Starting phenix.real_space_refine on Fri Aug 9 06:45:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zwo_11492/08_2024/6zwo_11492_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zwo_11492/08_2024/6zwo_11492.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zwo_11492/08_2024/6zwo_11492.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zwo_11492/08_2024/6zwo_11492.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zwo_11492/08_2024/6zwo_11492_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zwo_11492/08_2024/6zwo_11492_neut.cif" } resolution = 3.0 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= -0.002 sd= 0.102 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 12 5.49 5 S 159 5.16 5 C 15858 2.51 5 N 4396 2.21 5 O 4568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 804": "OE1" <-> "OE2" Residue "B GLU 812": "OE1" <-> "OE2" Residue "B GLU 819": "OE1" <-> "OE2" Residue "B ASP 826": "OD1" <-> "OD2" Residue "B GLU 866": "OE1" <-> "OE2" Residue "B ASP 928": "OD1" <-> "OD2" Residue "B TYR 929": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 933": "OE1" <-> "OE2" Residue "B ASP 944": "OD1" <-> "OD2" Residue "B GLU 945": "OE1" <-> "OE2" Residue "B PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1005": "OD1" <-> "OD2" Residue "B ASP 1032": "OD1" <-> "OD2" Residue "B ARG 1039": "NH1" <-> "NH2" Residue "B GLU 1066": "OE1" <-> "OE2" Residue "B ARG 1141": "NH1" <-> "NH2" Residue "B ASP 1147": "OD1" <-> "OD2" Residue "B ASP 1175": "OD1" <-> "OD2" Residue "B ARG 1215": "NH1" <-> "NH2" Residue "B GLU 1226": "OE1" <-> "OE2" Residue "B TYR 1232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1238": "NH1" <-> "NH2" Residue "B ASP 1279": "OD1" <-> "OD2" Residue "B GLU 1282": "OE1" <-> "OE2" Residue "B GLU 1328": "OE1" <-> "OE2" Residue "B ASP 1349": "OD1" <-> "OD2" Residue "B GLU 1352": "OE1" <-> "OE2" Residue "B GLU 1401": "OE1" <-> "OE2" Residue "B PHE 1404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1442": "OE1" <-> "OE2" Residue "B GLU 1457": "OE1" <-> "OE2" Residue "B ASP 1464": "OD1" <-> "OD2" Residue "B ASP 1473": "OD1" <-> "OD2" Residue "B ASP 1506": "OD1" <-> "OD2" Residue "B GLU 1507": "OE1" <-> "OE2" Residue "B GLU 1531": "OE1" <-> "OE2" Residue "B ASP 1539": "OD1" <-> "OD2" Residue "B PHE 1545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1555": "OD1" <-> "OD2" Residue "B ASP 1569": "OD1" <-> "OD2" Residue "B GLU 1610": "OE1" <-> "OE2" Residue "B GLU 1613": "OE1" <-> "OE2" Residue "B ARG 1683": "NH1" <-> "NH2" Residue "B TYR 1700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1712": "OD1" <-> "OD2" Residue "B GLU 1742": "OE1" <-> "OE2" Residue "B GLU 1799": "OE1" <-> "OE2" Residue "B ARG 1905": "NH1" <-> "NH2" Residue "B GLU 1925": "OE1" <-> "OE2" Residue "B ARG 1955": "NH1" <-> "NH2" Residue "B GLU 2014": "OE1" <-> "OE2" Residue "B GLU 2049": "OE1" <-> "OE2" Residue "B GLU 2052": "OE1" <-> "OE2" Residue "B TYR 2074": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2080": "OE1" <-> "OE2" Residue "B ARG 2086": "NH1" <-> "NH2" Residue "B ASP 2102": "OD1" <-> "OD2" Residue "B GLU 2122": "OE1" <-> "OE2" Residue "B ARG 2134": "NH1" <-> "NH2" Residue "B GLU 2181": "OE1" <-> "OE2" Residue "B PHE 2182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2190": "OE1" <-> "OE2" Residue "B ASP 2195": "OD1" <-> "OD2" Residue "B ASP 2252": "OD1" <-> "OD2" Residue "B ASP 2274": "OD1" <-> "OD2" Residue "B GLU 2311": "OE1" <-> "OE2" Residue "B ASP 2360": "OD1" <-> "OD2" Residue "B ASP 2433": "OD1" <-> "OD2" Residue "B ASP 2516": "OD1" <-> "OD2" Residue "B GLU 2526": "OE1" <-> "OE2" Residue "D PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 42": "OD1" <-> "OD2" Residue "D TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 95": "OE1" <-> "OE2" Residue "D ARG 98": "NH1" <-> "NH2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 142": "OE1" <-> "OE2" Residue "D ASP 147": "OD1" <-> "OD2" Residue "D ASP 179": "OD1" <-> "OD2" Residue "D GLU 206": "OE1" <-> "OE2" Residue "D TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 231": "OD1" <-> "OD2" Residue "D GLU 307": "OE1" <-> "OE2" Residue "D TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 322": "OD1" <-> "OD2" Residue "F ARG 39": "NH1" <-> "NH2" Residue "F GLU 40": "OE1" <-> "OE2" Residue "F ARG 47": "NH1" <-> "NH2" Residue "F ARG 55": "NH1" <-> "NH2" Residue "F GLU 75": "OE1" <-> "OE2" Residue "F ARG 89": "NH1" <-> "NH2" Residue "F ARG 105": "NH1" <-> "NH2" Residue "F ARG 205": "NH1" <-> "NH2" Residue "F ASP 247": "OD1" <-> "OD2" Residue "F GLU 275": "OE1" <-> "OE2" Residue "F ASP 276": "OD1" <-> "OD2" Residue "F GLU 278": "OE1" <-> "OE2" Residue "F ASP 333": "OD1" <-> "OD2" Residue "F GLU 345": "OE1" <-> "OE2" Residue "F ASP 354": "OD1" <-> "OD2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 406": "OE1" <-> "OE2" Residue "F GLU 410": "OE1" <-> "OE2" Residue "F PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 481": "OE1" <-> "OE2" Residue "F ASP 495": "OD1" <-> "OD2" Residue "F ASP 523": "OD1" <-> "OD2" Residue "F GLU 525": "OE1" <-> "OE2" Residue "F ASP 534": "OD1" <-> "OD2" Residue "F GLU 542": "OE1" <-> "OE2" Residue "F ARG 563": "NH1" <-> "NH2" Residue "F GLU 568": "OE1" <-> "OE2" Residue "F ARG 576": "NH1" <-> "NH2" Residue "F ASP 592": "OD1" <-> "OD2" Residue "F ASP 594": "OD1" <-> "OD2" Residue "F GLU 610": "OE1" <-> "OE2" Residue "F GLU 616": "OE1" <-> "OE2" Residue "F GLU 624": "OE1" <-> "OE2" Residue "F ASP 625": "OD1" <-> "OD2" Residue "F ASP 695": "OD1" <-> "OD2" Residue "F ARG 709": "NH1" <-> "NH2" Residue "F ASP 710": "OD1" <-> "OD2" Residue "F ARG 737": "NH1" <-> "NH2" Residue "F GLU 745": "OE1" <-> "OE2" Residue "F GLU 769": "OE1" <-> "OE2" Residue "F ASP 772": "OD1" <-> "OD2" Residue "F GLU 779": "OE1" <-> "OE2" Residue "F PHE 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 820": "OE1" <-> "OE2" Residue "F ARG 821": "NH1" <-> "NH2" Residue "F ASP 841": "OD1" <-> "OD2" Residue "F GLU 897": "OE1" <-> "OE2" Residue "F ASP 951": "OD1" <-> "OD2" Residue "F ASP 1441": "OD1" <-> "OD2" Residue "F GLU 1491": "OE1" <-> "OE2" Residue "F GLU 1514": "OE1" <-> "OE2" Residue "F TYR 1522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1527": "OE1" <-> "OE2" Residue "F GLU 1641": "OE1" <-> "OE2" Residue "F PHE 1665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 1666": "NH1" <-> "NH2" Residue "F GLU 1687": "OE1" <-> "OE2" Residue "F GLU 1688": "OE1" <-> "OE2" Residue "H ASP 35": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 24994 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 12841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1592, 12841 Classifications: {'peptide': 1592} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 64, 'TRANS': 1527} Chain breaks: 4 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "D" Number of atoms: 2465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2465 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 305} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 8931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1117, 8931 Classifications: {'peptide': 1117} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 37, 'TRANS': 1079} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "H" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 655 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'AGS': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 23377 SG CYS F1520 123.208 91.400 26.960 1.00 61.03 S ATOM 23403 SG CYS F1523 123.708 91.698 23.353 1.00 65.32 S ATOM 23877 SG CYS F1651 123.596 88.159 24.988 1.00 48.61 S Time building chain proxies: 14.04, per 1000 atoms: 0.56 Number of scatterers: 24994 At special positions: 0 Unit cell: (165.312, 163.968, 149.184, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 159 16.00 P 12 15.00 O 4568 8.00 N 4396 7.00 C 15858 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.12 Conformation dependent library (CDL) restraints added in 4.