.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.118607 restraints weight = 10766.024|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.1878

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= 0.182
  Angle     :  0.549   8.511  12450  Z= 0.260
  Chirality :  0.039   0.179   1504
  Planarity :  0.003   0.042   1513
  Dihedral  : 10.019 129.808   1300
  Min Nonbonded Distance : 1.910

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 10.86 %
    Favored  : 87.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.84 (0.25), residues: 1150
  helix:  2.48 (0.18), residues: 803
  sheet:  0.66 (0.65), residues: 61
  loop :  0.45 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 756 
 HIS   0.004   0.001   HIS A1065 
 PHE   0.017   0.001   PHE A 854 
 TYR   0.015   0.001   TYR A 228 
 ARG   0.002   0.000   ARG A 774 

*********************** 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
  129 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 113
  time to evaluate  : 0.896 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  225 LYS cc_start: 0.8129 (mtmt) cc_final: 0.7446 (tptt)
REVERT: A  239 HIS cc_start: 0.8168 (OUTLIER) cc_final: 0.7416 (m90)
REVERT: A  284 SER cc_start: 0.8674 (t) cc_final: 0.8279 (m)
REVERT: A  405 MET cc_start: 0.6753 (mmm) cc_final: 0.6462 (mmt)
REVERT: A  707 LYS cc_start: 0.7849 (ptpp) cc_final: 0.7633 (mtmm)
REVERT: A  910 MET cc_start: 0.6354 (OUTLIER) cc_final: 0.5451 (ttt)
REVERT: A 1091 ARG cc_start: 0.7351 (mmp80) cc_final: 0.7145 (mmp80)
REVERT: A 1123 MET cc_start: 0.8247 (tpp) cc_final: 0.7665 (tpp)
REVERT: A 1128 THR cc_start: 0.8771 (m) cc_final: 0.8171 (p)
REVERT: A 1289 TYR cc_start: 0.7625 (m-80) cc_final: 0.7292 (m-80)
REVERT: A 1322 LYS cc_start: 0.8618 (ttpt) cc_final: 0.8135 (tptt)
  outliers start: 16
  outliers final: 10
  residues processed: 122
  average time/residue: 0.2065
  time to fit residues: 35.8860
Evaluate side-chains
  113 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.992 
-------------------------------------------------------------------------------
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  865 VAL
Chi-restraints excluded: chain A residue  910 MET
Chi-restraints excluded: chain A residue 1072 ILE
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:   20.0000
   chunk 91 optimal weight:    3.9990
   chunk 113 optimal weight:    7.9990
   chunk 61 optimal weight:    0.9980
   chunk 105 optimal weight:    0.9990
   chunk 40 optimal weight:    9.9990
   chunk 2 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 85 optimal weight:    3.9990
   chunk 75 optimal weight:    0.7980
   chunk 50 optimal weight:    0.7980
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 = 0.3809 r_free = 0.3809 target = 0.149060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.116273 restraints weight = 12950.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.115661 restraints weight = 9485.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.116493 restraints weight = 7228.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.1995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9142  Z= 0.259
  Angle     :  0.575   8.286  12450  Z= 0.274
  Chirality :  0.040   0.177   1504
  Planarity :  0.004   0.044   1513
  Dihedral  :  9.881 134.732   1300
  Min Nonbonded Distance : 1.905

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 11.51 %
    Favored  : 86.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.69 (0.24), residues: 1150
  helix:  2.36 (0.18), residues: 802
  sheet:  0.84 (0.66), residues: 61
  loop :  0.41 (0.36), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1214 
 HIS   0.006   0.001   HIS A1065 
 PHE   0.016   0.001   PHE A 552 
 TYR   0.015   0.001   TYR A 228 
 ARG   0.002   0.000   ARG A 774 

