Starting phenix.real_space_refine
on Sat Aug 23 13:40:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ask_11895/08_2025/7ask_11895.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ask_11895/08_2025/7ask_11895.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ask_11895/08_2025/7ask_11895.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ask_11895/08_2025/7ask_11895.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ask_11895/08_2025/7ask_11895.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ask_11895/08_2025/7ask_11895.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     Mg      1      5.21       5
     S      66      5.16       5
     C    7744      2.51       5
     N    2170      2.21       5
     O    2302      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 57 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12285
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "F"
      Number of atoms: 12257
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1523, 12257
          Classifications: {'peptide': 1523}
          Link IDs: {'CIS': 45, 'PCIS': 3, 'PTRANS': 50, 'TRANS': 1424}
          Chain breaks: 15
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.63, per 1000 atoms: 0.21
  Number of scatterers: 12285
  At special positions: 0
  Unit cell: (156.96, 114.45, 160.23, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      66     16.00
     P       2     15.00
     Mg      1     11.99
     O    2302      8.00
     N    2170      7.00
     C    7744      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: 0.85
  Conformation dependent library (CDL) restraints added in 356.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2978 Ramachandran restraints generated.
    1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        pdb=" CB  TYR F 296 "
        pdb=" CB  TYR F 305 "
        pdb=" CB  ILE F1155 "
        pdb=" CB  ARG F1697 "
  Number of C-beta restraints generated:  2870

