Starting phenix.real_space_refine
on Tue May 20 02:23:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jb5_36141/05_2025/8jb5_36141.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jb5_36141/05_2025/8jb5_36141.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jb5_36141/05_2025/8jb5_36141.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jb5_36141/05_2025/8jb5_36141.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jb5_36141/05_2025/8jb5_36141.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jb5_36141/05_2025/8jb5_36141.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.005
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: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      47      5.16       5
     C   12183      2.51       5
     N    3022      2.21       5
     O    3774      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 324 residue(s): 0.07s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 19027
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 19026
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2355, 19026
          Classifications: {'peptide': 2355}
          Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 2298}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   5704  SG  CYS A 698      81.942  22.758  87.073  1.00 23.67           S

  Time building chain proxies: 10.66, per 1000 atoms: 0.56
  Number of scatterers: 19027
  At special positions: 0
  Unit cell: (180.442, 161.963, 208.704, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      47     16.00
     O    3774      8.00
     N    3022      7.00
     C   12183      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 4.86
  Conformation dependent library (CDL) restraints added in 2.5 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A3000 "
        pdb="ZN    ZN A3000 " - pdb=" SG  CYS A 698 "
        pdb="ZN    ZN A3000 " - pdb=" NE2 HIS A 757 "
        pdb="ZN    ZN A3000 " - pdb=" ND1 HIS A 653 "


  4702 Ramachandran restraints generated.
    2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4446

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 44 sheets defined
      31.8% alpha, 22.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 3.48
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 13
    Processing helix  chain 'A' and resid 21 through 36
    Processing helix  chain 'A' and resid 41 through 63
    Processing helix  chain 'A' and resid 68 through 87
    Processing helix  chain 'A' and resid 108 through 122
      removed outlier: 3.902A  pdb=" N   GLN A 117 " --> pdb=" O   ASN A 113 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   TRP A 118 " --> pdb=" O   TYR A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 156
      removed outlier: 3.553A  pdb=" N   LEU A 141 " --> pdb=" O   LEU A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 197
    Processing helix  chain 'A' and resid 201 through 214
      removed outlier: 3.521A  pdb=" N   ILE A 205 " --> pdb=" O   ILE A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 234
    Processing helix  chain 'A' and resid 248 through 261
    Processing helix  chain 'A' and resid 264 through 280
      removed outlier: 3.976A  pdb=" N   ILE A 274 " --> pdb=" O   ASP A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 324
    Processing helix  chain 'A' and resid 339 through 353
      removed outlier: 3.967A  pdb=" N   SER A 352 " --> pdb=" O   SER A 348 " (cutoff:3.500A)
      removed outlier: 4.545A  pdb=" N   LYS A 353 " --> pdb=" O   ALA A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 358
    Processing helix  chain 'A' and resid 393 through 420
      removed outlier: 3.533A  pdb=" N   ASP A 397 " --> pdb=" O   SER A 393 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ILE A 409 " --> pdb=" O   ASN A 405 " (cutoff:3.500A)
      Proline residue:  A 416  - end of helix
    Processing helix  chain 'A' and resid 423 through 438
    Processing helix  chain 'A' and resid 443 through 450
    Processing helix  chain 'A' and resid 452 through 456
    Processing helix  chain 'A' and resid 464 through 469
    Processing helix  chain 'A' and resid 470 through 484
      removed outlier: 3.955A  pdb=" N   TYR A 474 " --> pdb=" O   GLY A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 499
    Processing helix  chain 'A' and resid 500 through 502
      No H-bonds generated for 'chain 'A' and resid 500 through 502'
    Processing helix  chain 'A' and resid 504 through 506
      No H-bonds generated for 'chain 'A' and resid 504 through 506'
    Processing helix  chain 'A' and resid 512 through 519
    Processing helix  chain 'A' and resid 523 through 539
    Processing helix  chain 'A' and resid 558 through 568
    Processing helix  chain 'A' and resid 587 through 601
      removed outlier: 3.833A  pdb=" N   ASP A 601 " --> pdb=" O   LEU A 597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 637 through 642
      removed outlier: 4.531A  pdb=" N   ASN A 642 " --> pdb=" O   TYR A 638 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 667 through 683
    Processing helix  chain 'A' and resid 706 through 709
    Processing helix  chain 'A' and resid 710 through 727
      removed outlier: 4.662A  pdb=" N   ASP A 721 " --> pdb=" O   LEU A 717 " (cutoff:3.500A)
      removed outlier: 5.001A  pdb=" N   ARG A 722 " --> pdb=" O   LYS A 718 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 731 through 733
      No H-bonds generated for 'chain 'A' and resid 731 through 733'
    Processing helix  chain 'A' and resid 764 through 775
      removed outlier: 3.778A  pdb=" N   LYS A 775 " --> pdb=" O   ASP A 771 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 793 through 809
      removed outlier: 3.511A  pdb=" N   LEU A 797 " --> pdb=" O   TYR A 793 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   THR A 799 " --> pdb=" O   HIS A 795 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 814 through 839
    Processing helix  chain 'A' and resid 850 through 876
      removed outlier: 3.704A  pdb=" N   ASN A 876 " --> pdb=" O   LEU A 872 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 916 through 936
      removed outlier: 3.542A  pdb=" N   ALA A 922 " --> pdb=" O   PHE A 918 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   SER A 926 " --> pdb=" O   ALA A 922 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   THR A 935 " --> pdb=" O   ASN A 931 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 954 through 971
      removed outlier: 4.418A  pdb=" N   THR A 958 " --> pdb=" O   HIS A 954 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   PHE A 964 " --> pdb=" O   ASN A 960 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   ILE A 965 " --> pdb=" O   SER A 961 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 978 through 995
    Processing helix  chain 'A' and resid 997 through 1001
    Processing helix  chain 'A' and resid 1003 through 1017
    Processing helix  chain 'A' and resid 1042 through 1051
      removed outlier: 3.513A  pdb=" N   GLU A1050 " --> pdb=" O   LYS A1046 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1053 through 1065
    Processing helix  chain 'A' and resid 1072 through 1087
    Processing helix  chain 'A' and resid 1116 through 1133
      removed outlier: 4.213A  pdb=" N   ALA A1130 " --> pdb=" O   HIS A1126 " (cutoff:3.500A)
      removed outlier: 5.155A  pdb=" N   GLU A1131 " --> pdb=" O   ILE A1127 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   THR A1132 " --> pdb=" O   SER A1128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1203 through 1206
    Processing helix  chain 'A' and resid 1245 through 1258
    Processing helix  chain 'A' and resid 1305 through 1310
    Processing helix  chain 'A' and resid 1348 through 1352
    Processing helix  chain 'A' and resid 1370 through 1373
    Processing helix  chain 'A' and resid 1432 through 1439
    Processing helix  chain 'A' and resid 1439 through 1450
      removed outlier: 3.748A  pdb=" N   ILE A1450 " --> pdb=" O   LYS A1446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1558 through 1572
    Processing helix  chain 'A' and resid 1580 through 1589
    Processing helix  chain 'A' and resid 1651 through 1653
      No H-bonds generated for 'chain 'A' and resid 1651 through 1653'
    Processing helix  chain 'A' and resid 1680 through 1683
    Processing helix  chain 'A' and resid 1685 through 1689
      removed outlier: 3.758A  pdb=" N   VAL A1689 " --> pdb=" O   ASP A1686 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1774 through 1779
      removed outlier: 3.871A  pdb=" N   ALA A1778 " --> pdb=" O   SER A1774 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   ASP A1779 " --> pdb=" O   ASP A1775 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1774 through 1779'
    Processing helix  chain 'A' and resid 1792 through 1800
    Processing helix  chain 'A' and resid 1868 through 1872
      removed outlier: 3.588A  pdb=" N   SER A1872 " --> pdb=" O   PRO A1869 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 93
    Processing sheet with id=AA2, first strand: chain 'A' and resid 237 through 239
      removed outlier: 6.170A  pdb=" N   LEU A  98 " --> pdb=" O   LYS A 128 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   PHE A 130 " --> pdb=" O   LEU A  98 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   PHE A 100 " --> pdb=" O   PHE A 130 " (cutoff:3.500A)
      removed outlier: 5.097A  pdb=" N   ILE A 101 " --> pdb=" O   LEU A 285 " (cutoff:3.500A)
      removed outlier: 8.119A  pdb=" N   GLN A 385 " --> pdb=" O   LYS A 374 " (cutoff:3.500A)
      removed outlier: 11.302A  pdb=" N   LYS A 374 " --> pdb=" O   GLN A 385 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 360 through 361
      removed outlier: 4.520A  pdb=" N   GLY A 292 " --> pdb=" O   LEU A 361 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LEU A 290 " --> pdb=" O   SER A 509 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 605 through 609
      removed outlier: 6.746A  pdb=" N   ILE A 646 " --> pdb=" O   GLU A 692 " (cutoff:3.500A)
      removed outlier: 8.016A  pdb=" N   ASN A 694 " --> pdb=" O   ILE A 646 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   LEU A 648 " --> pdb=" O   ASN A 694 " (cutoff:3.500A)
      removed outlier: 7.550A  pdb=" N   LEU A 696 " --> pdb=" O   LEU A 648 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   PHE A 650 " --> pdb=" O   LEU A 696 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 617 through 622
    Processing sheet with id=AA6, first strand: chain 'A' and resid 744 through 746
    Processing sheet with id=AA7, first strand: chain 'A' and resid 777 through 781
      removed outlier: 4.610A  pdb=" N   TYR A 777 " --> pdb=" O   LYS A 790 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 882 through 884
    Processing sheet with id=AA9, first strand: chain 'A' and resid 882 through 884
    Processing sheet with id=AB1, first strand: chain 'A' and resid 938 through 940
      removed outlier: 3.810A  pdb=" N   ASP A 938 " --> pdb=" O   VAL A 945 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1035 through 1036
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1067 through 1068
      removed outlier: 5.485A  pdb=" N   ASP A1515 " --> pdb=" O   ASN A1530 " (cutoff:3.500A)
      removed outlier: 4.913A  pdb=" N   ASN A1530 " --> pdb=" O   ASP A1515 " (cutoff:3.500A)
      removed outlier: 7.315A  pdb=" N   LYS A1525 " --> pdb=" O   ILE A1544 " (cutoff:3.500A)
      removed outlier: 5.278A  pdb=" N   ILE A1544 " --> pdb=" O   LYS A1525 " (cutoff:3.500A)
      removed outlier: 7.811A  pdb=" N   LYS A1537 " --> pdb=" O   LEU A1557 " (cutoff:3.500A)
      removed outlier: 5.298A  pdb=" N   LEU A1557 " --> pdb=" O   LYS A1537 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   SER A1539 " --> pdb=" O   VAL A1555 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   VAL A1555 " --> pdb=" O   SER A1539 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   SER A1541 " --> pdb=" O   ASN A1553 " (cutoff:3.500A)
      removed outlier: 8.241A  pdb=" N   GLY A1554 " --> pdb=" O   ASP A1608 " (cutoff:3.500A)
      removed outlier: 11.142A  pdb=" N   ASN A1610 " --> pdb=" O   GLY A1554 " (cutoff:3.500A)
      removed outlier: 11.055A  pdb=" N   TYR A1556 " --> pdb=" O   ASN A1610 " (cutoff:3.500A)
      removed outlier: 11.380A  pdb=" N   ILE A1612 " --> pdb=" O   TYR A1556 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   PHE A1611 " --> pdb=" O   CYS A1626 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   CYS A1626 " --> pdb=" O   PHE A1611 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   GLN A1621 " --> pdb=" O   ILE A1637 " (cutoff:3.500A)
      removed outlier: 4.689A  pdb=" N   ILE A1637 " --> pdb=" O   GLN A1621 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   GLU A1623 " --> pdb=" O   TYR A1635 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   LEU A1656 " --> pdb=" O   ILE A1693 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   VAL A1718 " --> pdb=" O   ARG A1767 " (cutoff:3.500A)
      removed outlier: 4.747A  pdb=" N   SER A1801 " --> pdb=" O   TYR A1741 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 1105 through 1107
    Processing sheet with id=AB5, first strand: chain 'A' and resid 1136 through 1139
      removed outlier: 6.963A  pdb=" N   ILE A1144 " --> pdb=" O   VAL A1221 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   VAL A1345 " --> pdb=" O   TYR A1323 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   LEU A1325 " --> pdb=" O   VAL A1345 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   ASP A1347 " --> pdb=" O   LEU A1325 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   TRP A1344 " --> pdb=" O   SER A1403 " (cutoff:3.500A)
      removed outlier: 7.711A  pdb=" N   THR A1405 " --> pdb=" O   TRP A1344 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   ILE A1346 " --> pdb=" O   THR A1405 " (cutoff:3.500A)
      removed outlier: 8.551A  pdb=" N   SER A1407 " --> pdb=" O   ILE A1346 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 1161 through 1164
      removed outlier: 6.950A  pdb=" N   SER A1161 " --> pdb=" O   ILE A1155 " (cutoff:3.500A)
      removed outlier: 4.748A  pdb=" N   ILE A1155 " --> pdb=" O   SER A1161 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   THR A1163 " --> pdb=" O   SER A1153 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   SER A1153 " --> pdb=" O   ARG A1288 " (cutoff:3.500A)
      removed outlier: 8.093A  pdb=" N   ASN A1290 " --> pdb=" O   SER A1153 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   ILE A1155 " --> pdb=" O   ASN A1290 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   TYR A1314 " --> pdb=" O   ASP A1335 " (cutoff:3.500A)
      removed outlier: 8.260A  pdb=" N   ASN A1337 " --> pdb=" O   TYR A1314 " (cutoff:3.500A)
      removed outlier: 7.479A  pdb=" N   PHE A1316 " --> pdb=" O   ASN A1337 " (cutoff:3.500A)
      removed outlier: 7.593A  pdb=" N   THR A1388 " --> pdb=" O   ILE A1334 " (cutoff:3.500A)
      removed outlier: 9.004A  pdb=" N   LEU A1336 " --> pdb=" O   THR A1388 " (cutoff:3.500A)
      removed outlier: 7.290A  pdb=" N   ASN A1390 " --> pdb=" O   LEU A1336 " (cutoff:3.500A)
      removed outlier: 7.406A  pdb=" N   LEU A1338 " --> pdb=" O   ASN A1390 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   TYR A1392 " --> pdb=" O   LEU A1338 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 1168 through 1169
    Processing sheet with id=AB8, first strand: chain 'A' and resid 1171 through 1173
    Processing sheet with id=AB9, first strand: chain 'A' and resid 1179 through 1181
      removed outlier: 6.650A  pdb=" N   ASP A1185 " --> pdb=" O   PHE A1267 " (cutoff:3.500A)
      removed outlier: 5.318A  pdb=" N   ILE A1275 " --> pdb=" O   GLY A1235 " (cutoff:3.500A)
      removed outlier: 5.757A  pdb=" N   GLY A1235 " --> pdb=" O   ILE A1275 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'A' and resid 1353 through 1358
      removed outlier: 4.242A  pdb=" N   ASN A1354 " --> pdb=" O   GLY A1365 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'A' and resid 1459 through 1466
    Processing sheet with id=AC3, first strand: chain 'A' and resid 1674 through 1678
      removed outlier: 6.400A  pdb=" N   ILE A1675 " --> pdb=" O   ASN A1704 " (cutoff:3.500A)
      removed outlier: 7.938A  pdb=" N   THR A1706 " --> pdb=" O   ILE A1675 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   PHE A1677 " --> pdb=" O   THR A1706 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   ILE A1703 " --> pdb=" O   ASN A1733 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   ILE A1730 " --> pdb=" O   SER A1782 " (cutoff:3.500A)
      removed outlier: 7.440A  pdb=" N   ASN A1784 " --> pdb=" O   ILE A1730 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   VAL A1732 " --> pdb=" O   ASN A1784 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC3
    Processing sheet with id=AC4, first strand: chain 'A' and resid 1815 through 1819
    Processing sheet with id=AC5, first strand: chain 'A' and resid 1835 through 1839
      removed outlier: 3.722A  pdb=" N   ASN A1852 " --> pdb=" O   LYS A1847 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'A' and resid 1856 through 1860
    Processing sheet with id=AC7, first strand: chain 'A' and resid 1878 through 1882
    Processing sheet with id=AC8, first strand: chain 'A' and resid 1898 through 1902
      removed outlier: 3.765A  pdb=" N   GLU A1922 " --> pdb=" O   ALA A1910 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'A' and resid 1928 through 1932
    Processing sheet with id=AD1, first strand: chain 'A' and resid 1969 through 1973
      removed outlier: 4.567A  pdb=" N   TYR A1979 " --> pdb=" O   GLN A1987 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'A' and resid 1991 through 1992
    Processing sheet with id=AD3, first strand: chain 'A' and resid 2009 through 2013
    Processing sheet with id=AD4, first strand: chain 'A' and resid 2029 through 2033
    Processing sheet with id=AD5, first strand: chain 'A' and resid 2059 through 2063
    Processing sheet with id=AD6, first strand: chain 'A' and resid 2079 through 2082
    Processing sheet with id=AD7, first strand: chain 'A' and resid 2101 through 2105
    Processing sheet with id=AD8, first strand: chain 'A' and resid 2143 through 2145
    Processing sheet with id=AD9, first strand: chain 'A' and resid 2161 through 2165
      removed outlier: 4.695A  pdb=" N   TYR A2171 " --> pdb=" O   VAL A2187 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   GLN A2185 " --> pdb=" O   ALA A2173 " (cutoff:3.500A)
    Processing sheet with id=AE1, first strand: chain 'A' and resid 2191 through 2194
    Processing sheet with id=AE2, first strand: chain 'A' and resid 2211 through 2215
    Processing sheet with id=AE3, first strand: chain 'A' and resid 2232 through 2236
    Processing sheet with id=AE4, first strand: chain 'A' and resid 2252 through 2256
    Processing sheet with id=AE5, first strand: chain 'A' and resid 2272 through 2276
    Processing sheet with id=AE6, first strand: chain 'A' and resid 2292 through 2296
      removed outlier: 4.544A  pdb=" N   TYR A2302 " --> pdb=" O   ILE A2318 " (cutoff:3.500A)
    Processing sheet with id=AE7, first strand: chain 'A' and resid 2322 through 2326
    Processing sheet with id=AE8, first strand: chain 'A' and resid 2343 through 2346