*********************** 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
  126 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  225 LYS cc_start: 0.8138 (mtmt) cc_final: 0.7524 (tttp)
REVERT: A  239 HIS cc_start: 0.8212 (OUTLIER) cc_final: 0.7395 (m90)
REVERT: A  284 SER cc_start: 0.8810 (t) cc_final: 0.8404 (m)
REVERT: A  405 MET cc_start: 0.7005 (mmm) cc_final: 0.6707 (mmt)
REVERT: A  910 MET cc_start: 0.6132 (OUTLIER) cc_final: 0.5412 (ttt)
REVERT: A 1123 MET cc_start: 0.8415 (tpp) cc_final: 0.7738 (tpp)
REVERT: A 1128 THR cc_start: 0.8794 (m) cc_final: 0.8204 (p)
REVERT: A 1322 LYS cc_start: 0.8679 (ttpt) cc_final: 0.8082 (tptt)
REVERT: A 1445 PHE cc_start: 0.8359 (m-80) cc_final: 0.8062 (m-80)
  outliers start: 20
  outliers final: 16
  residues processed: 120
  average time/residue: 0.2090
  time to fit residues: 36.1772
Evaluate side-chains
  118 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
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  761 THR
Chi-restraints excluded: chain A residue  910 MET
Chi-restraints excluded: chain A residue 1072 ILE
Chi-restraints excluded: chain A residue 1162 SER
Chi-restraints excluded: chain A residue 1219 THR
Chi-restraints excluded: chain A residue 1283 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 1483 LEU
Chi-restraints excluded: chain A residue 1512 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 18 optimal weight:    0.1980
   chunk 109 optimal weight:    0.1980
   chunk 39 optimal weight:    7.9990
   chunk 97 optimal weight:   20.0000
   chunk 38 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0980
   chunk 49 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.3580

-------------------------------------------------------------------------------
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 = 0.3853 r_free = 0.3853 target = 0.152939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.120974 restraints weight = 12788.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.119918 restraints weight = 9475.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.120676 restraints weight = 7349.457|
|-----------------------------------------------------------------------------|
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
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      :  0.002   0.032   9142  Z= 0.150
  Angle     :  0.537   8.295  12450  Z= 0.252
  Chirality :  0.038   0.191   1504
  Planarity :  0.003   0.043   1513
  Dihedral  :  9.605 122.892   1300
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 12.17 %
    Favored  : 85.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.99 (0.25), residues: 1150
  helix:  2.61 (0.18), residues: 800
  sheet:  0.80 (0.59), residues: 71
  loop :  0.44 (0.37), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 230 
 HIS   0.002   0.000   HIS A1065 
 PHE   0.010   0.001   PHE A1356 
 TYR   0.009   0.001   TYR A 871 
 ARG   0.002   0.000   ARG A 774 

*********************** 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
  133 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 0.960 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  225 LYS cc_start: 0.8108 (mtmt) cc_final: 0.7353 (tptt)
REVERT: A  239 HIS cc_start: 0.7965 (OUTLIER) cc_final: 0.7069 (m90)
REVERT: A  284 SER cc_start: 0.8786 (t) cc_final: 0.8342 (m)
REVERT: A  405 MET cc_start: 0.6968 (mmm) cc_final: 0.6653 (mmt)
REVERT: A  707 LYS cc_start: 0.8010 (ptpp) cc_final: 0.7722 (mtmm)
REVERT: A  910 MET cc_start: 0.6101 (OUTLIER) cc_final: 0.5409 (ttt)
REVERT: A 1123 MET cc_start: 0.8208 (tpp) cc_final: 0.7631 (tpp)
REVERT: A 1128 THR cc_start: 0.8633 (m) cc_final: 0.8200 (p)
REVERT: A 1155 ASP cc_start: 0.8085 (t70) cc_final: 0.7884 (t0)
REVERT: A 1322 LYS cc_start: 0.8673 (ttpt) cc_final: 0.8030 (tptt)
REVERT: A 1445 PHE cc_start: 0.8322 (m-80) cc_final: 0.8068 (m-80)
  outliers start: 20
  outliers final: 13
  residues processed: 127
  average time/residue: 0.2157
  time to fit residues: 39.4654
Evaluate side-chains
  115 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 1.004 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 HIS
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  432 TRP
Chi-restraints excluded: chain A residue  493 ASN
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  910 MET
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 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 96 optimal weight:    7.9990
   chunk 59 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9990
   chunk 108 optimal weight:    2.9990
   chunk 58 optimal weight:   10.0000
   chunk 10 optimal weight:    0.8980
   chunk 93 optimal weight:    6.9990
   chunk 105 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    1.1386