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 3 sheets defined
      47.4% alpha, 3.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'F' and resid 1 through 16
      removed outlier: 4.871A  pdb=" N   ILE F   9 " --> pdb=" O   TYR F   5 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   ALA F  10 " --> pdb=" O   ARG F   6 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   GLU F  14 " --> pdb=" O   ALA F  10 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   PHE F  15 " --> pdb=" O   ILE F  11 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   LEU F  16 " --> pdb=" O   PHE F  12 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 31 through 38
      removed outlier: 3.631A  pdb=" N   THR F  35 " --> pdb=" O   GLY F  31 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 59 through 75
      removed outlier: 3.947A  pdb=" N   ASP F  64 " --> pdb=" O   ALA F  60 " (cutoff:3.500A)
      removed outlier: 5.021A  pdb=" N   ALA F  65 " --> pdb=" O   ARG F  61 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ASN F  71 " --> pdb=" O   ARG F  67 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 92 through 109
      removed outlier: 3.923A  pdb=" N   LEU F  96 " --> pdb=" O   GLU F  92 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   GLY F 103 " --> pdb=" O   LYS F  99 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   ALA F 104 " --> pdb=" O   PHE F 100 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ALA F 106 " --> pdb=" O   ILE F 102 " (cutoff:3.500A)
      removed outlier: 4.491A  pdb=" N   ALA F 107 " --> pdb=" O   GLY F 103 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   LYS F 108 " --> pdb=" O   ALA F 104 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ASN F 109 " --> pdb=" O   LEU F 105 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 111 through 130
      removed outlier: 3.822A  pdb=" N   VAL F 115 " --> pdb=" O   GLU F 111 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   GLU F 119 " --> pdb=" O   VAL F 115 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   VAL F 125 " --> pdb=" O   LEU F 121 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   TYR F 129 " --> pdb=" O   VAL F 125 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 140 through 144
      removed outlier: 3.584A  pdb=" N   LEU F 143 " --> pdb=" O   PHE F 140 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 153 through 161
    Processing helix  chain 'F' and resid 177 through 188
      removed outlier: 3.783A  pdb=" N   GLN F 181 " --> pdb=" O   ILE F 177 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 215 through 228
      removed outlier: 4.210A  pdb=" N   GLU F 228 " --> pdb=" O   MET F 224 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 249 through 256
      removed outlier: 4.032A  pdb=" N   TRP F 255 " --> pdb=" O   TYR F 251 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 271 through 287
      removed outlier: 3.579A  pdb=" N   GLN F 275 " --> pdb=" O   LEU F 271 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ALA F 276 " --> pdb=" O   ASN F 272 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   PHE F 277 " --> pdb=" O   PRO F 273 " (cutoff:3.500A)
      Proline residue:  F 281  - end of helix
    Processing helix  chain 'F' and resid 671 through 675
    Processing helix  chain 'F' and resid 686 through 695
      removed outlier: 3.842A  pdb=" N   HIS F 691 " --> pdb=" O   VAL F 687 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   ALA F 692 " --> pdb=" O   ASN F 688 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 738 through 764
      removed outlier: 4.540A  pdb=" N   ASP F 744 " --> pdb=" O   THR F 740 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ILE F 749 " --> pdb=" O   ARG F 745 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ILE F 752 " --> pdb=" O   SER F 748 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   GLN F 761 " --> pdb=" O   LYS F 757 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   GLU F 762 " --> pdb=" O   ARG F 758 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   PHE F 764 " --> pdb=" O   SER F 760 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 776 through 779
    Processing helix  chain 'F' and resid 780 through 792
      removed outlier: 3.798A  pdb=" N   LEU F 784 " --> pdb=" O   THR F 780 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLU F 787 " --> pdb=" O   PRO F 783 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 810 through 815
    Processing helix  chain 'F' and resid 816 through 823
      removed outlier: 3.782A  pdb=" N   LYS F 820 " --> pdb=" O   LYS F 816 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ASP F 823 " --> pdb=" O   SER F 819 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 836 through 845
      removed outlier: 3.680A  pdb=" N   PHE F 840 " --> pdb=" O   VAL F 836 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 853 through 860
      removed outlier: 3.587A  pdb=" N   ARG F 858 " --> pdb=" O   LEU F 854 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 866 through 901
      removed outlier: 3.909A  pdb=" N   LEU F 873 " --> pdb=" O   ALA F 869 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   LEU F 878 " --> pdb=" O   ARG F 874 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   PHE F 880 " --> pdb=" O   VAL F 876 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   HIS F 884 " --> pdb=" O   PHE F 880 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   LEU F 889 " --> pdb=" O   ILE F 885 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   VAL F 893 " --> pdb=" O   LEU F 889 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   LEU F 896 " --> pdb=" O   ARG F 892 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   LEU F 898 " --> pdb=" O   VAL F 894 " (cutoff:3.500A)
      removed outlier: 4.669A  pdb=" N   GLU F 899 " --> pdb=" O   LYS F 895 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ASN F 900 " --> pdb=" O   LEU F 896 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 901 through 907
      removed outlier: 3.866A  pdb=" N   ARG F 905 " --> pdb=" O   TRP F 901 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   GLU F 906 " --> pdb=" O   ARG F 902 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 921 through 932
    Processing helix  chain 'F' and resid 946 through 955
    Processing helix  chain 'F' and resid 962 through 976
      removed outlier: 3.536A  pdb=" N   LYS F 966 " --> pdb=" O   SER F 962 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ASP F 968 " --> pdb=" O   TYR F 964 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   GLN F 969 " --> pdb=" O   ASN F 965 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   CYS F 970 " --> pdb=" O   LYS F 966 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   ARG F 973 " --> pdb=" O   GLN F 969 " (cutoff:3.500A)
      removed outlier: 4.609A  pdb=" N   TRP F 974 " --> pdb=" O   CYS F 970 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1001 through 1007
      removed outlier: 3.855A  pdb=" N   MET F1005 " --> pdb=" O   GLN F1001 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   HIS F1007 " --> pdb=" O   ILE F1003 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1028 through 1037
      removed outlier: 4.968A  pdb=" N   ASP F1034 " --> pdb=" O   ARG F1030 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   ILE F1035 " --> pdb=" O   GLU F1031 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   VAL F1036 " --> pdb=" O   LEU F1032 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1053 through 1055
      No H-bonds generated for 'chain 'F' and resid 1053 through 1055'
    Processing helix  chain 'F' and resid 1056 through 1057
      No H-bonds generated for 'chain 'F' and resid 1056 through 1057'
    Processing helix  chain 'F' and resid 1059 through 1066
      removed outlier: 3.836A  pdb=" N   ARG F1066 " --> pdb=" O   LYS F1062 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1082 through 1092
      removed outlier: 4.597A  pdb=" N   VAL F1086 " --> pdb=" O   ILE F1082 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ARG F1092 " --> pdb=" O   ASP F1088 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1127 through 1137
    Processing helix  chain 'F' and resid 1140 through 1145
      removed outlier: 3.715A  pdb=" N   VAL F1144 " --> pdb=" O   TYR F1140 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   GLU F1145 " --> pdb=" O   THR F1141 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 1140 through 1145'
    Processing helix  chain 'F' and resid 1155 through 1162
      removed outlier: 3.714A  pdb=" N   ASN F1161 " --> pdb=" O   SER F1157 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1166 through 1171
      removed outlier: 3.613A  pdb=" N   ILE F1170 " --> pdb=" O   VAL F1166 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LEU F1171 " --> pdb=" O   TRP F1167 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 1166 through 1171'
    Processing helix  chain 'F' and resid 1188 through 1206
      removed outlier: 3.509A  pdb=" N   TRP F1194 " --> pdb=" O   GLN F1190 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1271 through 1278
      removed outlier: 3.947A  pdb=" N   GLN F1276 " --> pdb=" O   ALA F1272 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1290 through 1298
      removed outlier: 4.087A  pdb=" N   GLU F1295 " --> pdb=" O   VAL F1291 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LYS F1296 " --> pdb=" O   SER F1292 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1313 through 1331
      removed outlier: 4.969A  pdb=" N   GLN F1321 " --> pdb=" O   THR F1317 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   MET F1323 " --> pdb=" O   ARG F1319 " (cutoff:3.500A)
      removed outlier: 5.218A  pdb=" N   LEU F1324 " --> pdb=" O   ALA F1320 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   GLU F1326 " --> pdb=" O   LEU F1322 " (cutoff:3.500A)
      Proline residue:  F1327  - end of helix
      removed outlier: 3.568A  pdb=" N   TYR F1330 " --> pdb=" O   GLU F1326 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1342 through 1349
      removed outlier: 4.151A  pdb=" N   GLU F1346 " --> pdb=" O   ALA F1342 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ALA F1347 " --> pdb=" O   ARG F1343 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1349 through 1358
      removed outlier: 4.082A  pdb=" N   TYR F1355 " --> pdb=" O   ASN F1351 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   TRP F1356 " --> pdb=" O   ALA F1352 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1381 through 1401
      removed outlier: 3.804A  pdb=" N   ARG F1391 " --> pdb=" O   GLU F1387 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   THR F1392 " --> pdb=" O   SER F1388 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ALA F1394 " --> pdb=" O   LEU F1390 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLN F1395 " --> pdb=" O   ARG F1391 " (cutoff:3.500A)
      removed outlier: 4.769A  pdb=" N   LYS F1396 " --> pdb=" O   THR F1392 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ASN F1398 " --> pdb=" O   ALA F1394 " (cutoff:3.500A)
      removed outlier: 5.345A  pdb=" N   GLU F1399 " --> pdb=" O   GLN F1395 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   ASP F1400 " --> pdb=" O   LYS F1396 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   GLU F1401 " --> pdb=" O   LEU F1397 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1403 through 1420
      removed outlier: 3.682A  pdb=" N   ALA F1408 " --> pdb=" O   LEU F1404 " (cutoff:3.500A)
      removed outlier: 4.899A  pdb=" N   ALA F1409 " --> pdb=" O   GLU F1405 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1420 through 1436
      removed outlier: 3.849A  pdb=" N   HIS F1424 " --> pdb=" O   LEU F1420 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   LEU F1428 " --> pdb=" O   HIS F1424 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   GLN F1429 " --> pdb=" O   LEU F1425 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   GLU F1432 " --> pdb=" O   LEU F1428 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ASN F1435 " --> pdb=" O   GLN F1431 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1475 through 1488
      removed outlier: 3.569A  pdb=" N   ILE F1479 " --> pdb=" O   ILE F1475 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   LEU F1480 " --> pdb=" O   ARG F1476 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   ASN F1481 " --> pdb=" O   GLU F1477 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1503 through 1521
    Processing helix  chain 'F' and resid 1527 through 1553
      removed outlier: 3.692A  pdb=" N   ARG F1534 " --> pdb=" O   LEU F1530 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ILE F1535 " --> pdb=" O   TYR F1531 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ALA F1539 " --> pdb=" O   ILE F1535 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   LYS F1547 " --> pdb=" O   GLU F1543 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1588 through 1592
      removed outlier: 3.779A  pdb=" N   GLU F1591 " --> pdb=" O   VAL F1588 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1602 through 1617
      removed outlier: 4.207A  pdb=" N   VAL F1606 " --> pdb=" O   GLU F1602 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   LYS F1615 " --> pdb=" O   GLU F1611 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   GLU F1616 " --> pdb=" O   ASP F1612 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1620 through 1627
      removed outlier: 4.045A  pdb=" N   GLN F1626 " --> pdb=" O   LEU F1622 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1637 through 1650
      removed outlier: 3.615A  pdb=" N   ARG F1646 " --> pdb=" O   ALA F1642 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   LEU F1647 " --> pdb=" O   HIS F1643 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1660 through 1664
    Processing helix  chain 'F' and resid 1683 through 1692
      removed outlier: 4.009A  pdb=" N   GLN F1689 " --> pdb=" O   THR F1685 " (cutoff:3.500A)
      removed outlier: 4.892A  pdb=" N   MET F1690 " --> pdb=" O   GLN F1686 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   GLY F1692 " --> pdb=" O   ARG F1688 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1713 through 1720
      removed outlier: 4.017A  pdb=" N   ARG F1717 " --> pdb=" O   ARG F1713 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1733 through 1749
      removed outlier: 3.799A  pdb=" N   ASN F1737 " --> pdb=" O   ASP F1733 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   ASN F1747 " --> pdb=" O   LEU F1743 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   THR F1748 " --> pdb=" O   TYR F1744 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1754 through 1769
    Processing helix  chain 'F' and resid 1775 through 1780
    Processing helix  chain 'F' and resid 1791 through 1800
      removed outlier: 4.410A  pdb=" N   MET F1797 " --> pdb=" O   GLU F1793 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   GLY F1800 " --> pdb=" O   GLN F1796 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1821 through 1825
      removed outlier: 3.696A  pdb=" N   MET F1824 " --> pdb=" O   GLN F1821 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1827 through 1831
    Processing helix  chain 'F' and resid 1841 through 1847
    Processing helix  chain 'F' and resid 1848 through 1850
      No H-bonds generated for 'chain 'F' and resid 1848 through 1850'
    Processing helix  chain 'F' and resid 1857 through 1867
      removed outlier: 3.566A  pdb=" N   VAL F1865 " --> pdb=" O   LEU F1861 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ASP F1867 " --> pdb=" O   SER F1863 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'F' and resid 135 through 136
      removed outlier: 3.669A  pdb=" N   TYR F 305 " --> pdb=" O   GLU F 135 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   ARG F 306 " --> pdb=" O   LYS F 293 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   LYS F 293 " --> pdb=" O   ARG F 306 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   ILE F 260 " --> pdb=" O   ALA F 294 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ASP F 152 " --> pdb=" O   LEU F 261 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   PHE F 149 " --> pdb=" O   VAL F 196 " (cutoff:3.500A)
      removed outlier: 8.106A  pdb=" N   PHE F 198 " --> pdb=" O   PHE F 149 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   ILE F 151 " --> pdb=" O   PHE F 198 " (cutoff:3.500A)
      removed outlier: 7.892A  pdb=" N   SER F 238 " --> pdb=" O   HIS F 195 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   VAL F 197 " --> pdb=" O   SER F 238 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'F' and resid 1105 through 1107
      removed outlier: 6.757A  pdb=" N   VAL F1072 " --> pdb=" O   LEU F1124 " (cutoff:3.500A)
      removed outlier: 8.582A  pdb=" N   THR F1126 " --> pdb=" O   VAL F1072 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   TYR F1074 " --> pdb=" O   THR F1126 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   VAL F1179 " --> pdb=" O   VAL F1150 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   LEU F1152 " --> pdb=" O   VAL F1179 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   LEU F1181 " --> pdb=" O   LEU F1152 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   SER F1041 " --> pdb=" O   VAL F1218 " (cutoff:3.500A)
      removed outlier: 7.718A  pdb=" N   LEU F1220 " --> pdb=" O   SER F1041 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   VAL F1043 " --> pdb=" O   LEU F1220 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'F' and resid 1233 through 1236
      removed outlier: 7.121A  pdb=" N   THR F1494 " --> pdb=" O   ILE F1656 " (cutoff:3.500A)
      removed outlier: 8.468A  pdb=" N   SER F1658 " --> pdb=" O   THR F1494 " (cutoff:3.500A)
      removed outlier: 5.808A  pdb=" N   VAL F1496 " --> pdb=" O   SER F1658 " (cutoff:3.500A)

    371 hydrogen bonds defined for protein.
    1071 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.55

