Starting phenix.real_space_refine on Thu Mar 21 03:23:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g2h_4343/03_2024/6g2h_4343.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g2h_4343/03_2024/6g2h_4343.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g2h_4343/03_2024/6g2h_4343.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g2h_4343/03_2024/6g2h_4343.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g2h_4343/03_2024/6g2h_4343.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g2h_4343/03_2024/6g2h_4343.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 120 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 300 5.16 5 C 33150 2.51 5 N 9040 2.21 5 O 9554 1.98 5 H 51852 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 645": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 733": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 958": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 975": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 1131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 1146": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 1359": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 1428": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 1441": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 1448": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 1502": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 1531": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 1538": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 1691": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 2144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 645": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 733": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 958": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 1146": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 1538": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 1691": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 1699": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 1734": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 1758": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 1691": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 2144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 1691": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 2144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 645": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 733": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 958": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 1146": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 1538": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 645": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 733": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 958": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 1146": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 1538": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 103896 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 24416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1518, 24416 Classifications: {'peptide': 1518} Link IDs: {'CIS': 1, 'PTRANS': 65, 'TRANS': 1451} Chain breaks: 9 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 24416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1518, 24416 Classifications: {'peptide': 1518} Link IDs: {'CIS': 1, 'PTRANS': 65, 'TRANS': 1451} Chain breaks: 9 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 15171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 15171 Classifications: {'peptide': 948} Link IDs: {'CIS': 1, 'PTRANS': 47, 'TRANS': 899} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 15171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 15171 Classifications: {'peptide': 948} Link IDs: {'CIS': 1, 'PTRANS': 47, 'TRANS': 899} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 12361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 12361 Classifications: {'peptide': 761} Link IDs: {'PTRANS': 25, 'TRANS': 735} Chain breaks: 9 Chain: "A" Number of atoms: 12361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 12361 Classifications: {'peptide': 761} Link IDs: {'PTRANS': 25, 'TRANS': 735} Chain breaks: 9 Time building chain proxies: 34.51, per 1000 atoms: 0.33 Number of scatterers: 103896 At special positions: 0 Unit cell: (225.354, 263.442, 177.744, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 300 16.00 O 9554 8.00 N 9040 7.00 C 33150 6.00 H 51852 1.00 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 63.62 Conformation dependent library (CDL) restraints added in 7.7 seconds 12716 Ramachandran restraints generated. 6358 Oldfield, 0 Emsley, 6358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12220 Finding SS restraints... Secondary structure from input PDB file: 251 helices and 65 sheets defined 50.9% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.05 Creating SS restraints... Processing helix chain 'D' and resid 627 through 658 Processing helix chain 'D' and resid 662 through 667 Processing helix chain 'D' and resid 849 through 867 removed outlier: 4.132A pdb=" N GLY D 866 " --> pdb=" O ASN D 862 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR D 867 " --> pdb=" O VAL D 863 " (cutoff:3.500A) Processing helix chain 'D' and resid 873 through 891 removed outlier: 4.185A pdb=" N LYS D 879 " --> pdb=" O SER D 875 " (cutoff:3.500A) Processing helix chain 'D' and resid 893 through 906 Processing helix chain 'D' and resid 911 through 929 Processing helix chain 'D' and resid 937 through 953 Processing helix chain 'D' and resid 958 through 976 Processing helix chain 'D' and resid 978 through 1002 removed outlier: 4.105A pdb=" N VAL D 987 " --> pdb=" O MET D 983 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TYR D 994 " --> pdb=" O LEU D 990 " (cutoff:3.500A) Processing helix chain 'D' and resid 1005 through 1017 Processing helix chain 'D' and resid 1021 through 1031 Processing helix chain 'D' and resid 1033 through 1051 removed outlier: 3.552A pdb=" N LYS D1037 " --> pdb=" O GLN D1033 " (cutoff:3.500A) Processing helix chain 'D' and resid 1056 through 1068 removed outlier: 3.517A pdb=" N GLN D1068 " --> pdb=" O THR D1064 " (cutoff:3.500A) Processing helix chain 'D' and resid 1075 through 1088 removed outlier: 4.071A pdb=" N LEU D1079 " --> pdb=" O ALA D1075 " (cutoff:3.500A) Processing helix chain 'D' and resid 1093 through 1108 Processing helix chain 'D' and resid 1116 through 1125 Processing helix chain 'D' and resid 1133 through 1138 Processing helix chain 'D' and resid 1142 through 1158 Processing helix chain 'D' and resid 1241 through 1248 Processing helix chain 'D' and resid 1248 through 1253 removed outlier: 4.196A pdb=" N VAL D1252 " --> pdb=" O ILE D1248 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET D1253 " --> pdb=" O PHE D1249 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1248 through 1253' Processing helix chain 'D' and resid 1300 through 1315 Processing helix chain 'D' and resid 1316 through 1321 Processing helix chain 'D' and resid 1382 through 1387 removed outlier: 3.583A pdb=" N MET D1386 " --> pdb=" O LEU D1383 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG D1387 " --> pdb=" O ASN D1384 " (cutoff:3.500A) Processing helix chain 'D' and resid 1437 through 1464 Processing helix chain 'D' and resid 1485 through 1499 removed outlier: 3.875A pdb=" N TYR D1499 " --> pdb=" O MET D1495 " (cutoff:3.500A) Processing helix chain 'D' and resid 1500 through 1506 removed outlier: 3.997A pdb=" N TRP D1504 " --> pdb=" O GLY D1500 " (cutoff:3.500A) Processing helix chain 'D' and resid 1580 through 1593 Processing helix chain 'D' and resid 1597 through 1599 No H-bonds generated for 'chain 'D' and resid 1597 through 1599' Processing helix chain 'D' and resid 1600 through 1619 removed outlier: 3.649A pdb=" N SER D1617 " --> pdb=" O TRP D1613 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR D1618 " --> pdb=" O GLU D1614 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN D1619 " --> pdb=" O SER D1615 " (cutoff:3.500A) Processing helix chain 'D' and resid 1627 through 1631 Processing helix chain 'D' and resid 1686 through 1690 Processing helix chain 'D' and resid 1692 through 1710 Processing helix chain 'D' and resid 1727 through 1732 Processing helix chain 'D' and resid 1743 through 1746 Processing helix chain 'D' and resid 1754 through 1762 removed outlier: 4.401A pdb=" N ARG D1760 " --> pdb=" O GLN D1756 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL D1761 " --> pdb=" O ASP D1757 " (cutoff:3.500A) Processing helix chain 'D' and resid 1763 through 1765 No H-bonds generated for 'chain 'D' and resid 1763 through 1765' Processing helix chain 'D' and resid 1794 through 1814 Processing helix chain 'D' and resid 1826 through 1836 Processing helix chain 'D' and resid 1850 through 1858 Processing helix chain 'D' and resid 1865 through 1871 removed outlier: 3.729A pdb=" N LEU D1869 " --> pdb=" O SER D1865 " (cutoff:3.500A) Processing helix chain 'D' and resid 1871 through 1876 Processing helix chain 'D' and resid 1887 through 1900 Processing helix chain 'D' and resid 1933 through 1940 removed outlier: 3.804A pdb=" N MET D1937 " --> pdb=" O ASP D1933 " (cutoff:3.500A) Processing helix chain 'D' and resid 2019 through 2037 Processing helix chain 'D' and resid 2052 through 2058 Processing helix chain 'D' and resid 2059 through 2073 removed outlier: 4.207A pdb=" N PHE D2063 " --> pdb=" O GLN D2059 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL D2068 " --> pdb=" O GLY D2064 " (cutoff:3.500A) Processing helix chain 'D' and resid 2090 through 2095 Processing helix chain 'D' and resid 2096 through 