-------------------------------------------------------------------------------
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 = 0.3828 r_free = 0.3828 target = 0.150876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.118453 restraints weight = 12944.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.117494 restraints weight = 9374.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.118235 restraints weight = 7037.316|
|-----------------------------------------------------------------------------|
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.2251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9142  Z= 0.231
  Angle     :  0.564   8.440  12450  Z= 0.266
  Chirality :  0.039   0.171   1504
  Planarity :  0.003   0.044   1513
  Dihedral  :  9.562 129.032   1300
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 12.72 %
    Favored  : 84.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.91 (0.25), residues: 1150
  helix:  2.53 (0.18), residues: 798
  sheet:  0.90 (0.60), residues: 71
  loop :  0.48 (0.37), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1214 
 HIS   0.005   0.001   HIS A1001 
 PHE   0.014   0.001   PHE A 552 
 TYR   0.015   0.001   TYR A 228 
 ARG   0.002   0.000   ARG A 774 

*********************** 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
  128 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 1.055 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  225 LYS cc_start: 0.8124 (mtmt) cc_final: 0.7439 (tttp)
REVERT: A  239 HIS cc_start: 0.8064 (OUTLIER) cc_final: 0.7160 (m90)
REVERT: A  284 SER cc_start: 0.8802 (t) cc_final: 0.8352 (m)
REVERT: A  405 MET cc_start: 0.6974 (mmm) cc_final: 0.6662 (mmt)
REVERT: A  520 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.7033 (mtp)
REVERT: A  910 MET cc_start: 0.6064 (OUTLIER) cc_final: 0.5451 (ttt)
REVERT: A 1123 MET cc_start: 0.8316 (tpp) cc_final: 0.7647 (tpp)
REVERT: A 1128 THR cc_start: 0.8648 (m) cc_final: 0.8199 (p)
REVERT: A 1322 LYS cc_start: 0.8682 (ttpt) cc_final: 0.8045 (tptt)
REVERT: A 1376 LEU cc_start: 0.8514 (mt) cc_final: 0.8204 (mt)
REVERT: A 1445 PHE cc_start: 0.8405 (m-80) cc_final: 0.8114 (m-80)
  outliers start: 23
  outliers final: 19
  residues processed: 122
  average time/residue: 0.2165
  time to fit residues: 37.5763
Evaluate side-chains
  125 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 103
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
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  413 LEU
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  432 TRP
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  865 VAL
Chi-restraints excluded: chain A residue  910 MET
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 1277 LYS
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 108 optimal weight:    0.8980
   chunk 69 optimal weight:    0.2980
   chunk 94 optimal weight:    9.9990
   chunk 76 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 106 optimal weight:    0.0570
   chunk 72 optimal weight:    0.8980
   chunk 57 optimal weight:    0.3980
   chunk 93 optimal weight:   10.0000
   chunk 6 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.4698

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

Flipped N/Q/H residues before XYZ refinement:
A 399 ASN
A 493 ASN
** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1311 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.152894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.121237 restraints weight = 12990.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.120411 restraints weight = 10126.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.121254 restraints weight = 7697.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.2373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9142  Z= 0.168
  Angle     :  0.560  12.288  12450  Z= 0.260
  Chirality :  0.038   0.184   1504
  Planarity :  0.003   0.044   1513
  Dihedral  :  9.439 124.397   1300
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 12.72 %
    Favored  : 84.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.98 (0.25), residues: 1150
  helix:  2.56 (0.18), residues: 802
  sheet:  0.84 (0.61), residues: 72
  loop :  0.57 (0.38), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 906 
 HIS   0.003   0.000   HIS A1065 
 PHE   0.010   0.001   PHE A 552 
 TYR   0.011   0.001   TYR A 505 
 ARG   0.002   0.000   ARG A 774 