  Time building geometry restraints manager: 1.14 seconds

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

  Histogram of bond lengths:
        1.03 -     1.42: 5288
        1.42 -     1.81: 7130
        1.81 -     2.20: 106
        2.20 -     2.59: 0
        2.59 -     2.98: 1
  Bond restraints: 12525
  Sorted by residual:
  bond pdb=" C   ARG F1521 "
       pdb=" N   TYR F1522 "
    ideal  model  delta    sigma   weight residual
    1.335  2.980 -1.645 1.36e-02 5.41e+03 1.46e+04
  bond pdb=" C   TYR F1149 "
       pdb=" N   VAL F1150 "
    ideal  model  delta    sigma   weight residual
    1.331  1.724 -0.393 1.29e-02 6.01e+03 9.30e+02
  bond pdb=" CA  PRO F 304 "
       pdb=" C   PRO F 304 "
    ideal  model  delta    sigma   weight residual
    1.522  1.191  0.331 1.16e-02 7.43e+03 8.14e+02
  bond pdb=" CA  TYR F 305 "
       pdb=" C   TYR F 305 "
    ideal  model  delta    sigma   weight residual
    1.523  1.202  0.321 1.34e-02 5.57e+03 5.75e+02
  bond pdb=" CA  PHE F 259 "
       pdb=" C   PHE F 259 "
    ideal  model  delta    sigma   weight residual
    1.522  1.813 -0.291 1.24e-02 6.50e+03 5.51e+02
  ... (remaining 12520 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     8.67: 16641
        8.67 -    17.34: 179
       17.34 -    26.00: 56
       26.00 -    34.67: 5
       34.67 -    43.34: 6
  Bond angle restraints: 16887
  Sorted by residual:
  angle pdb=" O   GLY F1051 "
        pdb=" C   GLY F1051 "
        pdb=" N   LYS F1052 "
      ideal   model   delta    sigma   weight residual
     122.42   84.72   37.70 1.31e+00 5.83e-01 8.28e+02
  angle pdb=" CA  ASN F 303 "
        pdb=" C   ASN F 303 "
        pdb=" N   PRO F 304 "
      ideal   model   delta    sigma   weight residual
     117.68   97.94   19.74 7.10e-01 1.98e+00 7.73e+02
  angle pdb=" O   ARG F1521 "
        pdb=" C   ARG F1521 "
        pdb=" N   TYR F1522 "
      ideal   model   delta    sigma   weight residual
     122.22   90.29   31.93 1.17e+00 7.31e-01 7.45e+02
  angle pdb=" O   LEU F1136 "
        pdb=" C   LEU F1136 "
        pdb=" N   SER F1137 "
      ideal   model   delta    sigma   weight residual
     122.08  148.00  -25.92 1.07e+00 8.73e-01 5.87e+02
  angle pdb=" N   ILE F1155 "
        pdb=" CA  ILE F1155 "
        pdb=" CB  ILE F1155 "
      ideal   model   delta    sigma   weight residual
     111.50  150.54  -39.04 1.70e+00 3.46e-01 5.27e+02
  ... (remaining 16882 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.31: 7025
       25.31 -    50.63: 391
       50.63 -    75.94: 147
       75.94 -   101.26: 15
      101.26 -   126.57: 12
  Dihedral angle restraints: 7590
    sinusoidal: 3163
      harmonic: 4427
  Sorted by residual:
  dihedral pdb=" CA  GLY F1784 "
           pdb=" C   GLY F1784 "
           pdb=" N   GLY F1785 "
           pdb=" CA  GLY F1785 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -53.43 -126.57     0      5.00e+00 4.00e-02 6.41e+02
  dihedral pdb=" CA  ARG F1214 "
           pdb=" C   ARG F1214 "
           pdb=" N   ASP F1215 "
           pdb=" CA  ASP F1215 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   53.77  126.23     0      5.00e+00 4.00e-02 6.37e+02
  dihedral pdb=" CA  SER F 144 "
           pdb=" C   SER F 144 "
           pdb=" N   ALA F 145 "
           pdb=" CA  ALA F 145 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   56.28  123.72     0      5.00e+00 4.00e-02 6.12e+02
  ... (remaining 7587 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.858: 1817
       0.858 -    1.717: 8
       1.717 -    2.575: 0
       2.575 -    3.434: 3
       3.434 -    4.292: 1
  Chirality restraints: 1829
  Sorted by residual:
  chirality pdb=" CA  ARG F1697 "
            pdb=" N   ARG F1697 "
            pdb=" C   ARG F1697 "
            pdb=" CB  ARG F1697 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.78    4.29 2.00e-01 2.50e+01 4.61e+02
  chirality pdb=" CA  ILE F1155 "
            pdb=" N   ILE F1155 "
            pdb=" C   ILE F1155 "
            pdb=" CB  ILE F1155 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43   -0.52    2.95 2.00e-01 2.50e+01 2.18e+02
  chirality pdb=" CA  TYR F 305 "
            pdb=" N   TYR F 305 "
            pdb=" C   TYR F 305 "
            pdb=" CB  TYR F 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -0.40    2.91 2.00e-01 2.50e+01 2.12e+02
  ... (remaining 1826 not shown)

  Planarity restraints: 2193
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG F1521 "   -0.179 2.00e-02 2.50e+03   2.65e-01 7.02e+02
        pdb=" C   ARG F1521 "    0.443 2.00e-02 2.50e+03
        pdb=" O   ARG F1521 "   -0.227 2.00e-02 2.50e+03
        pdb=" N   TYR F1522 "   -0.038 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F1744 "   -0.305 2.00e-02 2.50e+03   1.57e-01 4.90e+02
        pdb=" CG  TYR F1744 "    0.117 2.00e-02 2.50e+03
        pdb=" CD1 TYR F1744 "    0.156 2.00e-02 2.50e+03
        pdb=" CD2 TYR F1744 "    0.135 2.00e-02 2.50e+03
        pdb=" CE1 TYR F1744 "    0.046 2.00e-02 2.50e+03
        pdb=" CE2 TYR F1744 "    0.064 2.00e-02 2.50e+03
        pdb=" CZ  TYR F1744 "   -0.013 2.00e-02 2.50e+03
        pdb=" OH  TYR F1744 "   -0.201 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER F 146 "   -0.111 2.00e-02 2.50e+03   1.89e-01 3.56e+02
        pdb=" C   SER F 146 "    0.326 2.00e-02 2.50e+03
        pdb=" O   SER F 146 "   -0.120 2.00e-02 2.50e+03
        pdb=" N   GLU F 147 "   -0.095 2.00e-02 2.50e+03
  ... (remaining 2190 not shown)

  Histogram of nonbonded interaction distances:
        0.77 -     1.59: 3
        1.59 -     2.42: 65
        2.42 -     3.25: 12022
        3.25 -     4.07: 29186
        4.07 -     4.90: 49247
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 90523
  Sorted by model distance:
  nonbonded pdb=" CG  ASP F 152 "
            pdb=" OD2 ASP F 200 "
     model   vdw
     0.766 3.270
  nonbonded pdb=" OD2 ASP F 152 "
            pdb=" OD2 ASP F 200 "
     model   vdw
     1.024 3.040
  nonbonded pdb=" OD1 ASP F 152 "
            pdb=" OD2 ASP F 200 "
     model   vdw
     1.257 3.040
  nonbonded pdb=" CZ  PHE F 149 "
            pdb=" CD1 LEU F 261 "
     model   vdw
     1.638 3.760
  nonbonded pdb=" OD1 ASN F 295 "
            pdb=" ND2 ASN F 303 "
     model   vdw
     1.729 3.120
  ... (remaining 90518 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.420
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.360
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5181
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      :  0.028   1.645  12526  Z= 1.946
  Angle     :  2.987  43.340  16887  Z= 1.949
  Chirality :  0.219   4.292   1829
  Planarity :  0.023   0.265   2193
  Dihedral  : 18.830 126.570   4720
  Min Nonbonded Distance : 0.766

Molprobity Statistics.
  All-atom Clashscore : 14.20
  Ramachandran Plot:
    Outliers :  9.67 %
    Allowed  : 16.72 %
    Favored  : 73.61 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  :  5.69 %
    Favored  : 91.73 %
  Cbeta Deviations :  3.27 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    Cis-general     : 2.75 %
    Twisted Proline : 13.21 %
    Twisted General : 9.98 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -6.06 (0.15), residues: 1489
  helix: -4.31 (0.12), residues: 570
  sheet: -2.84 (0.47), residues: 75
  loop : -4.10 (0.17), residues: 844

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F 292 
 TYR   0.305   0.023   TYR F1744 
 PHE   0.089   0.013   PHE F1648 
 TRP   0.106   0.018   TRP F 851 
 HIS   0.005   0.001   HIS F1852 

Details of bonding type rmsd
  covalent geometry    : bond        0.02810 (12525)
  covalent geometry    : angle       2.98681 (16887)
  hydrogen bonds       : bond        0.30092 (  371)
  hydrogen bonds       : angle       9.96829 ( 1071)
  Misc. bond           : bond        0.02279 (    1)