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN F4801 " pdb="ZN ZN F4801 " - pdb=" NE2 HIS F1515 " pdb="ZN ZN F4801 " - pdb=" SG CYS F1520 " pdb="ZN ZN F4801 " - pdb=" SG CYS F1523 " pdb="ZN ZN F4801 " - pdb=" SG CYS F1651 " Number of angles added : 3 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5968 Finding SS restraints... Secondary structure from input PDB file: 169 helices and 11 sheets defined 65.6% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'B' and resid 792 through 809 Processing helix chain 'B' and resid 816 through 829 removed outlier: 3.605A pdb=" N ASP B 826 " --> pdb=" O ILE B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 847 removed outlier: 4.086A pdb=" N ALA B 840 " --> pdb=" O LYS B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 861 removed outlier: 3.990A pdb=" N ARG B 859 " --> pdb=" O VAL B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 871 removed outlier: 3.846A pdb=" N PHE B 871 " --> pdb=" O VAL B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 877 through 892 Processing helix chain 'B' and resid 895 through 902 Processing helix chain 'B' and resid 929 through 936 removed outlier: 3.541A pdb=" N VAL B 936 " --> pdb=" O SER B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 960 removed outlier: 3.519A pdb=" N ILE B 958 " --> pdb=" O ALA B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 983 removed outlier: 3.781A pdb=" N GLY B 983 " --> pdb=" O PHE B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1004 Proline residue: B 995 - end of helix Processing helix chain 'B' and resid 1005 through 1007 No H-bonds generated for 'chain 'B' and resid 1005 through 1007' Processing helix chain 'B' and resid 1008 through 1023 removed outlier: 3.871A pdb=" N GLN B1014 " --> pdb=" O GLU B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1027 through 1029 No H-bonds generated for 'chain 'B' and resid 1027 through 1029' Processing helix chain 'B' and resid 1030 through 1039 removed outlier: 3.698A pdb=" N ILE B1034 " --> pdb=" O TYR B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1048 through 1064 removed outlier: 3.753A pdb=" N LEU B1054 " --> pdb=" O SER B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1070 Processing helix chain 'B' and resid 1071 through 1073 No H-bonds generated for 'chain 'B' and resid 1071 through 1073' Processing helix chain 'B' and resid 1074 through 1084 removed outlier: 3.595A pdb=" N MET B1078 " --> pdb=" O LEU B1074 " (cutoff:3.500A) Processing helix chain 'B' and resid 1090 through 1101 Processing helix chain 'B' and resid 1115 through 1123 removed outlier: 3.557A pdb=" N LEU B1121 " --> pdb=" O PRO B1117 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE B1122 " --> pdb=" O ILE B1118 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP B1123 " --> pdb=" O VAL B1119 " (cutoff:3.500A) Processing helix chain 'B' and resid 1128 through 1142 Processing helix chain 'B' and resid 1149 through 1151 No H-bonds generated for 'chain 'B' and resid 1149 through 1151' Processing helix chain 'B' and resid 1152 through 1165 removed outlier: 4.080A pdb=" N HIS B1157 " --> pdb=" O SER B1153 " (cutoff:3.500A) Proline residue: B1158 - end of helix removed outlier: 3.861A pdb=" N ASP B1164 " --> pdb=" O VAL B1160 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN B1165 " --> pdb=" O ARG B1161 " (cutoff:3.500A) Processing helix chain 'B' and resid 1169 through 1182 Processing helix chain 'B' and resid 1185 through 1189 removed outlier: 3.683A pdb=" N TYR B1188 " --> pdb=" O GLY B1185 " (cutoff:3.500A) Processing helix chain 'B' and resid 1191 through 1202 removed outlier: 3.942A pdb=" N LYS B1197 " --> pdb=" O PRO B1193 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL B1198 " --> pdb=" O MET B1194 " (cutoff:3.500A) Processing helix chain 'B' and resid 1206 through 1218 Processing helix chain 'B' and resid 1228 through 1238 Processing helix chain 'B' and resid 1265 through 1270 Processing helix chain 'B' and resid 1276 through 1294 removed outlier: 3.802A pdb=" N ASP B1294 " --> pdb=" O GLU B1290 " (cutoff:3.500A) Processing helix chain 'B' and resid 1297 through 1308 removed outlier: 4.164A pdb=" N ALA B1305 " --> pdb=" O ARG B1301 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU B1306 " --> pdb=" O SER B1302 " (cutoff:3.500A) Processing helix chain 'B' and resid 1310 through 1317 removed outlier: 3.698A pdb=" N ALA B1314 " --> pdb=" O TYR B1310 " (cutoff:3.500A) Processing helix chain 'B' and resid 1317 through 1327 Processing helix chain 'B' and resid 1330 through 1348 removed outlier: 4.051A pdb=" N GLN B1348 " --> pdb=" O ALA B1344 " (cutoff:3.500A) Processing helix chain 'B' and resid 1350 through 1366 removed outlier: 3.915A pdb=" N THR B1354 " --> pdb=" O ILE B1350 " (cutoff:3.500A) Processing helix chain 'B' and resid 1376 through 1378 No H-bonds generated for 'chain 'B' and resid 1376 through 1378' Processing helix chain 'B' and resid 1379 through 1389 removed outlier: 3.708A pdb=" N LYS B1389 " --> pdb=" O GLU B1385 " (cutoff:3.500A) Processing helix chain 'B' and resid 1392 through 1407 removed outlier: 3.875A pdb=" N LYS B1406 " --> pdb=" O LEU B1402 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY B1407 " --> pdb=" O GLU B1403 " (cutoff:3.500A) Processing helix chain 'B' and resid 1409 through 1423 removed outlier: 3.567A pdb=" N LYS B1422 " --> pdb=" O SER B1418 " (cutoff:3.500A) Processing helix chain 'B' and resid 1425 through 1440 removed outlier: 3.534A pdb=" N ALA B1429 " --> pdb=" O GLN B1425 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE B1440 " --> pdb=" O ALA B1436 " (cutoff:3.500A) Processing helix chain 'B' and resid 1446 through 1453 removed outlier: 3.785A pdb=" N TYR B1450 " --> pdb=" O GLN B1446 " (cutoff:3.500A) Processing helix chain 'B' and resid 1455 through 1468 Processing helix chain 'B' and resid 1476 through 1488 removed outlier: 3.887A pdb=" N ARG B1480 " --> pdb=" O LEU B1476 " (cutoff:3.500A) Processing helix chain 'B' and resid 1489 through 1499 removed outlier: 3.541A pdb=" N LEU B1493 " --> pdb=" O GLU B1489 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU B1499 " --> pdb=" O GLN B1495 " (cutoff:3.500A) Processing helix chain 'B' and resid 1505 through 1524 removed