Starting phenix.real_space_refine
on Wed Mar  4 09:51:08 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9wzx_66411/03_2026/9wzx_66411.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9wzx_66411/03_2026/9wzx_66411.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.72
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9wzx_66411/03_2026/9wzx_66411.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9wzx_66411/03_2026/9wzx_66411.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9wzx_66411/03_2026/9wzx_66411.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9wzx_66411/03_2026/9wzx_66411.cif"
  }
  resolution = 3.72
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.038
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: 4
    Type Number    sf(0)   Gaussians
     S      72      5.16       5
     C    7919      2.51       5
     N    2023      2.21       5
     O    2103      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12117
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "F"
      Number of atoms: 12117
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1485, 12117
          Classifications: {'peptide': 1485}
          Link IDs: {'PTRANS': 65, 'TRANS': 1419}
          Chain breaks: 10
  Time building chain proxies: 2.86, per 1000 atoms: 0.24
  Number of scatterers: 12117
  At special positions: 0
  Unit cell: (101.76, 115.54, 133.56, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      72     16.00
     O    2103      8.00
     N    2023      7.00
     C    7919      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS F 658 " - pdb=" SG  CYS F 669 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F1328 " - pdb=" SG  CYS F1345 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.03
  Conformation dependent library (CDL) restraints added in 557.9 milliseconds
  

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2826

  Finding SS restraints...
    Secondary structure from input PDB file:
      65 helices and 4 sheets defined
      65.4% alpha, 3.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.65
  Creating SS restraints...
    Processing helix  chain 'F' and resid 160 through 176
    Processing helix  chain 'F' and resid 178 through 196
      removed outlier: 3.564A  pdb=" N   ARG F 183 " --> pdb=" O   ARG F 179 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 201 through 214
      removed outlier: 3.775A  pdb=" N   LEU F 206 " --> pdb=" O   PRO F 202 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   LEU F 207 " --> pdb=" O   ASP F 203 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 219 through 228
      removed outlier: 3.554A  pdb=" N   LYS F 223 " --> pdb=" O   ALA F 219 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 232 through 243
    Processing helix  chain 'F' and resid 282 through 295
      removed outlier: 3.608A  pdb=" N   GLN F 295 " --> pdb=" O   ALA F 291 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 297 through 315
      removed outlier: 3.825A  pdb=" N   ARG F 301 " --> pdb=" O   SER F 297 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   VAL F 302 " --> pdb=" O   PRO F 298 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   ARG F 303 " --> pdb=" O   LEU F 299 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ALA F 315 " --> pdb=" O   CYS F 311 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 321 through 337
    Processing helix  chain 'F' and resid 338 through 344
    Processing helix  chain 'F' and resid 351 through 357
      removed outlier: 3.520A  pdb=" N   VAL F 357 " --> pdb=" O   PHE F 353 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 358 through 368
      removed outlier: 3.529A  pdb=" N   GLN F 368 " --> pdb=" O   PHE F 364 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 389 through 394
    Processing helix  chain 'F' and resid 395 through 398
      removed outlier: 3.540A  pdb=" N   TRP F 398 " --> pdb=" O   GLN F 395 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 395 through 398'
    Processing helix  chain 'F' and resid 399 through 405
    Processing helix  chain 'F' and resid 421 through 427
      removed outlier: 3.514A  pdb=" N   ARG F 425 " --> pdb=" O   GLU F 421 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLY F 427 " --> pdb=" O   TYR F 423 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 443 through 451
      removed outlier: 3.920A  pdb=" N   HIS F 447 " --> pdb=" O   ARG F 443 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   LEU F 448 " --> pdb=" O   THR F 444 " (cutoff:3.500A)
      removed outlier: 5.249A  pdb=" N   VAL F 449 " --> pdb=" O   TRP F 445 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   THR F 450 " --> pdb=" O   LEU F 446 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 452 through 471
      removed outlier: 4.047A  pdb=" N   TRP F 456 " --> pdb=" O   PHE F 452 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   VAL F 457 " --> pdb=" O   ASN F 453 " (cutoff:3.500A)
      removed outlier: 5.157A  pdb=" N   ILE F 462 " --> pdb=" O   MET F 458 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ASN F 470 " --> pdb=" O   TYR F 466 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   SER F 471 " --> pdb=" O   PHE F 467 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 489 through 496
    Processing helix  chain 'F' and resid 498 through 516
      removed outlier: 3.920A  pdb=" N   ALA F 503 " --> pdb=" O   GLY F 499 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   SER F 504 " --> pdb=" O   GLY F 500 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU F 505 " --> pdb=" O   THR F 501 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   SER F 516 " --> pdb=" O   LEU F 512 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 525 through 552
      removed outlier: 3.635A  pdb=" N   SER F 529 " --> pdb=" O   ALA F 525 " (cutoff:3.500A)
      Proline residue:  F 545  - end of helix
      removed outlier: 3.692A  pdb=" N   PHE F 550 " --> pdb=" O   ILE F 546 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   TYR F 552 " --> pdb=" O   PHE F 548 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 558 through 583
    Processing helix  chain 'F' and resid 616 through 653
      removed outlier: 3.981A  pdb=" N   PHE F 629 " --> pdb=" O   TRP F 625 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   TYR F 633 " --> pdb=" O   PHE F 629 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   SER F 634 " --> pdb=" O   ALA F 630 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   VAL F 641 " --> pdb=" O   TYR F 637 " (cutoff:3.500A)
      removed outlier: 5.407A  pdb=" N   LEU F 642 " --> pdb=" O   TYR F 638 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   SER F 643 " --> pdb=" O   PHE F 639 " (cutoff:3.500A)
      Proline residue:  F 647  - end of helix
      removed outlier: 4.510A  pdb=" N   THR F 653 " --> pdb=" O   ARG F 649 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 661 through 669
      removed outlier: 4.083A  pdb=" N   ALA F 666 " --> pdb=" O   TYR F 662 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   VAL F 667 " --> pdb=" O   TRP F 663 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 672 through 689
      removed outlier: 3.529A  pdb=" N   VAL F 676 " --> pdb=" O   GLN F 672 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   PHE F 689 " --> pdb=" O   PHE F 685 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 690 through 711
      removed outlier: 3.627A  pdb=" N   ILE F 697 " --> pdb=" O   TYR F 693 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ILE F 698 " --> pdb=" O   LEU F 694 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 725 through 734
    Processing helix  chain 'F' and resid 745 through 764
      removed outlier: 3.552A  pdb=" N   LEU F 749 " --> pdb=" O   LYS F 745 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   VAL F 753 " --> pdb=" O   LEU F 749 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 768 through 775
    Processing helix  chain 'F' and resid 809 through 812
      removed outlier: 3.686A  pdb=" N   ASP F 812 " --> pdb=" O   PHE F 809 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 809 through 812'
    Processing helix  chain 'F' and resid 813 through 828
      removed outlier: 4.209A  pdb=" N   ARG F 817 " --> pdb=" O   SER F 813 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU F 826 " --> pdb=" O   PHE F 822 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   SER F 827 " --> pdb=" O   ALA F 823 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   THR F 828 " --> pdb=" O   GLN F 824 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 835 through 839
      removed outlier: 3.939A  pdb=" N   MET F 839 " --> pdb=" O   VAL F 836 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 854 through 859
      removed outlier: 3.620A  pdb=" N   ARG F 858 " --> pdb=" O   LEU F 854 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 871 through 880
    Processing helix  chain 'F' and resid 880 through 896
      removed outlier: 3.502A  pdb=" N   TRP F 884 " --> pdb=" O   HIS F 880 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   PHE F 887 " --> pdb=" O   GLU F 883 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   VAL F 888 " --> pdb=" O   TRP F 884 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   LYS F 889 " --> pdb=" O   GLU F 885 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   LYS F 892 " --> pdb=" O   VAL F 888 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 933 through 946
    Processing helix  chain 'F' and resid 949 through 958
      removed outlier: 4.167A  pdb=" N   THR F 953 " --> pdb=" O   THR F 949 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 958 through 972
      removed outlier: 4.060A  pdb=" N   ARG F 962 " --> pdb=" O   MET F 958 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   LEU F 967 " --> pdb=" O   ALA F 963 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   GLU F 971 " --> pdb=" O   LEU F 967 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ASN F 972 " --> pdb=" O   TYR F 968 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 973 through 980
    Processing helix  chain 'F' and resid 982 through 997
    Processing helix  chain 'F' and resid 1006 through 1010
    Processing helix  chain 'F' and resid 1011 through 1025
      removed outlier: 4.022A  pdb=" N   GLU F1016 " --> pdb=" O   PRO F1012 " (cutoff:3.500A)
      removed outlier: 4.888A  pdb=" N   ASN F1017 " --> pdb=" O   HIS F1013 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ALA F1018 " --> pdb=" O   GLU F1014 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1082 through 1090
      removed outlier: 4.214A  pdb=" N   GLN F1086 " --> pdb=" O   LYS F1082 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1108 through 1113
      removed outlier: 4.220A  pdb=" N   LEU F1113 " --> pdb=" O   GLU F1110 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1114 through 1119
      removed outlier: 4.052A  pdb=" N   VAL F1118 " --> pdb=" O   LYS F1114 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1181 through 1185
    Processing helix  chain 'F' and resid 1191 through 1195
      removed outlier: 3.693A  pdb=" N   HIS F1195 " --> pdb=" O   HIS F1192 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1201 through 1207
      removed outlier: 3.559A  pdb=" N   THR F1206 " --> pdb=" O   THR F1202 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   ARG F1207 " --> pdb=" O   PHE F1203 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1223 through 1231
      removed outlier: 3.724A  pdb=" N   LEU F1231 " --> pdb=" O   MET F1227 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1268 through 1272
    Processing helix  chain 'F' and resid 1273 through 1282
      removed outlier: 3.641A  pdb=" N   GLN F1281 " --> pdb=" O   TYR F1277 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1283 through 1292
      removed outlier: 3.534A  pdb=" N   THR F1289 " --> pdb=" O   ASP F1285 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1294 through 1324
      removed outlier: 4.218A  pdb=" N   HIS F1298 " --> pdb=" O   HIS F1294 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   LEU F1313 " --> pdb=" O   GLN F1309 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   GLU F1324 " --> pdb=" O   SER F1320 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1349 through 1379
      removed outlier: 3.633A  pdb=" N   ASP F1353 " --> pdb=" O   GLN F1349 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   TRP F1367 " --> pdb=" O   PHE F1363 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ILE F1368 " --> pdb=" O   ILE F1364 " (cutoff:3.500A)
      Proline residue:  F1372  - end of helix
      removed outlier: 3.583A  pdb=" N   GLN F1376 " --> pdb=" O   PRO F1372 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1383 through 1391
      removed outlier: 4.023A  pdb=" N   THR F1387 " --> pdb=" O   LEU F1383 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1400 through 1418
      removed outlier: 4.226A  pdb=" N   PHE F1404 " --> pdb=" O   MET F1400 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1437 through 1467
      removed outlier: 4.284A  pdb=" N   ARG F1444 " --> pdb=" O   ILE F1440 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   PHE F1445 " --> pdb=" O   LEU F1441 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   GLY F1447 " --> pdb=" O   SER F1443 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   SER F1448 " --> pdb=" O   ARG F1444 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   ILE F1450 " --> pdb=" O   ALA F1446 " (cutoff:3.500A)
      removed outlier: 5.798A  pdb=" N   TYR F1451 " --> pdb=" O   GLY F1447 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   MET F1452 " --> pdb=" O   SER F1448 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   MET F1459 " --> pdb=" O   ARG F1455 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   GLY F1463 " --> pdb=" O   MET F1459 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1470 through 1489
      removed outlier: 4.055A  pdb=" N   TRP F1474 " --> pdb=" O   ALA F1470 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   PHE F1475 " --> pdb=" O   PRO F1471 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   SER F1478 " --> pdb=" O   TRP F1474 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   ALA F1485 " --> pdb=" O   SER F1481 " (cutoff:3.500A)
      Proline residue:  F1486  - end of helix
      removed outlier: 3.795A  pdb=" N   PHE F1489 " --> pdb=" O   ALA F1485 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1496 through 1513
      removed outlier: 3.711A  pdb=" N   PHE F1500 " --> pdb=" O   TRP F1496 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   LEU F1501 " --> pdb=" O   GLU F1497 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1559 through 1584
      Proline residue:  F1567  - end of helix
      removed outlier: 3.832A  pdb=" N   TYR F1571 " --> pdb=" O   PRO F1567 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1597 through 1624
      removed outlier: 3.736A  pdb=" N   ARG F1601 " --> pdb=" O   ASN F1597 " (cutoff:3.500A)
      Proline residue:  F1609  - end of helix
    Processing helix  chain 'F' and resid 1639 through 1665
      removed outlier: 3.804A  pdb=" N   HIS F1654 " --> pdb=" O   ALA F1650 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1672 through 1697
    Processing helix  chain 'F' and resid 1725 through 1760
      removed outlier: 3.654A  pdb=" N   GLU F1739 " --> pdb=" O   ILE F1735 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   PHE F1740 " --> pdb=" O   GLU F1736 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   ALA F1741 " --> pdb=" O   LEU F1737 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   ALA F1742 " --> pdb=" O   SER F1738 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ILE F1750 " --> pdb=" O   LEU F1746 " (cutoff:3.500A)
      Proline residue:  F1756  - end of helix
      removed outlier: 4.152A  pdb=" N   ILE F1760 " --> pdb=" O   PRO F1756 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1761 through 1774
    Processing helix  chain 'F' and resid 1786 through 1821
      removed outlier: 3.934A  pdb=" N   ARG F1791 " --> pdb=" O   LEU F1787 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   SER F1802 " --> pdb=" O   LYS F1798 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LEU F1803 " --> pdb=" O   LYS F1799 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   ILE F1815 " --> pdb=" O   PHE F1811 " (cutoff:3.500A)
      Proline residue:  F1818  - end of helix
    Processing sheet with id=AA1, first strand: chain 'F' and resid 371 through 372
    Processing sheet with id=AA2, first strand: chain 'F' and resid 778 through 781
    Processing sheet with id=AA3, first strand: chain 'F' and resid 1070 through 1072
      removed outlier: 4.543A  pdb=" N   ILE F1047 " --> pdb=" O   LEU F1072 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   PHE F1000 " --> pdb=" O   GLN F1029 " (cutoff:3.500A)
      removed outlier: 7.730A  pdb=" N   ALA F1031 " --> pdb=" O   PHE F1000 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   VAL F1002 " --> pdb=" O   ALA F1031 " (cutoff:3.500A)
      removed outlier: 8.714A  pdb=" N   LEU F1033 " --> pdb=" O   VAL F1002 " (cutoff:3.500A)
      removed outlier: 9.030A  pdb=" N   MET F1004 " --> pdb=" O   LEU F1033 " (cutoff:3.500A)
      removed outlier: 10.603A  pdb=" N   GLU F1035 " --> pdb=" O   MET F1004 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   PHE F 842 " --> pdb=" O   LYS F 999 " (cutoff:3.500A)
      removed outlier: 8.142A  pdb=" N   LEU F1001 " --> pdb=" O   PHE F 842 " (cutoff:3.500A)
      removed outlier: 5.760A  pdb=" N   VAL F 844 " --> pdb=" O   LEU F1001 " (cutoff:3.500A)
      removed outlier: 7.243A  pdb=" N   SER F1003 " --> pdb=" O   VAL F 844 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   THR F 846 " --> pdb=" O   SER F1003 " (cutoff:3.500A)
      removed outlier: 7.236A  pdb=" N   ALA F1149 " --> pdb=" O   ASN F1200 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'F' and resid 1153 through 1154
      removed outlier: 7.000A  pdb=" N   TYR F1241 " --> pdb=" O   ARG F1154 " (cutoff:3.500A)