    832 hydrogen bonds defined for protein.
    2232 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: 12.00

  Time building geometry restraints manager: 5.64 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 4718
        1.33 -     1.45: 3944
        1.45 -     1.57: 10663
        1.57 -     1.69: 0
        1.69 -     1.82: 84
  Bond restraints: 19409
  Sorted by residual:
  bond pdb=" C   ILE A 409 "
       pdb=" O   ILE A 409 "
    ideal  model  delta    sigma   weight residual
    1.237  1.307 -0.070 1.13e-02 7.83e+03 3.85e+01
  bond pdb=" C   ASN A 413 "
       pdb=" O   ASN A 413 "
    ideal  model  delta    sigma   weight residual
    1.237  1.293 -0.056 1.19e-02 7.06e+03 2.23e+01
  bond pdb=" C   ASP A 412 "
       pdb=" O   ASP A 412 "
    ideal  model  delta    sigma   weight residual
    1.236  1.285 -0.049 1.15e-02 7.56e+03 1.78e+01
  bond pdb=" C   ARG A 406 "
       pdb=" O   ARG A 406 "
    ideal  model  delta    sigma   weight residual
    1.237  1.280 -0.043 1.19e-02 7.06e+03 1.32e+01
  bond pdb=" N   ILE A1019 "
       pdb=" CA  ILE A1019 "
    ideal  model  delta    sigma   weight residual
    1.456  1.496 -0.039 1.14e-02 7.69e+03 1.19e+01
  ... (remaining 19404 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.67: 26125
        3.67 -     7.34: 126
        7.34 -    11.01: 8
       11.01 -    14.68: 1
       14.68 -    18.35: 1
  Bond angle restraints: 26261
  Sorted by residual:
  angle pdb=" CA  PRO A 416 "
        pdb=" N   PRO A 416 "
        pdb=" CD  PRO A 416 "
      ideal   model   delta    sigma   weight residual
     112.00   93.65   18.35 1.40e+00 5.10e-01 1.72e+02
  angle pdb=" C   VAL A1947 "
        pdb=" N   GLU A1948 "
        pdb=" CA  GLU A1948 "
      ideal   model   delta    sigma   weight residual
     121.54  132.77  -11.23 1.91e+00 2.74e-01 3.46e+01
  angle pdb=" N   VAL A1069 "
        pdb=" CA  VAL A1069 "
        pdb=" C   VAL A1069 "
      ideal   model   delta    sigma   weight residual
     111.91  107.22    4.69 8.90e-01 1.26e+00 2.78e+01
  angle pdb=" O   LEU A1021 "
        pdb=" C   LEU A1021 "
        pdb=" N   LEU A1022 "
      ideal   model   delta    sigma   weight residual
     122.09  127.29   -5.20 1.08e+00 8.57e-01 2.32e+01
  angle pdb=" CA  ASN A 415 "
        pdb=" C   ASN A 415 "
        pdb=" N   PRO A 416 "
      ideal   model   delta    sigma   weight residual
     120.52  124.43   -3.91 8.30e-01 1.45e+00 2.21e+01
  ... (remaining 26256 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 9886
       17.95 -    35.90: 1332
       35.90 -    53.85: 301
       53.85 -    71.81: 68
       71.81 -    89.76: 26
  Dihedral angle restraints: 11613
    sinusoidal: 4669
      harmonic: 6944
  Sorted by residual:
  dihedral pdb=" CA  GLY A1028 "
           pdb=" C   GLY A1028 "
           pdb=" N   LEU A1029 "
           pdb=" CA  LEU A1029 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   92.75   87.25     0      5.00e+00 4.00e-02 3.04e+02
  dihedral pdb=" CA  PHE A1452 "
           pdb=" C   PHE A1452 "
           pdb=" N   ASN A1453 "
           pdb=" CA  ASN A1453 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.03   31.97     0      5.00e+00 4.00e-02 4.09e+01
  dihedral pdb=" C   ASN A1602 "
           pdb=" N   ASN A1602 "
           pdb=" CA  ASN A1602 "
           pdb=" CB  ASN A1602 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.36   14.76     0      2.50e+00 1.60e-01 3.48e+01
  ... (remaining 11610 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.097: 2550
       0.097 -    0.193: 326
       0.193 -    0.290: 18
       0.290 -    0.387: 2
       0.387 -    0.484: 2
  Chirality restraints: 2898
  Sorted by residual:
  chirality pdb=" CA  ASN A1602 "
            pdb=" N   ASN A1602 "
            pdb=" C   ASN A1602 "
            pdb=" CB  ASN A1602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.85e+00
  chirality pdb=" CA  ASN A 419 "
            pdb=" N   ASN A 419 "
            pdb=" C   ASN A 419 "
            pdb=" CB  ASN A 419 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 3.99e+00
  chirality pdb=" CA  SER A 706 "
            pdb=" N   SER A 706 "
            pdb=" C   SER A 706 "
            pdb=" CB  SER A 706 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.44e+00
  ... (remaining 2895 not shown)