outlier: 4.006A pdb=" N GLN B1509 " --> pdb=" O ASN B1505 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B1510 " --> pdb=" O ASP B1506 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LYS B1511 " --> pdb=" O GLU B1507 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ARG B1514 " --> pdb=" O ALA B1510 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N MET B1515 " --> pdb=" O LYS B1511 " (cutoff:3.500A) Processing helix chain 'B' and resid 1525 through 1534 removed outlier: 3.759A pdb=" N GLU B1531 " --> pdb=" O ASP B1527 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS B1534 " --> pdb=" O GLU B1530 " (cutoff:3.500A) Processing helix chain 'B' and resid 1540 through 1554 removed outlier: 3.535A pdb=" N GLN B1554 " --> pdb=" O LEU B1550 " (cutoff:3.500A) Processing helix chain 'B' and resid 1558 through 1579 removed outlier: 3.685A pdb=" N ASP B1569 " --> pdb=" O ASP B1565 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU B1574 " --> pdb=" O LEU B1570 " (cutoff:3.500A) Processing helix chain 'B' and resid 1582 through 1598 removed outlier: 5.041A pdb=" N GLY B1588 " --> pdb=" O SER B1584 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ALA B1589 " --> pdb=" O ARG B1585 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER B1592 " --> pdb=" O GLY B1588 " (cutoff:3.500A) Processing helix chain 'B' and resid 1598 through 1608 Processing helix chain 'B' and resid 1611 through 1624 removed outlier: 3.730A pdb=" N TRP B1620 " --> pdb=" O ARG B1616 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN B1624 " --> pdb=" O TRP B1620 " (cutoff:3.500A) Processing helix chain 'B' and resid 1629 through 1641 removed outlier: 3.871A pdb=" N LYS B1635 " --> pdb=" O GLU B1631 " (cutoff:3.500A) Processing helix chain 'B' and resid 1650 through 1663 removed outlier: 4.008A pdb=" N LYS B1655 " --> pdb=" O ARG B1651 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR B1656 " --> pdb=" O THR B1652 " (cutoff:3.500A) Processing helix chain 'B' and resid 1665 through 1678 Processing helix chain 'B' and resid 1693 through 1708 removed outlier: 3.590A pdb=" N ALA B1708 " --> pdb=" O MET B1704 " (cutoff:3.500A) Processing helix chain 'B' and resid 1711 through 1729 removed outlier: 3.508A pdb=" N GLN B1715 " --> pdb=" O ILE B1711 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN B1727 " --> pdb=" O THR B1723 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA B1728 " --> pdb=" O MET B1724 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLN B1729 " --> pdb=" O GLN B1725 " (cutoff:3.500A) Processing helix chain 'B' and resid 1739 through 1763 Processing helix chain 'B' and resid 1768 through 1784 Processing helix chain 'B' and resid 1786 through 1809 removed outlier: 3.535A pdb=" N TRP B1790 " --> pdb=" O TRP B1786 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN B1808 " --> pdb=" O TYR B1804 " (cutoff:3.500A) Processing helix chain 'B' and resid 1875 through 1896 Proline residue: B1883 - end of helix removed outlier: 3.856A pdb=" N SER B1893 " --> pdb=" O PHE B1889 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU B1894 " --> pdb=" O ARG B1890 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER B1895 " --> pdb=" O SER B1891 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG B1896 " --> pdb=" O ILE B1892 " (cutoff:3.500A) Processing helix chain 'B' and resid 1899 through 1914 Processing helix chain 'B' and resid 1916 through 1930 removed outlier: 3.955A pdb=" N GLU B1921 " --> pdb=" O PRO B1917 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA B1922 " --> pdb=" O ASP B1918 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS B1928 " --> pdb=" O VAL B1924 " (cutoff:3.500A) Processing helix chain 'B' and resid 1932 through 1937 removed outlier: 3.732A pdb=" N TRP B1935 " --> pdb=" O ILE B1932 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLN B1937 " --> pdb=" O THR B1934 " (cutoff:3.500A) Processing helix chain 'B' and resid 1938 through 1944 Processing helix chain 'B' and resid 1950 through 1968 Processing helix chain 'B' and resid 1972 through 1981 removed outlier: 3.660A pdb=" N LYS B1981 " --> pdb=" O THR B1977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1984 through 1999 Processing helix chain 'B' and resid 2003 through 2021 removed outlier: 3.851A pdb=" N ARG B2018 " --> pdb=" O GLU B2014 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL B2019 " --> pdb=" O GLU B2015 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B2020 " --> pdb=" O LEU B2016 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE B2021 " --> pdb=" O ILE B2017 " (cutoff:3.500A) Processing helix chain 'B' and resid 2022 through 2042 removed outlier: 3.616A pdb=" N ARG B2036 " --> pdb=" O GLU B2032 " (cutoff:3.500A) Processing helix chain 'B' and resid 2043 through 2059 removed outlier: 4.072A pdb=" N GLU B2049 " --> pdb=" O LYS B2045 " (cutoff:3.500A) Proline residue: B2053 - end of helix Processing helix chain 'B' and resid 2064 through 2075 Processing helix chain 'B' and resid 2076 through 2091 removed outlier: 3.589A pdb=" N GLN B2082 " --> pdb=" O LEU B2078 " (cutoff:3.500A) Processing helix chain 'B' and resid 2093 through 2113 removed outlier: 3.710A pdb=" N LEU B2097 " --> pdb=" O ASN B2093 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLN B2099 " --> pdb=" O LYS B2095 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA B2100 " --> pdb=" O ASP B2096 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS B2113 " --> pdb=" O ARG B2109 " (cutoff:3.500A) Processing helix chain 'B' and resid 2123 through 2127 Processing helix chain 'B' and resid 2192 through 2211 removed outlier: 3.650A pdb=" N GLU B2196 " --> pdb=" O LEU B2192 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG B2197 " --> pdb=" O ARG B2193 " (cutoff:3.500A) Processing helix chain 'B' and resid 2212 through 2217 Processing helix chain 'B' and resid 2246 through 2257 removed outlier: 4.327A pdb=" N ASP B2252 " --> pdb=" O ALA B2248 " (cutoff:3.500A) Processing helix chain 'B' and resid 2262 through 2272 Processing helix chain 'B' and resid 2274 through 2278 removed outlier: 3.535A pdb=" N HIS B2277 " --> pdb=" O ASP B2274 " (cutoff:3.500A) Processing helix chain 'B' and resid 2279 through 2293 Processing helix chain 'B' and resid 2297 through 2306 removed outlier: 3.520A pdb=" N LYS B2306 " --> pdb=" O LEU B2302 " (cutoff:3.500A) Processing helix chain 'B' and resid 2309 through 2335 removed outlier: 3.534A pdb=" N TRP B2313 " --> pdb=" O SER B2309 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL B2326 " --> pdb=" O ARG B2322 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET B2327 " --> pdb=" O SER B2323 " (cutoff:3.500A) Processing helix chain 'B' and resid 2380 through 2385 Processing helix chain 'B' and resid 2394 through 2410 Processing helix chain 'B' and resid 2410 through 2423 removed outlier: 3.714A pdb=" N VAL B2414 " --> pdb=" O HIS B2410 " (cutoff:3.500A) Processing helix chain 'B' and resid 2429 through 2433 removed outlier: 3.686A pdb=" N MET B2432 " --> pdb=" O TRP B2429 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP B2433 " --> pdb=" O ARG B2430 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2429 through 2433' Processing helix chain 'B' and resid 2493 through 2508 removed outlier: 4.515A pdb=" N ALA B2497 " --> pdb=" O LEU B2493 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE B2498 " --> pdb=" O ASN B2494 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG B2503 " --> pdb=" O GLN B2499 " (cutoff:3.500A) Processing helix chain 'B' and resid 2520 through 2533 Processing helix chain 'B' and resid 2534 through 2539 Processing helix chain 'B' and resid 2540 through 2541 No H-bonds generated for 'chain 'B' and resid 2540 through 2541' Processing helix chain 'B' and resid 2542 through 2546 Processing helix chain 'F' and resid 32 through 46 Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' Processing helix chain 'F' and resid 52 through 70 Processing helix chain 'F' and resid 80 through 89 removed outlier: 3.791A pdb=" N ILE F 84 " --> pdb=" O HIS F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 109 Processing helix chain 'F' and resid 113 through 123 removed outlier: 3.539A pdb=" N LEU F 123 " --> pdb=" O LYS F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 134 removed outlier: 4.349A pdb=" N LEU F 128 " --> pdb=" O LYS F 124 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP F 134 " --> pdb=" O ALA F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 157 removed outlier: 3.663A pdb=" N GLN F 145 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA F 146 " --> pdb=" O GLU F 142 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU F 147 " --> pdb=" O ARG F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 161 removed outlier: 3.646A pdb=" N PHE F 161 " --> pdb=" O ALA F 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 158 through 161' Processing helix chain 'F' and resid 162 through 175 removed outlier: 3.568A pdb=" N THR F 166 " --> pdb=" O PRO F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 196 removed outlier: 3.686A pdb=" N ILE F 190 " --> pdb=" O ALA F 186 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU F 196 " --> pdb=" O CYS F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 205 removed outlier: 3.875A pdb=" N VAL F 202 " --> pdb=" O ASN F 198 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG F 205 " --> pdb=" O VAL F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 215 removed outlier: 3.849A pdb=" N THR F 210 " --> pdb=" O GLY F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 235 removed outlier: 3.945A pdb=" N THR F 230 " --> pdb=" O ALA F 226 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE F 231 " --> pdb=" O LEU F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 242 Processing helix chain 'F' and resid 249 through 253 removed outlier: 3.516A pdb=" N ILE F 253 " --> pdb=" O LEU F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 259 Processing helix chain 'F' and resid 273 through 292 removed outlier: 3.541A pdb=" N ARG F 277 " --> pdb=" O LEU F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 302 removed outlier: 3.553A pdb=" N ASN F 300 " --> pdb=" O ALA F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 315 removed outlier: 3.509A pdb=" N VAL F 315 " --> pdb=" O SER F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 318 No H-bonds generated for 'chain 'F' and resid 316 through 318' Processing helix chain 'F' and resid 323 through 335 removed outlier: 3.678A pdb=" N LEU F 328 " --> pdb=" O ARG F 324 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU F 329 " --> pdb=" O ARG F 325 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL F 330 " --> pdb=" O GLY F 326 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE F 335 " --> pdb=" O LEU F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 353 removed outlier: 3.625A pdb=" N ALA F 349 " --> pdb=" O GLU F 345 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU F 351 " --> pdb=" O ILE F 347 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER F 352 " --> pdb=" O GLU F 348 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL F 353 " --> pdb=" O ALA F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 362 Processing helix chain 'F' and resid 363 through 368 removed outlier: 4.071A pdb=" N PHE F 368 " --> pdb=" O LEU F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 377 removed outlier: 3.750A pdb=" N THR F 375 " --> pdb=" O ALA F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 402 removed outlier: 3.735A pdb=" N ASN F 390 " --> pdb=" O ASP F 386 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN F 402 " --> pdb=" O ALA F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 414 removed outlier: 3.709A pdb=" N GLY F 407 " --> pdb=" O GLY F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 438 removed outlier: 3.927A pdb=" N ARG F 422 " --> pdb=" O HIS F 418 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN F 435 " --> pdb=" O LEU F 431 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR F 436 " --> pdb=" O HIS F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 449 through 457 removed outlier: 3.775A pdb=" N MET F 455 " --> pdb=" O THR F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 486 removed outlier: 3.552A pdb=" N ARG F 466 " --> pdb=" O PRO F 462 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY F 486 " --> pdb=" O MET F 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 509 removed outlier: 3.510A pdb=" N HIS F 496 " --> pdb=" O LEU F 492 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP F 509 " --> pdb=" O HIS F 505 " (cutoff:3.500A) Processing helix chain 'F' and resid 525 through 535 removed outlier: 3.676A pdb=" N LEU F 529 " --> pdb=" O GLU F 525 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 557 Processing helix chain 'F' and resid 567 through 582 Processing helix chain 'F' and resid 598 through 615 removed outlier: 3.597A pdb=" N LEU F 613 " --> pdb=" O THR F 609 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER F 615 " --> pdb=" O PHE F 611 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 639 removed outlier: 3.708A pdb=" N LEU F 623 " --> pdb=" O GLY F 619 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP F 625 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY F 639 " --> pdb=" O ASN F 635 " (cutoff:3.500A) Processing helix chain 'F' and resid 647 through 652 Processing helix chain 'F' and resid 654 through 657 removed outlier: 3.724A pdb=" N GLN F 657 " --> pdb=" O THR F 654 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 654 through 657' Processing helix chain 'F' and resid 658 through 668 removed outlier: 3.534A pdb=" N PHE F 662 " --> pdb=" O HIS F 658 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE F 663 " --> pdb=" O TYR F 659 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS F 668 " --> pdb=" O GLY F 664 " (cutoff:3.500A) Processing helix chain 'F' and resid 669 through 679 removed outlier: 3.770A pdb=" N LYS F 674 " --> pdb=" O PRO F 670 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET F 675 " --> pdb=" O HIS F 671 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS F 679 " --> pdb=" O MET F 675 " (cutoff:3.500A) Processing helix chain 'F' and resid 681 through 689 Processing helix chain 'F' and resid 695 through 703 Processing helix chain 'F' and resid 711 through 723 removed outlier: 3.821A pdb=" N VAL F 715 " --> pdb=" O GLY F 711 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE F 716 " --> pdb=" O LEU F 712 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU F 717 " --> pdb=" O ALA F 713 " (cutoff:3.500A) Processing helix chain 'F' and resid 725 through 735 Processing helix chain 'F' and resid 736 through 741 Processing helix chain 'F' and resid 746 through 759 removed outlier: 3.937A pdb=" N TRP F 750 " --> pdb=" O PHE F 746 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ILE F 752 " --> pdb=" O ASN F 748 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLU F 753 " --> pdb=" O ASN F 749 " (cutoff:3.500A) Processing helix chain 'F' and resid 763 through 778 removed outlier: 3.540A pdb=" N SER F 767 " --> pdb=" O ASN F 763 " (cutoff:3.500A) Processing helix chain 'F' and resid 780 through 789 removed outlier: 3.543A pdb=" N ALA F 786 " --> pdb=" O ALA F 782 " (cutoff:3.500A) Processing helix chain 'F' and resid 798 through 806 removed outlier: 3.569A pdb=" N LEU F 802 " --> pdb=" O GLY F 798 " (cutoff:3.500A) Processing helix chain 'F' and resid 807 through 810 Processing helix chain 'F' and resid 811 through 821 removed outlier: 6.366A pdb=" N TYR F 817 " --> pdb=" O LYS F 813 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU F 820 " --> pdb=" O SER F 816 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG F 821 " --> pdb=" O TYR F 817 " (cutoff:3.500A) Processing helix chain 'F' and resid 823 through 834 removed outlier: 3.790A pdb=" N GLU F 829 " --> pdb=" O ALA F 825 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS F 830 " --> pdb=" O LYS F 826 " (cutoff:3.500A) Processing helix chain 'F' and resid 835 through 852 removed outlier: 4.197A pdb=" N VAL F 840 " --> pdb=" O ASN F 836 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP F 841 " --> pdb=" O SER F 837 " (cutoff:3.500A) Processing helix chain 'F' and resid 881 through 887 removed outlier: 3.610A pdb=" N VAL F 887 " --> pdb=" O TYR F 883 " (cutoff:3.500A) Processing helix chain 'F' and resid 890 through 898 removed outlier: 3.865A pdb=" N HIS F 894 " --> pdb=" O LYS F 890 " (cutoff:3.500A) Processing helix chain 'F' and resid 901 through 911 Processing helix chain 'F' and resid 917 through 934 Processing helix chain 'F' and resid 936 through 945 removed outlier: 3.626A pdb=" N ASN F 941 " --> pdb=" O ASN F 937 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU F 942 " --> pdb=" O TRP F 938 " (cutoff:3.500A) Processing helix chain 'F' and resid 948 through 959 removed outlier: 3.818A pdb=" N LYS F 957 " --> pdb=" O LEU F 953 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS F 959 " --> pdb=" O LEU F 955 " (cutoff:3.500A) Processing helix chain 'F' and resid 961 through 976 removed outlier: 3.638A pdb=" N VAL F 969 " --> pdb=" O ARG F 965 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA F 976 " --> pdb=" O LEU F 972 " (cutoff:3.500A) Processing helix chain 'F' and resid 978 through 988 removed outlier: 3.660A pdb=" N CYS F 987 " --> pdb=" O ASP F 983 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N HIS F 988 " --> pdb=" O ILE F 984 " (cutoff:3.500A) Processing helix chain 'F' and resid 1432 through 1436 removed outlier: 3.751A pdb=" N ILE F1436 " --> pdb=" O ILE F1433 " (cutoff:3.500A) Processing helix chain 'F' and resid 1480 through 1487 removed outlier: 4.002A pdb=" N GLN F1485 " --> pdb=" O HIS F1481 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLN F1486 " --> pdb=" O LEU F1482 " (cutoff:3.500A) Processing helix chain 'F' and resid 1488 through 1493 Processing helix chain 'F' and resid 1522 through 1529 removed outlier: 3.964A pdb=" N ILE F1526 " --> pdb=" O TYR F1522 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLU F1527 " --> pdb=" O CYS F1523 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE F1528 " --> pdb=" O VAL F1524 " (cutoff:3.500A) Processing helix chain 'F' and resid 1609 through 1623 removed outlier: 3.552A pdb=" N LYS F1614 " --> pdb=" O ILE F1610 " (cutoff:3.500A) Processing helix chain 'F' and resid 1628 through 1643 removed outlier: 4.018A pdb=" N HIS F1632 " --> pdb=" O SER F1628 " (cutoff:3.500A) Processing helix chain 'F' and resid 1649 through 1661 removed outlier: 3.861A pdb=" N GLU F1655 " --> pdb=" O CYS F1651 " (cutoff:3.500A) Processing helix chain 'F' and resid 1666 through 1677 removed outlier: 3.943A pdb=" N PHE F1677 " --> pdb=" O ILE F1673 " (cutoff:3.500A) Processing helix chain 'F' and resid 1682 through 1694 removed outlier: 3.550A pdb=" N HIS F1686 " --> pdb=" O PHE F1682 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 21 Processing helix chain 'H' and resid 25 through 31 removed outlier: 3.990A pdb=" N MET H 29 " --> pdb=" O GLY H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 101 removed outlier: 3.690A pdb=" N ASN H 99 " --> pdb=" O LYS H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 124 removed outlier: 4.040A pdb=" N SER H 122 " --> pdb=" O GLN H 118 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N PHE H 124 " --> pdb=" O LEU H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 146 Processing sheet with id=AA1, first strand: chain 'B' and resid 2120 through 2122 removed outlier: 4.234A pdb=" N GLN B2161 " --> pdb=" O LYS B2171 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 2153 through 2156 removed outlier: 6.443A pdb=" N SER B2234 " --> pdb=" O LEU B2230 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2243 through 2245 Processing sheet with id=AA4, first strand: chain 'D' and resid 34 through 39 removed outlier: 3.888A pdb=" N ARG D 36 " --> pdb=" O PHE D 26 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N THR D 23 " --> pdb=" O GLY D 19 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY D 19 " --> pdb=" O THR D 23 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU D 15 " --> pdb=" O TRP D 27 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS D 317 " --> pdb=" O ALA D 18 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 47 through 50 removed outlier: 3.676A pdb=" N ILE D 79 " --> pdb=" O MET D 67 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N SER D 80 " --> pdb=" O ILE H 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 88 through 93 removed outlier: 3.769A pdb=" N SER D 90 " --> pdb=" O GLY D 103 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N THR D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 131 through 136 removed outlier: 6.659A pdb=" N GLY D 146 " --> pdb=" O ASN D 132 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL D 134 " --> pdb=" O ILE D 144 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE D 144 " --> pdb=" O VAL D 134 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N LEU D 136 " --> pdb=" O GLU D 142 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLU D 142 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 173 through 178 