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

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

  2978 Ramachandran restraints generated.
    1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2978 Ramachandran restraints generated.
    1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  423 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 389
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F    1 MET cc_start: 0.4478 (mtp) cc_final: 0.1996 (ttt)
REVERT: F  308 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.5391 (tmm160)
REVERT: F  864 MET cc_start: 0.5894 (ttm) cc_final: 0.5251 (ttt)
REVERT: F  977 MET cc_start: 0.6275 (ttp) cc_final: 0.5542 (ttt)
REVERT: F 1097 LYS cc_start: 0.7817 (mttp) cc_final: 0.7434 (ttpt)
REVERT: F 1155 ILE cc_start: 0.4104 (mt) cc_final: 0.3524 (mt)
REVERT: F 1209 MET cc_start: 0.3159 (ttt) cc_final: 0.1448 (mpp)
REVERT: F 1298 HIS cc_start: 0.6478 (t-90) cc_final: 0.5356 (t-90)
REVERT: F 1358 TYR cc_start: 0.5015 (m-80) cc_final: 0.4762 (m-80)
REVERT: F 1386 VAL cc_start: 0.2922 (OUTLIER) cc_final: 0.1579 (t)
REVERT: F 1396 LYS cc_start: 0.6061 (pttp) cc_final: 0.5533 (ttpt)
REVERT: F 1515 LEU cc_start: 0.8172 (mp) cc_final: 0.7848 (mm)
REVERT: F 1558 LEU cc_start: 0.5742 (OUTLIER) cc_final: 0.5506 (pp)
REVERT: F 1633 HIS cc_start: 0.7703 (p90) cc_final: 0.7336 (p90)
REVERT: F 1688 ARG cc_start: 0.6523 (mtm180) cc_final: 0.5681 (mtp180)
REVERT: F 1847 VAL cc_start: 0.6863 (t) cc_final: 0.6632 (t)
  outliers start: 34
  outliers final: 9
  residues processed: 417
  average time/residue: 0.1155
  time to fit residues: 64.4462
Evaluate side-chains
  245 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 233
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    8.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:    0.0970
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    0.0970
   chunk 149 optimal weight:    5.9990
   overall best weight:    1.2382

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

Flipped N/Q/H residues before XYZ refinement:
** F 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 679 ASN
F 725 GLN
F 839 GLN
F 989 GLN
F1001 GLN
F1007 HIS
F1083 ASN
F1163 ASN
** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F1232 ASN
F1308 ASN
F1369 ASN
** F1481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F1632 HIS
F1643 HIS
F1683 ASN
** F1729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.175144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.159356 restraints weight = 42422.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.161947 restraints weight = 28413.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.163753 restraints weight = 20605.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.165145 restraints weight = 15955.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.166123 restraints weight = 12943.496|
|-----------------------------------------------------------------------------|
r_work (final): 0.4397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5970
moved from start:          0.4763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  12526  Z= 0.219
  Angle     :  1.217  14.105  16887  Z= 0.635
  Chirality :  0.091   2.465   1829
  Planarity :  0.008   0.094   2193
  Dihedral  : 13.178  84.188   1674
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 14.94
  Ramachandran Plot:
    Outliers :  2.88 %
    Allowed  : 16.63 %
    Favored  : 80.48 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  5.16 %
    Favored  : 94.46 %
  Cbeta Deviations :  0.28 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    Cis-general     : 3.03 %
    Twisted Proline : 11.32 %
    Twisted General : 4.47 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.61 (0.18), residues: 1491
  helix: -2.00 (0.18), residues: 594
  sheet: -1.73 (0.58), residues: 55
  loop : -4.20 (0.17), residues: 842

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG F 193 
 TYR   0.025   0.002   TYR F1149 
 PHE   0.028   0.003   PHE F 924 
 TRP   0.024   0.002   TRP F 204 
 HIS   0.014   0.002   HIS F1118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 (12525)
  covalent geometry    : angle       1.21699 (16887)
  hydrogen bonds       : bond        0.05938 (  371)
  hydrogen bonds       : angle       5.86153 ( 1071)
  Misc. bond           : bond        0.00012 (    1)

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

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

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 301
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F    1 MET cc_start: 0.3347 (mtp) cc_final: 0.2250 (ttt)
REVERT: F   27 MET cc_start: 0.4422 (mmt) cc_final: 0.4053 (mmt)
REVERT: F   32 GLU cc_start: 0.8172 (tp30) cc_final: 0.7909 (tp30)
REVERT: F   96 LEU cc_start: 0.8485 (tp) cc_final: 0.8185 (mm)
REVERT: F  158 MET cc_start: 0.7485 (tpp) cc_final: 0.7076 (ptp)
REVERT: F  193 ARG cc_start: 0.6002 (mpp-170) cc_final: 0.5427 (mpt-90)
REVERT: F  724 LYS cc_start: 0.8540 (ptpt) cc_final: 0.8010 (pttp)
REVERT: F  726 MET cc_start: 0.3881 (ttp) cc_final: 0.3250 (mtp)
REVERT: F  859 LYS cc_start: 0.8085 (mtmt) cc_final: 0.7866 (mtmt)
REVERT: F 1016 GLU cc_start: 0.7832 (tt0) cc_final: 0.7624 (tp30)
REVERT: F 1146 LEU cc_start: 0.8354 (mt) cc_final: 0.7951 (tp)
REVERT: F 1157 SER cc_start: 0.8689 (p) cc_final: 0.8247 (t)
REVERT: F 1209 MET cc_start: 0.2475 (ttt) cc_final: 0.1392 (mpp)
REVERT: F 1298 HIS cc_start: 0.8010 (t-90) cc_final: 0.7183 (t70)
REVERT: F 1491 MET cc_start: 0.5223 (OUTLIER) cc_final: 0.4761 (mmp)
REVERT: F 1499 PHE cc_start: 0.7141 (m-80) cc_final: 0.6756 (t80)
REVERT: F 1502 GLU cc_start: 0.4520 (mt-10) cc_final: 0.4251 (tp30)
REVERT: F 1510 TYR cc_start: 0.7974 (t80) cc_final: 0.7767 (t80)
REVERT: F 1610 MET cc_start: 0.7290 (mtp) cc_final: 0.7090 (mtm)
REVERT: F 1633 HIS cc_start: 0.8088 (p90) cc_final: 0.7863 (p90)
REVERT: F 1704 HIS cc_start: 0.8212 (m90) cc_final: 0.7741 (m90)
REVERT: F 1708 LEU cc_start: 0.5702 (tt) cc_final: 0.5225 (mp)
REVERT: F 1847 VAL cc_start: 0.8829 (t) cc_final: 0.8507 (p)
  outliers start: 5
  outliers final: 1
  residues processed: 303
  average time/residue: 0.1044
  time to fit residues: 43.5644
Evaluate side-chains
  209 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 207
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 43 optimal weight:    6.9990
   chunk 71 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9980
   chunk 86 optimal weight:   20.0000
   chunk 62 optimal weight:   10.0000
   chunk 68 optimal weight:    4.9990
   chunk 149 optimal weight:   20.0000
   chunk 105 optimal weight:    3.9990
   chunk 73 optimal weight:    6.9990
   chunk 81 optimal weight:    7.9990
   overall best weight:    3.1986

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

Flipped N/Q/H residues before XYZ refinement:
F 303 ASN
F 725 GLN
** F 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F1001 GLN
** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F1361 HIS
F1369 ASN
F1626 GLN
F1729 ASN
F1780 ASN
** F1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4463 r_free = 0.4463 target = 0.173990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.158949 restraints weight = 42831.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.161373 restraints weight = 28495.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.163020 restraints weight = 20682.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.164359 restraints weight = 16106.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.165131 restraints weight = 13057.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.4360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6049
moved from start:          0.5790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  12526  Z= 0.187
  Angle     :  1.077  13.660  16887  Z= 0.559
  Chirality :  0.064   1.236   1829
  Planarity :  0.007   0.093   2193
  Dihedral  : 11.231  73.308   1674
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 13.66
  Ramachandran Plot:
    Outliers :  2.55 %
    Allowed  : 16.97 %
    Favored  : 80.48 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  4.48 %
    Favored  : 95.45 %
  Cbeta Deviations :  0.21 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    Cis-general     : 3.09 %
    Twisted Proline : 9.43 %
    Twisted General : 2.96 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.88 (0.19), residues: 1491
  helix: -1.04 (0.20), residues: 604
  sheet: -1.62 (0.54), residues: 80
  loop : -4.15 (0.18), residues: 807

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG F 193 
 TYR   0.037   0.003   TYR F 828 
 PHE   0.039   0.003   PHE F1468 
 TRP   0.019   0.002   TRP F 851 
 HIS   0.008   0.001   HIS F1156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 (12525)
  covalent geometry    : angle       1.07726 (16887)
  hydrogen bonds       : bond        0.04860 (  371)
  hydrogen bonds       : angle       5.26313 ( 1071)
  Misc. bond           : bond        0.01092 (    1)