  Planarity restraints: 3394
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 415 "    0.120 5.00e-02 4.00e+02   1.65e-01 4.37e+01
        pdb=" N   PRO A 416 "   -0.285 5.00e-02 4.00e+02
        pdb=" CA  PRO A 416 "    0.075 5.00e-02 4.00e+02
        pdb=" CD  PRO A 416 "    0.090 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A2342 "    0.022 2.00e-02 2.50e+03   4.46e-02 1.99e+01
        pdb=" C   GLY A2342 "   -0.077 2.00e-02 2.50e+03
        pdb=" O   GLY A2342 "    0.029 2.00e-02 2.50e+03
        pdb=" N   SER A2343 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 413 "    0.020 2.00e-02 2.50e+03   4.03e-02 1.62e+01
        pdb=" C   ASN A 413 "   -0.070 2.00e-02 2.50e+03
        pdb=" O   ASN A 413 "    0.026 2.00e-02 2.50e+03
        pdb=" N   LEU A 414 "    0.024 2.00e-02 2.50e+03
  ... (remaining 3391 not shown)

  Histogram of nonbonded interaction distances:
        1.93 -     2.52: 135
        2.52 -     3.12: 14038
        3.12 -     3.71: 28177
        3.71 -     4.31: 42308
        4.31 -     4.90: 69264
  Nonbonded interactions: 153922
  Sorted by model distance:
  nonbonded pdb=" CG  PRO A1023 "
            pdb=" OH  TYR A1649 "
     model   vdw
     1.925 3.440
  nonbonded pdb=" O   ASP A1534 "
            pdb=" OD1 ASP A1535 "
     model   vdw
     1.962 3.040
  nonbonded pdb=" O   LYS A1795 "
            pdb=" OG1 THR A1799 "
     model   vdw
     2.029 3.040
  nonbonded pdb=" O   ILE A1507 "
            pdb=" OD1 ASN A1598 "
     model   vdw
     2.031 3.040
  nonbonded pdb=" OE2 GLU A 258 "
            pdb=" OH  TYR A 407 "
     model   vdw
     2.163 3.040
  ... (remaining 153917 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.850
  Check model and map are aligned:         0.140
  Set scattering table:                    0.180
  Process input model:                     52.580
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:11.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   66.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
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      :  0.008   0.431  19413  Z= 0.532
  Angle     :  0.884  18.347  26261  Z= 0.585
  Chirality :  0.062   0.484   2898
  Planarity :  0.006   0.165   3394
  Dihedral  : 17.400  89.757   7167
  Min Nonbonded Distance : 1.925

Molprobity Statistics.
  All-atom Clashscore : 14.17
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.74 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  6.34 %
    Allowed  : 17.18 %
    Favored  : 76.48 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.73 (0.16), residues: 2351
  helix:  0.08 (0.20), residues: 664
  sheet: -1.13 (0.22), residues: 453
  loop : -1.87 (0.15), residues: 1234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 102 
 HIS   0.005   0.001   HIS A  99 
 PHE   0.016   0.002   PHE A 503 
 TYR   0.019   0.002   TYR A1646 
 ARG   0.005   0.001   ARG A1241 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14813 (  830)
  hydrogen bonds       : angle       6.57421 ( 2232)
  metal coordination   : bond        0.17488 (    3)
  covalent geometry    : bond        0.00751 (19409)
  covalent geometry    : angle       0.88437 (26261)
  Misc. bond           : bond        0.43130 (    1)

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

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

  4702 Ramachandran restraints generated.
    2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4702 Ramachandran restraints generated.
    2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  335 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 135
    poor density    : 200
  time to evaluate  : 2.031 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 GLU cc_start: 0.6787 (tt0) cc_final: 0.6519 (tt0)
REVERT: A  197 ASN cc_start: 0.7715 (t0) cc_final: 0.7485 (t0)
REVERT: A  333 LYS cc_start: 0.8463 (ttpt) cc_final: 0.8257 (ttpt)
REVERT: A  428 MET cc_start: 0.8629 (tpt) cc_final: 0.8392 (mmm)
REVERT: A  651 ILE cc_start: 0.9497 (OUTLIER) cc_final: 0.9246 (mm)
REVERT: A 1327 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6843 (OUTLIER)
REVERT: A 1462 TYR cc_start: 0.7125 (OUTLIER) cc_final: 0.5038 (p90)
REVERT: A 1490 ASN cc_start: 0.7438 (p0) cc_final: 0.7042 (p0)
REVERT: A 1496 ASN cc_start: 0.7331 (t0) cc_final: 0.6567 (m-40)
REVERT: A 1499 MET cc_start: 0.6669 (tpp) cc_final: 0.5515 (ttp)
REVERT: A 1576 LEU cc_start: 0.2556 (OUTLIER) cc_final: 0.1786 (mp)
REVERT: A 1819 LEU cc_start: 0.8442 (mt) cc_final: 0.8229 (mt)
REVERT: A 1955 GLU cc_start: 0.5589 (OUTLIER) cc_final: 0.5352 (mp0)
REVERT: A 2181 ASN cc_start: 0.1215 (OUTLIER) cc_final: -0.0697 (m-40)
  outliers start: 135
  outliers final: 77
  residues processed: 320
  average time/residue: 1.0280
  time to fit residues: 381.9089
Evaluate side-chains
  211 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 82
    poor density    : 129
  time to evaluate  : 1.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  332 SER
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  464 SER
Chi-restraints excluded: chain A residue  469 SER
Chi-restraints excluded: chain A residue  508 ILE
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  535 LYS
Chi-restraints excluded: chain A residue  574 ASN
Chi-restraints excluded: chain A residue  651 ILE
Chi-restraints excluded: chain A residue  656 SER
Chi-restraints excluded: chain A residue  703 TYR
Chi-restraints excluded: chain A residue  865 ILE
Chi-restraints excluded: chain A residue  879 ASP
Chi-restraints excluded: chain A residue  884 ILE
Chi-restraints excluded: chain A residue  936 ILE
Chi-restraints excluded: chain A residue  958 THR
Chi-restraints excluded: chain A residue  968 LEU
Chi-restraints excluded: chain A residue 1002 THR
Chi-restraints excluded: chain A residue 1010 LEU
Chi-restraints excluded: chain A residue 1013 THR
Chi-restraints excluded: chain A residue 1019 ILE
Chi-restraints excluded: chain A residue 1055 LEU
Chi-restraints excluded: chain A residue 1143 ILE
Chi-restraints excluded: chain A residue 1144 ILE
Chi-restraints excluded: chain A residue 1167 CYS
Chi-restraints excluded: chain A residue 1205 VAL
Chi-restraints excluded: chain A residue 1285 THR
Chi-restraints excluded: chain A residue 1297 SER
Chi-restraints excluded: chain A residue 1305 THR
Chi-restraints excluded: chain A residue 1324 SER
Chi-restraints excluded: chain A residue 1327 LEU
Chi-restraints excluded: chain A residue 1368 ILE
Chi-restraints excluded: chain A residue 1392 TYR
Chi-restraints excluded: chain A residue 1433 CYS
Chi-restraints excluded: chain A residue 1462 TYR
Chi-restraints excluded: chain A residue 1515 ASP
Chi-restraints excluded: chain A residue 1543 THR
Chi-restraints excluded: chain A residue 1547 THR
Chi-restraints excluded: chain A residue 1576 LEU
Chi-restraints excluded: chain A residue 1591 ILE
Chi-restraints excluded: chain A residue 1598 ASN
Chi-restraints excluded: chain A residue 1602 ASN
Chi-restraints excluded: chain A residue 1618 SER
Chi-restraints excluded: chain A residue 1662 TYR
Chi-restraints excluded: chain A residue 1671 SER
Chi-restraints excluded: chain A residue 1726 ILE
Chi-restraints excluded: chain A residue 1771 VAL
Chi-restraints excluded: chain A residue 1776 THR
Chi-restraints excluded: chain A residue 1801 SER
Chi-restraints excluded: chain A residue 1814 PHE
Chi-restraints excluded: chain A residue 1821 ASN
Chi-restraints excluded: chain A residue 1870 THR
Chi-restraints excluded: chain A residue 1902 THR
Chi-restraints excluded: chain A residue 1914 THR
Chi-restraints excluded: chain A residue 1927 ILE
Chi-restraints excluded: chain A residue 1947 VAL
Chi-restraints excluded: chain A residue 1955 GLU
Chi-restraints excluded: chain A residue 1963 THR
Chi-restraints excluded: chain A residue 1988 THR
Chi-restraints excluded: chain A residue 1992 THR
Chi-restraints excluded: chain A residue 1995 ASP
Chi-restraints excluded: chain A residue 2005 VAL
Chi-restraints excluded: chain A residue 2078 VAL
Chi-restraints excluded: chain A residue 2181 ASN
Chi-restraints excluded: chain A residue 2235 VAL
Chi-restraints excluded: chain A residue 2259 ASN
Chi-restraints excluded: chain A residue 2362 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 235
   random chunks:
   chunk 198 optimal weight:    7.9990
   chunk 178 optimal weight:    0.1980
   chunk 98 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 120 optimal weight:   20.0000
   chunk 95 optimal weight:    0.9990
   chunk 184 optimal weight:    0.6980
   chunk 71 optimal weight:    0.6980
   chunk 112 optimal weight:    6.9990
   chunk 137 optimal weight:    5.9990
   chunk 213 optimal weight:    3.9990
   overall best weight:    0.7184

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

Flipped N/Q/H residues before XYZ refinement:
A   5 ASN
A   8 GLN
A 106 GLN
A 380 ASN
A 413 ASN
A 574 ASN
A 639 GLN
A 732 GLN
A 741 GLN
A 876 ASN
A 941 ASN
A 949 ASN
A 988 GLN
A1109 ASN
A1257 HIS
A1584 ASN
A1590 ASN
A1593 ASN
A1621 GLN
A1631 ASN
A1724 ASN
A1763 GLN
A2058 ASN
A2143 GLN
** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2319 ASN

Total number of N/Q/H flips: 25

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.198865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.122488 restraints weight = 27432.616|
|-----------------------------------------------------------------------------|
r_work (start): 0.3313 rms_B_bonded: 2.79
r_work: 0.3022 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
moved from start:          0.1763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061  19413  Z= 0.121
  Angle     :  0.559   9.687  26261  Z= 0.304
  Chirality :  0.045   0.170   2898
  Planarity :  0.004   0.092   3394
  Dihedral  :  7.230  68.177   2670
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  4.34 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 20.75 %
    Favored  : 75.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.17), residues: 2351
  helix:  1.56 (0.20), residues: 662
  sheet: -0.60 (0.22), residues: 475
  loop : -1.27 (0.16), residues: 1214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A1949 
 HIS   0.005   0.001   HIS A 924 
 PHE   0.017   0.001   PHE A 937 
 TYR   0.016   0.001   TYR A 990 
 ARG   0.002   0.000   ARG A 526 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04707 (  830)
  hydrogen bonds       : angle       4.95570 ( 2232)
  metal coordination   : bond        0.00905 (    3)
  covalent geometry    : bond        0.00258 (19409)
  covalent geometry    : angle       0.55893 (26261)
  Misc. bond           : bond        0.00673 (    1)