2101 removed outlier: 5.817A pdb=" N SER D2099 " --> pdb=" O ILE D2096 " (cutoff:3.500A) Processing helix chain 'D' and resid 2119 through 2128 Processing helix chain 'D' and resid 2129 through 2141 Processing helix chain 'D' and resid 2141 through 2152 Processing helix chain 'D' and resid 2157 through 2189 Proline residue: D2177 - end of helix Processing helix chain 'D' and resid 2192 through 2199 Processing helix chain 'D' and resid 2207 through 2236 removed outlier: 3.964A pdb=" N ARG D2212 " --> pdb=" O TRP D2208 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N THR D2213 " --> pdb=" O LYS D2209 " (cutoff:3.500A) Processing helix chain 'D' and resid 2240 through 2257 Processing helix chain 'D' and resid 2258 through 2265 removed outlier: 4.991A pdb=" N TYR D2262 " --> pdb=" O VAL D2259 " (cutoff:3.500A) Processing helix chain 'D' and resid 2266 through 2280 removed outlier: 3.635A pdb=" N LEU D2278 " --> pdb=" O LEU D2274 " (cutoff:3.500A) Processing helix chain 'D' and resid 2287 through 2311 Processing helix chain 'D' and resid 2314 through 2323 Processing helix chain 'D' and resid 2327 through 2337 Processing helix chain 'E' and resid 627 through 658 Processing helix chain 'E' and resid 662 through 667 Processing helix chain 'E' and resid 849 through 867 removed outlier: 4.051A pdb=" N GLY E 866 " --> pdb=" O ASN E 862 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR E 867 " --> pdb=" O VAL E 863 " (cutoff:3.500A) Processing helix chain 'E' and resid 873 through 891 removed outlier: 4.167A pdb=" N LYS E 879 " --> pdb=" O SER E 875 " (cutoff:3.500A) Processing helix chain 'E' and resid 893 through 906 Processing helix chain 'E' and resid 911 through 929 Processing helix chain 'E' and resid 937 through 953 Processing helix chain 'E' and resid 958 through 976 removed outlier: 3.582A pdb=" N TYR E 975 " --> pdb=" O LEU E 971 " (cutoff:3.500A) Processing helix chain 'E' and resid 977 through 1002 removed outlier: 4.598A pdb=" N GLY E 981 " --> pdb=" O SER E 977 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N HIS E 982 " --> pdb=" O GLY E 978 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL E 987 " --> pdb=" O MET E 983 " (cutoff:3.500A) Processing helix chain 'E' and resid 1005 through 1017 Processing helix chain 'E' and resid 1021 through 1033 removed outlier: 4.078A pdb=" N GLN E1033 " --> pdb=" O PHE E1029 " (cutoff:3.500A) Processing helix chain 'E' and resid 1033 through 1051 removed outlier: 3.506A pdb=" N LEU E1039 " --> pdb=" O THR E1035 " (cutoff:3.500A) Processing helix chain 'E' and resid 1056 through 1068 removed outlier: 3.814A pdb=" N GLN E1068 " --> pdb=" O THR E1064 " (cutoff:3.500A) Processing helix chain 'E' and resid 1075 through 1088 Processing helix chain 'E' and resid 1093 through 1108 Processing helix chain 'E' and resid 1116 through 1125 Processing helix chain 'E' and resid 1133 through 1138 Processing helix chain 'E' and resid 1142 through 1158 Processing helix chain 'E' and resid 1241 through 1253 removed outlier: 3.510A pdb=" N PHE E1245 " --> pdb=" O THR E1241 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ASP E1250 " --> pdb=" O VAL E1246 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N GLU E1251 " --> pdb=" O ARG E1247 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL E1252 " --> pdb=" O ILE E1248 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET E1253 " --> pdb=" O PHE E1249 " (cutoff:3.500A) Processing helix chain 'E' and resid 1300 through 1315 Processing helix chain 'E' and resid 1316 through 1321 Processing helix chain 'E' and resid 1374 through 1379 Processing helix chain 'E' and resid 1383 through 1387 removed outlier: 3.910A pdb=" N MET E1386 " --> pdb=" O LEU E1383 " (cutoff:3.500A) Processing helix chain 'E' and resid 1437 through 1464 Processing helix chain 'E' and resid 1484 through 1499 removed outlier: 4.175A pdb=" N ILE E1488 " --> pdb=" O ASP E1484 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR E1499 " --> pdb=" O MET E1495 " (cutoff:3.500A) Processing helix chain 'E' and resid 1500 through 1506 Processing helix chain 'E' and resid 1580 through 1593 Processing helix chain 'E' and resid 1597 through 1599 No H-bonds generated for 'chain 'E' and resid 1597 through 1599' Processing helix chain 'E' and resid 1600 through 1619 removed outlier: 3.599A pdb=" N SER E1617 " --> pdb=" O TRP E1613 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR E1618 " --> pdb=" O GLU E1614 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN E1619 " --> pdb=" O SER E1615 " (cutoff:3.500A) Processing helix chain 'E' and resid 1627 through 1630 Processing helix chain 'E' and resid 1686 through 1690 Processing helix chain 'E' and resid 1692 through 1710 Processing helix chain 'E' and resid 1727 through 1732 Processing helix chain 'E' and resid 1743 through 1746 Processing helix chain 'E' and resid 1754 through 1762 removed outlier: 4.061A pdb=" N ARG E1760 " --> pdb=" O GLN E1756 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL E1761 " --> pdb=" O ASP E1757 " (cutoff:3.500A) Processing helix chain 'E' and resid 1763 through 1765 No H-bonds generated for 'chain 'E' and resid 1763 through 1765' Processing helix chain 'E' and resid 1794 through 1814 Processing helix chain 'E' and resid 1826 through 1836 Processing helix chain 'E' and resid 1850 through 1858 Processing helix chain 'E' and resid 1865 through 1871 removed outlier: 3.705A pdb=" N LEU E1869 " --> pdb=" O SER E1865 " (cutoff:3.500A) Processing helix chain 'E' and resid 1871 through 1876 Processing helix chain 'E' and resid 1887 through 1900 Processing helix chain 'E' and resid 1933 through 1940 removed outlier: 3.786A pdb=" N MET E1937 " --> pdb=" O ASP E1933 " (cutoff:3.500A) Processing helix chain 'E' and resid 2019 through 2037 Processing helix chain 'E' and resid 2052 through 2058 Processing helix chain 'E' and resid 2059 through 2073 removed outlier: 4.106A pdb=" N PHE E2063 " --> pdb=" O GLN E2059 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL E2068 " --> pdb=" O GLY E2064 " (cutoff:3.500A) Processing helix chain 'E' and resid 2090 through 2095 Processing helix chain 'E' and resid 2096 through 2101 removed outlier: 5.893A pdb=" N SER E2099 " --> pdb=" O ILE E2096 " (cutoff:3.500A) Processing helix chain 'E' and resid 2119 through 2128 Processing helix chain 'E' and resid 2129 through 2141 Processing helix chain 'E' and resid 2141 through 2152 Processing helix chain 'E' and resid 2157 through 2189 Proline residue: E2177 - end of helix Processing helix chain 'E' and resid 2192 through 2199 Processing helix chain 'E' and resid 2207 through 2236 removed outlier: 4.048A pdb=" N ARG E2212 " --> pdb=" O TRP E2208 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N THR E2213 " --> pdb=" O LYS E2209 " (cutoff:3.500A) Processing helix chain 'E' and resid 2240 through 2257 Processing helix chain 'E' and resid 2258 through 2265 removed outlier: 4.991A pdb=" N TYR E2262 " --> pdb=" O VAL E2259 " (cutoff:3.500A) Processing helix chain 'E' and resid 2266 through 2280 Processing helix chain 'E' and resid 2287 through 2311 Processing helix chain 'E' and resid 2314 through 2323 removed outlier: 3.523A pdb=" N ILE E2320 " --> pdb=" O MET E2316 " (cutoff:3.500A) Processing helix chain 'E' and resid 2327 through 2337 Processing helix chain 'C' and resid 1383 through 1387 removed outlier: 3.809A pdb=" N MET C1386 " --> pdb=" O LEU C1383 " (cutoff:3.500A) Processing helix chain 'C' and resid 1437 through 1464 Processing helix chain 'C' and resid 1484 through 1499 removed outlier: 3.892A pdb=" N ILE C1488 " --> pdb=" O ASP C1484 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TYR C1499 " --> pdb=" O MET C1495 " (cutoff:3.500A) Processing helix chain 'C' and resid 1500 through 1507 Processing helix chain 'C' and resid 1580 through 1593 Processing helix chain 'C' and resid 1597 through 1599 No H-bonds generated for 'chain 'C' and resid 1597 through 1599' Processing helix chain 'C' and resid 1600 through 1620 removed outlier: 3.625A pdb=" N SER C1617 " --> pdb=" O TRP C1613 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR C1618 " --> pdb=" O GLU C1614 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN C1619 " --> pdb=" O SER C1615 " (cutoff:3.500A) Processing helix chain 'C' and resid 1627 through 1631 Processing helix chain 'C' and resid 1686 through 1690 Processing helix chain 'C' and resid 1692 through 1710 Processing helix chain 'C' and resid 1727 through 1732 Processing helix chain 'C' and resid 1743 through 1746 removed outlier: 3.502A pdb=" N LYS C1746 " --> pdb=" O ASP C1743 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1743 through 1746' Processing helix chain 'C' and resid 1754 through 1762 removed outlier: 4.512A pdb=" N ARG C1760 " --> pdb=" O GLN C1756 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL C1761 " --> pdb=" O ASP C1757 " (cutoff:3.500A) Processing helix chain 'C' and resid 1763 through 1765 No H-bonds generated for 'chain 'C' and resid 1763 through 1765' Processing helix chain 'C' and resid 1794 through 1814 Processing helix chain 'C' and resid 1826 through 1836 Processing helix chain 'C' and resid 1850 through 1858 Processing helix chain 'C' and resid 1865 through 1871 removed outlier: 3.775A pdb=" N LEU C1869 " --> pdb=" O SER C1865 " (cutoff:3.500A) Processing helix chain 'C' and resid 1871 through 1876 Processing helix chain 'C' and resid 1887 through 1900 Processing helix chain 'C' and resid 1933 through 1940 removed outlier: 3.999A pdb=" N MET C1937 " --> pdb=" O ASP C1933 " (cutoff:3.500A) Processing helix chain 'C' and resid 2019 through 2037 Processing helix chain 'C' and resid 2052 through 2058 Processing helix chain 'C' and resid 2059 through 2073 removed outlier: 3.682A pdb=" N VAL C2068 " --> pdb=" O GLY C2064 " (cutoff:3.500A) Processing helix chain 'C' and resid 2090 through 2095 Processing helix chain 'C' and resid 2096 through 2101 removed outlier: 5.725A pdb=" N SER C2099 " --> pdb=" O ILE C2096 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN C2101 " --> pdb=" O SER C2098 " (cutoff:3.500A) Processing helix chain 'C' and resid 2119 through 2128 Processing helix chain 'C' and resid 2129 through 2141 Processing helix chain 'C' and resid 2141 through 2152 Processing helix chain 'C' and resid 2157 through 2189 Proline residue: C2177 - end of helix removed outlier: 3.834A pdb=" N HIS C2180 " --> pdb=" O ILE C2176 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN C2181 " --> pdb=" O PRO C2177 " (cutoff:3.500A) Processing helix chain 'C' and resid 2192 through 2200 Processing helix chain 'C' and resid 2207 through 2209 No H-bonds generated for 'chain 'C' and resid 2207 through 2209' Processing helix chain 'C' and resid 2210 through 2236 Processing helix chain 'C' and resid 2240 through 2257 Processing helix chain 'C' and resid 2258 through 2265 removed outlier: 5.036A pdb=" N TYR C2262 " --> pdb=" O VAL C2259 " (cutoff:3.500A) Processing helix chain 'C' and resid 2266 through 2279 removed outlier: 3.700A pdb=" N LEU C2270 " --> pdb=" O ASN C2266 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA C2271 " --> pdb=" O ASN C2267 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLN C2277 " --> pdb=" O TRP C2273 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU C2278 " --> pdb=" O LEU C2274 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR C2279 " --> pdb=" O GLU C2275 " (cutoff:3.500A) Processing helix chain 'C' and resid 2286 through 2311 Processing helix chain 'C' and resid 2314 through 2323 removed outlier: 3.840A pdb=" N HIS C2321 " --> pdb=" O ASP C2317 " (cutoff:3.500A) Processing helix chain 'C' and resid 2326 through 2337 Processing helix chain 'F' and resid 1437 through 1464 Processing helix chain 'F' and resid 1484 through 1499 removed outlier: 3.859A pdb=" N ILE F1488 " --> pdb=" O ASP F1484 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N TYR F1499 " --> pdb=" O MET F1495 " (cutoff:3.500A) Processing helix chain 'F' and resid 1500 through 1507 Processing helix chain 'F' and resid 1580 through 1593 Processing helix chain 'F' and resid 1597 through 1599 No H-bonds generated for 'chain 'F' and resid 1597 through 1599' Processing helix chain 'F' and resid 1600 through 1620 removed outlier: 3.861A pdb=" N SER F1617 " --> pdb=" O TRP F1613 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR F1618 " --> pdb=" O GLU F1614 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN F1619 " --> pdb=" O SER F1615 " (cutoff:3.500A) Processing helix chain 'F' and resid 1627 through 1631 Processing helix chain 'F' and resid 1686 through 1690 Processing helix chain 'F' and resid 1692 through 1710 Processing helix chain 'F' and resid 1727 through 1732 Processing helix chain 'F' and resid 1743 through 1746 removed outlier: 3.527A pdb=" N LYS F1746 " --> pdb=" O ASP F1743 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1743 through 1746' Processing helix chain 'F' and resid 1754 through 1762 removed outlier: 4.515A pdb=" N ARG F1760 " --> pdb=" O GLN F1756 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL F1761 " --> pdb=" O ASP F1757 " (cutoff:3.500A) Processing helix chain 'F' and resid 1763 through 1765 No H-bonds generated for 'chain 'F' and resid 1763 through 1765' Processing helix chain 'F' and resid 1794 through 1814 removed outlier: 3.685A pdb=" N ASN F1812 " --> pdb=" O SER F1808 " (cutoff:3.500A) Processing helix chain 'F' and resid 1826 through 1836 Processing helix chain 'F' and resid 1850 through 1858 Processing helix chain 'F' and resid 1866 through 1871 Processing helix chain 'F' and resid 1871 through 1876 Processing helix chain 'F' and resid 1887 through 1900 Processing helix chain 'F' and resid 1933 through 1940 removed outlier: 4.087A pdb=" N MET F1937 " --> pdb=" O ASP F1933 " (cutoff:3.500A) Processing helix chain 'F' and resid 2019 through 2037 Processing helix chain 'F' and resid 2052 through 2058 Processing helix chain 'F' and resid 2059 through 2073 removed outlier: 3.591A pdb=" N PHE F2063 " --> pdb=" O GLN F2059 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL F2068 " --> pdb=" O GLY F2064 " (cutoff:3.500A) Processing helix chain 'F' and resid 2090 through 2095 Processing helix chain 'F' and resid 2096 through 2101 removed outlier: 5.865A pdb=" N SER F2099 " --> pdb=" O ILE F2096 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN F2101 " --> pdb=" O SER F2098 " (cutoff:3.500A) Processing helix chain 'F' and resid 2119 through 2128 Processing helix chain 'F' and resid 2129 through 2141 Processing helix chain 'F' and resid 2141 through 2152 Processing helix chain 'F' and resid 2157 through 2189 Proline residue: F2177 - end of helix removed outlier: 3.769A pdb=" N HIS F2180 " --> pdb=" O ILE F2176 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN F2181 " --> pdb=" O PRO F2177 " (cutoff:3.500A) Processing helix chain 'F' and resid 2192 through 2199 Processing helix chain 'F' and resid 2207 through 2209 No H-bonds generated for 'chain 'F' and resid 2207 through 2209' Processing helix chain 'F' and resid 2210 through 2236 Processing helix chain 'F' and resid 2240 through 2257 Processing helix chain 'F' and resid 2258 through 2265 removed outlier: 3.516A pdb=" N ALA F2261 " --> pdb=" O THR F2258 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N TYR F2262 " --> pdb=" O VAL F2259 " (cutoff:3.500A) Processing helix chain 'F' and resid 2266 through 2276 removed outlier: 3.671A pdb=" N LEU F2270 " --> pdb=" O ASN F2266 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA F2271 " --> pdb=" O ASN F2267 " (cutoff:3.500A) Processing helix chain 'F' and resid 2286 through 2311 Processing helix chain 'F' and resid 2314 through 2323 removed outlier: 3.890A pdb=" N HIS F2321 " --> pdb=" O ASP F2317 " (cutoff:3.500A) Processing helix chain 'F' and resid 2326 through 2337 removed outlier: 3.811A pdb=" N GLN F2330 " --> pdb=" O ILE F2326 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 657 Processing helix chain 'B' and resid 662 through 667 Processing helix chain 'B' and resid 849 through 865 Processing helix chain 'B' and resid 873 through 891 removed outlier: 4.327A pdb=" N LYS B 879 " --> pdb=" O SER B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 906 Processing helix chain 'B' and resid 911 through 929 Processing helix chain 'B' and resid 937 through 952 Processing helix chain 'B' and resid 958 through 976 removed outlier: 3.955A pdb=" N LEU B 971 " --> pdb=" O SER B 967 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR B 975 " --> pdb=" O LEU B 971 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG B 976 " --> pdb=" O VAL B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 1002 removed outlier: 4.143A pdb=" N VAL B 987 " --> pdb=" O MET B 983 " (cutoff:3.500A) Processing helix chain 'B' and resid 1005 through 1017 Processing helix chain 'B' and resid 1021 through 1031 Processing helix chain 'B' and resid 1033 through 1049 removed outlier: 3.672A pdb=" N LYS B1037 " --> pdb=" O GLN B1033 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1052 No H-bonds generated for 'chain 'B' and resid 1050 through 1052' Processing helix chain 'B' and resid 1056 through 1068 removed outlier: 4.054A pdb=" N GLN B1068 " --> pdb=" O THR B1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1090 removed outlier: 3.768A pdb=" N LEU B1079 " --> pdb=" O ALA B1075 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS B1089 " --> pdb=" O LEU B1085 " (cutoff:3.500A) Processing helix chain 'B' and resid 1093 through 1108 Processing helix chain 'B' and resid 1116 through 1125 Processing helix chain 'B' and resid 1133 through 1138 Processing helix chain 'B' and resid 1142 through 1158 Processing helix chain 'B' and resid 1241 through 1248 Processing helix chain 'B' and resid 1248 through 1253 removed outlier: 3.710A pdb=" N VAL B1252 " --> pdb=" O ILE B1248 " (cutoff:3.500A) Processing helix chain 'B' and resid 1300 through 1315 Processing helix chain 'B' and resid 1316 through 1321 Processing helix chain 'B' and resid 1374 through 1379 Processing helix chain 'B' and resid 1437 through 1464 Processing helix chain 'B' and resid 1484 through 1499 removed outlier: 3.651A pdb=" N ILE B1488 " --> pdb=" O ASP B1484 " (cutoff:3.500A) Processing helix chain 'B' and resid 1500 through 1507 Processing helix chain 'A' and resid 627 through 657 Processing helix chain 'A' and resid 662 through 667 Processing helix chain 'A' and resid 849 through 864 Processing helix chain 'A' and resid 873 through 891 removed outlier: 4.321A pdb=" N LYS A 879 " --> pdb=" O SER A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 906 Processing helix chain 'A' and resid 911 through 928 Processing helix chain 'A' and resid 937 through 953 Processing helix chain 'A' and resid 954 through 956 No H-bonds generated for 'chain 'A' and resid 954 through 956' Processing helix chain 'A' and resid 958 through 976 removed outlier: 3.954A pdb=" N LEU A 971 " --> pdb=" O SER A 967 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR A 975 " --> pdb=" O LEU A 971 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 976 " --> pdb=" O VAL A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 1002 removed outlier: 3.874A pdb=" N HIS A 982 " --> pdb=" O GLY A 978 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL A 987 " --> pdb=" O MET A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1017 Processing helix chain 'A' and resid 1021 through 1031 Processing helix chain 'A' and resid 1033 through 1052 Processing helix chain 'A' and resid 1056 through 1067 Processing helix chain 'A' and resid 1075 through 1090 removed outlier: 3.688A pdb=" N LEU A1079 " --> pdb=" O ALA A1075 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N HIS A1089 " --> pdb=" O LEU A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1108 Processing helix chain 'A' and resid 1116 through 1125 Processing helix chain 'A' and resid 1133 through 1138 removed outlier: 3.800A pdb=" N PHE A1137 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1159 Processing helix chain 'A' and resid 1241 through 1248 removed outlier: 3.545A pdb=" N PHE A1245 " --> pdb=" O THR A1241 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1253 Processing helix chain 'A' and resid 1300 through 1315 Processing helix chain 'A' and resid 1316 through 1321 Processing helix chain 'A' and resid 1374 through 1379 Processing helix chain 'A' and resid 1437 through 1464 Processing helix chain 'A' and resid 1484 through 1499 removed outlier: 3.621A pdb=" N TYR A1499 " --> pdb=" O MET A1495 " (cutoff:3.500A) Processing helix chain 'A' and resid 1500 through 1507 removed outlier: 3.554A pdb=" N TRP A1504 " --> pdb=" O GLY A1500 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 670 through 676 removed outlier: 4.334A pdb=" N ASP D 705 " --> pdb=" O SER D 717 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER D 717 " --> pdb=" O ASP D 705 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 726 through 729 Processing sheet with id=AA3, first strand: chain 'D' and resid 1162 through 1163 removed outlier: 4.112A pdb=" N GLU D1162 " --> pdb=" O MET D1183 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 1162 through 1163 removed outlier: 4.112A pdb=" N GLU D1162 " --> pdb=" O MET D1183 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N CYS D1176 " --> pdb=" O SER D1238 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER D1238 " --> pdb=" O CYS D1176 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N ILE D1288 " --> pdb=" O GLN D1231 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N MET D1233 " --> pdb=" O ILE D1288 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N ASN D1290 " --> pdb=" O MET D1233 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLY D1235 " --> pdb=" O ASN D1290 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ALA D1292 " --> pdb=" O GLY D1235 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL D1237 " --> pdb=" O ALA D1292 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG D1326 " --> pdb=" O HIS D1287 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 1390 through 1393 removed outlier: 8.287A pdb=" N HIS D1472 " --> pdb=" O TYR D1419 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N PHE D1421 " --> pdb=" O HIS D1472 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N PHE D1474 " --> pdb=" O PHE D1421 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL D1423 " --> pdb=" O PHE D1474 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ASN D1476 " --> pdb=" O VAL D1423 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ALA D1425 " --> pdb=" O ASN D1476 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N VAL D1478 " --> pdb=" O ALA D1425 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASN D1471 " --> pdb=" O GLN D1510 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N GLU D1512 " --> pdb=" O ASN D1471 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE D1473 " --> pdb=" O GLU D1512 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N LYS D1514 " --> pdb=" O ILE D1473 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU D1475 " --> pdb=" O LYS D1514 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N ASN D1516 " --> pdb=" O LEU D1475 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N PHE D1477 " --> pdb=" O ASN D1516 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N ARG D1518 " --> pdb=" O PHE D1477 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N LEU D1509 " --> pdb=" O ASN D1534 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN D1534 " --> pdb=" O LEU D1509 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA D1511 " --> pdb=" O LEU D1532 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE D1515 " --> pdb=" O ILE D1528 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 1546 through 1548 Processing sheet with id=AA7, first strand: chain 'D' and resid 1620 through 1621 removed outlier: 4.647A pdb=" N ASN D1914 " --> pdb=" O PHE D1621 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 1645 through 1648 removed outlier: 4.331A pdb=" N ALA D1661 " --> pdb=" O LEU D1637 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N LEU D1639 " --> pdb=" O MET D1659 " (cutoff:3.500A) removed outlier: 11.616A pdb=" N MET D1659 " --> pdb=" O LEU D1639 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 1735 through 1738 removed outlier: 3.807A pdb=" N TYR D1750 " --> pdb=" O ALA D1737 " (cutoff:3.500A) removed outlier: 16.189A pdb=" N ARG D1749 " --> pdb=" O ASP D1784 " (cutoff:3.500A) removed outlier: 11.673A pdb=" N ASP D1784 " --> pdb=" O ARG D1749 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU D1751 " --> pdb=" O ILE D1782 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N HIS D1768 " --> pdb=" O THR D1783 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 1823 through 1825 Processing sheet with id=AB2, first strand: chain 'D' and resid 1941 through 1942 Processing sheet with id=AB3, first strand: chain 'D' and resid 1961 through 1962 removed outlier: 6.104A pdb=" N LEU D2040 " --> pdb=" O LEU D2079 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N TYR D2081 " --> pdb=" O LEU D2040 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL D2042 " --> pdb=" O TYR D2081 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N VAL D2078 " --> pdb=" O GLU D2106 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N TYR D2108 " --> pdb=" O VAL D2078 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N VAL D2080 " --> pdb=" O TYR D2108 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 1993 through 1996 removed outlier: 3.518A pdb=" N VAL D1993 " --> pdb=" O GLN D2013 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 2017 through 2018 removed outlier: 3.810A pdb=" N TRP D2018 " --> pdb=" O GLY D2048 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 2087 through 2089 Processing sheet with id=AB7, first strand: chain 'E' and resid 670 through 676 removed outlier: 3.567A pdb=" N TYR E 676 " --> pdb=" O VAL E 679 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 716 through 717 Processing sheet with id=AB9, first strand: chain 'E' and resid 725 through 729 Processing sheet with id=AC1, first strand: chain 'E' and resid 1162 through 1163 removed outlier: 4.164A pdb=" N GLU E1162 " --> pdb=" O MET E1183 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 1162 through 1163 removed outlier: 4.164A pdb=" N GLU E1162 " --> pdb=" O MET E1183 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N CYS E1176 " --> pdb=" O SER E1238 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N SER E1238 " --> pdb=" O CYS E1176 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG E1232 " --> pdb=" O PHE E1182 " (cutoff:3.500A) removed outlier: 9.351A pdb=" N ILE E1288 " --> pdb=" O GLN E1231 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N MET E1233 " --> pdb=" O ILE E1288 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N ASN E1290 " --> pdb=" O MET E1233 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLY E1235 " --> pdb=" O ASN E1290 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ALA E1292 " --> pdb=" O GLY E1235 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL E1237 " --> pdb=" O ALA E1292 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG E1326 " --> pdb=" O HIS E1287 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 1390 through 1393 removed outlier: 3.518A pdb=" N ASP E1390 " --> pdb=" O ALA E1407 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N HIS E1472 " --> pdb=" O TYR E1419 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE E1421 " --> pdb=" O HIS E1472 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N PHE E1474 " --> pdb=" O PHE E1421 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL E1423 " --> pdb=" O PHE E1474 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ASN E1476 " --> pdb=" O VAL E1423 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ALA E1425 " --> pdb=" O ASN E1476 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N VAL E1478 " --> pdb=" O ALA E1425 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASN E1471 " --> pdb=" O GLN E1510 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N GLU E1512 " --> pdb=" O ASN E1471 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE E1473 " --> pdb=" O GLU E1512 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N LYS E1514 " --> pdb=" O ILE E1473 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LEU E1475 " --> pdb=" O LYS E1514 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N ASN E1516 " --> pdb=" O LEU E1475 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N PHE E1477 " --> pdb=" O ASN E1516 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 1390 through 1393 removed outlier: 3.518A pdb=" N ASP E1390 " --> pdb=" O ALA E1407 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N HIS E1472 " --> pdb=" O TYR E1419 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE E1421 " --> pdb=" O HIS E1472 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N PHE E1474 " --> pdb=" O PHE E1421 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL E1423 " --> pdb=" O PHE E1474 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ASN E1476 " --> pdb=" O VAL E1423 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ALA E1425 " --> pdb=" O ASN E1476 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N VAL E1478 " --> pdb=" O ALA E1425 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASN E1471 " --> pdb=" O GLN E1510 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N GLU E1512 " --> pdb=" O ASN E1471 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE E1473 " --> pdb=" O GLU E1512 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N LYS E1514 " --> pdb=" O ILE E1473 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LEU E1475 " --> pdb=" O LYS E1514 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N ASN E1516 " --> pdb=" O LEU E1475 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N PHE E1477 " --> pdb=" O ASN E1516 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA E1511 " --> pdb=" O LEU E1532 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 1620 through 1621 removed outlier: 4.775A pdb=" N ASN E1914 " --> pdb=" O PHE E1621 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 1645 through 1648 removed outlier: 4.186A pdb=" N ALA E1661 " --> pdb=" O LEU E1637 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N LEU E1639 " --> pdb=" O MET E1659 " (cutoff:3.500A) removed outlier: 11.334A pdb=" N MET E1659 " --> pdb=" O LEU E1639 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 1735 through 1738 removed outlier: 3.810A pdb=" N TYR E1750 " --> pdb=" O ALA E1737 " (cutoff:3.500A) removed outlier: 16.173A pdb=" N ARG E1749 " --> pdb=" O ASP E1784 " (cutoff:3.500A) removed outlier: 11.591A pdb=" N ASP E1784 " --> pdb=" O ARG E1749 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LEU E1751 " --> pdb=" O ILE E1782 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU E1753 " --> pdb=" O TYR E1780 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR E1780 " --> pdb=" O LEU E1753 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N HIS E1768 " --> pdb=" O THR E1783 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 1823 through 1825 removed outlier: 5.891A pdb=" N ALA E1824 " --> pdb=" O ILE E1847 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'E' and resid 1941 through 1942 Processing sheet with id=AD1, first strand: chain 'E' and resid 1961 through 1962 removed outlier: 3.504A pdb=" N ARG E1975 " --> pdb=" O SER E1961 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N MET E2041 " --> pdb=" O PRO E1982 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLY E1984 " --> pdb=" O MET E2041 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N PHE E2043 " --> pdb=" O GLY E1984 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL E1986 " --> pdb=" O PHE E2043 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU E2040 " --> pdb=" O LEU E2079 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N TYR E2081 " --> pdb=" O LEU E2040 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL E2042 " --> pdb=" O TYR E2081 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASP E2204 " --> pdb=" O MET E2107 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA E2109 " --> pdb=" O ASP E2204 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU E2206 " --> pdb=" O ALA E2109 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 1993 through 1996 Processing sheet with id=AD3, first strand: chain 'E' and resid 2017 through 2018 removed outlier: 3.821A pdb=" N TRP E2018 " --> pdb=" O GLY E2048 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'E' and resid 2087 through 2089 Processing sheet with id=AD5, first strand: chain 'C' and resid 1390 through 1394 removed outlier: 4.640A pdb=" N LEU C1403 " --> pdb=" O ILE C1394 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ASN C1471 " --> pdb=" O GLN C1510 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLU C1512 " --> pdb=" O ASN C1471 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILE C1473 " --> pdb=" O GLU C1512 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N LYS C1514 " --> pdb=" O ILE C1473 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU C1475 " --> pdb=" O LYS C1514 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N ASN C1516 " --> pdb=" O LEU C1475 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N PHE C1477 " --> pdb=" O ASN C1516 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1390 through 1394 removed outlier: 4.640A pdb=" N LEU C1403 " --> pdb=" O ILE C1394 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ASN C1471 " --> pdb=" O GLN C1510 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLU C1512 " --> pdb=" O ASN C1471 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILE C1473 " --> pdb=" O GLU C1512 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N LYS C1514 " --> pdb=" O ILE C1473 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU C1475 " --> pdb=" O LYS C1514 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N ASN C1516 " --> pdb=" O LEU C1475 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N PHE C1477 " --> pdb=" O ASN C1516 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU C1509 " --> pdb=" O ASN C1534 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASN C1534 " --> pdb=" O LEU C1509 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA C1511 " --> pdb=" O LEU C1532 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 1547 through 1548 Processing sheet with id=AD8, first strand: chain 'C' and resid 1645 through 1648 removed outlier: 4.735A pdb=" N ALA C1661 " --> pdb=" O LEU C1637 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N LEU C1639 " --> pdb=" O MET C1659 " (cutoff:3.500A) removed outlier: 12.168A pdb=" N MET C1659 " --> pdb=" O LEU C1639 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 1735 through 1738 removed outlier: 6.284A pdb=" N HIS C1735 " --> pdb=" O LEU C1751 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU C1751 " --> pdb=" O HIS C1735 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA C1737 " --> pdb=" O ARG C1749 " (cutoff:3.500A) removed outlier: 17.017A pdb=" N ARG C1749 " --> pdb=" O ASP C1784 " (cutoff:3.500A) removed outlier: 12.723A pdb=" N ASP C1784 " --> pdb=" O ARG C1749 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU C1751 " --> pdb=" O ILE C1782 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N SER C1778 " --> pdb=" O ASP C1774 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASP C1774 " --> pdb=" O SER C1778 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N TYR C1780 " --> pdb=" O VAL C1772 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL C1772 " --> pdb=" O TYR C1780 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ILE C1782 " --> pdb=" O GLU C1770 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU C1770 " --> pdb=" O ILE C1782 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 1824 through 1825 removed outlier: 5.548A pdb=" N ALA C1824 " --> pdb=" O ILE C1847 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 1941 through 1942 Processing sheet with id=AE3, first strand: chain 'C' and resid 1961 through 1963 removed outlier: 4.728A pdb=" N VAL C1973 " --> pdb=" O ILE C1963 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N MET C2041 " --> pdb=" O PRO C1982 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLY C1984 " --> pdb=" O MET C2041 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N PHE C2043 " --> pdb=" O GLY C1984 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL C1986 " --> pdb=" O PHE C2043 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU C2040 " --> pdb=" O LEU C2079 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N TYR C2081 " --> pdb=" O LEU C2040 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL C2042 " --> pdb=" O TYR C2081 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP C2204 " --> pdb=" O MET C2107 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 1993 through 1997 Processing sheet with id=AE5, first strand: chain 'C' and resid 2087 through 2089 Processing sheet with id=AE6, first strand: chain 'F' and resid 1390 through 1394 removed outlier: 4.654A pdb=" N LEU F1403 " --> pdb=" O ILE F1394 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ILE F1473 " --> pdb=" O GLU F1512 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N LYS F1514 " --> pdb=" O ILE F1473 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU F1475 " --> pdb=" O LYS F1514 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N ASN F1516 " --> pdb=" O LEU F1475 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N PHE F1477 " --> pdb=" O ASN F1516 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 1390 through 1394 removed outlier: 4.654A pdb=" N LEU F1403 " --> pdb=" O ILE F1394 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ILE F1473 " --> pdb=" O GLU F1512 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N LYS F1514 " --> pdb=" O ILE F1473 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU F1475 " --> pdb=" O LYS F1514 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N ASN F1516 " --> pdb=" O LEU F1475 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N PHE F1477 " --> pdb=" O ASN F1516 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA F1511 " --> pdb=" O LEU F1532 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 1547 through 1548 Processing sheet with id=AE9, first strand: chain 'F' and resid 1645 through 1648 removed outlier: 4.711A pdb=" N ALA F1661 " --> pdb=" O LEU F1637 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N LEU F1639 " --> pdb=" O MET F1659 " (cutoff:3.500A) removed outlier: 12.194A pdb=" N MET F1659 " --> pdb=" O LEU F1639 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA F1718 " --> pdb=" O ASN F1682 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR F1821 " --> pdb=" O SER F1717 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N ASN F1719 " --> pdb=" O THR F1821 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ARG F1823 " --> pdb=" O ASN F1719 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N ILE F1847 " --> pdb=" O CYS F1822 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ALA F1824 " --> pdb=" O ILE F1847 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 1645 through 1648 removed outlier: 4.711A pdb=" N ALA F1661 " --> pdb=" O LEU F1637 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N LEU F1639 " --> pdb=" O MET F1659 " (cutoff:3.500A) removed outlier: 12.194A pdb=" N MET F1659 " --> pdb=" O LEU F1639 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA F1718 " --> pdb=" O ASN F1682 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR F1821 " --> pdb=" O SER F1717 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N ASN F1719 " --> pdb=" O THR F1821 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ARG F1823 " --> pdb=" O ASN F1719 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N CYS F1822 " --> pdb=" O VAL F1841 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 1735 through 1738 removed outlier: 6.210A pdb=" N HIS F1735 " --> pdb=" O LEU F1751 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU F1751 " --> pdb=" O HIS F1735 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA F1737 " --> pdb=" O ARG F1749 " (cutoff:3.500A) removed outlier: 16.798A pdb=" N ARG F1749 " --> pdb=" O ASP F1784 " (cutoff:3.500A) removed outlier: 12.597A pdb=" N ASP F1784 " --> pdb=" O ARG F1749 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LEU F1751 " --> pdb=" O ILE F1782 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N SER F1778 " --> pdb=" O ASP F1774 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASP F1774 " --> pdb=" O SER F1778 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N TYR F1780 " --> pdb=" O VAL F1772 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL F1772 " --> pdb=" O TYR F1780 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ILE F1782 " --> pdb=" O GLU F1770 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLU F1770 " --> pdb=" O ILE F1782 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 1941 through 1942 Processing sheet with id=AF4, first strand: chain 'F' and resid 1961 through 1963 removed outlier: 4.707A pdb=" N VAL F1973 " --> pdb=" O ILE F1963 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N MET F2041 " --> pdb=" O PRO F1982 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY F1984 " --> pdb=" O MET F2041 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N PHE F2043 " --> pdb=" O GLY F1984 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL F1986 " --> pdb=" O PHE F2043 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU F2040 " --> pdb=" O LEU F2079 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N TYR F2081 " --> pdb=" O LEU F2040 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL F2042 " --> pdb=" O TYR F2081 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL F2078 " --> pdb=" O GLU F2106 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N TYR F2108 " --> pdb=" O VAL F2078 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL F2080 " --> pdb=" O TYR F2108 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP F2110 " --> pdb=" O VAL F2080 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE F2082 " --> pdb=" O ASP F2110 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N LEU F2206 " --> pdb=" O MET F2107 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ALA F2109 " --> pdb=" O LEU F2206 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 1993 through 1997 Processing sheet with id=AF6, first strand: chain 'F' and resid 2017 through 2018 Processing sheet with id=AF7, first strand: chain 'F' and resid 2087 through 2089 Processing sheet with id=AF8, first strand: chain 'B' and resid 672 through 676 removed outlier: 6.400A pdb=" N SER B 692 " --> pdb=" O GLN B 688 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 716 through 717 removed outlier: 3.662A pdb=" N LEU B 716 " --> pdb=" O TYR B 723 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 726 through 729 Processing sheet with id=AG2, first strand: chain 'B' and resid 1168 through 1171 removed outlier: 5.123A pdb=" N CYS B1176 " --> pdb=" O SER B1238 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER B1238 " --> pdb=" O CYS B1176 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N ILE B1288 " --> pdb=" O GLN B1231 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N MET B1233 " --> pdb=" O ILE B1288 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ASN B1290 " --> pdb=" O MET B1233 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLY B1235 " --> pdb=" O ASN B1290 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA B1292 " --> pdb=" O GLY B1235 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL B1237 " --> pdb=" O ALA B1292 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG B1326 " --> pdb=" O HIS B1287 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 1390 through 1394 removed outlier: 3.666A pdb=" N THR B1392 " --> pdb=" O LEU B1405 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU B1405 " --> pdb=" O THR B1392 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE B1394 " --> pdb=" O LEU B1403 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LEU B1403 " --> pdb=" O ILE B1394 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N HIS B1472 " --> pdb=" O TYR B1419 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N PHE B1421 " --> pdb=" O HIS B1472 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N PHE B1474 " --> pdb=" O PHE B1421 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL B1423 " --> pdb=" O PHE B1474 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N ASN B1476 " --> pdb=" O VAL B1423 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ASN B1471 " --> pdb=" O GLN B1510 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N GLU B1512 " --> pdb=" O ASN B1471 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE B1473 " --> pdb=" O GLU B1512 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LYS B1514 " --> pdb=" O ILE B1473 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU B1475 " --> pdb=" O LYS B1514 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N ASN B1516 " --> pdb=" O LEU B1475 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N PHE B1477 " --> pdb=" O ASN B1516 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 1390 through 1394 removed outlier: 3.666A pdb=" N THR B1392 " --> pdb=" O LEU B1405 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU B1405 " --> pdb=" O THR B1392 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE B1394 " --> pdb=" O LEU B1403 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LEU B1403 " --> pdb=" O ILE B1394 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N HIS B1472 " --> pdb=" O TYR B1419 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N PHE B1421 " --> pdb=" O HIS B1472 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N PHE B1474 " --> pdb=" O PHE B1421 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL B1423 " --> pdb=" O PHE B1474 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N ASN B1476 " --> pdb=" O VAL B1423 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ASN B1471 " --> pdb=" O GLN B1510 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N GLU B1512 " --> pdb=" O ASN B1471 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE B1473 " --> pdb=" O GLU B1512 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LYS B1514 " --> pdb=" O ILE B1473 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU B1475 " --> pdb=" O LYS B1514 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N ASN B1516 " --> pdb=" O LEU B1475 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N PHE B1477 " --> pdb=" O ASN B1516 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU B1509 " --> pdb=" O ASN B1534 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B1511 " --> pdb=" O LEU B1532 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 1547 through 1548 Processing sheet with id=AG6, first strand: chain 'A' and resid 702 through 705 removed outlier: 3.685A pdb=" N VAL A 679 " --> pdb=" O TYR A 676 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLU A 746 " --> pdb=" O ILE A 675 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'A' and resid 716 through 717 removed outlier: 4.058A pdb=" N LEU A 716 " --> pdb=" O TYR A 723 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR A 723 " --> pdb=" O LEU A 716 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'A' and resid 1168 through 1171 removed outlier: 5.310A pdb=" N CYS A1176 " --> pdb=" O SER A1238 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER A1238 " --> pdb=" O CYS A1176 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N ILE A1288 " --> pdb=" O GLN A1231 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N MET A1233 " --> pdb=" O ILE A1288 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N ASN A1290 " --> pdb=" O MET A1233 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N GLY A1235 " --> pdb=" O ASN A1290 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ALA A1292 " --> pdb=" O GLY A1235 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL A1237 " --> pdb=" O ALA A1292 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N HIS A1287 " --> pdb=" O ARG A1326 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N THR A1328 " --> pdb=" O HIS A1287 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU A1289 " --> pdb=" O THR A1328 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU A1330 " --> pdb=" O LEU A1289 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL A1291 " --> pdb=" O LEU A1330 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'A' and resid 1390 through 1394 removed outlier: 4.264A pdb=" N LEU A1403 " --> pdb=" O ILE A1394 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN A1476 " --> pdb=" O ALA A1425 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ASN A1471 " --> pdb=" O GLN A1510 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N GLU A1512 " --> pdb=" O ASN A1471 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE A1473 " --> pdb=" O GLU A1512 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N LYS A1514 " --> pdb=" O ILE A1473 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU A1475 " --> pdb=" O LYS A1514 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N ASN A1516 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N PHE A1477 " --> pdb=" O ASN A1516 " (cutoff:3.500A) removed outlier: 10.707A pdb=" N ARG A1518 " --> pdb=" O PHE A1477 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'A' and resid 1390 through 1394 removed outlier: 4.264A pdb=" N LEU A1403 " --> pdb=" O ILE A1394 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN A1476 " --> pdb=" O ALA A1425 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ASN A1471 " --> pdb=" O GLN A1510 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N GLU A1512 " --> pdb=" O ASN A1471 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE A1473 " --> pdb=" O GLU A1512 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N LYS A1514 " --> pdb=" O ILE A1473 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU A1475 " --> pdb=" O LYS A1514 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N ASN A1516 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N PHE A1477 " --> pdb=" O ASN A1516 " (cutoff:3.500A) removed outlier: 10.707A pdb=" N ARG A1518 " --> pdb=" O PHE A1477 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU A1509 " --> pdb=" O ASN A1534 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'A' and resid 1547 through 1548 2854 hydrogen bonds defined for protein. 8157 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: 51.68 Time building geometry restraints manager: 67.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 51763 1.01 - 1.22: 108 1.22 - 1.42: 22274 1.42 - 1.62: 30316 1.62 - 1.83: 515 Bond restraints: 104976 Sorted by residual: bond pdb=" CA ILE D1601 " pdb=" CB ILE D1601 " ideal model delta sigma weight residual 1.539 1.486 0.053 5.40e-03 3.43e+04 9.62e+01 bond pdb=" CA PRO E1625 " pdb=" C PRO E1625 " ideal model delta sigma weight residual 1.514 1.464 0.051 5.50e-03 3.31e+04 8.53e+01 bond pdb=" CA PRO F1625 " pdb=" C PRO F1625 " ideal model delta sigma weight residual 1.514 1.475 0.040 5.50e-03 3.31e+04 5.16e+01 bond pdb=" CA PRO D1625 " pdb=" C PRO D1625 " ideal model delta sigma weight residual 1.514 1.481 0.033 5.50e-03 3.31e+04 3.56e+01 bond pdb=" CG1 ILE D1711 " pdb=" CD1 ILE D1711 " ideal model delta sigma weight residual 1.513 1.327 0.186 3.90e-02 6.57e+02 2.28e+01 ... (remaining 104971 not shown) Histogram of bond angle deviations from ideal: 58.90 - 75.41: 86 75.41 - 91.93: 85 91.93 - 108.44: 39868 108.44 - 124.96: 145181 124.96 - 141.48: 4402 Bond angle restraints: 189622 Sorted by residual: angle pdb=" C ALA D1393 " pdb=" N ILE D1394 " pdb=" H ILE D1394 " ideal model delta sigma weight residual 123.63 67.34 56.29 3.00e+00 1.11e-01 3.52e+02 angle pdb=" CA ALA D1460 " pdb=" N ALA D1460 " pdb=" H ALA D1460 " ideal model delta sigma weight residual 114.71 58.90 55.81 3.00e+00 1.11e-01 3.46e+02 angle pdb=" C PHE D1461 " pdb=" N ASN D1462 " pdb=" H ASN D1462 " ideal model delta sigma weight residual 124.93 69.25 55.68 3.00e+00 1.11e-01 3.45e+02 angle pdb=" C GLY D1500 " pdb=" N SER D1501 " pdb=" H SER D1501 " ideal model delta sigma weight residual 125.01 70.08 54.93 3.00e+00 1.11e-01 3.35e+02 angle pdb=" CA ASN D1462 " pdb=" N ASN D1462 " pdb=" H ASN D1462 " ideal model delta sigma weight residual 114.63 60.00 54.63 3.00e+00 1.11e-01 3.32e+02 ... (remaining 189617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 42886 17.87 - 35.74: 4769 35.74 - 53.61: 1124 53.61 - 71.47: 284 71.47 - 89.34: 27 Dihedral angle restraints: 49090 sinusoidal: 27032 harmonic: 22058 Sorted by residual: dihedral pdb=" CA LEU E1171 " pdb=" C LEU E1171 " pdb=" N LYS E1172 " pdb=" CA LYS E1172 " ideal model delta harmonic sigma weight residual -180.00 -99.59 -80.41 0 5.00e+00 4.00e-02 2.59e+02 dihedral pdb=" CA LEU D1171 " pdb=" C LEU D1171 " pdb=" N LYS D1172 " pdb=" CA LYS D1172 " ideal model delta harmonic sigma weight residual -180.00 -103.71 -76.29 0 5.00e+00 4.00e-02 2.33e+02 dihedral pdb=" CA LEU B1171 " pdb=" C LEU B1171 " pdb=" N LYS B1172 " pdb=" CA LYS B1172 " ideal model delta harmonic sigma weight residual -180.00 -104.06 -75.94 0 5.00e+00 4.00e-02 2.31e+02 ... (remaining 49087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.396: 8014 0.396 - 0.792: 30 0.792 - 1.188: 3 1.188 - 1.584: 4 1.584 - 1.980: 3 Chirality restraints: 8054 Sorted by residual: chirality pdb=" CG LEU D1079 " pdb=" CB LEU D1079 " pdb=" CD1 LEU D1079 " pdb=" CD2 LEU D1079 " both_signs ideal model delta sigma weight residual False -2.59 -0.61 -1.98 2.00e-01 2.50e+01 9.81e+01 chirality pdb=" CB ILE D1488 " pdb=" CA ILE D1488 " pdb=" CG1 ILE D1488 " pdb=" CG2 ILE D1488 " both_signs ideal model delta sigma weight residual False 2.64 0.92 1.72 2.00e-01 2.50e+01 7.43e+01 chirality pdb=" CG LEU D1373 " pdb=" CB LEU D1373 " pdb=" CD1 LEU D1373 " pdb=" CD2 LEU D1373 " both_signs ideal model delta sigma weight residual False -2.59 -0.88 -1.71 2.00e-01 2.50e+01 7.33e+01 ... (remaining 8051 not shown) Planarity restraints: 15372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B1510 " -0.127 2.00e-02 2.50e+03 4.19e-01 2.63e+03 pdb=" CD GLN B1510 " 0.003 2.00e-02 2.50e+03 pdb=" OE1 GLN B1510 " 0.122 2.00e-02 2.50e+03 pdb=" NE2 GLN B1510 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN B1510 " 0.715 2.00e-02 2.50e+03 pdb="HE22 GLN B1510 " -0.715 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN E2059 " -0.148 2.00e-02 2.50e+03 4.12e-01 2.55e+03 pdb=" CD GLN E2059 " 0.026 2.00e-02 2.50e+03 pdb=" OE1 GLN E2059 " 0.138 2.00e-02 2.50e+03 pdb=" NE2 GLN E2059 " 0.005 2.00e-02 2.50e+03 pdb="HE21 GLN E2059 " 0.689 2.00e-02 2.50e+03 pdb="HE22 GLN E2059 " -0.710 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D2059 " 0.153 2.00e-02 2.50e+03 4.10e-01 2.52e+03 pdb=" CD GLN D2059 " -0.021 2.00e-02 2.50e+03 pdb=" OE1 GLN D2059 " -0.148 2.00e-02 2.50e+03 pdb=" NE2 GLN D2059 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN D2059 " -0.684 2.00e-02 2.50e+03 pdb="HE22 GLN D2059 " 0.702 2.00e-02 2.50e+03 ... (remaining 15369 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.10: 2914 2.10 - 2.73: 187349 2.73 - 3.35: 305161 3.35 - 3.98: 377240 3.98 - 4.60: 582091 Nonbonded interactions: 1454755 Sorted by model distance: nonbonded pdb=" H ILE D1394 " pdb=" HA ILE D1394 " model vdw 1.478 1.816 nonbonded pdb=" H ASN D1649 " pdb=" HA ASN D1649 " model vdw 1.486 1.816 nonbonded pdb=" H LYS D1546 " pdb=" HA LYS D1546 " model vdw 1.518 1.816 nonbonded pdb=" O PHE E1925 " pdb=" HE1 TRP E2208 " model vdw 1.536 1.850 nonbonded pdb=" H GLY D2090 " pdb=" O SER D2116 " model vdw 1.568 1.850 ... (remaining 1454750 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'D' selection = chain 'E' } Set up NCS constraints Number of NCS constrained groups: 3 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'D' selection = chain 'E' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.440 Construct map_model_manager: 1.080 Extract box with map and model: 14.230 Check model and map are aligned: 1.130 Set scattering table: 0.690 Process input model: 265.460 Find NCS groups from input model: 2.980 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.030 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 293.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 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 : 0.013 0.186 53124 Z= 0.880 Angle : 1.942 25.175 71882 Z= 1.111 Chirality : 0.112 1.980 8054 Planarity : 0.012 0.094 9240 Dihedral : 13.541 89.342 19918 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.72 % Allowed : 8.30 % Favored : 90.97 % Rotamer: Outliers : 2.29 % Allowed : 10.65 % Favored : 87.06 % Cbeta Deviations : 0.75 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 1.46 % Twisted General : 0.70 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.09), residues: 6358 helix: -1.93 (0.08), residues: 2802 sheet: -0.98 (0.15), residues: 1070 loop : -2.43 (0.11), residues: 2486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.127 0.008 TRP F2093 HIS 0.038 0.005 HIS D 638 PHE 0.096 0.007 PHE D1389 TYR 0.111 0.008 TYR E1370 ARG 0.087 0.006 ARG B 976 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12716 Ramachandran restraints generated. 6358 Oldfield, 0 Emsley, 6358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12716 Ramachandran restraints generated. 6358 Oldfield, 0 Emsley, 6358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 2213 is missing expected H atoms. Skipping. Residue THR 2213 is missing expected H atoms. Skipping. Residue THR 2213 is missing expected H atoms. Skipping. Residue THR 2213 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 107 time to evaluate : 0.752 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 986 VAL cc_start: 0.6034 (OUTLIER) cc_final: 0.5676 (m) REVERT: A 995 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8478 (tt) REVERT: A 1042 THR cc_start: 0.8105 (m) cc_final: 0.7775 (p) REVERT: A 1083 GLN cc_start: 0.8336 (pt0) cc_final: 0.7864 (mt0) REVERT: A 1233 MET cc_start: 0.6464 (ptp) cc_final: 0.6196 (ptp) REVERT: A 1307 MET cc_start: 0.6160 (tmt) cc_final: 0.5945 (tmm) REVERT: A 1436 GLU cc_start: 0.7253 (pm20) cc_final: 0.6696 (pp20) REVERT: A 1538 TYR cc_start: 0.3846 (m-80) cc_final: 0.3439 (t80) outliers start: 21 outliers final: 2 residues processed: 128 average time/residue: 0.3641 time to fit residues: 59.4758 Evaluate side-chains 80 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 0.729 Evaluate side-chains 158 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 141 time to evaluate : 0.886 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1497 MET cc_start: 0.8718 (ppp) cc_final: 0.8441 (ppp) REVERT: C 1833 ARG cc_start: 0.7569 (tpt170) cc_final: 0.6799 (ttt180) REVERT: C 1941 ARG cc_start: 0.7731 (ptm160) cc_final: 0.7490 (ptm160) REVERT: C 2033 PHE cc_start: 0.8507 (m-10) cc_final: 0.8186 (m-10) REVERT: C 2195 ARG cc_start: 0.4481 (ttt180) cc_final: 0.3945 (mmt180) REVERT: C 2291 ASN cc_start: 0.8655 (m-40) cc_final: 0.8164 (m-40) outliers start: 17 outliers final: 7 residues processed: 156 average time/residue: 0.4476 time to fit residues: 88.6724 Evaluate side-chains 97 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 0.882 Evaluate side-chains 280 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 249 time to evaluate : 1.423 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 873 PHE cc_start: 0.7237 (m-10) cc_final: 0.6799 (t80) REVERT: D 963 MET cc_start: 0.6794 (ttt) cc_final: 0.6432 (ptt) REVERT: D 1021 MET cc_start: 0.9126 (mpp) cc_final: 0.8756 (mtt) REVERT: D 1022 ASN cc_start: 0.9390 (t160) cc_final: 0.9097 (m-40) REVERT: D 1300 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8342 (mp0) REVERT: D 1540 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7816 (pp) outliers start: 31 outliers final: 9 residues processed: 277 average time/residue: 0.4765 time to fit residues: 184.6773 Evaluate side-chains 169 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 159 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 542 optimal weight: 0.9990 chunk 486 optimal weight: 0.8980 chunk 270 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 328 optimal weight: 8.9990 chunk 259 optimal weight: 3.9990 chunk 503 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 305 optimal weight: 10.0000 chunk 374 optimal weight: 2.9990 chunk 583 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 940 GLN ** A 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1181 GLN A1314 GLN ** A1333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1465 ASN F1565 GLN ** F1607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2234 ASN Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 859 ASN ** E 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 940 GLN E 964 ASN E1000 GLN ** E1026 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1099 GLN ** E1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1119 ASN E1181 GLN ** E1315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1384 ASN E1443 GLN ** E1444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1465 ASN E1584 GLN ** E1589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1655 ASN ** E1796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1969 GLN ** E2045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.5244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 53124 Z= 0.351 Angle : 0.988 16.701 71882 Z= 0.541 Chirality : 0.098 1.893 8054 Planarity : 0.007 0.129 9240 Dihedral : 7.363 68.320 7076 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 23.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.79 % Favored : 94.09 % Rotamer: Outliers : 0.24 % Allowed : 3.02 % Favored : 96.73 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 1.46 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.09), residues: 6358 helix: -1.13 (0.09), residues: 2904 sheet: -0.85 (0.15), residues: 1056 loop : -2.16 (0.11), residues: 2398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP D1662 HIS 0.020 0.002 HIS D1735 PHE 0.043 0.003 PHE A1029 TYR 0.034 0.002 TYR E1441 ARG 0.018 0.001 ARG C2139 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 2213 is missing expected H atoms. Skipping. Residue THR 2213 is missing expected H atoms. Skipping. Residue THR 2213 is missing expected H atoms. Skipping. Residue THR 2213 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 0.737 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: 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: symmetry clash revert: symmetry clash REVERT: A 628 THR cc_start: 0.7885 (p) cc_final: 0.7657 (p) REVERT: A 1083 GLN cc_start: 0.8442 (pt0) cc_final: 0.7899 (mt0) REVERT: A 1436 GLU cc_start: 0.7084 (pm20) cc_final: 0.6579 (pp20) REVERT: A 1538 TYR cc_start: 0.3855 (m-80) cc_final: 0.3546 (t80) outliers start: 1 outliers final: 1 residues processed: 91 average time/residue: 0.2964 time to fit residues: 36.3585 Evaluate side-chains 74 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 0.723 Evaluate side-chains 123 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 121 time to evaluate : 0.885 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1833 ARG cc_start: 0.7297 (tpt170) cc_final: 0.6561 (ttt180) REVERT: F 2033 PHE cc_start: 0.8590 (m-10) cc_final: 0.8147 (m-10) REVERT: F 2053 MET cc_start: 0.7664 (tmm) cc_final: 0.7105 (tmm) REVERT: F 2195 ARG cc_start: 0.4362 (ttt180) cc_final: 0.3865 (mmt180) outliers start: 2 outliers final: 0 residues processed: 123 average time/residue: 0.5133 time to fit residues: 78.3694 Evaluate side-chains 98 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.888 Evaluate side-chains 214 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 210 time to evaluate : 1.418 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 873 PHE cc_start: 0.7188 (m-10) cc_final: 0.6836 (t80) REVERT: E 1021 MET cc_start: 0.8874 (mpp) cc_final: 0.8666 (mtt) REVERT: E 1022 ASN cc_start: 0.9296 (t0) cc_final: 0.9076 (m-40) REVERT: E 1386 MET cc_start: 0.5406 (mpp) cc_final: 0.4762 (mpp) REVERT: E 1398 ASN cc_start: 0.6991 (m110) cc_final: 0.6627 (t0) REVERT: E 2041 MET cc_start: 0.7533 (mmt) cc_final: 0.7139 (mmt) REVERT: E 2053 MET cc_start: 0.1754 (ppp) cc_final: 0.0878 (ptt) REVERT: E 2219 LEU cc_start: 0.9035 (tp) cc_final: 0.8818 (tt) outliers start: 4 outliers final: 2 residues processed: 214 average time/residue: 0.4619 time to fit residues: 141.6095 Evaluate side-chains 164 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 162 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 798, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.7056 > 50: distance: 0 - 1: 3.192 distance: 0 - 9: 3.126 distance: 1 - 4: 3.516 distance: 1 - 10: 3.278 distance: 2 - 3: 16.300 distance: 2 - 15: 5.145 distance: 3 - 54: 17.202 distance: 4 - 11: 3.887 distance: 5 - 6: 4.208 distance: 5 - 13: 3.487 distance: 5 - 14: 3.327 distance: 15 - 16: 3.977 distance: 15 - 20: 15.847 distance: 16 - 17: 8.663 distance: 16 - 19: 6.365 distance: 16 - 21: 8.239 distance: 17 - 18: 3.932 distance: 17 - 25: 5.543 distance: 18 - 69: 5.485 distance: 19 - 22: 3.912 distance: 19 - 23: 8.017 distance: 19 - 24: 8.408 distance: 25 - 26: 4.398 distance: 25 - 33: 19.034 distance: 26 - 27: 4.576 distance: 26 - 29: 6.790 distance: 26 - 34: 5.594 distance: 27 - 28: 5.824 distance: 27 - 42: 4.832 distance: 28 - 88: 10.643 distance: 29 - 30: 4.213 distance: 29 - 35: 3.364 distance: 29 - 36: 5.188 distance: 30 - 31: 4.225 distance: 30 - 37: 3.056 distance: 42 - 50: 6.459 distance: 43 - 46: 4.454 distance: 43 - 51: 5.533 distance: 44 - 54: 3.424 distance: 45 - 103: 13.718 distance: 54 - 55: 5.342 distance: 54 - 63: 3.027 distance: 55 - 56: 5.557 distance: 55 - 58: 10.925 distance: 55 - 64: 21.607 distance: 56 - 57: 11.518 distance: 56 - 69: 4.605 distance: 57 - 119: 19.081 distance: 58 - 59: 13.655 distance: 58 - 65: 23.020 distance: 58 - 66: 22.669 distance: 59 - 60: 12.049 distance: 59 - 67: 11.939 distance: 59 - 68: 14.696 distance: 60 - 62: 8.110 distance: 69 - 77: 3.654 distance: 70 - 71: 5.586 distance: 70 - 73: 3.915 distance: 70 - 78: 8.266 distance: 71 - 72: 10.273 distance: 71 - 88: 9.025 distance: 72 - 129: 8.223 distance: 73 - 79: 8.876 distance: 73 - 80: 10.250 distance: 74 - 75: 5.252 distance: 74 - 76: 5.667 distance: 74 - 81: 4.778 distance: 75 - 82: 5.014 distance: 75 - 83: 3.578 distance: 76 - 85: 7.794 distance: 76 - 86: 4.718 distance: 76 - 87: 17.898 distance: 88 - 89: 10.072 distance: 88 - 97: 21.487 distance: 89 - 90: 15.824 distance: 89 - 92: 7.545 distance: 89 - 98: 7.832 distance: 90 - 91: 14.060 distance: 90 - 103: 8.993 distance: 92 - 93: 5.737 distance: 92 - 99: 7.445 distance: 92 - 100: 6.158 distance: 93 - 94: 4.660 distance: 93 - 101: 6.213 distance: 93 - 102: 6.715 distance: 94 - 95: 3.489 distance: 103 - 104: 10.310 distance: 103 - 110: 32.495 distance: 104 - 105: 23.178 distance: 104 - 107: 21.232 distance: 104 - 111: 27.396 distance: 105 - 106: 24.911 distance: 105 - 119: 19.285 distance: 107 - 108: 6.649 distance: 107 - 109: 10.896 distance: 108 - 113: 4.365 distance: 108 - 114: 4.091 distance: 119 - 120: 13.233 distance: 119 - 124: 4.535 distance: 120 - 121: 9.946 distance: 120 - 123: 8.152 distance: 120 - 125: 12.740 distance: 121 - 122: 4.720 distance: 121 - 129: 6.746 distance: 123 - 126: 4.368 distance: 123 - 127: 34.849 distance: 123 - 128: 28.220 distance: 129 - 130: 3.446 distance: 129 - 140: 3.104 distance: 130 - 131: 7.597 distance: 130 - 133: 3.520 distance: 130 - 141: 5.980 distance: 133 - 134: 3.083 distance: 133 - 143: 3.138