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

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

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 266
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F    1 MET cc_start: 0.3641 (mtp) cc_final: 0.2771 (ttt)
REVERT: F   58 GLU cc_start: 0.7503 (tt0) cc_final: 0.6725 (tt0)
REVERT: F   62 ARG cc_start: 0.6770 (tpp-160) cc_final: 0.6279 (tpt170)
REVERT: F  139 MET cc_start: 0.1300 (pmm) cc_final: 0.0844 (pmm)
REVERT: F  158 MET cc_start: 0.7474 (tpp) cc_final: 0.7225 (ptp)
REVERT: F  187 MET cc_start: 0.6996 (mmp) cc_final: 0.6011 (ttm)
REVERT: F  193 ARG cc_start: 0.5967 (mpp-170) cc_final: 0.5549 (mpp-170)
REVERT: F  207 GLU cc_start: 0.8638 (pm20) cc_final: 0.8423 (pm20)
REVERT: F  724 LYS cc_start: 0.8737 (ptpt) cc_final: 0.8127 (pttt)
REVERT: F  726 MET cc_start: 0.4059 (ttp) cc_final: 0.3659 (mtp)
REVERT: F  864 MET cc_start: 0.7011 (ttm) cc_final: 0.6371 (ttm)
REVERT: F 1016 GLU cc_start: 0.7983 (tt0) cc_final: 0.7328 (tp30)
REVERT: F 1146 LEU cc_start: 0.8520 (mt) cc_final: 0.7833 (tt)
REVERT: F 1157 SER cc_start: 0.8348 (p) cc_final: 0.7955 (t)
REVERT: F 1209 MET cc_start: 0.1616 (ttt) cc_final: 0.0888 (mpp)
REVERT: F 1502 GLU cc_start: 0.4731 (mt-10) cc_final: 0.4466 (tp30)
REVERT: F 1622 LEU cc_start: 0.8786 (tp) cc_final: 0.8523 (tp)
REVERT: F 1723 MET cc_start: 0.6177 (mmt) cc_final: 0.5938 (mmt)
REVERT: F 1849 ASP cc_start: 0.7927 (t0) cc_final: 0.7584 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 267
  average time/residue: 0.1026
  time to fit residues: 37.7088
Evaluate side-chains
  192 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 70 optimal weight:    8.9990
   chunk 3 optimal weight:    4.9990
   chunk 148 optimal weight:    5.9990
   chunk 124 optimal weight:   10.0000
   chunk 138 optimal weight:    6.9990
   chunk 75 optimal weight:   10.0000
   chunk 134 optimal weight:   10.0000
   chunk 9 optimal weight:   10.0000
   chunk 6 optimal weight:    0.0040
   chunk 25 optimal weight:    7.9990
   chunk 106 optimal weight:   20.0000
   overall best weight:    5.2000

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

Flipped N/Q/H residues before XYZ refinement:
F 675 ASN
F 678 ASN
F 725 GLN
** F 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 965 ASN
F1001 GLN
F1118 HIS
F1156 HIS
F1163 ASN
** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F1369 ASN
F1481 ASN
F1704 HIS
F1751 HIS
F1754 ASN
** F1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4428 r_free = 0.4428 target = 0.168995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.156845 restraints weight = 47619.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.158480 restraints weight = 34321.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.159514 restraints weight = 26434.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 59)----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.160513 restraints weight = 21681.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.161143 restraints weight = 18500.038|
|-----------------------------------------------------------------------------|
r_work (final): 0.4300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6174
moved from start:          0.6473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068  12526  Z= 0.202
  Angle     :  1.050  12.994  16887  Z= 0.544
  Chirality :  0.057   0.904   1829
  Planarity :  0.007   0.093   2193
  Dihedral  : 10.419  67.074   1674
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 17.11
  Ramachandran Plot:
    Outliers :  2.08 %
    Allowed  : 17.37 %
    Favored  : 80.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    Cis-general     : 3.09 %
    Twisted Proline : 9.43 %
    Twisted General : 2.20 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.70 (0.20), residues: 1491
  helix: -0.81 (0.20), residues: 618
  sheet: -1.19 (0.62), residues: 68
  loop : -4.18 (0.18), residues: 805

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG F1201 
 TYR   0.027   0.002   TYR F 828 
 PHE   0.022   0.002   PHE F 150 
 TRP   0.027   0.002   TRP F 851 
 HIS   0.010   0.002   HIS F1643 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 (12525)
  covalent geometry    : angle       1.04952 (16887)
  hydrogen bonds       : bond        0.04585 (  371)
  hydrogen bonds       : angle       5.22222 ( 1071)
  Misc. bond           : bond        0.00022 (    1)

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

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

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 260
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F    1 MET cc_start: 0.5005 (mtp) cc_final: 0.3265 (ttt)
REVERT: F   27 MET cc_start: 0.5239 (mmp) cc_final: 0.4477 (mmp)
REVERT: F   58 GLU cc_start: 0.7597 (tt0) cc_final: 0.6964 (tt0)
REVERT: F   62 ARG cc_start: 0.6696 (tpp-160) cc_final: 0.6173 (tpt170)
REVERT: F  187 MET cc_start: 0.7224 (mmp) cc_final: 0.6300 (ttm)
REVERT: F  306 ARG cc_start: 0.7788 (mmm-85) cc_final: 0.7526 (mmm-85)
REVERT: F  726 MET cc_start: 0.4295 (ttp) cc_final: 0.3668 (mtp)
REVERT: F  864 MET cc_start: 0.7067 (ttm) cc_final: 0.6509 (ttm)
REVERT: F  937 ASP cc_start: 0.7489 (t0) cc_final: 0.7202 (t70)
REVERT: F  983 LEU cc_start: 0.7429 (mp) cc_final: 0.6862 (tt)
REVERT: F 1016 GLU cc_start: 0.7461 (tt0) cc_final: 0.6959 (tp30)
REVERT: F 1024 ASN cc_start: 0.8900 (m-40) cc_final: 0.8428 (t0)
REVERT: F 1065 ARG cc_start: 0.5987 (tpt170) cc_final: 0.5403 (tpt170)
REVERT: F 1146 LEU cc_start: 0.8762 (mt) cc_final: 0.8212 (tt)
REVERT: F 1157 SER cc_start: 0.8020 (p) cc_final: 0.7513 (t)
REVERT: F 1209 MET cc_start: 0.1043 (ttt) cc_final: 0.0840 (mpp)
REVERT: F 1323 MET cc_start: 0.6927 (ptm) cc_final: 0.6467 (ppp)
REVERT: F 1510 TYR cc_start: 0.7887 (t80) cc_final: 0.7508 (t80)
REVERT: F 1549 ARG cc_start: 0.7997 (ttt-90) cc_final: 0.7756 (ttt-90)
REVERT: F 1723 MET cc_start: 0.6841 (mmt) cc_final: 0.6508 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 260
  average time/residue: 0.0967
  time to fit residues: 34.9416
Evaluate side-chains
  194 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 110 optimal weight:    8.9990
   chunk 58 optimal weight:    0.5980
   chunk 29 optimal weight:    2.9990
   chunk 69 optimal weight:    6.9990
   chunk 118 optimal weight:    6.9990
   chunk 23 optimal weight:    0.2980
   chunk 20 optimal weight:   20.0000
   chunk 151 optimal weight:    5.9990
   chunk 49 optimal weight:   20.0000
   chunk 61 optimal weight:    7.9990
   chunk 88 optimal weight:   20.0000
   overall best weight:    3.3786

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

Flipped N/Q/H residues before XYZ refinement:
F 288 HIS
F 678 ASN
F 725 GLN
F 839 GLN
** F 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F1001 GLN
F1122 GLN
** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F1339 GLN
F1478 HIS
F1704 HIS
F1772 ASN
** F1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.170697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.159085 restraints weight = 47611.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.160591 restraints weight = 33988.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.161511 restraints weight = 26046.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.162510 restraints weight = 21414.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.163030 restraints weight = 18059.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.4323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6131
moved from start:          0.7007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12526  Z= 0.166
  Angle     :  0.992  12.992  16887  Z= 0.510
  Chirality :  0.053   0.818   1829
  Planarity :  0.006   0.093   2193
  Dihedral  :  9.722  63.474   1674
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 15.14
  Ramachandran Plot:
    Outliers :  2.01 %
    Allowed  : 17.44 %
    Favored  : 80.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    Cis-general     : 3.09 %
    Twisted Proline : 9.43 %
    Twisted General : 1.65 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.47 (0.20), residues: 1491
  helix: -0.57 (0.20), residues: 612
  sheet: -0.99 (0.64), residues: 68
  loop : -4.08 (0.18), residues: 811

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG F 193 
 TYR   0.025   0.002   TYR F 828 
 PHE   0.023   0.002   PHE F1468 
 TRP   0.023   0.002   TRP F 851 
 HIS   0.012   0.002   HIS F1643 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (12525)
  covalent geometry    : angle       0.99212 (16887)
  hydrogen bonds       : bond        0.04075 (  371)
  hydrogen bonds       : angle       4.95431 ( 1071)
  Misc. bond           : bond        0.00080 (    1)

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

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

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 247
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F    1 MET cc_start: 0.5975 (mtp) cc_final: 0.4124 (ttt)
REVERT: F   58 GLU cc_start: 0.7529 (tt0) cc_final: 0.6894 (tt0)
REVERT: F  207 GLU cc_start: 0.8302 (pm20) cc_final: 0.8040 (pm20)
REVERT: F  285 ASN cc_start: 0.7116 (m-40) cc_final: 0.6860 (p0)
REVERT: F  723 HIS cc_start: 0.6368 (m-70) cc_final: 0.5958 (m-70)
REVERT: F  724 LYS cc_start: 0.8514 (ptpt) cc_final: 0.7767 (pttt)
REVERT: F  726 MET cc_start: 0.3909 (ttp) cc_final: 0.3331 (mtp)
REVERT: F  859 LYS cc_start: 0.8093 (mttt) cc_final: 0.7860 (mtpt)
REVERT: F  864 MET cc_start: 0.6648 (ttm) cc_final: 0.6241 (ttt)
REVERT: F  983 LEU cc_start: 0.7657 (mp) cc_final: 0.7066 (tt)
REVERT: F 1016 GLU cc_start: 0.7289 (tt0) cc_final: 0.6867 (tp30)
REVERT: F 1024 ASN cc_start: 0.8767 (m-40) cc_final: 0.8363 (t0)
REVERT: F 1146 LEU cc_start: 0.8762 (mt) cc_final: 0.8250 (tt)
REVERT: F 1157 SER cc_start: 0.7776 (p) cc_final: 0.7417 (t)
REVERT: F 1323 MET cc_start: 0.6885 (ptm) cc_final: 0.6376 (ppp)
REVERT: F 1510 TYR cc_start: 0.7902 (t80) cc_final: 0.7471 (t80)
REVERT: F 1545 ARG cc_start: 0.7051 (mpt180) cc_final: 0.6842 (mpt180)
REVERT: F 1549 ARG cc_start: 0.7974 (ttt-90) cc_final: 0.7560 (ttt-90)
REVERT: F 1614 GLU cc_start: 0.8300 (tt0) cc_final: 0.8001 (tt0)
REVERT: F 1643 HIS cc_start: 0.7720 (m170) cc_final: 0.7500 (m-70)
REVERT: F 1719 MET cc_start: 0.7688 (tmm) cc_final: 0.7478 (tmm)
REVERT: F 1723 MET cc_start: 0.6791 (mmt) cc_final: 0.6482 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 247
  average time/residue: 0.1039
  time to fit residues: 36.1908
Evaluate side-chains
  193 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 102 optimal weight:    7.9990
   chunk 52 optimal weight:    8.9990
   chunk 28 optimal weight:    0.5980
   chunk 66 optimal weight:    0.0070
   chunk 78 optimal weight:    0.8980
   chunk 123 optimal weight:   20.0000
   chunk 16 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0670
   chunk 137 optimal weight:    6.9990
   chunk 99 optimal weight:   10.0000
   chunk 148 optimal weight:    8.9990
   overall best weight:    1.1138

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

Flipped N/Q/H residues before XYZ refinement:
F 725 GLN
** F 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 956 HIS
F1001 GLN
F1017 HIS
** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F1219 HIS
** F1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F1339 GLN
F1704 HIS
** F1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4479 r_free = 0.4479 target = 0.173708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.161589 restraints weight = 47358.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.163131 restraints weight = 34098.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.164362 restraints weight = 26428.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.165133 restraints weight = 21631.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 70)----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.166025 restraints weight = 18516.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.4354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6021
moved from start:          0.7393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  12526  Z= 0.162
  Angle     :  0.957  12.746  16887  Z= 0.492
  Chirality :  0.052   0.751   1829
  Planarity :  0.006   0.089   2193
  Dihedral  :  9.100  57.664   1674
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 13.75
  Ramachandran Plot:
    Outliers :  1.88 %
    Allowed  : 16.83 %
    Favored  : 81.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Cbeta Deviations :  0.07 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    Cis-general     : 3.09 %
    Twisted Proline : 9.43 %
    Twisted General : 1.03 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.24 (0.20), residues: 1491
  helix: -0.20 (0.21), residues: 608
  sheet: -0.71 (0.68), residues: 61
  loop : -4.08 (0.18), residues: 822

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG F  63 
 TYR   0.021   0.002   TYR F1104 
 PHE   0.023   0.002   PHE F 277 
 TRP   0.017   0.001   TRP F 851 
 HIS   0.008   0.001   HIS F1643 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (12525)
  covalent geometry    : angle       0.95671 (16887)
  hydrogen bonds       : bond        0.03825 (  371)
  hydrogen bonds       : angle       4.74706 ( 1071)
  Misc. bond           : bond        0.00034 (    1)

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

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

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 251
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F    1 MET cc_start: 0.5933 (mtp) cc_final: 0.4117 (tmm)
REVERT: F   27 MET cc_start: 0.5087 (mmp) cc_final: 0.4322 (mmp)
REVERT: F  147 GLU cc_start: 0.8168 (tp30) cc_final: 0.7947 (tm-30)
REVERT: F  207 GLU cc_start: 0.8278 (pm20) cc_final: 0.7954 (pm20)
REVERT: F  723 HIS cc_start: 0.6061 (m-70) cc_final: 0.5707 (m-70)
REVERT: F  724 LYS cc_start: 0.8790 (ptpt) cc_final: 0.8048 (pttm)
REVERT: F  726 MET cc_start: 0.3736 (ttp) cc_final: 0.3195 (mtp)
REVERT: F  859 LYS cc_start: 0.7986 (mttt) cc_final: 0.7701 (mtpt)
REVERT: F  983 LEU cc_start: 0.7827 (mp) cc_final: 0.7146 (tt)
REVERT: F 1024 ASN cc_start: 0.8697 (m-40) cc_final: 0.8206 (t0)
REVERT: F 1146 LEU cc_start: 0.8715 (mt) cc_final: 0.8224 (tt)
REVERT: F 1157 SER cc_start: 0.7335 (p) cc_final: 0.7039 (t)
REVERT: F 1262 ARG cc_start: 0.5477 (mmm-85) cc_final: 0.5004 (mmm160)
REVERT: F 1323 MET cc_start: 0.7041 (ptm) cc_final: 0.6461 (ppp)
REVERT: F 1396 LYS cc_start: 0.6572 (ttpt) cc_final: 0.6253 (tttt)
REVERT: F 1472 ARG cc_start: 0.7101 (tmm-80) cc_final: 0.6725 (ptm-80)
REVERT: F 1510 TYR cc_start: 0.7800 (t80) cc_final: 0.7541 (t80)
REVERT: F 1643 HIS cc_start: 0.7680 (m170) cc_final: 0.7164 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 251
  average time/residue: 0.0996
  time to fit residues: 34.5599
Evaluate side-chains
  193 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 96 optimal weight:    5.9990
   chunk 111 optimal weight:    0.9980
   chunk 52 optimal weight:    7.9990
   chunk 148 optimal weight:    0.5980
   chunk 88 optimal weight:    5.9990
   chunk 56 optimal weight:    0.9980
   chunk 81 optimal weight:    0.0270
   chunk 141 optimal weight:   20.0000
   chunk 135 optimal weight:    5.9990
   chunk 27 optimal weight:   10.0000
   chunk 72 optimal weight:    0.3980
   overall best weight:    0.6038

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

Flipped N/Q/H residues before XYZ refinement:
F 725 GLN
** F 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F1001 GLN
** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F1339 GLN
** F1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.175569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.164412 restraints weight = 47461.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.165963 restraints weight = 35349.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.166420 restraints weight = 28584.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4403 r_free = 0.4403 target = 0.167191 restraints weight = 23333.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.167792 restraints weight = 19289.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.4411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5883
moved from start:          0.7737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12526  Z= 0.153
  Angle     :  0.947  14.024  16887  Z= 0.483
  Chirality :  0.051   0.755   1829
  Planarity :  0.006   0.148   2193
  Dihedral  :  8.695  55.779   1674
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 13.66
  Ramachandran Plot:
    Outliers :  1.68 %
    Allowed  : 17.10 %
    Favored  : 81.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    Cis-general     : 3.09 %
    Twisted Proline : 9.43 %
    Twisted General : 0.89 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.19 (0.20), residues: 1491
  helix: -0.15 (0.21), residues: 619
  sheet: -0.79 (0.60), residues: 76
  loop : -4.15 (0.18), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG F1201 
 TYR   0.024   0.002   TYR F 305 
 PHE   0.020   0.002   PHE F1468 
 TRP   0.014   0.001   TRP F 851 
 HIS   0.011   0.001   HIS F1751 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (12525)
  covalent geometry    : angle       0.94726 (16887)
  hydrogen bonds       : bond        0.03573 (  371)
  hydrogen bonds       : angle       4.60571 ( 1071)
  Misc. bond           : bond        0.00034 (    1)

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

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

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F    1 MET cc_start: 0.6037 (mtp) cc_final: 0.4330 (tmm)
REVERT: F   27 MET cc_start: 0.4559 (mmp) cc_final: 0.4282 (mmp)
REVERT: F   58 GLU cc_start: 0.7465 (tt0) cc_final: 0.7184 (tt0)
REVERT: F  187 MET cc_start: 0.7464 (ttp) cc_final: 0.6923 (ttt)
REVERT: F  193 ARG cc_start: 0.3989 (pmt170) cc_final: 0.3671 (ptt-90)
REVERT: F  723 HIS cc_start: 0.5854 (m-70) cc_final: 0.5502 (m-70)
REVERT: F  724 LYS cc_start: 0.8416 (ptpt) cc_final: 0.7952 (pttm)
REVERT: F  726 MET cc_start: 0.3599 (ttp) cc_final: 0.3078 (mtp)
REVERT: F  883 MET cc_start: 0.8219 (ttm) cc_final: 0.8006 (ttm)
REVERT: F  983 LEU cc_start: 0.7932 (mp) cc_final: 0.7239 (tt)
REVERT: F 1146 LEU cc_start: 0.8345 (mt) cc_final: 0.8073 (tt)
REVERT: F 1323 MET cc_start: 0.6800 (ptm) cc_final: 0.6269 (ppp)
REVERT: F 1472 ARG cc_start: 0.6715 (tmm-80) cc_final: 0.6404 (ptm-80)
REVERT: F 1473 GLN cc_start: 0.3010 (tp-100) cc_final: 0.2518 (tp-100)
REVERT: F 1486 LEU cc_start: 0.7195 (pp) cc_final: 0.6614 (tt)
REVERT: F 1510 TYR cc_start: 0.7584 (t80) cc_final: 0.7263 (t80)
REVERT: F 1723 MET cc_start: 0.6818 (mmt) cc_final: 0.6523 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 242
  average time/residue: 0.1270
  time to fit residues: 42.1204
Evaluate side-chains
  194 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 92 optimal weight:    0.0870
   chunk 101 optimal weight:   20.0000
   chunk 59 optimal weight:   10.0000
   chunk 109 optimal weight:    8.9990
   chunk 65 optimal weight:    0.9990
   chunk 90 optimal weight:    5.9990
   chunk 93 optimal weight:   10.0000
   chunk 29 optimal weight:    0.3980
   chunk 132 optimal weight:    0.0570
   chunk 103 optimal weight:   20.0000
   chunk 36 optimal weight:    7.9990
   overall best weight:    1.5080

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

Flipped N/Q/H residues before XYZ refinement:
F  78 HIS
F 725 GLN
** F 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F1001 GLN
F1190 GLN
** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.175843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.163824 restraints weight = 47761.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.165411 restraints weight = 34544.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.166454 restraints weight = 26658.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.167377 restraints weight = 21813.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 58)----------------|
| r_work = 0.4411 r_free = 0.4411 target = 0.168154 restraints weight = 18671.487|
|-----------------------------------------------------------------------------|
r_work (final): 0.4413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5871
moved from start:          0.8002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  12526  Z= 0.152
  Angle     :  0.945  13.216  16887  Z= 0.481
  Chirality :  0.051   0.764   1829
  Planarity :  0.006   0.104   2193
  Dihedral  :  8.400  55.405   1674
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 14.24
  Ramachandran Plot:
    Outliers :  1.61 %
    Allowed  : 16.97 %
    Favored  : 81.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    Cis-general     : 3.09 %
    Twisted Proline : 7.55 %
    Twisted General : 0.76 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.12 (0.21), residues: 1491
  helix: -0.02 (0.21), residues: 612
  sheet: -1.11 (0.64), residues: 61
  loop : -4.06 (0.18), residues: 818

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG F  63 
 TYR   0.027   0.002   TYR F1019 
 PHE   0.017   0.001   PHE F1468 
 TRP   0.015   0.001   TRP F 851 
 HIS   0.008   0.001   HIS F  78 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (12525)
  covalent geometry    : angle       0.94515 (16887)
  hydrogen bonds       : bond        0.03506 (  371)
  hydrogen bonds       : angle       4.55193 ( 1071)
  Misc. bond           : bond        0.00129 (    1)

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

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

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 229
  time to evaluate  : 0.499 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F    1 MET cc_start: 0.6075 (mtp) cc_final: 0.4440 (tmm)
REVERT: F  147 GLU cc_start: 0.8125 (tp30) cc_final: 0.7777 (tm-30)
REVERT: F  292 ARG cc_start: 0.6102 (tmt170) cc_final: 0.5783 (mmp80)
REVERT: F  723 HIS cc_start: 0.5721 (m-70) cc_final: 0.5327 (m-70)
REVERT: F  724 LYS cc_start: 0.8426 (ptpt) cc_final: 0.7941 (pttm)
REVERT: F  726 MET cc_start: 0.3330 (ttp) cc_final: 0.2741 (mtp)
REVERT: F  983 LEU cc_start: 0.7724 (mp) cc_final: 0.7161 (tt)
REVERT: F 1130 THR cc_start: 0.7074 (p) cc_final: 0.6816 (p)
REVERT: F 1146 LEU cc_start: 0.8392 (mt) cc_final: 0.8107 (tt)
REVERT: F 1149 TYR cc_start: 0.5837 (t80) cc_final: 0.5585 (t80)
REVERT: F 1323 MET cc_start: 0.6721 (ptm) cc_final: 0.6225 (ppp)
REVERT: F 1374 ASP cc_start: 0.5998 (t70) cc_final: 0.5004 (p0)
REVERT: F 1384 MET cc_start: 0.7594 (ptt) cc_final: 0.7131 (ptm)
REVERT: F 1418 MET cc_start: 0.6010 (tmm) cc_final: 0.5799 (tmm)
REVERT: F 1486 LEU cc_start: 0.7219 (pp) cc_final: 0.6561 (tt)
REVERT: F 1510 TYR cc_start: 0.7539 (t80) cc_final: 0.7324 (t80)
REVERT: F 1643 HIS cc_start: 0.7188 (m170) cc_final: 0.6759 (m-70)
REVERT: F 1723 MET cc_start: 0.6941 (mmt) cc_final: 0.6570 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 229
  average time/residue: 0.1351
  time to fit residues: 42.6280
Evaluate side-chains
  185 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 46 optimal weight:    0.0980
   chunk 11 optimal weight:    0.0070
   chunk 47 optimal weight:   20.0000
   chunk 25 optimal weight:    0.0770
   chunk 7 optimal weight:    8.9990
   chunk 31 optimal weight:    6.9990
   chunk 93 optimal weight:    4.9990
   chunk 144 optimal weight:    6.9990
   chunk 74 optimal weight:   10.0000
   chunk 48 optimal weight:   10.0000
   chunk 121 optimal weight:    3.9990
   overall best weight:    1.8360

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

Flipped N/Q/H residues before XYZ refinement:
F 725 GLN
** F 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 850 HIS
F1001 GLN
** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4502 r_free = 0.4502 target = 0.175326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.164142 restraints weight = 47859.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.165848 restraints weight = 35482.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.166270 restraints weight = 28686.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.167030 restraints weight = 23326.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.167440 restraints weight = 20130.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.4405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5887
moved from start:          0.8283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  12526  Z= 0.154
  Angle     :  0.949  14.046  16887  Z= 0.480
  Chirality :  0.051   0.759   1829
  Planarity :  0.006   0.093   2193
  Dihedral  :  8.243  53.996   1674
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 15.06
  Ramachandran Plot:
    Outliers :  1.61 %
    Allowed  : 17.17 %
    Favored  : 81.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.07 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    Cis-general     : 3.09 %
    Twisted Proline : 7.55 %
    Twisted General : 0.62 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.02 (0.21), residues: 1491
  helix:  0.04 (0.21), residues: 613
  sheet: -1.08 (0.62), residues: 71
  loop : -4.01 (0.18), residues: 807

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG F  63 
 TYR   0.018   0.002   TYR F1744 
 PHE   0.016   0.001   PHE F1294 
 TRP   0.027   0.002   TRP F1356 
 HIS   0.013   0.001   HIS F1643 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (12525)
  covalent geometry    : angle       0.94872 (16887)
  hydrogen bonds       : bond        0.03624 (  371)
  hydrogen bonds       : angle       4.64013 ( 1071)
  Misc. bond           : bond        0.00058 (    1)

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

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

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 225
  time to evaluate  : 0.523 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F    1 MET cc_start: 0.6106 (mtp) cc_final: 0.4488 (tmm)
REVERT: F  147 GLU cc_start: 0.8100 (tp30) cc_final: 0.7831 (tm-30)
REVERT: F  292 ARG cc_start: 0.6241 (tmt170) cc_final: 0.5940 (mmp80)
REVERT: F  723 HIS cc_start: 0.5800 (m-70) cc_final: 0.5383 (m-70)
REVERT: F  724 LYS cc_start: 0.8377 (ptpt) cc_final: 0.7895 (pttm)
REVERT: F  983 LEU cc_start: 0.7967 (mp) cc_final: 0.7325 (tt)
REVERT: F 1146 LEU cc_start: 0.8379 (mt) cc_final: 0.8064 (tt)
REVERT: F 1323 MET cc_start: 0.6801 (ptm) cc_final: 0.6328 (ppp)
REVERT: F 1374 ASP cc_start: 0.6336 (t70) cc_final: 0.5526 (m-30)
REVERT: F 1384 MET cc_start: 0.7694 (ptt) cc_final: 0.7268 (ptm)
REVERT: F 1396 LYS cc_start: 0.5997 (pttt) cc_final: 0.4976 (ttpt)
REVERT: F 1486 LEU cc_start: 0.7161 (pp) cc_final: 0.6493 (tt)
REVERT: F 1510 TYR cc_start: 0.7611 (t80) cc_final: 0.7409 (t80)
REVERT: F 1719 MET cc_start: 0.7156 (tmm) cc_final: 0.6908 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 225
  average time/residue: 0.1340
  time to fit residues: 41.7385
Evaluate side-chains
  182 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 55 optimal weight:   20.0000
   chunk 14 optimal weight:    7.9990
   chunk 112 optimal weight:    3.9990
   chunk 52 optimal weight:    8.9990
   chunk 101 optimal weight:    4.9990
   chunk 100 optimal weight:    7.9990
   chunk 81 optimal weight:    4.9990
   chunk 78 optimal weight:    2.9990
   chunk 104 optimal weight:    7.9990
   chunk 107 optimal weight:    7.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
F 218 ASN
F 725 GLN
** F 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F1001 GLN
F1118 HIS
** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F1361 HIS
** F1780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.170359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.159393 restraints weight = 48051.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.161388 restraints weight = 34226.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.161934 restraints weight = 26284.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.162346 restraints weight = 20688.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.162612 restraints weight = 18768.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.4348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6054
moved from start:          0.8355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  12526  Z= 0.187
  Angle     :  0.991  15.364  16887  Z= 0.504
  Chirality :  0.053   0.818   1829
  Planarity :  0.007   0.093   2193
  Dihedral  :  8.499  54.379   1674
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 17.23
  Ramachandran Plot:
    Outliers :  1.61 %
    Allowed  : 17.84 %
    Favored  : 80.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.07 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    Cis-general     : 3.09 %
    Twisted Proline : 7.55 %
    Twisted General : 0.89 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.15 (0.21), residues: 1491
  helix: -0.14 (0.21), residues: 611
  sheet: -0.81 (0.64), residues: 65
  loop : -4.02 (0.19), residues: 815

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG F  77 
 TYR   0.021   0.002   TYR F1744 
 PHE   0.022   0.002   PHE F1294 
 TRP   0.029   0.003   TRP F 851 
 HIS   0.013   0.002   HIS F1643 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 (12525)
  covalent geometry    : angle       0.99067 (16887)
  hydrogen bonds       : bond        0.04069 (  371)
  hydrogen bonds       : angle       4.88200 ( 1071)
  Misc. bond           : bond        0.00103 (    1)

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

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

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 0.493 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F    1 MET cc_start: 0.5770 (mtp) cc_final: 0.4339 (tmm)
REVERT: F   27 MET cc_start: 0.3699 (mmp) cc_final: 0.3316 (mmp)
REVERT: F  147 GLU cc_start: 0.8194 (tp30) cc_final: 0.7894 (tm-30)
REVERT: F  215 MET cc_start: 0.6718 (mmm) cc_final: 0.6184 (mmm)
REVERT: F  723 HIS cc_start: 0.6196 (m-70) cc_final: 0.5770 (m170)
REVERT: F  724 LYS cc_start: 0.8647 (ptpt) cc_final: 0.7849 (pttp)
REVERT: F  726 MET cc_start: 0.4783 (ttp) cc_final: 0.4341 (mtp)
REVERT: F  807 MET cc_start: 0.5548 (mpp) cc_final: 0.5093 (mpp)
REVERT: F  864 MET cc_start: 0.7084 (ttm) cc_final: 0.6731 (ttm)
REVERT: F  942 MET cc_start: 0.4972 (ttp) cc_final: 0.4720 (ttp)
REVERT: F  951 ARG cc_start: 0.6813 (mtt180) cc_final: 0.6390 (mtp85)
REVERT: F  983 LEU cc_start: 0.8040 (mp) cc_final: 0.7535 (tt)
REVERT: F 1146 LEU cc_start: 0.8309 (mt) cc_final: 0.7991 (tt)
REVERT: F 1157 SER cc_start: 0.7104 (p) cc_final: 0.6818 (t)
REVERT: F 1323 MET cc_start: 0.6830 (ptm) cc_final: 0.6320 (ppp)
REVERT: F 1374 ASP cc_start: 0.5445 (t70) cc_final: 0.4962 (m-30)
REVERT: F 1384 MET cc_start: 0.7752 (ptt) cc_final: 0.7376 (ptm)
REVERT: F 1486 LEU cc_start: 0.7221 (pp) cc_final: 0.6496 (tt)
REVERT: F 1609 LEU cc_start: 0.7322 (mt) cc_final: 0.7050 (mt)
REVERT: F 1723 MET cc_start: 0.7094 (mmt) cc_final: 0.6891 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 220
  average time/residue: 0.1329
  time to fit residues: 40.9075
Evaluate side-chains
  175 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 51 optimal weight:   20.0000
   chunk 31 optimal weight:    0.9980
   chunk 18 optimal weight:    7.9990
   chunk 118 optimal weight:    8.9990
   chunk 61 optimal weight:    5.9990
   chunk 92 optimal weight:    0.0020
   chunk 129 optimal weight:    8.9990
   chunk 65 optimal weight:    4.9990
   chunk 124 optimal weight:    0.2980
   chunk 80 optimal weight:    9.9990
   chunk 145 optimal weight:    4.9990
   overall best weight:    2.2592

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

Flipped N/Q/H residues before XYZ refinement:
F 694 GLN
** F 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F1001 GLN
** F1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F1780 ASN
** F1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4474 r_free = 0.4474 target = 0.172901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.161854 restraints weight = 46996.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.163166 restraints weight = 35935.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.164217 restraints weight = 29490.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.164655 restraints weight = 23455.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.164928 restraints weight = 19547.218|
|-----------------------------------------------------------------------------|
r_work (final): 0.4342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6101
moved from start:          0.8564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12526  Z= 0.155
  Angle     :  0.955  14.114  16887  Z= 0.483
  Chirality :  0.051   0.755   1829
  Planarity :  0.006   0.088   2193
  Dihedral  :  8.224  54.246   1674
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 15.47
  Ramachandran Plot:
    Outliers :  1.54 %
    Allowed  : 17.10 %
    Favored  : 81.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Cbeta Deviations :  0.07 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    Cis-general     : 3.09 %
    Twisted Proline : 7.55 %
    Twisted General : 0.55 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.00 (0.21), residues: 1491
  helix:  0.05 (0.21), residues: 603
  sheet: -0.83 (0.66), residues: 64
  loop : -3.95 (0.19), residues: 824

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG F  63 
 TYR   0.025   0.002   TYR F 305 
 PHE   0.027   0.001   PHE F1294 
 TRP   0.033   0.002   TRP F1028 
 HIS   0.006   0.001   HIS F1633 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (12525)
  covalent geometry    : angle       0.95519 (16887)
  hydrogen bonds       : bond        0.03638 (  371)
  hydrogen bonds       : angle       4.78115 ( 1071)
  Misc. bond           : bond        0.00093 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1984.83 seconds
wall clock time: 35 minutes 4.47 seconds (2104.47 seconds total)