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

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

  4702 Ramachandran restraints generated.
    2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4702 Ramachandran restraints generated.
    2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 80
    poor density    : 153
  time to evaluate  : 2.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  223 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8465 (tptp)
REVERT: A  535 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8767 (mtmm)
REVERT: A  646 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8713 (tp)
REVERT: A  760 LYS cc_start: 0.8948 (mttt) cc_final: 0.8669 (mmtp)
REVERT: A 1027 GLU cc_start: 0.7595 (tt0) cc_final: 0.7035 (tm-30)
REVERT: A 1212 LYS cc_start: 0.0698 (OUTLIER) cc_final: 0.0471 (mmtm)
REVERT: A 1230 PHE cc_start: 0.0161 (OUTLIER) cc_final: -0.0266 (m-80)
REVERT: A 1302 VAL cc_start: 0.5435 (OUTLIER) cc_final: 0.4823 (p)
REVERT: A 1332 MET cc_start: 0.4477 (pmm) cc_final: 0.0893 (ttp)
REVERT: A 1462 TYR cc_start: 0.6699 (OUTLIER) cc_final: 0.3702 (p90)
REVERT: A 1470 LYS cc_start: 0.7843 (ttmt) cc_final: 0.7491 (mtmt)
REVERT: A 1477 TYR cc_start: 0.7617 (t80) cc_final: 0.6849 (t80)
REVERT: A 1490 ASN cc_start: 0.7342 (p0) cc_final: 0.6997 (p0)
REVERT: A 1499 MET cc_start: 0.6551 (tpp) cc_final: 0.5163 (ttp)
REVERT: A 1567 LYS cc_start: 0.9086 (ttmt) cc_final: 0.8634 (ttpm)
REVERT: A 1576 LEU cc_start: 0.2583 (OUTLIER) cc_final: 0.1951 (mp)
REVERT: A 1775 ASP cc_start: 0.4940 (OUTLIER) cc_final: 0.3796 (m-30)
REVERT: A 2006 MET cc_start: 0.4326 (tpt) cc_final: 0.2604 (ttt)
  outliers start: 80
  outliers final: 33
  residues processed: 226
  average time/residue: 1.1723
  time to fit residues: 307.1019
Evaluate side-chains
  170 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 128
  time to evaluate  : 2.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  192 SER
Chi-restraints excluded: chain A residue  223 LYS
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  469 SER
Chi-restraints excluded: chain A residue  535 LYS
Chi-restraints excluded: chain A residue  574 ASN
Chi-restraints excluded: chain A residue  576 GLU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  646 ILE
Chi-restraints excluded: chain A residue  837 VAL
Chi-restraints excluded: chain A residue  865 ILE
Chi-restraints excluded: chain A residue  874 HIS
Chi-restraints excluded: chain A residue 1018 THR
Chi-restraints excluded: chain A residue 1019 ILE
Chi-restraints excluded: chain A residue 1034 THR
Chi-restraints excluded: chain A residue 1080 THR
Chi-restraints excluded: chain A residue 1150 LEU
Chi-restraints excluded: chain A residue 1167 CYS
Chi-restraints excluded: chain A residue 1212 LYS
Chi-restraints excluded: chain A residue 1213 ILE
Chi-restraints excluded: chain A residue 1230 PHE
Chi-restraints excluded: chain A residue 1234 MET
Chi-restraints excluded: chain A residue 1302 VAL
Chi-restraints excluded: chain A residue 1305 THR
Chi-restraints excluded: chain A residue 1368 ILE
Chi-restraints excluded: chain A residue 1418 ILE
Chi-restraints excluded: chain A residue 1462 TYR
Chi-restraints excluded: chain A residue 1547 THR
Chi-restraints excluded: chain A residue 1576 LEU
Chi-restraints excluded: chain A residue 1662 TYR
Chi-restraints excluded: chain A residue 1726 ILE
Chi-restraints excluded: chain A residue 1775 ASP
Chi-restraints excluded: chain A residue 1776 THR
Chi-restraints excluded: chain A residue 1814 PHE
Chi-restraints excluded: chain A residue 1842 SER
Chi-restraints excluded: chain A residue 1988 THR
Chi-restraints excluded: chain A residue 2143 GLN
Chi-restraints excluded: chain A residue 2235 VAL
Chi-restraints excluded: chain A residue 2253 LEU
Chi-restraints excluded: chain A residue 2362 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 235
   random chunks:
   chunk 139 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9990
   chunk 121 optimal weight:    9.9990
   chunk 161 optimal weight:    0.9980
   chunk 198 optimal weight:    8.9990
   chunk 43 optimal weight:    1.9990
   chunk 155 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 202 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 133 optimal weight:    9.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
A 238 ASN
A 487 ASN
A1530 ASN
A1580 ASN
A1633 GLN
A1724 ASN
A2058 ASN
** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2260 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.196617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.120009 restraints weight = 27071.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 2.69
r_work: 0.2991 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2855 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8504
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  19413  Z= 0.153
  Angle     :  0.560   8.055  26261  Z= 0.305
  Chirality :  0.046   0.172   2898
  Planarity :  0.004   0.089   3394
  Dihedral  :  5.885  56.594   2579
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 20.85 %
    Favored  : 75.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.17), residues: 2351
  helix:  1.84 (0.20), residues: 663
  sheet: -0.48 (0.23), residues: 470
  loop : -1.02 (0.17), residues: 1218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 118 
 HIS   0.005   0.001   HIS A 492 
 PHE   0.027   0.001   PHE A 937 
 TYR   0.013   0.001   TYR A1646 
 ARG   0.007   0.000   ARG A2118 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05311 (  830)
  hydrogen bonds       : angle       4.83446 ( 2232)
  metal coordination   : bond        0.00838 (    3)
  covalent geometry    : bond        0.00358 (19409)
  covalent geometry    : angle       0.56039 (26261)
  Misc. bond           : bond        0.00576 (    1)

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

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

  4702 Ramachandran restraints generated.
    2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4702 Ramachandran restraints generated.
    2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 87
    poor density    : 139
  time to evaluate  : 2.044 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    2 ASN cc_start: 0.8786 (OUTLIER) cc_final: 0.8413 (t0)
REVERT: A  227 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8232 (mt-10)
REVERT: A  238 ASN cc_start: 0.8326 (OUTLIER) cc_final: 0.7874 (m-40)
REVERT: A  279 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7786 (mt-10)
REVERT: A  333 LYS cc_start: 0.8741 (tmmt) cc_final: 0.8338 (mtmm)
REVERT: A  543 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7842 (mt)
REVERT: A  646 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.8847 (tp)
REVERT: A  751 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8376 (mttm)
REVERT: A  760 LYS cc_start: 0.9136 (mttt) cc_final: 0.8786 (mmtp)
REVERT: A 1027 GLU cc_start: 0.7670 (tt0) cc_final: 0.7045 (tm-30)
REVERT: A 1212 LYS cc_start: 0.0713 (OUTLIER) cc_final: 0.0447 (mmtm)
REVERT: A 1230 PHE cc_start: 0.0070 (OUTLIER) cc_final: -0.0471 (m-80)
REVERT: A 1302 VAL cc_start: 0.5669 (OUTLIER) cc_final: 0.5031 (p)
REVERT: A 1327 LEU cc_start: 0.6424 (OUTLIER) cc_final: 0.6122 (OUTLIER)
REVERT: A 1332 MET cc_start: 0.4316 (pmm) cc_final: 0.0856 (ttp)
REVERT: A 1462 TYR cc_start: 0.7034 (OUTLIER) cc_final: 0.3763 (p90)
REVERT: A 1470 LYS cc_start: 0.7985 (ttmt) cc_final: 0.7641 (mtmt)
REVERT: A 1477 TYR cc_start: 0.7562 (t80) cc_final: 0.6905 (t80)
REVERT: A 1484 PHE cc_start: 0.8538 (m-80) cc_final: 0.8334 (m-80)
REVERT: A 1490 ASN cc_start: 0.7381 (p0) cc_final: 0.7054 (p0)
REVERT: A 1567 LYS cc_start: 0.9157 (ttmt) cc_final: 0.8697 (ttpm)
REVERT: A 1775 ASP cc_start: 0.4934 (OUTLIER) cc_final: 0.3770 (m-30)
REVERT: A 1788 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8869 (mttp)
REVERT: A 2006 MET cc_start: 0.4382 (tpt) cc_final: 0.2698 (ttt)
  outliers start: 87
  outliers final: 41
  residues processed: 212
  average time/residue: 1.0706
  time to fit residues: 263.9898
Evaluate side-chains
  178 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 126
  time to evaluate  : 2.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 ASN
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  192 SER
Chi-restraints excluded: chain A residue  238 ASN
Chi-restraints excluded: chain A residue  288 ASP
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  469 SER
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  572 THR
Chi-restraints excluded: chain A residue  574 ASN
Chi-restraints excluded: chain A residue  576 GLU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  646 ILE
Chi-restraints excluded: chain A residue  751 LYS
Chi-restraints excluded: chain A residue  837 VAL
Chi-restraints excluded: chain A residue  865 ILE
Chi-restraints excluded: chain A residue  873 LYS
Chi-restraints excluded: chain A residue  874 HIS
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue  958 THR
Chi-restraints excluded: chain A residue 1018 THR
Chi-restraints excluded: chain A residue 1019 ILE
Chi-restraints excluded: chain A residue 1080 THR
Chi-restraints excluded: chain A residue 1167 CYS
Chi-restraints excluded: chain A residue 1212 LYS
Chi-restraints excluded: chain A residue 1213 ILE
Chi-restraints excluded: chain A residue 1230 PHE
Chi-restraints excluded: chain A residue 1234 MET
Chi-restraints excluded: chain A residue 1302 VAL
Chi-restraints excluded: chain A residue 1305 THR
Chi-restraints excluded: chain A residue 1327 LEU
Chi-restraints excluded: chain A residue 1368 ILE
Chi-restraints excluded: chain A residue 1418 ILE
Chi-restraints excluded: chain A residue 1462 TYR
Chi-restraints excluded: chain A residue 1547 THR
Chi-restraints excluded: chain A residue 1591 ILE
Chi-restraints excluded: chain A residue 1626 CYS
Chi-restraints excluded: chain A residue 1650 VAL
Chi-restraints excluded: chain A residue 1662 TYR
Chi-restraints excluded: chain A residue 1726 ILE
Chi-restraints excluded: chain A residue 1775 ASP
Chi-restraints excluded: chain A residue 1776 THR
Chi-restraints excluded: chain A residue 1779 ASP
Chi-restraints excluded: chain A residue 1788 LYS
Chi-restraints excluded: chain A residue 1842 SER
Chi-restraints excluded: chain A residue 1927 ILE
Chi-restraints excluded: chain A residue 1947 VAL
Chi-restraints excluded: chain A residue 1988 THR
Chi-restraints excluded: chain A residue 2125 ILE
Chi-restraints excluded: chain A residue 2235 VAL
Chi-restraints excluded: chain A residue 2362 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 235
   random chunks:
   chunk 93 optimal weight:    6.9990
   chunk 105 optimal weight:    0.9990
   chunk 160 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 167 optimal weight:    2.9990
   chunk 185 optimal weight:    3.9990
   chunk 123 optimal weight:    6.9990
   chunk 222 optimal weight:    0.0070
   chunk 150 optimal weight:    9.9990
   chunk 183 optimal weight:    0.5980
   chunk 38 optimal weight:    3.9990
   overall best weight:    1.1204

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

Flipped N/Q/H residues before XYZ refinement:
A 334 ASN
A 487 ASN
A 795 HIS
A 972 ASN
A1580 ASN
A1724 ASN
A2058 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.198722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.122371 restraints weight = 27218.286|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 2.78
r_work: 0.3007 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2869 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8489
moved from start:          0.2281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  19413  Z= 0.124
  Angle     :  0.528   8.911  26261  Z= 0.285
  Chirality :  0.045   0.192   2898
  Planarity :  0.004   0.088   3394
  Dihedral  :  5.427  59.953   2570
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 21.92 %
    Favored  : 74.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.04 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.17), residues: 2351
  helix:  2.10 (0.21), residues: 663
  sheet: -0.30 (0.23), residues: 478
  loop : -0.87 (0.17), residues: 1210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 118 
 HIS   0.004   0.001   HIS A 924 
 PHE   0.027   0.001   PHE A1474 
 TYR   0.019   0.001   TYR A 990 
 ARG   0.002   0.000   ARG A1495 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04503 (  830)
  hydrogen bonds       : angle       4.63678 ( 2232)
  metal coordination   : bond        0.00613 (    3)
  covalent geometry    : bond        0.00280 (19409)
  covalent geometry    : angle       0.52814 (26261)
  Misc. bond           : bond        0.00551 (    1)

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

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

  4702 Ramachandran restraints generated.
    2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4702 Ramachandran restraints generated.
    2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 80
    poor density    : 139
  time to evaluate  : 2.084 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.8327 (tpt) cc_final: 0.8032 (tpt)
REVERT: A  197 ASN cc_start: 0.7471 (m-40) cc_final: 0.6826 (t0)
REVERT: A  279 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7816 (mt-10)
REVERT: A  333 LYS cc_start: 0.8699 (tmmt) cc_final: 0.8255 (mmtt)
REVERT: A  543 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7801 (mt)
REVERT: A  646 ILE cc_start: 0.9311 (OUTLIER) cc_final: 0.8844 (tp)
REVERT: A  814 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7514 (p0)
REVERT: A 1027 GLU cc_start: 0.7649 (tt0) cc_final: 0.7206 (tm-30)
REVERT: A 1230 PHE cc_start: 0.0097 (OUTLIER) cc_final: -0.0473 (m-80)
REVERT: A 1302 VAL cc_start: 0.5564 (OUTLIER) cc_final: 0.4921 (p)
REVERT: A 1332 MET cc_start: 0.4168 (pmm) cc_final: 0.0652 (ttp)
REVERT: A 1462 TYR cc_start: 0.6928 (OUTLIER) cc_final: 0.3931 (p90)
REVERT: A 1470 LYS cc_start: 0.7970 (ttmt) cc_final: 0.7506 (mtmm)
REVERT: A 1477 TYR cc_start: 0.7576 (t80) cc_final: 0.6915 (t80)
REVERT: A 1490 ASN cc_start: 0.7427 (p0) cc_final: 0.7110 (p0)
REVERT: A 1495 ARG cc_start: 0.8309 (ttm-80) cc_final: 0.7974 (mmm-85)
REVERT: A 1499 MET cc_start: 0.6893 (tpp) cc_final: 0.5574 (ttp)
REVERT: A 1567 LYS cc_start: 0.9173 (ttmt) cc_final: 0.8729 (ttpm)
REVERT: A 1775 ASP cc_start: 0.4784 (OUTLIER) cc_final: 0.3647 (m-30)
REVERT: A 2006 MET cc_start: 0.4257 (tpt) cc_final: 0.2528 (ttt)
REVERT: A 2289 MET cc_start: -0.0461 (tpt) cc_final: -0.2342 (ptm)
  outliers start: 80
  outliers final: 42
  residues processed: 206
  average time/residue: 1.0255
  time to fit residues: 246.9420
Evaluate side-chains
  175 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 126
  time to evaluate  : 2.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  192 SER
Chi-restraints excluded: chain A residue  381 SER
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  574 ASN
Chi-restraints excluded: chain A residue  576 GLU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  646 ILE
Chi-restraints excluded: chain A residue  814 ASP
Chi-restraints excluded: chain A residue  837 VAL
Chi-restraints excluded: chain A residue  865 ILE
Chi-restraints excluded: chain A residue  873 LYS
Chi-restraints excluded: chain A residue  874 HIS
Chi-restraints excluded: chain A residue  884 ILE
Chi-restraints excluded: chain A residue  890 SER
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue  958 THR
Chi-restraints excluded: chain A residue 1019 ILE
Chi-restraints excluded: chain A residue 1080 THR
Chi-restraints excluded: chain A residue 1150 LEU
Chi-restraints excluded: chain A residue 1167 CYS
Chi-restraints excluded: chain A residue 1205 VAL
Chi-restraints excluded: chain A residue 1213 ILE
Chi-restraints excluded: chain A residue 1230 PHE
Chi-restraints excluded: chain A residue 1234 MET
Chi-restraints excluded: chain A residue 1302 VAL
Chi-restraints excluded: chain A residue 1305 THR
Chi-restraints excluded: chain A residue 1328 SER
Chi-restraints excluded: chain A residue 1368 ILE
Chi-restraints excluded: chain A residue 1418 ILE
Chi-restraints excluded: chain A residue 1462 TYR
Chi-restraints excluded: chain A residue 1547 THR
Chi-restraints excluded: chain A residue 1591 ILE
Chi-restraints excluded: chain A residue 1626 CYS
Chi-restraints excluded: chain A residue 1662 TYR
Chi-restraints excluded: chain A residue 1726 ILE
Chi-restraints excluded: chain A residue 1775 ASP
Chi-restraints excluded: chain A residue 1776 THR
Chi-restraints excluded: chain A residue 1842 SER
Chi-restraints excluded: chain A residue 1927 ILE
Chi-restraints excluded: chain A residue 1947 VAL
Chi-restraints excluded: chain A residue 1988 THR
Chi-restraints excluded: chain A residue 2125 ILE
Chi-restraints excluded: chain A residue 2235 VAL
Chi-restraints excluded: chain A residue 2253 LEU
Chi-restraints excluded: chain A residue 2362 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 235
   random chunks:
   chunk 173 optimal weight:    0.4980
   chunk 88 optimal weight:    0.3980
   chunk 185 optimal weight:    0.0870
   chunk 119 optimal weight:   30.0000
   chunk 151 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 130 optimal weight:    0.8980
   chunk 161 optimal weight:    3.9990
   chunk 128 optimal weight:   10.0000
   chunk 228 optimal weight:    9.9990
   overall best weight:    0.5760

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

Flipped N/Q/H residues before XYZ refinement:
A 487 ASN
A1580 ASN
A1584 ASN
A1724 ASN
A2058 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.200118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.121113 restraints weight = 27594.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 2.39
r_work: 0.3070 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2934 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.2609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  19413  Z= 0.098
  Angle     :  0.495  10.457  26261  Z= 0.267
  Chirality :  0.045   0.194   2898
  Planarity :  0.003   0.082   3394
  Dihedral  :  5.062  58.810   2569
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 22.44 %
    Favored  : 74.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.17), residues: 2351
  helix:  2.35 (0.21), residues: 666
  sheet: -0.15 (0.23), residues: 490
  loop : -0.68 (0.18), residues: 1195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 118 
 HIS   0.003   0.001   HIS A 924 
 PHE   0.030   0.001   PHE A1474 
 TYR   0.012   0.001   TYR A 793 
 ARG   0.004   0.000   ARG A1495 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03737 (  830)
  hydrogen bonds       : angle       4.42696 ( 2232)
  metal coordination   : bond        0.00359 (    3)
  covalent geometry    : bond        0.00210 (19409)
  covalent geometry    : angle       0.49510 (26261)
  Misc. bond           : bond        0.00527 (    1)

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

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

  4702 Ramachandran restraints generated.
    2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4702 Ramachandran restraints generated.
    2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 149
  time to evaluate  : 2.037 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.8347 (tpt) cc_final: 0.8041 (tpt)
REVERT: A  333 LYS cc_start: 0.8668 (tmmt) cc_final: 0.8251 (mtmm)
REVERT: A  543 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7669 (mt)
REVERT: A  570 MET cc_start: 0.9209 (OUTLIER) cc_final: 0.8188 (mmt)
REVERT: A  646 ILE cc_start: 0.9264 (OUTLIER) cc_final: 0.8831 (tp)
REVERT: A  751 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8379 (mttm)
REVERT: A  814 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7370 (p0)
REVERT: A 1027 GLU cc_start: 0.7366 (tt0) cc_final: 0.7097 (tm-30)
REVERT: A 1230 PHE cc_start: 0.0077 (OUTLIER) cc_final: -0.0476 (m-80)
REVERT: A 1332 MET cc_start: 0.4119 (pmm) cc_final: 0.0613 (ttp)
REVERT: A 1418 ILE cc_start: 0.6342 (OUTLIER) cc_final: 0.5787 (tp)
REVERT: A 1462 TYR cc_start: 0.6725 (OUTLIER) cc_final: 0.3959 (p90)
REVERT: A 1470 LYS cc_start: 0.7951 (ttmt) cc_final: 0.7539 (mtmm)
REVERT: A 1477 TYR cc_start: 0.7594 (t80) cc_final: 0.6981 (t80)
REVERT: A 1490 ASN cc_start: 0.7371 (p0) cc_final: 0.7053 (p0)
REVERT: A 1495 ARG cc_start: 0.8165 (ttm-80) cc_final: 0.7687 (mmm-85)
REVERT: A 1499 MET cc_start: 0.6447 (tpp) cc_final: 0.5173 (ttp)
REVERT: A 1567 LYS cc_start: 0.9172 (ttmt) cc_final: 0.8741 (ttpm)
REVERT: A 1906 LEU cc_start: 0.7740 (mm) cc_final: 0.7428 (mp)
REVERT: A 1947 VAL cc_start: 0.6460 (OUTLIER) cc_final: 0.6209 (m)
REVERT: A 2006 MET cc_start: 0.4104 (tpt) cc_final: 0.2546 (ttt)
REVERT: A 2289 MET cc_start: -0.0246 (tpt) cc_final: -0.2195 (ptm)
  outliers start: 70
  outliers final: 31
  residues processed: 207
  average time/residue: 1.0408
  time to fit residues: 249.8973
Evaluate side-chains
  169 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 129
  time to evaluate  : 1.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  192 SER
Chi-restraints excluded: chain A residue  381 SER
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  570 MET
Chi-restraints excluded: chain A residue  572 THR
Chi-restraints excluded: chain A residue  574 ASN
Chi-restraints excluded: chain A residue  576 GLU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  646 ILE
Chi-restraints excluded: chain A residue  702 SER
Chi-restraints excluded: chain A residue  751 LYS
Chi-restraints excluded: chain A residue  814 ASP
Chi-restraints excluded: chain A residue  865 ILE
Chi-restraints excluded: chain A residue  874 HIS
Chi-restraints excluded: chain A residue  890 SER
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue 1019 ILE
Chi-restraints excluded: chain A residue 1080 THR
Chi-restraints excluded: chain A residue 1150 LEU
Chi-restraints excluded: chain A residue 1167 CYS
Chi-restraints excluded: chain A residue 1205 VAL
Chi-restraints excluded: chain A residue 1230 PHE
Chi-restraints excluded: chain A residue 1234 MET
Chi-restraints excluded: chain A residue 1368 ILE
Chi-restraints excluded: chain A residue 1418 ILE
Chi-restraints excluded: chain A residue 1462 TYR
Chi-restraints excluded: chain A residue 1547 THR
Chi-restraints excluded: chain A residue 1591 ILE
Chi-restraints excluded: chain A residue 1626 CYS
Chi-restraints excluded: chain A residue 1726 ILE
Chi-restraints excluded: chain A residue 1807 ASP
Chi-restraints excluded: chain A residue 1842 SER
Chi-restraints excluded: chain A residue 1927 ILE
Chi-restraints excluded: chain A residue 1947 VAL
Chi-restraints excluded: chain A residue 1988 THR
Chi-restraints excluded: chain A residue 2235 VAL
Chi-restraints excluded: chain A residue 2253 LEU
Chi-restraints excluded: chain A residue 2361 VAL
Chi-restraints excluded: chain A residue 2362 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 235
   random chunks:
   chunk 133 optimal weight:    0.0570
   chunk 95 optimal weight:    5.9990
   chunk 45 optimal weight:    0.5980
   chunk 126 optimal weight:    1.9990
   chunk 184 optimal weight:    0.7980
   chunk 102 optimal weight:    0.9990
   chunk 146 optimal weight:    9.9990
   chunk 177 optimal weight:    5.9990
   chunk 79 optimal weight:    0.6980
   chunk 56 optimal weight:    0.7980
   chunk 121 optimal weight:    8.9990
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
A 487 ASN
A1445 GLN
A1724 ASN
A2001 ASN
A2058 ASN
A2143 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.200162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.121170 restraints weight = 27504.803|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 2.38
r_work: 0.3064 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2928 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.2779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  19413  Z= 0.098
  Angle     :  0.491   9.587  26261  Z= 0.265
  Chirality :  0.044   0.197   2898
  Planarity :  0.003   0.078   3394
  Dihedral  :  4.848  58.205   2565
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 22.96 %
    Favored  : 73.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.18), residues: 2351
  helix:  2.41 (0.21), residues: 666
  sheet: -0.03 (0.23), residues: 489
  loop : -0.61 (0.18), residues: 1196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 118 
 HIS   0.003   0.001   HIS A 924 
 PHE   0.031   0.001   PHE A 937 
 TYR   0.018   0.001   TYR A 990 
 ARG   0.003   0.000   ARG A1495 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03723 (  830)
  hydrogen bonds       : angle       4.36528 ( 2232)
  metal coordination   : bond        0.00373 (    3)
  covalent geometry    : bond        0.00211 (19409)
  covalent geometry    : angle       0.49061 (26261)
  Misc. bond           : bond        0.00517 (    1)