removed outlier: 6.983A pdb=" N VAL D 188 " --> pdb=" O THR D 174 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ALA D 176 " --> pdb=" O ALA D 186 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA D 186 " --> pdb=" O ALA D 176 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N CYS D 194 " --> pdb=" O LYS D 215 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LYS D 215 " --> pdb=" O CYS D 194 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL D 196 " --> pdb=" O LYS D 213 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE D 211 " --> pdb=" O ASN D 198 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 223 through 228 removed outlier: 3.597A pdb=" N GLN D 225 " --> pdb=" O CYS D 238 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR D 243 " --> pdb=" O SER D 239 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ARG D 248 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU D 254 " --> pdb=" O ARG D 248 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 273 through 277 removed outlier: 6.681A pdb=" N ALA D 294 " --> pdb=" O GLU D 307 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU D 307 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU D 296 " --> pdb=" O LYS D 305 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 990 through 992 1281 hydrogen bonds defined for protein. 3795 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: 10.55 Time building geometry restraints manager: 11.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.37: 8481 1.37 - 1.51: 6388 1.51 - 1.65: 10389 1.65 - 1.79: 22 1.79 - 1.93: 225 Bond restraints: 25505 Sorted by residual: bond pdb=" C5 AGS B2601 " pdb=" C6 AGS B2601 " ideal model delta sigma weight residual 1.409 1.329 0.080 1.00e-02 1.00e+04 6.35e+01 bond pdb=" C5 AGS F4802 " pdb=" C6 AGS F4802 " ideal model delta sigma weight residual 1.409 1.331 0.078 1.00e-02 1.00e+04 6.02e+01 bond pdb=" C2 AGS F4802 " pdb=" N3 AGS F4802 " ideal model delta sigma weight residual 1.335 1.397 -0.062 1.00e-02 1.00e+04 3.83e+01 bond pdb=" C2 AGS F4802 " pdb=" N1 AGS F4802 " ideal model delta sigma weight residual 1.335 1.396 -0.061 1.00e-02 1.00e+04 3.66e+01 bond pdb=" C2 AGS B2601 " pdb=" N3 AGS B2601 " ideal model delta sigma weight residual 1.335 1.394 -0.059 1.00e-02 1.00e+04 3.49e+01 ... (remaining 25500 not shown) Histogram of bond angle deviations from ideal: 94.94 - 102.76: 146 102.76 - 110.57: 7419 110.57 - 118.38: 12618 118.38 - 126.20: 13944 126.20 - 134.01: 467 Bond angle restraints: 34594 Sorted by residual: angle pdb=" N1 AGS F4802 " pdb=" C2 AGS F4802 " pdb=" N3 AGS F4802 " ideal model delta sigma weight residual 128.80 118.12 10.68 8.41e-01 1.41e+00 1.61e+02 angle pdb=" N1 AGS B2601 " pdb=" C2 AGS B2601 " pdb=" N3 AGS B2601 " ideal model delta sigma weight residual 128.80 118.21 10.59 8.41e-01 1.41e+00 1.59e+02 angle pdb=" C5 AGS F4802 " pdb=" N7 AGS F4802 " pdb=" C8 AGS F4802 " ideal model delta sigma weight residual 103.67 108.06 -4.39 4.26e-01 5.51e+00 1.06e+02 angle pdb=" C5 AGS B2601 " pdb=" N7 AGS B2601 " pdb=" C8 AGS B2601 " ideal model delta sigma weight residual 103.67 107.97 -4.30 4.26e-01 5.51e+00 1.02e+02 angle pdb=" C5 AGS F4802 " pdb=" C4 AGS F4802 " pdb=" N3 AGS F4802 " ideal model delta sigma weight residual 126.80 120.41 6.39 7.41e-01 1.82e+00 7.44e+01 ... (remaining 34589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.11: 14953 31.11 - 62.22: 459 62.22 - 93.33: 35 93.33 - 124.45: 1 124.45 - 155.56: 2 Dihedral angle restraints: 15450 sinusoidal: 6280 harmonic: 9170 Sorted by residual: dihedral pdb=" CA GLY F 367 " pdb=" C GLY F 367 " pdb=" N PHE F 368 " pdb=" CA PHE F 368 " ideal model delta harmonic sigma weight residual -180.00 -149.27 -30.73 0 5.00e+00 4.00e-02 3.78e+01 dihedral pdb=" O1B AGS B2601 " pdb=" O3B AGS B2601 " pdb=" PB AGS B2601 " pdb=" PG AGS B2601 " ideal model delta sinusoidal sigma weight residual 68.91 -86.65 155.56 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" CA GLY B 892 " pdb=" C GLY B 892 " pdb=" N ALA B 893 " pdb=" CA ALA B 893 " ideal model delta harmonic sigma weight residual 180.00 157.89 22.11 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 15447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3002 0.045 - 0.090: 793 0.090 - 0.135: 132 0.135 - 0.181: 6 0.181 - 0.226: 6 Chirality restraints: 3939 Sorted by residual: chirality pdb=" C3 IHP B2602 " pdb=" C2 IHP B2602 " pdb=" C4 IHP B2602 " pdb=" O13 IHP B2602 " both_signs ideal model delta sigma weight residual False -2.34 -2.56 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" C1' AGS B2601 " pdb=" C2' AGS B2601 " pdb=" N9 AGS B2601 " pdb=" O4' AGS B2601 " both_signs ideal model delta sigma weight residual False 2.41 2.62 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" C1 IHP B2602 " pdb=" C2 IHP B2602 " pdb=" C6 IHP B2602 " pdb=" O11 IHP B2602 " both_signs ideal model delta sigma weight residual False 2.32 2.53 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 3936 not shown) Planarity restraints: 4391 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 76 " -0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO D 77 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 77 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 77 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 384 " 0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO F 385 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO F 385 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 385 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B1473 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO B1474 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO B1474 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B1474 " -0.023 5.00e-02 4.00e+02 ... (remaining 4388 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 669 2.71 - 3.26: 25105 3.26 - 3.81: 38637 3.81 - 4.35: 50548 4.35 - 4.90: 85416 Nonbonded interactions: 200375 Sorted by model distance: nonbonded pdb=" O LEU B 894 " pdb=" OH TYR B1583 " model vdw 2.167 3.040 nonbonded pdb=" OD1 ASP D 53 " pdb=" OG SER D 55 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR B2332 " pdb=" OD2 ASP B2512 " model vdw 2.251 3.040 nonbonded pdb=" OE2 GLU B2025 " pdb=" NH2 ARG B2170 " model vdw 2.270 3.120 nonbonded pdb=" NH2 ARG F 910 " pdb=" O GLU F 946 " model vdw 2.281 3.120 ... (remaining 200370 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 74.430 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 25505 Z= 0.243 Angle : 0.582 10.681 34594 Z= 0.362 Chirality : 0.040 0.226 3939 Planarity : 0.003 0.043 4391 Dihedral : 14.573 155.556 9482 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.26 % Allowed : 9.93 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.70 (0.14), residues: 3096 helix: -1.26 (0.11), residues: 1869 sheet: -1.92 (0.34), residues: 184 loop : -2.51 (0.17), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 297 HIS 0.004 0.001 HIS B2340 PHE 0.015 0.001 PHE F 573 TYR 0.021 0.001 TYR F1522 ARG 0.009 0.000 ARG F 533 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 383 time to evaluate : 2.894 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 2045 LYS cc_start: 0.8641 (mptt) cc_final: 0.8289 (mptt) REVERT: B 2143 THR cc_start: 0.8098 (t) cc_final: 0.7782 (t) REVERT: D 155 TRP cc_start: 0.6719 (t60) cc_final: 0.6395 (t60) REVERT: D 185 MET cc_start: 0.8135 (tmm) cc_final: 0.7679 (tmt) REVERT: F 57 LEU cc_start: 0.7608 (pp) cc_final: 0.7312 (tp) REVERT: F 137 GLN cc_start: 0.7664 (tm-30) cc_final: 0.7447 (tm-30) REVERT: F 247 ASP cc_start: 0.7287 (m-30) cc_final: 0.7058 (m-30) REVERT: F 453 MET cc_start: 0.8364 (mmm) cc_final: 0.8160 (mmm) REVERT: F 852 THR cc_start: 0.8250 (OUTLIER) cc_final: 0.7885 (m) REVERT: F 1617 LEU cc_start: 0.8492 (mt) cc_final: 0.8259 (mt) outliers start: 34 outliers final: 16 residues processed: 413 average time/residue: 1.4846 time to fit residues: 700.9367 Evaluate side-chains 260 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 243 time to evaluate : 2.