*********************** 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
  129 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 106
  time to evaluate  : 1.042 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  225 LYS cc_start: 0.8077 (mtmt) cc_final: 0.7400 (tttp)
REVERT: A  239 HIS cc_start: 0.7961 (OUTLIER) cc_final: 0.6986 (m90)
REVERT: A  284 SER cc_start: 0.8806 (t) cc_final: 0.8349 (m)
REVERT: A  405 MET cc_start: 0.6890 (mmm) cc_final: 0.6587 (mmt)
REVERT: A  520 MET cc_start: 0.7359 (OUTLIER) cc_final: 0.6992 (mtp)
REVERT: A  910 MET cc_start: 0.6003 (OUTLIER) cc_final: 0.5406 (ttt)
REVERT: A 1123 MET cc_start: 0.8253 (tpp) cc_final: 0.7643 (tpp)
REVERT: A 1128 THR cc_start: 0.8625 (m) cc_final: 0.8213 (p)
REVERT: A 1322 LYS cc_start: 0.8666 (ttpt) cc_final: 0.8078 (tptt)
REVERT: A 1376 LEU cc_start: 0.8461 (mt) cc_final: 0.8188 (mt)
REVERT: A 1445 PHE cc_start: 0.8315 (m-80) cc_final: 0.8090 (m-80)
REVERT: A 1468 MET cc_start: 0.7383 (mtt) cc_final: 0.7130 (mtt)
  outliers start: 23
  outliers final: 18
  residues processed: 120
  average time/residue: 0.1934
  time to fit residues: 33.7956
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  : 1.060 
-------------------------------------------------------------------------------
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  413 LEU
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  432 TRP
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  910 MET
Chi-restraints excluded: chain A residue  993 MET
Chi-restraints excluded: chain A residue 1072 ILE
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1146 GLN
Chi-restraints excluded: chain A residue 1219 THR
Chi-restraints excluded: chain A residue 1277 LYS
Chi-restraints excluded: chain A residue 1399 ILE
Chi-restraints excluded: chain A residue 1403 LEU
Chi-restraints excluded: chain A residue 1437 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 93 optimal weight:    3.9990
   chunk 26 optimal weight:    0.3980
   chunk 107 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 36 optimal weight:    0.7980
   chunk 11 optimal weight:    0.8980
   chunk 108 optimal weight:    0.9990
   chunk 95 optimal weight:    5.9990
   chunk 62 optimal weight:    0.1980
   chunk 37 optimal weight:    0.0050
   chunk 73 optimal weight:    0.1980
   overall best weight:    0.2994

-------------------------------------------------------------------------------
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 = 0.3866 r_free = 0.3866 target = 0.154121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.122258 restraints weight = 12932.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.121630 restraints weight = 9670.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.122741 restraints weight = 7316.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.2514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9142  Z= 0.157
  Angle     :  0.568  11.621  12450  Z= 0.266
  Chirality :  0.038   0.192   1504
  Planarity :  0.005   0.122   1513
  Dihedral  :  9.339 122.291   1300
  Min Nonbonded Distance : 2.004

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 13.27 %
    Favored  : 84.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.02 (0.25), residues: 1150
  helix:  2.62 (0.18), residues: 804
  sheet:  0.84 (0.60), residues: 72
  loop :  0.47 (0.38), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 906 
 HIS   0.002   0.000   HIS A1065 
 PHE   0.010   0.001   PHE A1149 
 TYR   0.014   0.001   TYR A 505 
 ARG   0.013   0.000   ARG A1091 

*********************** 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
  130 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.944 
Fit side-chains
   revert: symmetry clash
REVERT: A  225 LYS cc_start: 0.8049 (mtmt) cc_final: 0.7408 (tttp)
REVERT: A  239 HIS cc_start: 0.7876 (OUTLIER) cc_final: 0.6896 (m90)
REVERT: A  284 SER cc_start: 0.8774 (t) cc_final: 0.8324 (m)
REVERT: A  405 MET cc_start: 0.6864 (mmm) cc_final: 0.6545 (mmt)
REVERT: A  520 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.7030 (mtp)
REVERT: A  910 MET cc_start: 0.6013 (OUTLIER) cc_final: 0.5374 (ttt)
REVERT: A 1123 MET cc_start: 0.8209 (tpp) cc_final: 0.7623 (tpp)
REVERT: A 1128 THR cc_start: 0.8580 (m) cc_final: 0.8211 (p)
REVERT: A 1155 ASP cc_start: 0.8064 (t70) cc_final: 0.7847 (t0)
REVERT: A 1322 LYS cc_start: 0.8666 (ttpt) cc_final: 0.8068 (tptt)
REVERT: A 1376 LEU cc_start: 0.8509 (mt) cc_final: 0.8200 (mt)
  outliers start: 19
  outliers final: 15
  residues processed: 124
  average time/residue: 0.1996
  time to fit residues: 35.8217
Evaluate side-chains
  121 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 1.039 
-------------------------------------------------------------------------------
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  413 LEU
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  432 TRP
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  910 MET
Chi-restraints excluded: chain A residue 1072 ILE
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1146 GLN
Chi-restraints excluded: chain A residue 1219 THR
Chi-restraints excluded: chain A residue 1403 LEU
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 106 optimal weight:    8.9990
   chunk 8 optimal weight:    0.5980
   chunk 52 optimal weight:    4.9990
   chunk 3 optimal weight:    0.7980
   chunk 83 optimal weight:    2.9990
   chunk 109 optimal weight:    9.9990
   chunk 70 optimal weight:    0.7980
   chunk 48 optimal weight:    3.9990
   chunk 59 optimal weight:   10.0000
   chunk 107 optimal weight:    0.9980
   chunk 101 optimal weight:    0.9990
   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 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 = 0.3849 r_free = 0.3849 target = 0.152763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.120005 restraints weight = 12965.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.119637 restraints weight = 9234.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.120993 restraints weight = 7061.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.2547

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= 0.198
  Angle     :  0.569  11.432  12450  Z= 0.268
  Chirality :  0.039   0.178   1504
  Planarity :  0.004   0.052   1513
  Dihedral  :  9.298 125.713   1300
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 13.38 %
    Favored  : 84.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.90 (0.25), residues: 1150
  helix:  2.53 (0.18), residues: 804
  sheet:  0.93 (0.61), residues: 70
  loop :  0.40 (0.38), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 906 
 HIS   0.004   0.001   HIS A1001 
 PHE   0.012   0.001   PHE A1445 
 TYR   0.023   0.001   TYR A 903 
 ARG   0.008   0.000   ARG A1091 

********************** 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
  121 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 1.059 
Fit side-chains
   revert: symmetry clash
REVERT: A  225 LYS cc_start: 0.8112 (mtmt) cc_final: 0.7447 (tttp)
REVERT: A  239 HIS cc_start: 0.7942 (OUTLIER) cc_final: 0.6975 (m90)
REVERT: A  284 SER cc_start: 0.8734 (t) cc_final: 0.8322 (m)
REVERT: A  405 MET cc_start: 0.6917 (mmm) cc_final: 0.6598 (mmt)
REVERT: A  520 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.7065 (mtp)
REVERT: A  892 LEU cc_start: 0.8721 (tp) cc_final: 0.8507 (tp)
REVERT: A  910 MET cc_start: 0.5996 (OUTLIER) cc_final: 0.5433 (ttt)
REVERT: A 1123 MET cc_start: 0.8278 (tpp) cc_final: 0.7665 (tpp)
REVERT: A 1128 THR cc_start: 0.8550 (OUTLIER) cc_final: 0.8160 (p)
REVERT: A 1322 LYS cc_start: 0.8678 (ttpt) cc_final: 0.8059 (tptt)
REVERT: A 1376 LEU cc_start: 0.8536 (mt) cc_final: 0.8195 (mt)
REVERT: A 1426 MET cc_start: 0.7911 (tpp) cc_final: 0.7698 (tpp)
  outliers start: 18
  outliers final: 13
  residues processed: 115
  average time/residue: 0.2151
  time to fit residues: 36.9870
Evaluate side-chains
  120 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
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  413 LEU
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  432 TRP
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  910 MET
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 1437 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 113 optimal weight:   40.0000
   chunk 110 optimal weight:   20.0000
   chunk 70 optimal weight:    1.9990
   chunk 59 optimal weight:    9.9990
   chunk 90 optimal weight:    0.7980
   chunk 52 optimal weight:    0.0170
   chunk 98 optimal weight:    0.0980
   chunk 75 optimal weight:    0.6980
   chunk 15 optimal weight:    0.0670
   chunk 78 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.2956

-------------------------------------------------------------------------------
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 = 0.3871 r_free = 0.3871 target = 0.154688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.123070 restraints weight = 12916.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.122038 restraints weight = 9279.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.122685 restraints weight = 6993.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.2635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9142  Z= 0.151
  Angle     :  0.559  11.305  12450  Z= 0.260
  Chirality :  0.038   0.189   1504
  Planarity :  0.004   0.063   1513
  Dihedral  :  9.181 121.751   1300
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 13.49 %
    Favored  : 84.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.00 (0.25), residues: 1150
  helix:  2.62 (0.18), residues: 804
  sheet:  0.91 (0.61), residues: 70
  loop :  0.37 (0.38), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 906 
 HIS   0.002   0.000   HIS A1001 
 PHE   0.010   0.001   PHE A1149 
 TYR   0.015   0.001   TYR A 505 
 ARG   0.007   0.000   ARG A1091 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2536.45 seconds
wall clock time: 46 minutes 42.88 seconds (2802.88 seconds total)