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

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

  4702 Ramachandran restraints generated.
    2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4702 Ramachandran restraints generated.
    2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 133
  time to evaluate  : 2.120 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.8361 (tpt) cc_final: 0.8056 (tpt)
REVERT: A  333 LYS cc_start: 0.8687 (tmmt) cc_final: 0.8306 (mtmm)
REVERT: A  543 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7650 (mt)
REVERT: A  570 MET cc_start: 0.9201 (OUTLIER) cc_final: 0.8159 (mmt)
REVERT: A  639 GLN cc_start: 0.8164 (mt0) cc_final: 0.7656 (mt0)
REVERT: A  646 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.8830 (tp)
REVERT: A  751 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8355 (mttm)
REVERT: A  814 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7482 (p0)
REVERT: A 1027 GLU cc_start: 0.7319 (tt0) cc_final: 0.7101 (tm-30)
REVERT: A 1230 PHE cc_start: 0.0048 (OUTLIER) cc_final: -0.0526 (m-80)
REVERT: A 1332 MET cc_start: 0.4067 (pmm) cc_final: 0.0539 (ttp)
REVERT: A 1418 ILE cc_start: 0.6318 (OUTLIER) cc_final: 0.5772 (tp)
REVERT: A 1462 TYR cc_start: 0.6750 (OUTLIER) cc_final: 0.4010 (p90)
REVERT: A 1470 LYS cc_start: 0.7946 (ttmt) cc_final: 0.7548 (mtmm)
REVERT: A 1477 TYR cc_start: 0.7617 (t80) cc_final: 0.7018 (t80)
REVERT: A 1490 ASN cc_start: 0.7373 (p0) cc_final: 0.7047 (p0)
REVERT: A 1495 ARG cc_start: 0.8193 (ttm-80) cc_final: 0.7870 (mmm-85)
REVERT: A 1499 MET cc_start: 0.6393 (tpp) cc_final: 0.5151 (ttp)
REVERT: A 1567 LYS cc_start: 0.9171 (ttmt) cc_final: 0.8885 (tttp)
REVERT: A 1641 ILE cc_start: 0.8486 (mt) cc_final: 0.8230 (mt)
REVERT: A 1775 ASP cc_start: 0.4220 (OUTLIER) cc_final: 0.3161 (m-30)
REVERT: A 1906 LEU cc_start: 0.7841 (mm) cc_final: 0.7556 (mp)
REVERT: A 1947 VAL cc_start: 0.6383 (OUTLIER) cc_final: 0.6150 (m)
REVERT: A 2006 MET cc_start: 0.4288 (tpt) cc_final: 0.2595 (ttt)
REVERT: A 2289 MET cc_start: -0.0035 (tpt) cc_final: -0.1978 (ptm)
  outliers start: 70
  outliers final: 39
  residues processed: 191
  average time/residue: 0.9851
  time to fit residues: 222.0883
Evaluate side-chains
  175 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 126
  time to evaluate  : 2.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  192 SER
Chi-restraints excluded: chain A residue  381 SER
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  570 MET
Chi-restraints excluded: chain A residue  572 THR
Chi-restraints excluded: chain A residue  574 ASN
Chi-restraints excluded: chain A residue  576 GLU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  646 ILE
Chi-restraints excluded: chain A residue  702 SER
Chi-restraints excluded: chain A residue  751 LYS
Chi-restraints excluded: chain A residue  814 ASP
Chi-restraints excluded: chain A residue  820 MET
Chi-restraints excluded: chain A residue  865 ILE
Chi-restraints excluded: chain A residue  874 HIS
Chi-restraints excluded: chain A residue  890 SER
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue 1055 LEU
Chi-restraints excluded: chain A residue 1080 THR
Chi-restraints excluded: chain A residue 1150 LEU
Chi-restraints excluded: chain A residue 1167 CYS
Chi-restraints excluded: chain A residue 1205 VAL
Chi-restraints excluded: chain A residue 1213 ILE
Chi-restraints excluded: chain A residue 1230 PHE
Chi-restraints excluded: chain A residue 1234 MET
Chi-restraints excluded: chain A residue 1264 TRP
Chi-restraints excluded: chain A residue 1328 SER
Chi-restraints excluded: chain A residue 1343 THR
Chi-restraints excluded: chain A residue 1368 ILE
Chi-restraints excluded: chain A residue 1418 ILE
Chi-restraints excluded: chain A residue 1462 TYR
Chi-restraints excluded: chain A residue 1547 THR
Chi-restraints excluded: chain A residue 1591 ILE
Chi-restraints excluded: chain A residue 1626 CYS
Chi-restraints excluded: chain A residue 1662 TYR
Chi-restraints excluded: chain A residue 1726 ILE
Chi-restraints excluded: chain A residue 1775 ASP
Chi-restraints excluded: chain A residue 1842 SER
Chi-restraints excluded: chain A residue 1927 ILE
Chi-restraints excluded: chain A residue 1947 VAL
Chi-restraints excluded: chain A residue 1988 THR
Chi-restraints excluded: chain A residue 2235 VAL
Chi-restraints excluded: chain A residue 2253 LEU
Chi-restraints excluded: chain A residue 2269 MET
Chi-restraints excluded: chain A residue 2361 VAL
Chi-restraints excluded: chain A residue 2362 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 235
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 187 optimal weight:    0.5980
   chunk 109 optimal weight:    7.9990
   chunk 179 optimal weight:    0.5980
   chunk 110 optimal weight:    5.9990
   chunk 232 optimal weight:    9.9990
   chunk 163 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9980
   chunk 160 optimal weight:    6.9990
   chunk 36 optimal weight:    0.1980
   chunk 197 optimal weight:    9.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 487 ASN
A 874 HIS
A1724 ASN
A1931 ASN
A2058 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.201531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.125529 restraints weight = 27193.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 2.73
r_work: 0.3068 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2934 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.2873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  19413  Z= 0.100
  Angle     :  0.496  11.821  26261  Z= 0.265
  Chirality :  0.045   0.206   2898
  Planarity :  0.003   0.076   3394
  Dihedral  :  4.702  57.157   2563
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 23.29 %
    Favored  : 73.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.18), residues: 2351
  helix:  2.46 (0.21), residues: 667
  sheet:  0.05 (0.23), residues: 492
  loop : -0.54 (0.18), residues: 1192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 118 
 HIS   0.003   0.001   HIS A 924 
 PHE   0.031   0.001   PHE A1474 
 TYR   0.017   0.001   TYR A 793 
 ARG   0.002   0.000   ARG A1495 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03779 (  830)
  hydrogen bonds       : angle       4.32476 ( 2232)
  metal coordination   : bond        0.00417 (    3)
  covalent geometry    : bond        0.00218 (19409)
  covalent geometry    : angle       0.49589 (26261)
  Misc. bond           : bond        0.00531 (    1)

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

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

  4702 Ramachandran restraints generated.
    2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4702 Ramachandran restraints generated.
    2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 136
  time to evaluate  : 2.035 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.8359 (tpt) cc_final: 0.8053 (tpt)
REVERT: A  333 LYS cc_start: 0.8667 (tmmt) cc_final: 0.8186 (mttm)
REVERT: A  543 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7642 (mt)
REVERT: A  570 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8170 (mmt)
REVERT: A  639 GLN cc_start: 0.8157 (mt0) cc_final: 0.7688 (mt0)
REVERT: A  646 ILE cc_start: 0.9269 (OUTLIER) cc_final: 0.8830 (tp)
REVERT: A  751 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8310 (mttm)
REVERT: A  814 ASP cc_start: 0.7705 (OUTLIER) cc_final: 0.7439 (p0)
REVERT: A  890 SER cc_start: 0.5060 (OUTLIER) cc_final: 0.4712 (t)
REVERT: A 1230 PHE cc_start: 0.0168 (OUTLIER) cc_final: -0.0497 (m-80)
REVERT: A 1332 MET cc_start: 0.4114 (pmm) cc_final: 0.0485 (ttp)
REVERT: A 1418 ILE cc_start: 0.6228 (OUTLIER) cc_final: 0.5693 (tp)
REVERT: A 1462 TYR cc_start: 0.6806 (OUTLIER) cc_final: 0.4040 (p90)
REVERT: A 1470 LYS cc_start: 0.7950 (ttmt) cc_final: 0.7529 (mtmm)
REVERT: A 1477 TYR cc_start: 0.7609 (t80) cc_final: 0.7026 (t80)
REVERT: A 1490 ASN cc_start: 0.7327 (p0) cc_final: 0.7018 (p0)
REVERT: A 1495 ARG cc_start: 0.8141 (ttm-80) cc_final: 0.7878 (mmm-85)
REVERT: A 1499 MET cc_start: 0.6352 (tpp) cc_final: 0.5102 (ttp)
REVERT: A 1567 LYS cc_start: 0.9156 (ttmt) cc_final: 0.8724 (ttpm)
REVERT: A 1641 ILE cc_start: 0.8473 (mt) cc_final: 0.8207 (mt)
REVERT: A 1906 LEU cc_start: 0.7813 (mm) cc_final: 0.7568 (mp)
REVERT: A 1947 VAL cc_start: 0.6217 (OUTLIER) cc_final: 0.5997 (m)
REVERT: A 2006 MET cc_start: 0.4283 (tpt) cc_final: 0.2607 (ttt)
REVERT: A 2289 MET cc_start: -0.0055 (tpt) cc_final: -0.2081 (ptm)
  outliers start: 63
  outliers final: 35
  residues processed: 189
  average time/residue: 1.0733
  time to fit residues: 235.2558
Evaluate side-chains
  168 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 123
  time to evaluate  : 2.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  192 SER
Chi-restraints excluded: chain A residue  381 SER
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  570 MET
Chi-restraints excluded: chain A residue  572 THR
Chi-restraints excluded: chain A residue  574 ASN
Chi-restraints excluded: chain A residue  576 GLU
Chi-restraints excluded: chain A residue  646 ILE
Chi-restraints excluded: chain A residue  702 SER
Chi-restraints excluded: chain A residue  751 LYS
Chi-restraints excluded: chain A residue  814 ASP
Chi-restraints excluded: chain A residue  837 VAL
Chi-restraints excluded: chain A residue  865 ILE
Chi-restraints excluded: chain A residue  890 SER
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue 1025 LEU
Chi-restraints excluded: chain A residue 1055 LEU
Chi-restraints excluded: chain A residue 1064 ILE
Chi-restraints excluded: chain A residue 1150 LEU
Chi-restraints excluded: chain A residue 1167 CYS
Chi-restraints excluded: chain A residue 1205 VAL
Chi-restraints excluded: chain A residue 1213 ILE
Chi-restraints excluded: chain A residue 1230 PHE
Chi-restraints excluded: chain A residue 1234 MET
Chi-restraints excluded: chain A residue 1264 TRP
Chi-restraints excluded: chain A residue 1324 SER
Chi-restraints excluded: chain A residue 1328 SER
Chi-restraints excluded: chain A residue 1343 THR
Chi-restraints excluded: chain A residue 1368 ILE
Chi-restraints excluded: chain A residue 1418 ILE
Chi-restraints excluded: chain A residue 1462 TYR
Chi-restraints excluded: chain A residue 1547 THR
Chi-restraints excluded: chain A residue 1626 CYS
Chi-restraints excluded: chain A residue 1662 TYR
Chi-restraints excluded: chain A residue 1726 ILE
Chi-restraints excluded: chain A residue 1842 SER
Chi-restraints excluded: chain A residue 1927 ILE
Chi-restraints excluded: chain A residue 1947 VAL
Chi-restraints excluded: chain A residue 1988 THR
Chi-restraints excluded: chain A residue 2253 LEU
Chi-restraints excluded: chain A residue 2361 VAL
Chi-restraints excluded: chain A residue 2362 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 235
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 160 optimal weight:    1.9990
   chunk 102 optimal weight:    5.9990
   chunk 55 optimal weight:    4.9990
   chunk 86 optimal weight:    1.9990
   chunk 178 optimal weight:    0.0010
   chunk 38 optimal weight:    3.9990
   chunk 123 optimal weight:    8.9990
   chunk 208 optimal weight:    8.9990
   chunk 37 optimal weight:    1.9990
   chunk 26 optimal weight:    0.2980
   overall best weight:    1.2592

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

Flipped N/Q/H residues before XYZ refinement:
A1724 ASN
** A2058 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 = 0.4315 r_free = 0.4315 target = 0.198776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.123242 restraints weight = 27387.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.3339 rms_B_bonded: 3.13
r_work: 0.3022 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work: 0.2888 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
moved from start:          0.2837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  19413  Z= 0.129
  Angle     :  0.532  12.528  26261  Z= 0.285
  Chirality :  0.046   0.221   2898
  Planarity :  0.004   0.073   3394
  Dihedral  :  4.808  55.240   2562
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 23.71 %
    Favored  : 73.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.18), residues: 2351
  helix:  2.38 (0.20), residues: 666
  sheet:  0.05 (0.23), residues: 487
  loop : -0.54 (0.18), residues: 1198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 118 
 HIS   0.003   0.001   HIS A1456 
 PHE   0.032   0.001   PHE A1474 
 TYR   0.021   0.001   TYR A1459 
 ARG   0.003   0.000   ARG A1517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04440 (  830)
  hydrogen bonds       : angle       4.40996 ( 2232)
  metal coordination   : bond        0.00678 (    3)
  covalent geometry    : bond        0.00299 (19409)
  covalent geometry    : angle       0.53176 (26261)
  Misc. bond           : bond        0.00514 (    1)

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

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

  4702 Ramachandran restraints generated.
    2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4702 Ramachandran restraints generated.
    2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 132
  time to evaluate  : 2.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.8320 (tpt) cc_final: 0.8016 (tpt)
REVERT: A    2 ASN cc_start: 0.8748 (OUTLIER) cc_final: 0.8371 (t0)
REVERT: A  333 LYS cc_start: 0.8662 (tmmt) cc_final: 0.8298 (mtmm)
REVERT: A  543 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7730 (mt)
REVERT: A  570 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.8285 (mmt)
REVERT: A  646 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.8821 (tp)
REVERT: A  751 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8358 (mttm)
REVERT: A  814 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7404 (p0)
REVERT: A 1230 PHE cc_start: 0.0131 (OUTLIER) cc_final: -0.0464 (m-80)
REVERT: A 1327 LEU cc_start: 0.6292 (OUTLIER) cc_final: 0.5999 (tp)
REVERT: A 1462 TYR cc_start: 0.6950 (OUTLIER) cc_final: 0.3827 (p90)
REVERT: A 1470 LYS cc_start: 0.7918 (ttmt) cc_final: 0.7491 (mtmm)
REVERT: A 1477 TYR cc_start: 0.7625 (t80) cc_final: 0.7037 (t80)
REVERT: A 1490 ASN cc_start: 0.7217 (p0) cc_final: 0.6945 (p0)
REVERT: A 1495 ARG cc_start: 0.8127 (ttm-80) cc_final: 0.7773 (mmm-85)
REVERT: A 1499 MET cc_start: 0.6381 (tpp) cc_final: 0.5102 (ttp)
REVERT: A 1567 LYS cc_start: 0.9194 (ttmt) cc_final: 0.8753 (ttpm)
REVERT: A 1641 ILE cc_start: 0.8539 (mt) cc_final: 0.8279 (mt)
REVERT: A 1775 ASP cc_start: 0.4578 (OUTLIER) cc_final: 0.3525 (m-30)
REVERT: A 1906 LEU cc_start: 0.7868 (mm) cc_final: 0.7625 (mp)
REVERT: A 1927 ILE cc_start: 0.6268 (OUTLIER) cc_final: 0.5928 (pp)
REVERT: A 1947 VAL cc_start: 0.6196 (OUTLIER) cc_final: 0.5995 (m)
REVERT: A 2006 MET cc_start: 0.4181 (tpt) cc_final: 0.2605 (ttt)
REVERT: A 2289 MET cc_start: 0.0007 (tpt) cc_final: -0.1997 (ptm)
  outliers start: 59
  outliers final: 37
  residues processed: 181
  average time/residue: 1.0437
  time to fit residues: 221.1195
Evaluate side-chains
  177 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 128
  time to evaluate  : 2.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 ASN
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  192 SER
Chi-restraints excluded: chain A residue  381 SER
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  570 MET
Chi-restraints excluded: chain A residue  572 THR
Chi-restraints excluded: chain A residue  574 ASN
Chi-restraints excluded: chain A residue  576 GLU
Chi-restraints excluded: chain A residue  646 ILE
Chi-restraints excluded: chain A residue  702 SER
Chi-restraints excluded: chain A residue  751 LYS
Chi-restraints excluded: chain A residue  814 ASP
Chi-restraints excluded: chain A residue  837 VAL
Chi-restraints excluded: chain A residue  865 ILE
Chi-restraints excluded: chain A residue  890 SER
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue 1025 LEU
Chi-restraints excluded: chain A residue 1055 LEU
Chi-restraints excluded: chain A residue 1064 ILE
Chi-restraints excluded: chain A residue 1150 LEU
Chi-restraints excluded: chain A residue 1205 VAL
Chi-restraints excluded: chain A residue 1213 ILE
Chi-restraints excluded: chain A residue 1230 PHE
Chi-restraints excluded: chain A residue 1234 MET
Chi-restraints excluded: chain A residue 1264 TRP
Chi-restraints excluded: chain A residue 1324 SER
Chi-restraints excluded: chain A residue 1327 LEU
Chi-restraints excluded: chain A residue 1328 SER
Chi-restraints excluded: chain A residue 1343 THR
Chi-restraints excluded: chain A residue 1368 ILE
Chi-restraints excluded: chain A residue 1418 ILE
Chi-restraints excluded: chain A residue 1462 TYR
Chi-restraints excluded: chain A residue 1547 THR
Chi-restraints excluded: chain A residue 1591 ILE
Chi-restraints excluded: chain A residue 1626 CYS
Chi-restraints excluded: chain A residue 1662 TYR
Chi-restraints excluded: chain A residue 1726 ILE
Chi-restraints excluded: chain A residue 1775 ASP
Chi-restraints excluded: chain A residue 1842 SER
Chi-restraints excluded: chain A residue 1927 ILE
Chi-restraints excluded: chain A residue 1947 VAL
Chi-restraints excluded: chain A residue 1988 THR
Chi-restraints excluded: chain A residue 2253 LEU
Chi-restraints excluded: chain A residue 2361 VAL
Chi-restraints excluded: chain A residue 2362 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 235
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 226 optimal weight:    6.9990
   chunk 167 optimal weight:    2.9990
   chunk 187 optimal weight:    0.8980
   chunk 158 optimal weight:    7.9990
   chunk 136 optimal weight:    8.9990
   chunk 117 optimal weight:   10.0000
   chunk 132 optimal weight:    4.9990
   chunk 114 optimal weight:   30.0000
   chunk 197 optimal weight:    0.3980
   chunk 203 optimal weight:    9.9990
   overall best weight:    2.2586

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

Flipped N/Q/H residues before XYZ refinement:
A 574 ASN
** A1652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1724 ASN
** A2058 ASN ** 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 = 0.4284 r_free = 0.4284 target = 0.195813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.119732 restraints weight = 27302.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 3.28
r_work: 0.2941 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.2805 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8544
moved from start:          0.2647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061  19413  Z= 0.192
  Angle     :  0.594  13.031  26261  Z= 0.318
  Chirality :  0.048   0.240   2898
  Planarity :  0.004   0.073   3394
  Dihedral  :  5.034  50.031   2561
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  4.85 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 23.62 %
    Favored  : 73.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.17), residues: 2351
  helix:  2.09 (0.20), residues: 665
  sheet: -0.08 (0.23), residues: 480
  loop : -0.66 (0.18), residues: 1206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 118 
 HIS   0.004   0.001   HIS A1456 
 PHE   0.033   0.002   PHE A1474 
 TYR   0.018   0.002   TYR A1646 
 ARG   0.008   0.001   ARG A1653 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05567 (  830)
  hydrogen bonds       : angle       4.65809 ( 2232)
  metal coordination   : bond        0.01101 (    3)
  covalent geometry    : bond        0.00465 (19409)
  covalent geometry    : angle       0.59356 (26261)
  Misc. bond           : bond        0.00506 (    1)