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1172 THR Chi-restraints excluded: chain B residue 1593 CYS Chi-restraints excluded: chain B residue 1639 VAL Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1768 THR Chi-restraints excluded: chain B residue 1988 HIS Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2326 VAL Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain F residue 765 THR Chi-restraints excluded: chain F residue 852 THR Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 29 MET Chi-restraints excluded: chain H residue 36 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 4.9990 chunk 234 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 158 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 242 optimal weight: 0.2980 chunk 94 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 180 optimal weight: 4.9990 chunk 281 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 797 ASN B 838 GLN B 967 HIS B1014 GLN B1045 ASN B1106 ASN B1202 HIS B1687 HIS B1715 GLN B1719 HIS B1722 GLN B1744 HIS B1809 GLN B2117 GLN B2340 HIS B2401 HIS D 41 GLN D 44 GLN D 71 ASN ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 ASN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 GLN F 94 ASN F 145 GLN F 219 GLN F 359 GLN ** F 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 390 ASN F 418 HIS F 447 HIS F 496 HIS F 505 HIS F 539 GLN F 540 HIS F 549 ASN F 648 ASN F 846 GLN F 848 ASN F 908 ASN F 958 GLN F1535 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25505 Z= 0.183 Angle : 0.548 9.612 34594 Z= 0.281 Chirality : 0.040 0.196 3939 Planarity : 0.004 0.046 4391 Dihedral : 6.585 152.343 3485 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.93 % Allowed : 15.75 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.15), residues: 3096 helix: -0.27 (0.12), residues: 1905 sheet: -1.54 (0.37), residues: 182 loop : -2.08 (0.19), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 99 HIS 0.006 0.001 HIS B2410 PHE 0.014 0.001 PHE B1011 TYR 0.016 0.001 TYR B1700 ARG 0.012 0.001 ARG B1955 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 268 time to evaluate : 3.142 Fit side-chains revert: symmetry clash REVERT: B 853 TYR cc_start: 0.8044 (OUTLIER) cc_final: 0.7118 (t80) REVERT: B 994 MET cc_start: 0.8291 (tpp) cc_final: 0.8035 (mmm) REVERT: B 1174 MET cc_start: 0.8314 (mmm) cc_final: 0.8102 (mmm) REVERT: B 1896 ARG cc_start: 0.7584 (tmt-80) cc_final: 0.7375 (tmt-80) REVERT: B 2045 LYS cc_start: 0.8609 (mptt) cc_final: 0.8257 (mptt) REVERT: B 2143 THR cc_start: 0.8137 (t) cc_final: 0.7740 (t) REVERT: D 155 TRP cc_start: 0.6700 (t60) cc_final: 0.6430 (t60) REVERT: D 185 MET cc_start: 0.7933 (tmm) cc_final: 0.7560 (tmt) REVERT: D 273 MET cc_start: 0.8128 (mmt) cc_final: 0.7678 (mmt) REVERT: F 137 GLN cc_start: 0.7571 (tm-30) cc_final: 0.7323 (tm-30) REVERT: F 247 ASP cc_start: 0.7280 (m-30) cc_final: 0.7050 (m-30) REVERT: F 254 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.7932 (pp) REVERT: F 453 MET cc_start: 0.8382 (mmm) cc_final: 0.8160 (mmm) REVERT: F 648 ASN cc_start: 0.6524 (OUTLIER) cc_final: 0.6247 (p0) REVERT: F 1516 THR cc_start: 0.8268 (OUTLIER) cc_final: 0.8049 (p) REVERT: F 1679 ASP cc_start: 0.7355 (t0) cc_final: 0.6954 (m-30) outliers start: 79 outliers final: 29 residues processed: 319 average time/residue: 1.3963 time to fit residues: 515.8019 Evaluate side-chains 262 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 229 time to evaluate : 2.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 804 GLU Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 966 HIS Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1381 VAL Chi-restraints excluded: chain B residue 1572 ASP Chi-restraints excluded: chain B residue 1593 CYS Chi-restraints excluded: chain B residue 1639 VAL Chi-restraints excluded: chain B residue 1692 VAL Chi-restraints excluded: chain B residue 1988 HIS Chi-restraints excluded: chain B residue 2089 MET Chi-restraints excluded: chain B residue 2164 THR Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2327 MET Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 648 ASN Chi-restraints excluded: chain F residue 765 THR Chi-restraints excluded: chain F residue 852 THR Chi-restraints excluded: chain F residue 893 CYS Chi-restraints excluded: chain F residue 1514 GLU Chi-restraints excluded: chain F residue 1516 THR Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 36 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 234 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 282 optimal weight: 3.9990 chunk 304 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 chunk 279 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1049 GLN B2385 ASN D 64 HIS ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN ** F 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 648 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 25505 Z= 0.301 Angle : 0.591 9.853 34594 Z= 0.299 Chirality : 0.043 0.218 3939 Planarity : 0.004 0.054 4391 Dihedral : 6.578 156.056 3477 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.19 % Allowed : 17.30 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.15), residues: 3096 helix: -0.01 (0.12), residues: 1932 sheet: -1.28 (0.36), residues: 192 loop : -2.05 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 99 HIS 0.007 0.001 HIS B1594 PHE 0.018 0.001 PHE B1122 TYR 0.014 0.002 TYR F 839 ARG 0.013 0.001 ARG B1955 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 247 time to evaluate : 2.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 853 TYR cc_start: 0.8272 (OUTLIER) cc_final: 0.7226 (t80) REVERT: B 1141 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.6935 (ttp-110) REVERT: B 1235 ARG cc_start: 0.8446 (mtm110) cc_final: 0.8242 (mtm110) REVERT: B 1529 MET cc_start: 0.8557 (ttt) cc_final: 0.8135 (ttt) REVERT: B 1896 ARG cc_start: 0.7770 (tmt-80) cc_final: 0.7541 (tmt-80) REVERT: B 2045 LYS cc_start: 0.8697 (mptt) cc_final: 0.8339 (mptt) REVERT: B 2429 TRP cc_start: 0.7270 (OUTLIER) cc_final: 0.7051 (p90) REVERT: B 2515 HIS cc_start: 0.6894 (OUTLIER) cc_final: 0.6656 (t70) REVERT: D 185 MET cc_start: 0.8011 (tmm) cc_final: 0.7637 (tmt) REVERT: F 247 ASP cc_start: 0.7352 (m-30) cc_final: 0.7148 (m-30) REVERT: F 254 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8293 (pp) REVERT: F 709 ARG cc_start: 0.7546 (ptm-80) cc_final: 0.7325 (ptm-80) REVERT: F 1679 ASP cc_start: 0.7281 (t0) cc_final: 0.6932 (m-30) outliers start: 86 outliers final: 53 residues processed: 305 average time/residue: 1.2944 time to fit residues: 461.5424 Evaluate side-chains 286 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 228 time to evaluate : 2.