    607 hydrogen bonds defined for protein.
    1785 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: 2.59

  Time building geometry restraints manager: 1.43 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3687
        1.34 -     1.46: 2250
        1.46 -     1.58: 6390
        1.58 -     1.70: 0
        1.70 -     1.82: 116
  Bond restraints: 12443
  Sorted by residual:
  bond pdb=" C   ILE F 830 "
       pdb=" N   PRO F 831 "
    ideal  model  delta    sigma   weight residual
    1.331  1.495 -0.164 1.31e-02 5.83e+03 1.57e+02
  bond pdb=" N   ARG F1154 "
       pdb=" CA  ARG F1154 "
    ideal  model  delta    sigma   weight residual
    1.455  1.490 -0.035 1.27e-02 6.20e+03 7.72e+00
  bond pdb=" N   THR F1851 "
       pdb=" CA  THR F1851 "
    ideal  model  delta    sigma   weight residual
    1.455  1.490 -0.035 1.29e-02 6.01e+03 7.37e+00
  bond pdb=" N   ARG F1381 "
       pdb=" CA  ARG F1381 "
    ideal  model  delta    sigma   weight residual
    1.455  1.489 -0.035 1.29e-02 6.01e+03 7.31e+00
  bond pdb=" N   ILE F 830 "
       pdb=" CA  ILE F 830 "
    ideal  model  delta    sigma   weight residual
    1.462  1.490 -0.028 1.04e-02 9.25e+03 7.28e+00
  ... (remaining 12438 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.68: 16766
        3.68 -     7.37: 100
        7.37 -    11.05: 8
       11.05 -    14.74: 2
       14.74 -    18.42: 3
  Bond angle restraints: 16879
  Sorted by residual:
  angle pdb=" C   ILE F 830 "
        pdb=" N   PRO F 831 "
        pdb=" CA  PRO F 831 "
      ideal   model   delta    sigma   weight residual
     119.85  138.27  -18.42 1.01e+00 9.80e-01 3.33e+02
  angle pdb=" CB  MET F 569 "
        pdb=" CG  MET F 569 "
        pdb=" SD  MET F 569 "
      ideal   model   delta    sigma   weight residual
     112.70  128.74  -16.04 3.00e+00 1.11e-01 2.86e+01
  angle pdb=" CA  ASP F 231 "
        pdb=" C   ASP F 231 "
        pdb=" N   MET F 232 "
      ideal   model   delta    sigma   weight residual
     119.98  115.97    4.01 8.50e-01 1.38e+00 2.22e+01
  angle pdb=" N   MET F 569 "
        pdb=" CA  MET F 569 "
        pdb=" CB  MET F 569 "
      ideal   model   delta    sigma   weight residual
     110.12  115.95   -5.83 1.47e+00 4.63e-01 1.57e+01
  angle pdb=" C   PHE F1657 "
        pdb=" N   PHE F1658 "
        pdb=" CA  PHE F1658 "
      ideal   model   delta    sigma   weight residual
     121.58  113.96    7.62 1.95e+00 2.63e-01 1.53e+01
  ... (remaining 16874 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 6185
       17.91 -    35.83: 889
       35.83 -    53.74: 220
       53.74 -    71.66: 28
       71.66 -    89.57: 9
  Dihedral angle restraints: 7331
    sinusoidal: 2962
      harmonic: 4369
  Sorted by residual:
  dihedral pdb=" CB  CYS F 658 "
           pdb=" SG  CYS F 658 "
           pdb=" SG  CYS F 669 "
           pdb=" CB  CYS F 669 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -152.84   66.84     1      1.00e+01 1.00e-02 5.82e+01
  dihedral pdb=" CB  CYS F1328 "
           pdb=" SG  CYS F1328 "
           pdb=" SG  CYS F1345 "
           pdb=" CB  CYS F1345 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  156.10  -63.10     1      1.00e+01 1.00e-02 5.26e+01
  dihedral pdb=" CA  PHE F1475 "
           pdb=" C   PHE F1475 "
           pdb=" N   TRP F1476 "
           pdb=" CA  TRP F1476 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.20  -18.80     0      5.00e+00 4.00e-02 1.41e+01
  ... (remaining 7328 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 1481
       0.054 -    0.108: 327
       0.108 -    0.161: 49
       0.161 -    0.215: 2
       0.215 -    0.269: 3
  Chirality restraints: 1862
  Sorted by residual:
  chirality pdb=" CA  ILE F 830 "
            pdb=" N   ILE F 830 "
            pdb=" C   ILE F 830 "
            pdb=" CB  ILE F 830 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.70   -0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" CG  LEU F 876 "
            pdb=" CB  LEU F 876 "
            pdb=" CD1 LEU F 876 "
            pdb=" CD2 LEU F 876 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.37   -0.22 2.00e-01 2.50e+01 1.19e+00
  chirality pdb=" CA  MET F 569 "
            pdb=" N   MET F 569 "
            pdb=" C   MET F 569 "
            pdb=" CB  MET F 569 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.19e+00
  ... (remaining 1859 not shown)

  Planarity restraints: 2115
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS F1195 "   -0.071 5.00e-02 4.00e+02   1.07e-01 1.82e+01
        pdb=" N   PRO F1196 "    0.185 5.00e-02 4.00e+02
        pdb=" CA  PRO F1196 "   -0.056 5.00e-02 4.00e+02
        pdb=" CD  PRO F1196 "   -0.058 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER F 297 "    0.012 2.00e-02 2.50e+03   2.45e-02 6.03e+00
        pdb=" C   SER F 297 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   SER F 297 "    0.015 2.00e-02 2.50e+03
        pdb=" N   PRO F 298 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F1409 "   -0.013 2.00e-02 2.50e+03   1.73e-02 5.99e+00
        pdb=" CG  TYR F1409 "    0.043 2.00e-02 2.50e+03
        pdb=" CD1 TYR F1409 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 TYR F1409 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE1 TYR F1409 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR F1409 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR F1409 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR F1409 "    0.003 2.00e-02 2.50e+03
  ... (remaining 2112 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 310
        2.69 -     3.24: 12668
        3.24 -     3.80: 19145
        3.80 -     4.35: 23344
        4.35 -     4.90: 38700
  Nonbonded interactions: 94167
  Sorted by model distance:
  nonbonded pdb=" CE  MET F 232 "
            pdb=" O   SER F 281 "
     model   vdw
     2.138 3.460
  nonbonded pdb=" O   ALA F1201 "
            pdb=" OG1 THR F1205 "
     model   vdw
     2.152 3.040
  nonbonded pdb=" OE1 GLU F1036 "
            pdb=" OH  TYR F1048 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" OH  TYR F 362 "
            pdb=" O   ASN F1075 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" NH1 ARG F 199 "
            pdb=" O   GLU F1124 "
     model   vdw
     2.226 3.120
  ... (remaining 94162 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:             5.660
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     12.770
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7378
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   0.164  12445  Z= 0.232
  Angle     :  0.786  18.419  16883  Z= 0.427
  Chirality :  0.045   0.269   1862
  Planarity :  0.005   0.107   2115
  Dihedral  : 17.232  89.573   4499
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 18.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  : 34.05 %
    Favored  : 65.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.74 (0.22), residues: 1463
  helix:  0.72 (0.19), residues: 822
  sheet: -0.66 (0.71), residues: 52
  loop : -2.29 (0.25), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F 818 
 TYR   0.043   0.002   TYR F1409 
 PHE   0.033   0.002   PHE F1404 
 TRP   0.014   0.001   TRP F 663 
 HIS   0.011   0.001   HIS F 848 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 (12443)
  covalent geometry    : angle       0.78554 (16879)
  SS BOND              : bond        0.00201 (    2)
  SS BOND              : angle       0.81022 (    4)
  hydrogen bonds       : bond        0.13813 (  607)
  hydrogen bonds       : angle       5.95241 ( 1785)

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

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

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 173
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F 1512 ARG cc_start: 0.3897 (mmp-170) cc_final: 0.3683 (mmm160)
  outliers start: 4
  outliers final: 2
  residues processed: 176
  average time/residue: 0.1005
  time to fit residues: 26.5018
Evaluate side-chains
  164 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 162
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  448 LEU
Chi-restraints excluded: chain F residue 1310 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    0.4980
   chunk 66 optimal weight:    0.5980
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    0.0570
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    0.2980
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.4898

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

Flipped N/Q/H residues before XYZ refinement:
F1099 GLN
** F1681 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 = 0.4254 r_free = 0.4254 target = 0.159030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.127613 restraints weight = 23297.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.126863 restraints weight = 19859.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.128235 restraints weight = 20619.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.128651 restraints weight = 13813.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.129407 restraints weight = 12764.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7368
moved from start:          0.0828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12445  Z= 0.135
  Angle     :  0.655  11.022  16883  Z= 0.325
  Chirality :  0.043   0.266   1862
  Planarity :  0.005   0.076   2115
  Dihedral  :  4.395  36.587   1637
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 29.15 %
    Favored  : 66.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.40 (0.22), residues: 1463
  helix:  0.92 (0.18), residues: 830
  sheet:  0.24 (0.71), residues: 60
  loop : -2.17 (0.25), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F 938 
 TYR   0.029   0.001   TYR F1409 
 PHE   0.016   0.001   PHE F1445 
 TRP   0.011   0.001   TRP F 664 
 HIS   0.006   0.001   HIS F 848 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (12443)
  covalent geometry    : angle       0.65457 (16879)
  SS BOND              : bond        0.00204 (    2)
  SS BOND              : angle       1.11232 (    4)
  hydrogen bonds       : bond        0.04658 (  607)
  hydrogen bonds       : angle       4.80814 ( 1785)

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

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

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 186
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  146 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.6194 (pm20)
REVERT: F  501 THR cc_start: 0.7173 (p) cc_final: 0.6896 (p)
REVERT: F  725 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7888 (ptp-170)
REVERT: F  957 PHE cc_start: 0.8318 (OUTLIER) cc_final: 0.7443 (t80)
REVERT: F 1110 GLU cc_start: 0.7972 (pm20) cc_final: 0.7620 (pt0)
REVERT: F 1479 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8140 (tt)
REVERT: F 1694 MET cc_start: 0.6613 (mmm) cc_final: 0.6396 (mmt)
REVERT: F 1795 ARG cc_start: 0.7955 (tpt90) cc_final: 0.7712 (tpt90)
REVERT: F 1800 TYR cc_start: 0.6162 (m-10) cc_final: 0.5326 (m-10)
REVERT: F 1851 THR cc_start: 0.7135 (m) cc_final: 0.6769 (t)
  outliers start: 54
  outliers final: 22
  residues processed: 231
  average time/residue: 0.0994
  time to fit residues: 34.3639
Evaluate side-chains
  191 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 165
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  146 GLU
Chi-restraints excluded: chain F residue  148 TYR
Chi-restraints excluded: chain F residue  170 ASP
Chi-restraints excluded: chain F residue  473 THR
Chi-restraints excluded: chain F residue  546 ILE
Chi-restraints excluded: chain F residue  644 LEU
Chi-restraints excluded: chain F residue  690 LEU
Chi-restraints excluded: chain F residue  721 ASN
Chi-restraints excluded: chain F residue  725 ARG
Chi-restraints excluded: chain F residue  734 ILE
Chi-restraints excluded: chain F residue  737 THR
Chi-restraints excluded: chain F residue  797 VAL
Chi-restraints excluded: chain F residue  830 ILE
Chi-restraints excluded: chain F residue  855 LEU
Chi-restraints excluded: chain F residue  873 LEU
Chi-restraints excluded: chain F residue  888 VAL
Chi-restraints excluded: chain F residue  957 PHE
Chi-restraints excluded: chain F residue 1088 HIS
Chi-restraints excluded: chain F residue 1306 LEU
Chi-restraints excluded: chain F residue 1443 SER
Chi-restraints excluded: chain F residue 1479 LEU
Chi-restraints excluded: chain F residue 1496 TRP
Chi-restraints excluded: chain F residue 1621 MET
Chi-restraints excluded: chain F residue 1693 LEU
Chi-restraints excluded: chain F residue 1774 LEU
Chi-restraints excluded: chain F residue 1837 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 42 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 91 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   chunk 137 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** F 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F1099 GLN
F1376 GLN
** F1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.155252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.123403 restraints weight = 23623.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.121649 restraints weight = 21424.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.123112 restraints weight = 23134.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.123635 restraints weight = 14970.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.124713 restraints weight = 13847.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
moved from start:          0.1134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12445  Z= 0.192
  Angle     :  0.696  10.797  16883  Z= 0.343
  Chirality :  0.045   0.301   1862
  Planarity :  0.004   0.064   2115
  Dihedral  :  4.324  19.086   1632
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 11.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.38 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 28.46 %
    Favored  : 66.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.48 (0.22), residues: 1463
  helix:  0.82 (0.18), residues: 835
  sheet:  0.18 (0.67), residues: 60
  loop : -2.15 (0.26), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F 938 
 TYR   0.021   0.002   TYR F1409 
 PHE   0.020   0.002   PHE F1462 
 TRP   0.012   0.001   TRP F1474 
 HIS   0.009   0.001   HIS F1767 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 (12443)
  covalent geometry    : angle       0.69639 (16879)
  SS BOND              : bond        0.00430 (    2)
  SS BOND              : angle       1.04848 (    4)
  hydrogen bonds       : bond        0.04825 (  607)
  hydrogen bonds       : angle       4.83278 ( 1785)

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

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

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 173
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  146 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.6253 (pm20)
REVERT: F  182 MET cc_start: 0.7177 (tmm) cc_final: 0.6872 (tmm)
REVERT: F  501 THR cc_start: 0.7408 (OUTLIER) cc_final: 0.6974 (p)
REVERT: F  725 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7947 (ptp-170)
REVERT: F  957 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.7427 (t80)
REVERT: F 1110 GLU cc_start: 0.7984 (pm20) cc_final: 0.7566 (pt0)
REVERT: F 1199 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8102 (tt)
REVERT: F 1400 MET cc_start: 0.4045 (tpt) cc_final: 0.3712 (tpp)
REVERT: F 1561 ILE cc_start: 0.6242 (OUTLIER) cc_final: 0.5973 (pp)
REVERT: F 1687 PHE cc_start: 0.8399 (m-80) cc_final: 0.7908 (m-80)
REVERT: F 1694 MET cc_start: 0.6534 (mmm) cc_final: 0.6318 (mmt)
REVERT: F 1772 PHE cc_start: 0.7584 (OUTLIER) cc_final: 0.7205 (t80)
REVERT: F 1828 HIS cc_start: 0.6194 (OUTLIER) cc_final: 0.5860 (t-90)
REVERT: F 1851 THR cc_start: 0.7311 (m) cc_final: 0.6937 (t)
  outliers start: 69
  outliers final: 38
  residues processed: 225
  average time/residue: 0.0897
  time to fit residues: 30.8695
Evaluate side-chains
  210 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 164
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  146 GLU
Chi-restraints excluded: chain F residue  148 TYR
Chi-restraints excluded: chain F residue  170 ASP
Chi-restraints excluded: chain F residue  175 LEU
Chi-restraints excluded: chain F residue  213 TYR
Chi-restraints excluded: chain F residue  214 ILE
Chi-restraints excluded: chain F residue  311 CYS
Chi-restraints excluded: chain F residue  373 VAL
Chi-restraints excluded: chain F residue  448 LEU
Chi-restraints excluded: chain F residue  449 VAL
Chi-restraints excluded: chain F residue  473 THR
Chi-restraints excluded: chain F residue  501 THR
Chi-restraints excluded: chain F residue  546 ILE
Chi-restraints excluded: chain F residue  651 LEU
Chi-restraints excluded: chain F residue  725 ARG
Chi-restraints excluded: chain F residue  734 ILE
Chi-restraints excluded: chain F residue  737 THR
Chi-restraints excluded: chain F residue  749 LEU
Chi-restraints excluded: chain F residue  797 VAL
Chi-restraints excluded: chain F residue  830 ILE
Chi-restraints excluded: chain F residue  845 LEU
Chi-restraints excluded: chain F residue  855 LEU
Chi-restraints excluded: chain F residue  873 LEU
Chi-restraints excluded: chain F residue  888 VAL
Chi-restraints excluded: chain F residue  957 PHE
Chi-restraints excluded: chain F residue  975 ILE
Chi-restraints excluded: chain F residue 1030 ILE
Chi-restraints excluded: chain F residue 1039 LEU
Chi-restraints excluded: chain F residue 1088 HIS
Chi-restraints excluded: chain F residue 1183 THR
Chi-restraints excluded: chain F residue 1199 ILE
Chi-restraints excluded: chain F residue 1228 ASN
Chi-restraints excluded: chain F residue 1289 THR
Chi-restraints excluded: chain F residue 1306 LEU
Chi-restraints excluded: chain F residue 1378 LEU
Chi-restraints excluded: chain F residue 1496 TRP
Chi-restraints excluded: chain F residue 1561 ILE
Chi-restraints excluded: chain F residue 1566 ILE
Chi-restraints excluded: chain F residue 1576 PHE
Chi-restraints excluded: chain F residue 1621 MET
Chi-restraints excluded: chain F residue 1693 LEU
Chi-restraints excluded: chain F residue 1755 LEU
Chi-restraints excluded: chain F residue 1772 PHE
Chi-restraints excluded: chain F residue 1774 LEU
Chi-restraints excluded: chain F residue 1828 HIS
Chi-restraints excluded: chain F residue 1837 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 141 optimal weight:    6.9990
   chunk 70 optimal weight:    0.8980
   chunk 80 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 107 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 147 optimal weight:    4.9990
   chunk 113 optimal weight:    7.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** F 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F1099 GLN
F1218 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.154149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.122067 restraints weight = 23712.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.120932 restraints weight = 20984.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.122097 restraints weight = 23470.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.122550 restraints weight = 14796.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.122922 restraints weight = 13533.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.1444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  12445  Z= 0.198
  Angle     :  0.716  12.818  16883  Z= 0.351
  Chirality :  0.045   0.291   1862
  Planarity :  0.004   0.054   2115
  Dihedral  :  4.390  18.647   1632
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.38 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  6.89 %
    Allowed  : 27.77 %
    Favored  : 65.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.65 (0.22), residues: 1463
  helix:  0.69 (0.18), residues: 845
  sheet: -0.16 (0.64), residues: 62
  loop : -2.27 (0.25), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F 938 
 TYR   0.022   0.002   TYR F 148 
 PHE   0.017   0.002   PHE F1363 
 TRP   0.011   0.001   TRP F1474 
 HIS   0.010   0.001   HIS F1767 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 (12443)
  covalent geometry    : angle       0.71561 (16879)
  SS BOND              : bond        0.00331 (    2)
  SS BOND              : angle       1.11898 (    4)
  hydrogen bonds       : bond        0.04806 (  607)
  hydrogen bonds       : angle       4.78763 ( 1785)

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

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

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 90
    poor density    : 176
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  146 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.6250 (pm20)
REVERT: F  182 MET cc_start: 0.7225 (tmm) cc_final: 0.6952 (tmm)
REVERT: F  501 THR cc_start: 0.7483 (OUTLIER) cc_final: 0.7213 (p)
REVERT: F  725 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7933 (ptp-170)
REVERT: F  769 ILE cc_start: 0.7176 (mm) cc_final: 0.6154 (tp)
REVERT: F  957 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.7561 (t80)
REVERT: F 1110 GLU cc_start: 0.8000 (pm20) cc_final: 0.7566 (pt0)
REVERT: F 1227 MET cc_start: 0.7526 (tmm) cc_final: 0.7107 (ttm)
REVERT: F 1400 MET cc_start: 0.4085 (tpt) cc_final: 0.3828 (tpp)
REVERT: F 1512 ARG cc_start: 0.4713 (mmp-170) cc_final: 0.4507 (mmm160)
REVERT: F 1561 ILE cc_start: 0.6349 (OUTLIER) cc_final: 0.6070 (pp)
REVERT: F 1687 PHE cc_start: 0.8346 (m-80) cc_final: 0.7802 (m-80)
REVERT: F 1772 PHE cc_start: 0.7546 (OUTLIER) cc_final: 0.7201 (t80)
REVERT: F 1828 HIS cc_start: 0.6186 (OUTLIER) cc_final: 0.5826 (t-90)
REVERT: F 1851 THR cc_start: 0.7291 (m) cc_final: 0.6889 (t)
REVERT: F 1855 MET cc_start: 0.7348 (pmm) cc_final: 0.6161 (pmm)
  outliers start: 90
  outliers final: 53
  residues processed: 248
  average time/residue: 0.0987
  time to fit residues: 36.6752
Evaluate side-chains
  220 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 160
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  146 GLU
Chi-restraints excluded: chain F residue  148 TYR
Chi-restraints excluded: chain F residue  152 THR
Chi-restraints excluded: chain F residue  170 ASP
Chi-restraints excluded: chain F residue  175 LEU
Chi-restraints excluded: chain F residue  213 TYR
Chi-restraints excluded: chain F residue  214 ILE
Chi-restraints excluded: chain F residue  282 LEU
Chi-restraints excluded: chain F residue  311 CYS
Chi-restraints excluded: chain F residue  373 VAL
Chi-restraints excluded: chain F residue  448 LEU
Chi-restraints excluded: chain F residue  473 THR
Chi-restraints excluded: chain F residue  498 LEU
Chi-restraints excluded: chain F residue  501 THR
Chi-restraints excluded: chain F residue  546 ILE
Chi-restraints excluded: chain F residue  651 LEU
Chi-restraints excluded: chain F residue  725 ARG
Chi-restraints excluded: chain F residue  734 ILE
Chi-restraints excluded: chain F residue  737 THR
Chi-restraints excluded: chain F residue  749 LEU
Chi-restraints excluded: chain F residue  757 ILE
Chi-restraints excluded: chain F residue  797 VAL
Chi-restraints excluded: chain F residue  830 ILE
Chi-restraints excluded: chain F residue  845 LEU
Chi-restraints excluded: chain F residue  855 LEU
Chi-restraints excluded: chain F residue  873 LEU
Chi-restraints excluded: chain F residue  879 LEU
Chi-restraints excluded: chain F residue  888 VAL
Chi-restraints excluded: chain F residue  957 PHE
Chi-restraints excluded: chain F residue  975 ILE
Chi-restraints excluded: chain F residue 1030 ILE
Chi-restraints excluded: chain F residue 1039 LEU
Chi-restraints excluded: chain F residue 1088 HIS
Chi-restraints excluded: chain F residue 1098 ILE
Chi-restraints excluded: chain F residue 1183 THR
Chi-restraints excluded: chain F residue 1199 ILE
Chi-restraints excluded: chain F residue 1228 ASN
Chi-restraints excluded: chain F residue 1306 LEU
Chi-restraints excluded: chain F residue 1314 THR
Chi-restraints excluded: chain F residue 1378 LEU
Chi-restraints excluded: chain F residue 1383 LEU
Chi-restraints excluded: chain F residue 1395 LEU
Chi-restraints excluded: chain F residue 1410 SER
Chi-restraints excluded: chain F residue 1441 LEU
Chi-restraints excluded: chain F residue 1443 SER
Chi-restraints excluded: chain F residue 1476 TRP
Chi-restraints excluded: chain F residue 1496 TRP
Chi-restraints excluded: chain F residue 1561 ILE
Chi-restraints excluded: chain F residue 1576 PHE
Chi-restraints excluded: chain F residue 1621 MET
Chi-restraints excluded: chain F residue 1688 HIS
Chi-restraints excluded: chain F residue 1689 CYS
Chi-restraints excluded: chain F residue 1693 LEU
Chi-restraints excluded: chain F residue 1735 ILE
Chi-restraints excluded: chain F residue 1737 LEU
Chi-restraints excluded: chain F residue 1755 LEU
Chi-restraints excluded: chain F residue 1772 PHE
Chi-restraints excluded: chain F residue 1774 LEU
Chi-restraints excluded: chain F residue 1828 HIS
Chi-restraints excluded: chain F residue 1837 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 77 optimal weight:    0.4980
   chunk 61 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 37 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9980
   chunk 132 optimal weight:    0.6980
   chunk 122 optimal weight:    6.9990
   chunk 85 optimal weight:    0.7980
   chunk 139 optimal weight:    2.9990
   chunk 69 optimal weight:    8.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** F 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1839 ASN ** 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 = 0.4214 r_free = 0.4214 target = 0.155555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.123631 restraints weight = 23573.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.122026 restraints weight = 20622.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.123529 restraints weight = 21773.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.123815 restraints weight = 14034.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.125648 restraints weight = 13188.087|
|-----------------------------------------------------------------------------|
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.1641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12445  Z= 0.146
  Angle     :  0.683  12.400  16883  Z= 0.333
  Chirality :  0.044   0.328   1862
  Planarity :  0.004   0.062   2115
  Dihedral  :  4.332  18.669   1632
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 11.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  6.35 %
    Allowed  : 28.46 %
    Favored  : 65.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.49 (0.22), residues: 1463
  helix:  0.84 (0.18), residues: 839
  sheet: -0.15 (0.63), residues: 62
  loop : -2.21 (0.25), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG F1795 
 TYR   0.021   0.001   TYR F 148 
 PHE   0.019   0.001   PHE F1462 
 TRP   0.010   0.001   TRP F 663 
 HIS   0.010   0.001   HIS F1767 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (12443)
  covalent geometry    : angle       0.68314 (16879)
  SS BOND              : bond        0.00129 (    2)
  SS BOND              : angle       0.98268 (    4)
  hydrogen bonds       : bond        0.04398 (  607)
  hydrogen bonds       : angle       4.65510 ( 1785)

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

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

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 167
  time to evaluate  : 0.466 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  146 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.6221 (pm20)
REVERT: F  182 MET cc_start: 0.7303 (tmm) cc_final: 0.7009 (tmm)
REVERT: F  370 TYR cc_start: 0.7784 (m-80) cc_final: 0.7584 (m-80)
REVERT: F  501 THR cc_start: 0.7636 (OUTLIER) cc_final: 0.7374 (p)
REVERT: F  957 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.7534 (t80)
REVERT: F 1110 GLU cc_start: 0.7941 (pm20) cc_final: 0.7539 (pt0)
REVERT: F 1310 MET cc_start: 0.7291 (ttm) cc_final: 0.7015 (tpt)
REVERT: F 1561 ILE cc_start: 0.6342 (OUTLIER) cc_final: 0.6049 (pp)
REVERT: F 1687 PHE cc_start: 0.8358 (m-80) cc_final: 0.7908 (m-80)
REVERT: F 1772 PHE cc_start: 0.7538 (OUTLIER) cc_final: 0.7159 (t80)
REVERT: F 1800 TYR cc_start: 0.6652 (m-10) cc_final: 0.5590 (m-10)
REVERT: F 1851 THR cc_start: 0.7241 (m) cc_final: 0.6891 (t)
REVERT: F 1855 MET cc_start: 0.7443 (pmm) cc_final: 0.6365 (pmm)
  outliers start: 83
  outliers final: 53
  residues processed: 235
  average time/residue: 0.0921
  time to fit residues: 33.3831
Evaluate side-chains
  212 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 154
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  146 GLU
Chi-restraints excluded: chain F residue  148 TYR
Chi-restraints excluded: chain F residue  170 ASP
Chi-restraints excluded: chain F residue  175 LEU
Chi-restraints excluded: chain F residue  208 SER
Chi-restraints excluded: chain F residue  213 TYR
Chi-restraints excluded: chain F residue  214 ILE
Chi-restraints excluded: chain F residue  373 VAL
Chi-restraints excluded: chain F residue  414 LEU
Chi-restraints excluded: chain F residue  448 LEU
Chi-restraints excluded: chain F residue  473 THR
Chi-restraints excluded: chain F residue  498 LEU
Chi-restraints excluded: chain F residue  501 THR
Chi-restraints excluded: chain F residue  546 ILE
Chi-restraints excluded: chain F residue  641 VAL
Chi-restraints excluded: chain F residue  651 LEU
Chi-restraints excluded: chain F residue  684 ASP
Chi-restraints excluded: chain F residue  690 LEU
Chi-restraints excluded: chain F residue  734 ILE
Chi-restraints excluded: chain F residue  737 THR
Chi-restraints excluded: chain F residue  749 LEU
Chi-restraints excluded: chain F residue  797 VAL
Chi-restraints excluded: chain F residue  830 ILE
Chi-restraints excluded: chain F residue  855 LEU
Chi-restraints excluded: chain F residue  873 LEU
Chi-restraints excluded: chain F residue  879 LEU
Chi-restraints excluded: chain F residue  888 VAL
Chi-restraints excluded: chain F residue  957 PHE
Chi-restraints excluded: chain F residue 1030 ILE
Chi-restraints excluded: chain F residue 1039 LEU
Chi-restraints excluded: chain F residue 1088 HIS
Chi-restraints excluded: chain F residue 1093 TYR
Chi-restraints excluded: chain F residue 1098 ILE
Chi-restraints excluded: chain F residue 1199 ILE
Chi-restraints excluded: chain F residue 1228 ASN
Chi-restraints excluded: chain F residue 1289 THR
Chi-restraints excluded: chain F residue 1306 LEU
Chi-restraints excluded: chain F residue 1313 LEU
Chi-restraints excluded: chain F residue 1323 HIS
Chi-restraints excluded: chain F residue 1364 ILE
Chi-restraints excluded: chain F residue 1395 LEU
Chi-restraints excluded: chain F residue 1410 SER
Chi-restraints excluded: chain F residue 1441 LEU
Chi-restraints excluded: chain F residue 1443 SER
Chi-restraints excluded: chain F residue 1476 TRP
Chi-restraints excluded: chain F residue 1496 TRP
Chi-restraints excluded: chain F residue 1561 ILE
Chi-restraints excluded: chain F residue 1566 ILE
Chi-restraints excluded: chain F residue 1576 PHE
Chi-restraints excluded: chain F residue 1621 MET
Chi-restraints excluded: chain F residue 1693 LEU
Chi-restraints excluded: chain F residue 1735 ILE
Chi-restraints excluded: chain F residue 1737 LEU
Chi-restraints excluded: chain F residue 1755 LEU
Chi-restraints excluded: chain F residue 1772 PHE
Chi-restraints excluded: chain F residue 1774 LEU
Chi-restraints excluded: chain F residue 1837 VAL
Chi-restraints excluded: chain F residue 1839 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 21 optimal weight:    0.2980
   chunk 43 optimal weight:    2.9990
   chunk 51 optimal weight:    7.9990
   chunk 124 optimal weight:    1.9990
   chunk 122 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 139 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 140 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** F 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F1839 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.153470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.121674 restraints weight = 23609.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.120673 restraints weight = 21393.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.121507 restraints weight = 23748.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.122015 restraints weight = 14875.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.122770 restraints weight = 13347.831|
|-----------------------------------------------------------------------------|
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.1847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12445  Z= 0.194
  Angle     :  0.718  13.212  16883  Z= 0.354
  Chirality :  0.045   0.345   1862
  Planarity :  0.005   0.055   2115
  Dihedral  :  4.423  18.391   1632
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.34 %
    Favored  : 91.66 %
  Rotamer:
    Outliers :  7.04 %
    Allowed  : 27.62 %
    Favored  : 65.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.64 (0.22), residues: 1463
  helix:  0.71 (0.18), residues: 838
  sheet:  0.05 (0.63), residues: 60
  loop : -2.26 (0.25), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F 938 
 TYR   0.023   0.002   TYR F 148 
 PHE   0.023   0.002   PHE F1445 
 TRP   0.010   0.001   TRP F 663 
 HIS   0.010   0.001   HIS F1767 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 (12443)
  covalent geometry    : angle       0.71810 (16879)
  SS BOND              : bond        0.00327 (    2)
  SS BOND              : angle       1.16376 (    4)
  hydrogen bonds       : bond        0.04691 (  607)
  hydrogen bonds       : angle       4.75596 ( 1785)

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

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

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 92
    poor density    : 159
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  146 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.6216 (pm20)
REVERT: F  182 MET cc_start: 0.7380 (tmm) cc_final: 0.7087 (tmm)
REVERT: F  185 MET cc_start: 0.8392 (tpt) cc_final: 0.8017 (tpt)
REVERT: F  370 TYR cc_start: 0.7822 (m-80) cc_final: 0.7617 (m-80)
REVERT: F  501 THR cc_start: 0.7719 (OUTLIER) cc_final: 0.7465 (p)
REVERT: F  725 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7933 (mtt90)
REVERT: F  769 ILE cc_start: 0.7275 (mm) cc_final: 0.6683 (tp)
REVERT: F  957 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.7589 (t80)
REVERT: F  965 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.6637 (ptpt)
REVERT: F 1110 GLU cc_start: 0.8005 (pm20) cc_final: 0.7642 (pt0)
REVERT: F 1273 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.6672 (ttm110)
REVERT: F 1561 ILE cc_start: 0.6376 (OUTLIER) cc_final: 0.6089 (pp)
REVERT: F 1687 PHE cc_start: 0.8370 (m-80) cc_final: 0.7943 (m-80)
REVERT: F 1693 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7425 (mt)
REVERT: F 1772 PHE cc_start: 0.7546 (OUTLIER) cc_final: 0.7225 (t80)
REVERT: F 1851 THR cc_start: 0.7319 (m) cc_final: 0.6912 (t)
REVERT: F 1855 MET cc_start: 0.7458 (pmm) cc_final: 0.6412 (pmm)
  outliers start: 92
  outliers final: 63
  residues processed: 231
  average time/residue: 0.1046
  time to fit residues: 35.8388
Evaluate side-chains
  225 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 153
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  146 GLU
Chi-restraints excluded: chain F residue  148 TYR
Chi-restraints excluded: chain F residue  170 ASP
Chi-restraints excluded: chain F residue  175 LEU
Chi-restraints excluded: chain F residue  208 SER
Chi-restraints excluded: chain F residue  213 TYR
Chi-restraints excluded: chain F residue  311 CYS
Chi-restraints excluded: chain F residue  373 VAL
Chi-restraints excluded: chain F residue  414 LEU
Chi-restraints excluded: chain F residue  448 LEU
Chi-restraints excluded: chain F residue  473 THR
Chi-restraints excluded: chain F residue  498 LEU
Chi-restraints excluded: chain F residue  501 THR
Chi-restraints excluded: chain F residue  546 ILE
Chi-restraints excluded: chain F residue  641 VAL
Chi-restraints excluded: chain F residue  651 LEU
Chi-restraints excluded: chain F residue  676 VAL
Chi-restraints excluded: chain F residue  721 ASN
Chi-restraints excluded: chain F residue  725 ARG
Chi-restraints excluded: chain F residue  734 ILE
Chi-restraints excluded: chain F residue  737 THR
Chi-restraints excluded: chain F residue  749 LEU
Chi-restraints excluded: chain F residue  757 ILE
Chi-restraints excluded: chain F residue  797 VAL
Chi-restraints excluded: chain F residue  830 ILE
Chi-restraints excluded: chain F residue  845 LEU
Chi-restraints excluded: chain F residue  855 LEU
Chi-restraints excluded: chain F residue  873 LEU
Chi-restraints excluded: chain F residue  879 LEU
Chi-restraints excluded: chain F residue  888 VAL
Chi-restraints excluded: chain F residue  957 PHE
Chi-restraints excluded: chain F residue  965 LYS
Chi-restraints excluded: chain F residue  975 ILE
Chi-restraints excluded: chain F residue 1030 ILE
Chi-restraints excluded: chain F residue 1039 LEU
Chi-restraints excluded: chain F residue 1088 HIS
Chi-restraints excluded: chain F residue 1090 LEU
Chi-restraints excluded: chain F residue 1093 TYR
Chi-restraints excluded: chain F residue 1112 CYS
Chi-restraints excluded: chain F residue 1183 THR
Chi-restraints excluded: chain F residue 1199 ILE
Chi-restraints excluded: chain F residue 1210 VAL
Chi-restraints excluded: chain F residue 1228 ASN
Chi-restraints excluded: chain F residue 1273 ARG
Chi-restraints excluded: chain F residue 1289 THR
Chi-restraints excluded: chain F residue 1306 LEU
Chi-restraints excluded: chain F residue 1313 LEU
Chi-restraints excluded: chain F residue 1314 THR
Chi-restraints excluded: chain F residue 1323 HIS
Chi-restraints excluded: chain F residue 1378 LEU
Chi-restraints excluded: chain F residue 1383 LEU
Chi-restraints excluded: chain F residue 1395 LEU
Chi-restraints excluded: chain F residue 1410 SER
Chi-restraints excluded: chain F residue 1441 LEU
Chi-restraints excluded: chain F residue 1442 TYR
Chi-restraints excluded: chain F residue 1476 TRP
Chi-restraints excluded: chain F residue 1496 TRP
Chi-restraints excluded: chain F residue 1561 ILE
Chi-restraints excluded: chain F residue 1566 ILE
Chi-restraints excluded: chain F residue 1576 PHE
Chi-restraints excluded: chain F residue 1614 LEU
Chi-restraints excluded: chain F residue 1621 MET
Chi-restraints excluded: chain F residue 1658 PHE
Chi-restraints excluded: chain F residue 1688 HIS
Chi-restraints excluded: chain F residue 1689 CYS
Chi-restraints excluded: chain F residue 1693 LEU
Chi-restraints excluded: chain F residue 1735 ILE
Chi-restraints excluded: chain F residue 1737 LEU
Chi-restraints excluded: chain F residue 1755 LEU
Chi-restraints excluded: chain F residue 1772 PHE
Chi-restraints excluded: chain F residue 1774 LEU
Chi-restraints excluded: chain F residue 1837 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 56 optimal weight:    0.3980
   chunk 11 optimal weight:    0.9980
   chunk 119 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 104 optimal weight:    0.3980
   chunk 97 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 99 optimal weight:    2.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
** F 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1839 ASN ** 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 = 0.4211 r_free = 0.4211 target = 0.155482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.124333 restraints weight = 23425.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.122894 restraints weight = 21230.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.124036 restraints weight = 22968.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.124922 restraints weight = 14798.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.125791 restraints weight = 13126.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.3800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12445  Z= 0.141
  Angle     :  0.685  13.563  16883  Z= 0.337
  Chirality :  0.044   0.343   1862
  Planarity :  0.004   0.056   2115
  Dihedral  :  4.324  18.250   1632
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 28.69 %
    Favored  : 65.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.47 (0.22), residues: 1463
  helix:  0.84 (0.18), residues: 841
  sheet:  0.18 (0.65), residues: 60
  loop : -2.22 (0.25), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG F 938 
 TYR   0.021   0.001   TYR F 148 
 PHE   0.023   0.001   PHE F1462 
 TRP   0.011   0.001   TRP F1773 
 HIS   0.009   0.001   HIS F1767 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (12443)
  covalent geometry    : angle       0.68490 (16879)
  SS BOND              : bond        0.00106 (    2)
  SS BOND              : angle       1.03406 (    4)
  hydrogen bonds       : bond        0.04312 (  607)
  hydrogen bonds       : angle       4.62070 ( 1785)

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

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

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 168
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  146 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.6226 (pm20)
REVERT: F  182 MET cc_start: 0.7325 (tmm) cc_final: 0.7057 (tmm)
REVERT: F  501 THR cc_start: 0.7708 (OUTLIER) cc_final: 0.7470 (p)
REVERT: F  725 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7887 (ptp-170)
REVERT: F  769 ILE cc_start: 0.7298 (mm) cc_final: 0.6732 (tp)
REVERT: F  957 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.7561 (t80)
REVERT: F  965 LYS cc_start: 0.7377 (OUTLIER) cc_final: 0.6609 (ptpt)
REVERT: F 1006 ARG cc_start: 0.8413 (ptt90) cc_final: 0.8098 (ptt-90)
REVERT: F 1110 GLU cc_start: 0.7974 (pm20) cc_final: 0.7617 (pt0)
REVERT: F 1273 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.6600 (ttm110)
REVERT: F 1404 PHE cc_start: 0.6038 (m-80) cc_final: 0.5414 (m-80)
REVERT: F 1561 ILE cc_start: 0.6308 (OUTLIER) cc_final: 0.6037 (pp)
REVERT: F 1687 PHE cc_start: 0.8341 (m-80) cc_final: 0.7949 (m-80)
REVERT: F 1693 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7402 (mt)
REVERT: F 1772 PHE cc_start: 0.7493 (OUTLIER) cc_final: 0.7206 (t80)
REVERT: F 1793 ARG cc_start: 0.7741 (ptt90) cc_final: 0.7532 (ptt-90)
REVERT: F 1795 ARG cc_start: 0.8281 (tpt90) cc_final: 0.7722 (tpm170)
REVERT: F 1811 PHE cc_start: 0.7431 (OUTLIER) cc_final: 0.6802 (m-80)
REVERT: F 1851 THR cc_start: 0.7165 (m) cc_final: 0.6804 (t)
REVERT: F 1855 MET cc_start: 0.7512 (pmm) cc_final: 0.6537 (pmm)
  outliers start: 72
  outliers final: 46
  residues processed: 225
  average time/residue: 0.1037
  time to fit residues: 34.7897
Evaluate side-chains
  215 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 159
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  146 GLU
Chi-restraints excluded: chain F residue  148 TYR
Chi-restraints excluded: chain F residue  170 ASP
Chi-restraints excluded: chain F residue  208 SER
Chi-restraints excluded: chain F residue  311 CYS
Chi-restraints excluded: chain F residue  373 VAL
Chi-restraints excluded: chain F residue  414 LEU
Chi-restraints excluded: chain F residue  448 LEU
Chi-restraints excluded: chain F residue  473 THR
Chi-restraints excluded: chain F residue  498 LEU
Chi-restraints excluded: chain F residue  501 THR
Chi-restraints excluded: chain F residue  546 ILE
Chi-restraints excluded: chain F residue  641 VAL
Chi-restraints excluded: chain F residue  651 LEU
Chi-restraints excluded: chain F residue  684 ASP
Chi-restraints excluded: chain F residue  690 LEU
Chi-restraints excluded: chain F residue  725 ARG
Chi-restraints excluded: chain F residue  734 ILE
Chi-restraints excluded: chain F residue  737 THR
Chi-restraints excluded: chain F residue  749 LEU
Chi-restraints excluded: chain F residue  797 VAL
Chi-restraints excluded: chain F residue  830 ILE
Chi-restraints excluded: chain F residue  855 LEU
Chi-restraints excluded: chain F residue  873 LEU
Chi-restraints excluded: chain F residue  879 LEU
Chi-restraints excluded: chain F residue  888 VAL
Chi-restraints excluded: chain F residue  957 PHE
Chi-restraints excluded: chain F residue  965 LYS
Chi-restraints excluded: chain F residue 1030 ILE
Chi-restraints excluded: chain F residue 1039 LEU
Chi-restraints excluded: chain F residue 1088 HIS
Chi-restraints excluded: chain F residue 1090 LEU
Chi-restraints excluded: chain F residue 1093 TYR
Chi-restraints excluded: chain F residue 1112 CYS
Chi-restraints excluded: chain F residue 1199 ILE
Chi-restraints excluded: chain F residue 1228 ASN
Chi-restraints excluded: chain F residue 1273 ARG
Chi-restraints excluded: chain F residue 1306 LEU
Chi-restraints excluded: chain F residue 1313 LEU
Chi-restraints excluded: chain F residue 1323 HIS
Chi-restraints excluded: chain F residue 1395 LEU
Chi-restraints excluded: chain F residue 1441 LEU
Chi-restraints excluded: chain F residue 1442 TYR
Chi-restraints excluded: chain F residue 1476 TRP
Chi-restraints excluded: chain F residue 1496 TRP
Chi-restraints excluded: chain F residue 1561 ILE
Chi-restraints excluded: chain F residue 1566 ILE
Chi-restraints excluded: chain F residue 1576 PHE
Chi-restraints excluded: chain F residue 1621 MET
Chi-restraints excluded: chain F residue 1669 PHE
Chi-restraints excluded: chain F residue 1689 CYS
Chi-restraints excluded: chain F residue 1693 LEU
Chi-restraints excluded: chain F residue 1737 LEU
Chi-restraints excluded: chain F residue 1755 LEU
Chi-restraints excluded: chain F residue 1772 PHE
Chi-restraints excluded: chain F residue 1811 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 62 optimal weight:    0.0870
   chunk 137 optimal weight:    1.9990
   chunk 121 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 93 optimal weight:    0.0470
   chunk 50 optimal weight:    0.8980
   chunk 63 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 54 optimal weight:    0.1980
   chunk 116 optimal weight:    1.9990
   chunk 90 optimal weight:    0.6980
   overall best weight:    0.3656

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

Flipped N/Q/H residues before XYZ refinement:
F1228 ASN
** F1839 ASN ** 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 = 0.4247 r_free = 0.4247 target = 0.158055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.126445 restraints weight = 23179.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.125345 restraints weight = 20288.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.126745 restraints weight = 21258.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.127147 restraints weight = 13567.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.129175 restraints weight = 12651.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7397
moved from start:          0.2098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12445  Z= 0.125
  Angle     :  0.678  14.406  16883  Z= 0.331
  Chirality :  0.043   0.334   1862
  Planarity :  0.004   0.057   2115
  Dihedral  :  4.230  17.819   1632
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.25 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 29.15 %
    Favored  : 65.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.34 (0.23), residues: 1463
  helix:  0.97 (0.19), residues: 839
  sheet:  0.29 (0.65), residues: 60
  loop : -2.18 (0.26), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG F 938 
 TYR   0.020   0.001   TYR F 148 
 PHE   0.021   0.001   PHE F1462 
 TRP   0.012   0.001   TRP F1773 
 HIS   0.008   0.001   HIS F1767 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (12443)
  covalent geometry    : angle       0.67761 (16879)
  SS BOND              : bond        0.00056 (    2)
  SS BOND              : angle       0.92746 (    4)
  hydrogen bonds       : bond        0.04048 (  607)
  hydrogen bonds       : angle       4.50607 ( 1785)

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

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

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 161
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  146 GLU cc_start: 0.6638 (OUTLIER) cc_final: 0.6106 (pm20)
REVERT: F  182 MET cc_start: 0.7239 (tmm) cc_final: 0.6990 (tmm)
REVERT: F  241 MET cc_start: 0.7844 (tmm) cc_final: 0.7563 (tmm)
REVERT: F  501 THR cc_start: 0.7820 (OUTLIER) cc_final: 0.7572 (p)
REVERT: F  725 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7798 (mtt90)
REVERT: F  957 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.7391 (t80)
REVERT: F  965 LYS cc_start: 0.7360 (OUTLIER) cc_final: 0.6644 (ptpt)
REVERT: F 1110 GLU cc_start: 0.7906 (pm20) cc_final: 0.7572 (pt0)
REVERT: F 1273 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.6739 (ttm110)
REVERT: F 1407 GLN cc_start: 0.8250 (mt0) cc_final: 0.7891 (tm-30)
REVERT: F 1561 ILE cc_start: 0.6369 (OUTLIER) cc_final: 0.6129 (pp)
REVERT: F 1687 PHE cc_start: 0.8349 (m-80) cc_final: 0.7888 (m-80)
REVERT: F 1693 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7408 (mt)
REVERT: F 1772 PHE cc_start: 0.7353 (OUTLIER) cc_final: 0.7126 (t80)
REVERT: F 1851 THR cc_start: 0.7015 (m) cc_final: 0.6682 (t)
REVERT: F 1855 MET cc_start: 0.7521 (pmm) cc_final: 0.6537 (pmm)
  outliers start: 68
  outliers final: 44
  residues processed: 215
  average time/residue: 0.1037
  time to fit residues: 33.0310
Evaluate side-chains
  205 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 152
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  146 GLU
Chi-restraints excluded: chain F residue  148 TYR
Chi-restraints excluded: chain F residue  170 ASP
Chi-restraints excluded: chain F residue  208 SER
Chi-restraints excluded: chain F residue  311 CYS
Chi-restraints excluded: chain F residue  350 GLU
Chi-restraints excluded: chain F residue  373 VAL
Chi-restraints excluded: chain F residue  448 LEU
Chi-restraints excluded: chain F residue  473 THR
Chi-restraints excluded: chain F residue  501 THR
Chi-restraints excluded: chain F residue  546 ILE
Chi-restraints excluded: chain F residue  651 LEU
Chi-restraints excluded: chain F residue  690 LEU
Chi-restraints excluded: chain F residue  725 ARG
Chi-restraints excluded: chain F residue  734 ILE
Chi-restraints excluded: chain F residue  737 THR
Chi-restraints excluded: chain F residue  749 LEU
Chi-restraints excluded: chain F residue  797 VAL
Chi-restraints excluded: chain F residue  830 ILE
Chi-restraints excluded: chain F residue  855 LEU
Chi-restraints excluded: chain F residue  873 LEU
Chi-restraints excluded: chain F residue  888 VAL
Chi-restraints excluded: chain F residue  957 PHE
Chi-restraints excluded: chain F residue  965 LYS
Chi-restraints excluded: chain F residue 1030 ILE
Chi-restraints excluded: chain F residue 1039 LEU
Chi-restraints excluded: chain F residue 1088 HIS
Chi-restraints excluded: chain F residue 1090 LEU
Chi-restraints excluded: chain F residue 1093 TYR
Chi-restraints excluded: chain F residue 1112 CYS
Chi-restraints excluded: chain F residue 1199 ILE
Chi-restraints excluded: chain F residue 1210 VAL
Chi-restraints excluded: chain F residue 1228 ASN
Chi-restraints excluded: chain F residue 1273 ARG
Chi-restraints excluded: chain F residue 1306 LEU
Chi-restraints excluded: chain F residue 1310 MET
Chi-restraints excluded: chain F residue 1313 LEU
Chi-restraints excluded: chain F residue 1441 LEU
Chi-restraints excluded: chain F residue 1442 TYR
Chi-restraints excluded: chain F residue 1443 SER
Chi-restraints excluded: chain F residue 1476 TRP
Chi-restraints excluded: chain F residue 1496 TRP
Chi-restraints excluded: chain F residue 1561 ILE
Chi-restraints excluded: chain F residue 1566 ILE
Chi-restraints excluded: chain F residue 1576 PHE
Chi-restraints excluded: chain F residue 1621 MET
Chi-restraints excluded: chain F residue 1658 PHE
Chi-restraints excluded: chain F residue 1689 CYS
Chi-restraints excluded: chain F residue 1693 LEU
Chi-restraints excluded: chain F residue 1735 ILE
Chi-restraints excluded: chain F residue 1737 LEU
Chi-restraints excluded: chain F residue 1755 LEU
Chi-restraints excluded: chain F residue 1772 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 118 optimal weight:    0.5980
   chunk 46 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0770
   chunk 16 optimal weight:    3.9990
   chunk 40 optimal weight:    4.9990
   chunk 131 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 130 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 36 optimal weight:    9.9990
   overall best weight:    1.3344

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

Flipped N/Q/H residues before XYZ refinement:
** F 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F1228 ASN
F1789 GLN
F1839 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.153554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.122139 restraints weight = 23307.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.120783 restraints weight = 21211.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.121733 restraints weight = 24029.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.122484 restraints weight = 15169.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.124634 restraints weight = 13453.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.2159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  12445  Z= 0.202
  Angle     :  0.742  13.909  16883  Z= 0.363
  Chirality :  0.046   0.345   1862
  Planarity :  0.005   0.064   2115
  Dihedral  :  4.397  18.544   1632
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.72 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 29.92 %
    Favored  : 64.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.51 (0.22), residues: 1463
  helix:  0.79 (0.18), residues: 835
  sheet:  0.03 (0.64), residues: 62
  loop : -2.16 (0.25), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG F 852 
 TYR   0.022   0.002   TYR F 148 
 PHE   0.018   0.002   PHE F1462 
 TRP   0.012   0.001   TRP F1773 
 HIS   0.009   0.001   HIS F1767 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 (12443)
  covalent geometry    : angle       0.74187 (16879)
  SS BOND              : bond        0.00260 (    2)
  SS BOND              : angle       0.89089 (    4)
  hydrogen bonds       : bond        0.04487 (  607)
  hydrogen bonds       : angle       4.67917 ( 1785)

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

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

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 155
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
REVERT: F  146 GLU cc_start: 0.6649 (OUTLIER) cc_final: 0.6162 (pm20)
REVERT: F  182 MET cc_start: 0.7359 (tmm) cc_final: 0.7110 (tmm)
REVERT: F  185 MET cc_start: 0.8412 (mmt) cc_final: 0.7824 (tpt)
REVERT: F  725 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7818 (mtt90)
REVERT: F  769 ILE cc_start: 0.7306 (mm) cc_final: 0.6826 (tp)
REVERT: F  957 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.7433 (t80)
REVERT: F  965 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.6659 (ptpt)
REVERT: F 1110 GLU cc_start: 0.7965 (pm20) cc_final: 0.7619 (pt0)
REVERT: F 1273 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.6680 (ttm110)
REVERT: F 1310 MET cc_start: 0.7292 (OUTLIER) cc_final: 0.7023 (tpt)
REVERT: F 1561 ILE cc_start: 0.6379 (OUTLIER) cc_final: 0.6132 (pp)
REVERT: F 1687 PHE cc_start: 0.8348 (m-10) cc_final: 0.7974 (m-80)
REVERT: F 1693 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7504 (mt)
REVERT: F 1772 PHE cc_start: 0.7425 (OUTLIER) cc_final: 0.7221 (t80)
REVERT: F 1811 PHE cc_start: 0.7558 (OUTLIER) cc_final: 0.6823 (m-80)
REVERT: F 1839 ASN cc_start: 0.7342 (OUTLIER) cc_final: 0.6924 (t0)
REVERT: F 1851 THR cc_start: 0.7248 (m) cc_final: 0.6895 (t)
REVERT: F 1855 MET cc_start: 0.7509 (pmm) cc_final: 0.6530 (pmm)
  outliers start: 72
  outliers final: 52
  residues processed: 215
  average time/residue: 0.1066
  time to fit residues: 33.8790
Evaluate side-chains
  216 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 153
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  146 GLU
Chi-restraints excluded: chain F residue  148 TYR
Chi-restraints excluded: chain F residue  170 ASP
Chi-restraints excluded: chain F residue  175 LEU
Chi-restraints excluded: chain F residue  194 ASP
Chi-restraints excluded: chain F residue  208 SER
Chi-restraints excluded: chain F residue  213 TYR
Chi-restraints excluded: chain F residue  311 CYS
Chi-restraints excluded: chain F residue  350 GLU
Chi-restraints excluded: chain F residue  373 VAL
Chi-restraints excluded: chain F residue  414 LEU
Chi-restraints excluded: chain F residue  448 LEU
Chi-restraints excluded: chain F residue  473 THR
Chi-restraints excluded: chain F residue  498 LEU
Chi-restraints excluded: chain F residue  501 THR
Chi-restraints excluded: chain F residue  546 ILE
Chi-restraints excluded: chain F residue  641 VAL
Chi-restraints excluded: chain F residue  651 LEU
Chi-restraints excluded: chain F residue  725 ARG
Chi-restraints excluded: chain F residue  734 ILE
Chi-restraints excluded: chain F residue  737 THR
Chi-restraints excluded: chain F residue  749 LEU
Chi-restraints excluded: chain F residue  778 HIS
Chi-restraints excluded: chain F residue  797 VAL
Chi-restraints excluded: chain F residue  830 ILE
Chi-restraints excluded: chain F residue  845 LEU
Chi-restraints excluded: chain F residue  873 LEU
Chi-restraints excluded: chain F residue  879 LEU
Chi-restraints excluded: chain F residue  888 VAL
Chi-restraints excluded: chain F residue  957 PHE
Chi-restraints excluded: chain F residue  965 LYS
Chi-restraints excluded: chain F residue 1030 ILE
Chi-restraints excluded: chain F residue 1039 LEU
Chi-restraints excluded: chain F residue 1088 HIS
Chi-restraints excluded: chain F residue 1090 LEU
Chi-restraints excluded: chain F residue 1093 TYR
Chi-restraints excluded: chain F residue 1112 CYS
Chi-restraints excluded: chain F residue 1199 ILE
Chi-restraints excluded: chain F residue 1210 VAL
Chi-restraints excluded: chain F residue 1273 ARG
Chi-restraints excluded: chain F residue 1306 LEU
Chi-restraints excluded: chain F residue 1310 MET
Chi-restraints excluded: chain F residue 1313 LEU
Chi-restraints excluded: chain F residue 1379 ILE
Chi-restraints excluded: chain F residue 1395 LEU
Chi-restraints excluded: chain F residue 1441 LEU
Chi-restraints excluded: chain F residue 1442 TYR
Chi-restraints excluded: chain F residue 1443 SER
Chi-restraints excluded: chain F residue 1476 TRP
Chi-restraints excluded: chain F residue 1496 TRP
Chi-restraints excluded: chain F residue 1561 ILE
Chi-restraints excluded: chain F residue 1566 ILE
Chi-restraints excluded: chain F residue 1576 PHE
Chi-restraints excluded: chain F residue 1621 MET
Chi-restraints excluded: chain F residue 1669 PHE
Chi-restraints excluded: chain F residue 1689 CYS
Chi-restraints excluded: chain F residue 1693 LEU
Chi-restraints excluded: chain F residue 1735 ILE
Chi-restraints excluded: chain F residue 1737 LEU
Chi-restraints excluded: chain F residue 1755 LEU
Chi-restraints excluded: chain F residue 1772 PHE
Chi-restraints excluded: chain F residue 1811 PHE
Chi-restraints excluded: chain F residue 1839 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 145 optimal weight:    9.9990
   chunk 51 optimal weight:    7.9990
   chunk 33 optimal weight:    3.9990
   chunk 119 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 126 optimal weight:    0.9980
   chunk 41 optimal weight:    0.0030
   chunk 120 optimal weight:    3.9990
   chunk 103 optimal weight:    0.7980
   chunk 100 optimal weight:    0.9980
   overall best weight:    0.7390

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

Flipped N/Q/H residues before XYZ refinement:
** F 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F1839 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.155074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.124495 restraints weight = 23532.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.124625 restraints weight = 22443.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.125169 restraints weight = 23864.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.126589 restraints weight = 14800.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.126746 restraints weight = 12482.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.3826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7411
moved from start:          0.2253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12445  Z= 0.149
  Angle     :  0.724  13.621  16883  Z= 0.352
  Chirality :  0.045   0.356   1862
  Planarity :  0.005   0.074   2115
  Dihedral  :  4.363  18.992   1632
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.25 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  4.97 %
    Allowed  : 30.60 %
    Favored  : 64.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.46 (0.22), residues: 1463
  helix:  0.81 (0.18), residues: 842
  sheet:  0.01 (0.63), residues: 62
  loop : -2.14 (0.26), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG F 852 
 TYR   0.026   0.001   TYR F1506 
 PHE   0.025   0.001   PHE F1462 
 TRP   0.014   0.001   TRP F1773 
 HIS   0.008   0.001   HIS F1767 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (12443)
  covalent geometry    : angle       0.72393 (16879)
  SS BOND              : bond        0.00135 (    2)
  SS BOND              : angle       0.86586 (    4)
  hydrogen bonds       : bond        0.04298 (  607)
  hydrogen bonds       : angle       4.60345 ( 1785)

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

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

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 154
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
REVERT: F  146 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.6196 (pm20)
REVERT: F  182 MET cc_start: 0.7295 (tmm) cc_final: 0.7026 (tmm)
REVERT: F  185 MET cc_start: 0.8388 (mmt) cc_final: 0.7759 (tpt)
REVERT: F  241 MET cc_start: 0.7958 (tmm) cc_final: 0.7623 (tmm)
REVERT: F  501 THR cc_start: 0.7967 (OUTLIER) cc_final: 0.7737 (p)
REVERT: F  725 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7775 (mtt90)
REVERT: F  769 ILE cc_start: 0.7287 (mm) cc_final: 0.6820 (tp)
REVERT: F  957 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.7520 (t80)
REVERT: F  965 LYS cc_start: 0.7468 (OUTLIER) cc_final: 0.6694 (ptpt)
REVERT: F 1110 GLU cc_start: 0.7930 (pm20) cc_final: 0.7593 (pt0)
REVERT: F 1273 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.6804 (ttm110)
REVERT: F 1310 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.7083 (tpt)
REVERT: F 1404 PHE cc_start: 0.5857 (m-80) cc_final: 0.4697 (m-80)
REVERT: F 1561 ILE cc_start: 0.6252 (OUTLIER) cc_final: 0.5999 (pp)
REVERT: F 1687 PHE cc_start: 0.8225 (m-10) cc_final: 0.7811 (m-80)
REVERT: F 1693 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7406 (mt)
REVERT: F 1811 PHE cc_start: 0.7395 (OUTLIER) cc_final: 0.6697 (m-80)
REVERT: F 1839 ASN cc_start: 0.7509 (OUTLIER) cc_final: 0.6830 (t0)
REVERT: F 1851 THR cc_start: 0.7087 (m) cc_final: 0.6731 (t)
REVERT: F 1855 MET cc_start: 0.7572 (pmm) cc_final: 0.6607 (pmm)
  outliers start: 65
  outliers final: 46
  residues processed: 206
  average time/residue: 0.0988
  time to fit residues: 30.0340
Evaluate side-chains
  208 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 151
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  146 GLU
Chi-restraints excluded: chain F residue  148 TYR
Chi-restraints excluded: chain F residue  170 ASP
Chi-restraints excluded: chain F residue  208 SER
Chi-restraints excluded: chain F residue  213 TYR
Chi-restraints excluded: chain F residue  311 CYS
Chi-restraints excluded: chain F residue  350 GLU
Chi-restraints excluded: chain F residue  373 VAL
Chi-restraints excluded: chain F residue  414 LEU
Chi-restraints excluded: chain F residue  448 LEU
Chi-restraints excluded: chain F residue  473 THR
Chi-restraints excluded: chain F residue  501 THR
Chi-restraints excluded: chain F residue  546 ILE
Chi-restraints excluded: chain F residue  651 LEU
Chi-restraints excluded: chain F residue  725 ARG
Chi-restraints excluded: chain F residue  734 ILE
Chi-restraints excluded: chain F residue  737 THR
Chi-restraints excluded: chain F residue  749 LEU
Chi-restraints excluded: chain F residue  778 HIS
Chi-restraints excluded: chain F residue  797 VAL
Chi-restraints excluded: chain F residue  830 ILE
Chi-restraints excluded: chain F residue  873 LEU
Chi-restraints excluded: chain F residue  879 LEU
Chi-restraints excluded: chain F residue  888 VAL
Chi-restraints excluded: chain F residue  957 PHE
Chi-restraints excluded: chain F residue  965 LYS
Chi-restraints excluded: chain F residue 1030 ILE
Chi-restraints excluded: chain F residue 1039 LEU
Chi-restraints excluded: chain F residue 1088 HIS
Chi-restraints excluded: chain F residue 1090 LEU
Chi-restraints excluded: chain F residue 1093 TYR
Chi-restraints excluded: chain F residue 1112 CYS
Chi-restraints excluded: chain F residue 1199 ILE
Chi-restraints excluded: chain F residue 1210 VAL
Chi-restraints excluded: chain F residue 1273 ARG
Chi-restraints excluded: chain F residue 1306 LEU
Chi-restraints excluded: chain F residue 1310 MET
Chi-restraints excluded: chain F residue 1313 LEU
Chi-restraints excluded: chain F residue 1379 ILE
Chi-restraints excluded: chain F residue 1395 LEU
Chi-restraints excluded: chain F residue 1441 LEU
Chi-restraints excluded: chain F residue 1442 TYR
Chi-restraints excluded: chain F residue 1443 SER
Chi-restraints excluded: chain F residue 1476 TRP
Chi-restraints excluded: chain F residue 1496 TRP
Chi-restraints excluded: chain F residue 1561 ILE
Chi-restraints excluded: chain F residue 1566 ILE
Chi-restraints excluded: chain F residue 1576 PHE
Chi-restraints excluded: chain F residue 1621 MET
Chi-restraints excluded: chain F residue 1669 PHE
Chi-restraints excluded: chain F residue 1689 CYS
Chi-restraints excluded: chain F residue 1693 LEU
Chi-restraints excluded: chain F residue 1735 ILE
Chi-restraints excluded: chain F residue 1737 LEU
Chi-restraints excluded: chain F residue 1755 LEU
Chi-restraints excluded: chain F residue 1811 PHE
Chi-restraints excluded: chain F residue 1839 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 87 optimal weight:    0.3980
   chunk 109 optimal weight:    0.9980
   chunk 64 optimal weight:    0.4980
   chunk 22 optimal weight:    0.7980
   chunk 91 optimal weight:    0.7980
   chunk 114 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   chunk 128 optimal weight:    0.9980
   chunk 16 optimal weight:   10.0000
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** F 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F1839 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.155270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.124367 restraints weight = 23392.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.123053 restraints weight = 20372.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.124257 restraints weight = 22469.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.124827 restraints weight = 14679.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.126953 restraints weight = 13231.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7420
moved from start:          0.2316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12445  Z= 0.146
  Angle     :  0.722  13.741  16883  Z= 0.352
  Chirality :  0.045   0.331   1862
  Planarity :  0.005   0.071   2115
  Dihedral  :  4.351  19.770   1632
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  4.97 %
    Allowed  : 30.37 %
    Favored  : 64.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.43 (0.22), residues: 1463
  helix:  0.84 (0.18), residues: 843
  sheet:  0.02 (0.64), residues: 62
  loop : -2.12 (0.26), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG F1793 
 TYR   0.025   0.001   TYR F1506 
 PHE   0.028   0.002   PHE F1772 
 TRP   0.019   0.001   TRP F1773 
 HIS   0.008   0.001   HIS F1767 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (12443)
  covalent geometry    : angle       0.72225 (16879)
  SS BOND              : bond        0.00125 (    2)
  SS BOND              : angle       0.75865 (    4)
  hydrogen bonds       : bond        0.04234 (  607)
  hydrogen bonds       : angle       4.61161 ( 1785)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1886.75 seconds
wall clock time: 33 minutes 33.78 seconds (2013.78 seconds total)