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

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

  4702 Ramachandran restraints generated.
    2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4702 Ramachandran restraints generated.
    2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 129
  time to evaluate  : 2.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.8292 (tpt) cc_final: 0.7980 (tpt)
REVERT: A  333 LYS cc_start: 0.8658 (tmmt) cc_final: 0.8271 (mtmm)
REVERT: A  543 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7820 (mt)
REVERT: A  646 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.8755 (tp)
REVERT: A  751 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8425 (mttm)
REVERT: A  814 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7600 (p0)
REVERT: A 1055 LEU cc_start: 0.6884 (OUTLIER) cc_final: 0.6541 (tm)
REVERT: A 1230 PHE cc_start: 0.0205 (OUTLIER) cc_final: -0.0393 (m-80)
REVERT: A 1327 LEU cc_start: 0.6297 (OUTLIER) cc_final: 0.5969 (tp)
REVERT: A 1391 PHE cc_start: 0.6332 (OUTLIER) cc_final: 0.5685 (p90)
REVERT: A 1470 LYS cc_start: 0.7944 (ttmt) cc_final: 0.7489 (mtmm)
REVERT: A 1477 TYR cc_start: 0.7610 (t80) cc_final: 0.6991 (t80)
REVERT: A 1490 ASN cc_start: 0.7208 (p0) cc_final: 0.6934 (p0)
REVERT: A 1495 ARG cc_start: 0.8215 (ttm-80) cc_final: 0.7841 (mmm-85)
REVERT: A 1499 MET cc_start: 0.6476 (tpp) cc_final: 0.5142 (ttp)
REVERT: A 1641 ILE cc_start: 0.8539 (mt) cc_final: 0.8306 (mt)
REVERT: A 1906 LEU cc_start: 0.7813 (mm) cc_final: 0.7543 (mp)
REVERT: A 2006 MET cc_start: 0.4079 (tpt) cc_final: 0.2842 (ttt)
REVERT: A 2289 MET cc_start: -0.0091 (tpt) cc_final: -0.2162 (ptm)
  outliers start: 61
  outliers final: 41
  residues processed: 181
  average time/residue: 0.9700
  time to fit residues: 206.7491
Evaluate side-chains
  169 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 120
  time to evaluate  : 1.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  192 SER
Chi-restraints excluded: chain A residue  381 SER
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  572 THR
Chi-restraints excluded: chain A residue  574 ASN
Chi-restraints excluded: chain A residue  576 GLU
Chi-restraints excluded: chain A residue  646 ILE
Chi-restraints excluded: chain A residue  751 LYS
Chi-restraints excluded: chain A residue  814 ASP
Chi-restraints excluded: chain A residue  837 VAL
Chi-restraints excluded: chain A residue  865 ILE
Chi-restraints excluded: chain A residue  890 SER
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue 1025 LEU
Chi-restraints excluded: chain A residue 1055 LEU
Chi-restraints excluded: chain A residue 1064 ILE
Chi-restraints excluded: chain A residue 1080 THR
Chi-restraints excluded: chain A residue 1150 LEU
Chi-restraints excluded: chain A residue 1205 VAL
Chi-restraints excluded: chain A residue 1213 ILE
Chi-restraints excluded: chain A residue 1230 PHE
Chi-restraints excluded: chain A residue 1234 MET
Chi-restraints excluded: chain A residue 1264 TRP
Chi-restraints excluded: chain A residue 1324 SER
Chi-restraints excluded: chain A residue 1327 LEU
Chi-restraints excluded: chain A residue 1328 SER
Chi-restraints excluded: chain A residue 1343 THR
Chi-restraints excluded: chain A residue 1368 ILE
Chi-restraints excluded: chain A residue 1391 PHE
Chi-restraints excluded: chain A residue 1418 ILE
Chi-restraints excluded: chain A residue 1462 TYR
Chi-restraints excluded: chain A residue 1547 THR
Chi-restraints excluded: chain A residue 1591 ILE
Chi-restraints excluded: chain A residue 1626 CYS
Chi-restraints excluded: chain A residue 1662 TYR
Chi-restraints excluded: chain A residue 1726 ILE
Chi-restraints excluded: chain A residue 1842 SER
Chi-restraints excluded: chain A residue 1927 ILE
Chi-restraints excluded: chain A residue 1947 VAL
Chi-restraints excluded: chain A residue 1988 THR
Chi-restraints excluded: chain A residue 2226 THR
Chi-restraints excluded: chain A residue 2235 VAL
Chi-restraints excluded: chain A residue 2253 LEU
Chi-restraints excluded: chain A residue 2361 VAL
Chi-restraints excluded: chain A residue 2362 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 235
   random chunks:
   chunk 153 optimal weight:    8.9990
   chunk 103 optimal weight:    0.0570
   chunk 52 optimal weight:    0.9980
   chunk 160 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 80 optimal weight:    2.9990
   chunk 195 optimal weight:    0.7980
   chunk 97 optimal weight:    0.8980
   chunk 90 optimal weight:    3.9990
   overall best weight:    0.7298

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

Flipped N/Q/H residues before XYZ refinement:
A 874 HIS
A1724 ASN
** A2058 ASN ** 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 = 0.4315 r_free = 0.4315 target = 0.198801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.124831 restraints weight = 27387.613|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 2.47
r_work: 0.3035 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2902 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8450
moved from start:          0.2953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  19413  Z= 0.105
  Angle     :  0.520  13.064  26261  Z= 0.277
  Chirality :  0.045   0.224   2898
  Planarity :  0.003   0.076   3394
  Dihedral  :  4.665  49.541   2561
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  4.08 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 24.55 %
    Favored  : 73.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.18), residues: 2351
  helix:  2.37 (0.20), residues: 666
  sheet:  0.09 (0.24), residues: 481
  loop : -0.57 (0.18), residues: 1204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 118 
 HIS   0.003   0.001   HIS A 924 
 PHE   0.032   0.001   PHE A1474 
 TYR   0.020   0.001   TYR A 990 
 ARG   0.005   0.000   ARG A1653 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03879 (  830)
  hydrogen bonds       : angle       4.39863 ( 2232)
  metal coordination   : bond        0.00425 (    3)
  covalent geometry    : bond        0.00230 (19409)
  covalent geometry    : angle       0.51994 (26261)
  Misc. bond           : bond        0.00519 (    1)

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

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

  4702 Ramachandran restraints generated.
    2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4702 Ramachandran restraints generated.
    2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 128
  time to evaluate  : 2.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.8343 (tpt) cc_final: 0.8028 (tpt)
REVERT: A  201 ILE cc_start: 0.8607 (pt) cc_final: 0.8390 (mt)
REVERT: A  333 LYS cc_start: 0.8661 (tmmt) cc_final: 0.8300 (mtmm)
REVERT: A  543 LEU cc_start: 0.7988 (mt) cc_final: 0.7680 (mt)
REVERT: A  646 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.8794 (tp)
REVERT: A  751 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8419 (mttm)
REVERT: A  814 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7399 (p0)
REVERT: A 1055 LEU cc_start: 0.6877 (OUTLIER) cc_final: 0.6555 (tm)
REVERT: A 1230 PHE cc_start: 0.0290 (OUTLIER) cc_final: -0.0453 (m-80)
REVERT: A 1327 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.6305 (tp)
REVERT: A 1332 MET cc_start: 0.4579 (pmm) cc_final: 0.1204 (ttp)
REVERT: A 1470 LYS cc_start: 0.8013 (ttmt) cc_final: 0.7574 (mtmm)
REVERT: A 1477 TYR cc_start: 0.7555 (t80) cc_final: 0.7058 (t80)
REVERT: A 1490 ASN cc_start: 0.7174 (p0) cc_final: 0.6898 (p0)
REVERT: A 1495 ARG cc_start: 0.8117 (ttm-80) cc_final: 0.7780 (mmm-85)
REVERT: A 1499 MET cc_start: 0.6578 (tpp) cc_final: 0.5245 (ttp)
REVERT: A 1567 LYS cc_start: 0.9197 (ttmt) cc_final: 0.8766 (ttpm)
REVERT: A 1641 ILE cc_start: 0.8480 (mt) cc_final: 0.8201 (mt)
REVERT: A 1746 ASP cc_start: 0.8390 (t70) cc_final: 0.7964 (m-30)
REVERT: A 1906 LEU cc_start: 0.7856 (mm) cc_final: 0.7589 (mp)
REVERT: A 1927 ILE cc_start: 0.6277 (OUTLIER) cc_final: 0.5950 (pp)
REVERT: A 1947 VAL cc_start: 0.6123 (OUTLIER) cc_final: 0.5849 (m)
REVERT: A 2006 MET cc_start: 0.3937 (tpt) cc_final: 0.2633 (ttt)
REVERT: A 2235 VAL cc_start: 0.0821 (OUTLIER) cc_final: 0.0617 (p)
REVERT: A 2289 MET cc_start: -0.0095 (tpt) cc_final: -0.2159 (ptm)
  outliers start: 50
  outliers final: 34
  residues processed: 170
  average time/residue: 1.0822
  time to fit residues: 214.3106
Evaluate side-chains
  166 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 123
  time to evaluate  : 2.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  192 SER
Chi-restraints excluded: chain A residue  381 SER
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  572 THR
Chi-restraints excluded: chain A residue  574 ASN
Chi-restraints excluded: chain A residue  576 GLU
Chi-restraints excluded: chain A residue  646 ILE
Chi-restraints excluded: chain A residue  702 SER
Chi-restraints excluded: chain A residue  751 LYS
Chi-restraints excluded: chain A residue  814 ASP
Chi-restraints excluded: chain A residue  837 VAL
Chi-restraints excluded: chain A residue  865 ILE
Chi-restraints excluded: chain A residue  890 SER
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue 1055 LEU
Chi-restraints excluded: chain A residue 1080 THR
Chi-restraints excluded: chain A residue 1150 LEU
Chi-restraints excluded: chain A residue 1213 ILE
Chi-restraints excluded: chain A residue 1230 PHE
Chi-restraints excluded: chain A residue 1234 MET
Chi-restraints excluded: chain A residue 1264 TRP
Chi-restraints excluded: chain A residue 1324 SER
Chi-restraints excluded: chain A residue 1327 LEU
Chi-restraints excluded: chain A residue 1328 SER
Chi-restraints excluded: chain A residue 1343 THR
Chi-restraints excluded: chain A residue 1368 ILE
Chi-restraints excluded: chain A residue 1418 ILE
Chi-restraints excluded: chain A residue 1547 THR
Chi-restraints excluded: chain A residue 1591 ILE
Chi-restraints excluded: chain A residue 1626 CYS
Chi-restraints excluded: chain A residue 1807 ASP
Chi-restraints excluded: chain A residue 1842 SER
Chi-restraints excluded: chain A residue 1927 ILE
Chi-restraints excluded: chain A residue 1947 VAL
Chi-restraints excluded: chain A residue 1988 THR
Chi-restraints excluded: chain A residue 2226 THR
Chi-restraints excluded: chain A residue 2235 VAL
Chi-restraints excluded: chain A residue 2253 LEU
Chi-restraints excluded: chain A residue 2361 VAL
Chi-restraints excluded: chain A residue 2362 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 235
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 191 optimal weight:    2.9990
   chunk 92 optimal weight:    1.9990
   chunk 207 optimal weight:    6.9990
   chunk 208 optimal weight:    0.0040
   chunk 10 optimal weight:    0.9990
   chunk 103 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 233 optimal weight:   40.0000
   chunk 73 optimal weight:    3.9990
   chunk 139 optimal weight:   20.0000
   overall best weight:    1.8000

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

Flipped N/Q/H residues before XYZ refinement:
A 874 HIS
** A1652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1724 ASN
** A2058 ASN ** 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 = 0.4294 r_free = 0.4294 target = 0.196802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.120204 restraints weight = 27182.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 2.84
r_work: 0.2984 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2854 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.2810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  19413  Z= 0.159
  Angle     :  0.559  12.761  26261  Z= 0.299
  Chirality :  0.047   0.236   2898
  Planarity :  0.004   0.075   3394
  Dihedral  :  4.691  48.771   2557
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  4.68 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 24.46 %
    Favored  : 72.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.17), residues: 2351
  helix:  2.21 (0.20), residues: 666
  sheet:  0.01 (0.24), residues: 472
  loop : -0.63 (0.18), residues: 1213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 118 
 HIS   0.004   0.001   HIS A1456 
 PHE   0.034   0.001   PHE A1474 
 TYR   0.014   0.001   TYR A1646 
 ARG   0.011   0.000   ARG A1653 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04971 (  830)
  hydrogen bonds       : angle       4.52118 ( 2232)
  metal coordination   : bond        0.00860 (    3)
  covalent geometry    : bond        0.00379 (19409)
  covalent geometry    : angle       0.55878 (26261)
  Misc. bond           : bond        0.00532 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 20771.45 seconds
wall clock time: 357 minutes 30.27 seconds (21450.27 seconds total)