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 804 GLU Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 966 HIS Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1030 TYR Chi-restraints excluded: chain B residue 1141 ARG Chi-restraints excluded: chain B residue 1172 THR Chi-restraints excluded: chain B residue 1236 MET Chi-restraints excluded: chain B residue 1313 MET Chi-restraints excluded: chain B residue 1381 VAL Chi-restraints excluded: chain B residue 1572 ASP Chi-restraints excluded: chain B residue 1593 CYS Chi-restraints excluded: chain B residue 1639 VAL Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1692 VAL Chi-restraints excluded: chain B residue 1953 VAL Chi-restraints excluded: chain B residue 1988 HIS Chi-restraints excluded: chain B residue 1998 MET Chi-restraints excluded: chain B residue 2004 THR Chi-restraints excluded: chain B residue 2010 MET Chi-restraints excluded: chain B residue 2164 THR Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2228 ILE Chi-restraints excluded: chain B residue 2261 LEU Chi-restraints excluded: chain B residue 2276 ASP Chi-restraints excluded: chain B residue 2326 VAL Chi-restraints excluded: chain B residue 2327 MET Chi-restraints excluded: chain B residue 2429 TRP Chi-restraints excluded: chain B residue 2509 THR Chi-restraints excluded: chain B residue 2515 HIS Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 535 SER Chi-restraints excluded: chain F residue 550 LEU Chi-restraints excluded: chain F residue 676 LEU Chi-restraints excluded: chain F residue 702 VAL Chi-restraints excluded: chain F residue 842 LEU Chi-restraints excluded: chain F residue 852 THR Chi-restraints excluded: chain F residue 893 CYS Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1514 GLU Chi-restraints excluded: chain F residue 1521 LEU Chi-restraints excluded: chain F residue 1649 ASP Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 36 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 0.6980 chunk 212 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 chunk 189 optimal weight: 10.0000 chunk 283 optimal weight: 1.9990 chunk 299 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 268 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN F 237 HIS ** F 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 758 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25505 Z= 0.174 Angle : 0.533 9.988 34594 Z= 0.270 Chirality : 0.040 0.182 3939 Planarity : 0.004 0.055 4391 Dihedral : 6.448 155.042 3476 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.48 % Allowed : 17.71 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.15), residues: 3096 helix: 0.32 (0.12), residues: 1921 sheet: -1.09 (0.36), residues: 192 loop : -1.82 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B2101 HIS 0.004 0.001 HIS B1594 PHE 0.014 0.001 PHE B1122 TYR 0.014 0.001 TYR B2275 ARG 0.013 0.000 ARG B1955 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 251 time to evaluate : 2.928 Fit side-chains revert: symmetry clash REVERT: B 853 TYR cc_start: 0.8153 (OUTLIER) cc_final: 0.7076 (t80) REVERT: B 994 MET cc_start: 0.8212 (tpp) cc_final: 0.7966 (mmm) REVERT: B 1174 MET cc_start: 0.8256 (mmm) cc_final: 0.8048 (mmm) REVERT: B 1235 ARG cc_start: 0.8408 (mtm110) cc_final: 0.8144 (mtm110) REVERT: B 1352 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6900 (mm-30) REVERT: B 1529 MET cc_start: 0.8567 (ttt) cc_final: 0.8145 (ttt) REVERT: B 1896 ARG cc_start: 0.7777 (tmt-80) cc_final: 0.7546 (tmt-80) REVERT: B 2045 LYS cc_start: 0.8684 (mptt) cc_final: 0.8337 (mptt) REVERT: B 2429 TRP cc_start: 0.7269 (OUTLIER) cc_final: 0.7037 (p90) REVERT: B 2515 HIS cc_start: 0.6894 (OUTLIER) cc_final: 0.6506 (t70) REVERT: D 135 CYS cc_start: 0.7077 (t) cc_final: 0.6867 (p) REVERT: D 155 TRP cc_start: 0.6669 (t60) cc_final: 0.6392 (t60) REVERT: D 185 MET cc_start: 0.7973 (tmm) cc_final: 0.7654 (tmt) REVERT: F 57 LEU cc_start: 0.7584 (pp) cc_final: 0.7301 (tp) REVERT: F 254 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8023 (pp) REVERT: F 587 LEU cc_start: 0.8546 (mt) cc_final: 0.8281 (mt) REVERT: F 709 ARG cc_start: 0.7533 (ptm-80) cc_final: 0.7310 (ptm-80) REVERT: F 852 THR cc_start: 0.8539 (OUTLIER) cc_final: 0.8102 (m) REVERT: F 960 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.6553 (mm-30) REVERT: F 1679 ASP cc_start: 0.7329 (t0) cc_final: 0.6958 (m-30) outliers start: 94 outliers final: 46 residues processed: 314 average time/residue: 1.0758 time to fit residues: 396.8373 Evaluate side-chains 290 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 237 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 804 GLU Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 966 HIS Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1030 TYR Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1352 GLU Chi-restraints excluded: chain B residue 1572 ASP Chi-restraints excluded: chain B residue 1593 CYS Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1685 LEU Chi-restraints excluded: chain B residue 1692 VAL Chi-restraints excluded: chain B residue 1766 GLU Chi-restraints excluded: chain B residue 1988 HIS Chi-restraints excluded: chain B residue 1998 MET Chi-restraints excluded: chain B residue 2057 MET Chi-restraints excluded: chain B residue 2089 MET Chi-restraints excluded: chain B residue 2164 THR Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2261 LEU Chi-restraints excluded: chain B residue 2263 ILE Chi-restraints excluded: chain B residue 2326 VAL Chi-restraints excluded: chain B residue 2327 MET Chi-restraints excluded: chain B residue 2413 SER Chi-restraints excluded: chain B residue 2429 TRP Chi-restraints excluded: chain B residue 2509 THR Chi-restraints excluded: chain B residue 2515 HIS Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 482 MET Chi-restraints excluded: chain F residue 535 SER Chi-restraints excluded: chain F residue 702 VAL Chi-restraints excluded: chain F residue 765 THR Chi-restraints excluded: chain F residue 852 THR Chi-restraints excluded: chain F residue 893 CYS Chi-restraints excluded: chain F residue 960 GLU Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1514 GLU Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 36 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 249 optimal weight: 7.9990 chunk 170 optimal weight: 0.8980 chunk 4 optimal weight: 9.9990 chunk 223 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 255 optimal weight: 4.9990 chunk 207 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 268 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: