Starting phenix.real_space_refine (version: 1.21rc1) on Wed Jul 12 03:44:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zwo_11492/07_2023/6zwo_11492_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zwo_11492/07_2023/6zwo_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_11492/07_2023/6zwo_11492.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zwo_11492/07_2023/6zwo_11492.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zwo_11492/07_2023/6zwo_11492_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zwo_11492/07_2023/6zwo_11492_neut_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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: 11.28, per 1000 atoms: 0.45 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: 10.01 Conformation dependent library (CDL) restraints added in 3.6 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... running ksdssp... Secondary structure from input PDB file: 155 helices and 12 sheets defined 57.1% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.52 Creating SS restraints... Processing helix chain 'B' and resid 793 through 808 Processing helix chain 'B' and resid 817 through 828 removed outlier: 3.605A pdb=" N ASP B 826 " --> pdb=" O ILE B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 846 Processing helix chain 'B' and resid 856 through 860 Processing helix chain 'B' and resid 864 through 872 removed outlier: 3.846A pdb=" N PHE B 871 " --> pdb=" O VAL B 867 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU B 872 " --> pdb=" O LEU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 891 Processing helix chain 'B' and resid 896 through 901 Processing helix chain 'B' and resid 930 through 935 Processing helix chain 'B' and resid 947 through 959 removed outlier: 3.519A pdb=" N ILE B 958 " --> pdb=" O ALA B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 982 Processing helix chain 'B' and resid 990 through 1003 Proline residue: B 995 - end of helix Processing helix chain 'B' and resid 1006 through 1022 removed outlier: 4.200A pdb=" N GLU B1010 " --> pdb=" O ALA B1007 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N PHE B1013 " --> pdb=" O GLU B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1038 removed outlier: 5.536A pdb=" N ASP B1032 " --> pdb=" O PRO B1029 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU B1033 " --> pdb=" O TYR B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1049 through 1063 removed outlier: 3.753A pdb=" N LEU B1054 " --> pdb=" O SER B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1069 No H-bonds generated for 'chain 'B' and resid 1067 through 1069' Processing helix chain 'B' and resid 1072 through 1083 Proline residue: B1076 - end of helix removed outlier: 4.371A pdb=" N MET B1083 " --> pdb=" O ARG B1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 1091 through 1102 removed outlier: 4.198A pdb=" N LEU B1102 " --> pdb=" O ALA B1098 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1122 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) Processing helix chain 'B' and resid 1129 through 1143 removed outlier: 3.938A pdb=" N THR B1143 " --> pdb=" O VAL B1139 " (cutoff:3.500A) Processing helix chain 'B' and resid 1150 through 1164 removed outlier: 4.669A pdb=" N SER B1153 " --> pdb=" O ASP B1150 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ARG B1154 " --> pdb=" O TYR B1151 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE B1156 " --> pdb=" O SER B1153 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N HIS B1157 " --> pdb=" O ARG B1154 " (cutoff:3.500A) Proline residue: B1158 - end of helix removed outlier: 3.717A pdb=" N LEU B1163 " --> pdb=" O VAL B1160 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP B1164 " --> pdb=" O ARG B1161 " (cutoff:3.500A) Processing helix chain 'B' and resid 1170 through 1183 removed outlier: 4.131A pdb=" N GLN B1183 " --> pdb=" O SER B1179 " (cutoff:3.500A) Processing helix chain 'B' and resid 1186 through 1188 No H-bonds generated for 'chain 'B' and resid 1186 through 1188' Processing helix chain 'B' and resid 1192 through 1201 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 1207 through 1217 Processing helix chain 'B' and resid 1229 through 1237 Processing helix chain 'B' and resid 1266 through 1269 No H-bonds generated for 'chain 'B' and resid 1266 through 1269' Processing helix chain 'B' and resid 1277 through 1293 Processing helix chain 'B' and resid 1298 through 1307 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 1311 through 1316 Processing helix chain 'B' and resid 1318 through 1328 removed outlier: 4.153A pdb=" N GLU B1328 " --> pdb=" O SER B1324 " (cutoff:3.500A) Processing helix chain 'B' and resid 1331 through 1347 Processing helix chain 'B' and resid 1351 through 1365 Processing helix chain 'B' and resid 1377 through 1389 removed outlier: 3.592A pdb=" N ILE B1380 " --> pdb=" O ASP B1377 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N VAL B1381 " --> pdb=" O ASN B1378 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU B1383 " --> pdb=" O ILE B1380 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY B1384 " --> pdb=" O VAL B1381 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA B1388 " --> pdb=" O GLU B1385 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS B1389 " --> pdb=" O ARG B1386 " (cutoff:3.500A) Processing helix chain 'B' and resid 1393 through 1406 removed outlier: 3.875A pdb=" N LYS B1406 " --> pdb=" O LEU B1402 " (cutoff:3.500A) Processing helix chain 'B' and resid 1410 through 1422 removed outlier: 3.567A pdb=" N LYS B1422 " --> pdb=" O SER B1418 " (cutoff:3.500A) Processing helix chain 'B' and resid 1426 through 1439 Processing helix chain 'B' and resid 1447 through 1452 Processing helix chain 'B' and resid 1456 through 1467 Processing helix chain 'B' and resid 1477 through 1487 Processing helix chain 'B' and resid 1490 through 1500 removed outlier: 3.564A pdb=" N GLU B1499 " --> pdb=" O GLN B1495 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS B1500 " --> pdb=" O GLN B1496 " (cutoff:3.500A) Processing helix chain 'B' and resid 1506 through 1523 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 1526 through 1535 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) removed outlier: 4.443A pdb=" N MET B1535 " --> pdb=" O GLU B1531 " (cutoff:3.500A) Processing helix chain 'B' and resid 1541 through 1553 Processing helix chain 'B' and resid 1559 through 1578 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 1583 through 1597 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 1599 through 1607 Processing helix chain 'B' and resid 1609 through 1623 removed outlier: 3.760A pdb=" N ARG B1612 " --> pdb=" O PRO B1609 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLU B1613 " --> pdb=" O GLU B1610 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B1615 " --> pdb=" O ARG B1612 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TRP B1619 " --> pdb=" O ARG B1616 " (cutoff:3.500A) Processing helix chain 'B' and resid 1630 through 1640 removed outlier: 3.871A pdb=" N LYS B1635 " --> pdb=" O GLU B1631 " (cutoff:3.500A) Processing helix chain 'B' and resid 1651 through 1662 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 1666 through 1677 Processing helix chain 'B' and resid 1694 through 1707 Processing helix chain 'B' and resid 1712 through 1728 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) Processing helix chain 'B' and resid 1740 through 1762 Processing helix chain 'B' and resid 1769 through 1783 Processing helix chain 'B' and resid 1787 through 1808 removed outlier: 3.508A pdb=" N ASN B1808 " --> pdb=" O TYR B1804 " (cutoff:3.500A) Processing helix chain 'B' and resid 1876 through 1895 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) Processing helix chain 'B' and resid 1900 through 1913 Processing helix chain 'B' and resid 1917 through 1929 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 1933 through 1945 removed outlier: 4.596A pdb=" N GLN B1937 " --> pdb=" O THR B1934 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE B1939 " --> pdb=" O LEU B1936 " (cutoff:3.500A) Proline residue: B1940 - end of helix removed outlier: 3.946A pdb=" N ALA B1944 " --> pdb=" O GLN B1941 " (cutoff:3.500A) Processing helix chain 'B' and resid 1951 through 1967 Processing helix chain 'B' and resid 1973 through 1980 Processing helix chain 'B' and resid 1985 through 1998 Processing helix chain 'B' and resid 2004 through 2020 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) Processing helix chain 'B' and resid 2023 through 2041 removed outlier: 3.616A pdb=" N ARG B2036 " --> pdb=" O GLU B2032 " (cutoff:3.500A) Processing helix chain 'B' and resid 2044 through 2058 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 2065 through 2090 removed outlier: 5.438A pdb=" N ARG B2076 " --> pdb=" O GLN B2072 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ASP B2077 " --> pdb=" O ALA B2073 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET B2079 " --> pdb=" O GLY B2075 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN B2082 " --> pdb=" O LEU B2078 " (cutoff:3.500A) Processing helix chain 'B' and resid 2094 through 2112 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) Processing helix chain 'B' and resid 2123 through 2126 No H-bonds generated for 'chain 'B' and resid 2123 through 2126' Processing helix chain 'B' and resid 2193 through 2210 removed outlier: 3.835A pdb=" N ARG B2197 " --> pdb=" O ARG B2193 " (cutoff:3.500A) Processing helix chain 'B' and resid 2213 through 2216 No H-bonds generated for 'chain 'B' and resid 2213 through 2216' Processing helix chain 'B' and resid 2247 through 2256 removed outlier: 4.327A pdb=" N ASP B2252 " --> pdb=" O ALA B2248 " (cutoff:3.500A) Processing helix chain 'B' and resid 2263 through 2271 Processing helix chain 'B' and resid 2275 through 2277 No H-bonds generated for 'chain 'B' and resid 2275 through 2277' Processing helix chain 'B' and resid 2280 through 2292 Processing helix chain 'B' and resid 2298 through 2305 Processing helix chain 'B' and resid 2310 through 2334 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 2381 through 2384 No H-bonds generated for 'chain 'B' and resid 2381 through 2384' Processing helix chain 'B' and resid 2395 through 2409 Processing helix chain 'B' and resid 2411 through 2422 Processing helix chain 'B' and resid 2430 through 2432 No H-bonds generated for 'chain 'B' and resid 2430 through 2432' Processing helix chain 'B' and resid 2493 through 2507 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 2521 through 2532 Processing helix chain 'B' and resid 2535 through 2540 removed outlier: 4.315A pdb=" N GLN B2540 " --> pdb=" O GLU B2536 " (cutoff:3.500A) Processing helix chain 'B' and resid 2543 through 2545 No H-bonds generated for 'chain 'B' and resid 2543 through 2545' Processing helix chain 'F' and resid 33 through 48 removed outlier: 5.996A pdb=" N ARG F 47 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU F 48 " --> pdb=" O ASN F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 69 Processing helix chain 'F' and resid 81 through 88 Processing helix chain 'F' and resid 97 through 108 Processing helix chain 'F' and resid 114 through 122 Processing helix chain 'F' and resid 125 through 133 Processing helix chain 'F' and resid 142 through 156 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 160 No H-bonds generated for 'chain 'F' and resid 158 through 160' Processing helix chain 'F' and resid 163 through 174 Processing helix chain 'F' and resid 184 through 195 removed outlier: 3.686A pdb=" N ILE F 190 " --> pdb=" O ALA F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 204 Processing helix chain 'F' and resid 207 through 214 Processing helix chain 'F' and resid 221 through 234 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 238 through 243 removed outlier: 5.182A pdb=" N TYR F 243 " --> pdb=" O LYS F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 258 removed outlier: 3.516A pdb=" N ILE F 253 " --> pdb=" O LEU F 250 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU F 254 " --> pdb=" O GLU F 251 " (cutoff:3.500A) Proline residue: F 256 - end of helix Processing helix chain 'F' and resid 274 through 291 Processing helix chain 'F' and resid 295 through 301 removed outlier: 3.553A pdb=" N ASN F 300 " --> pdb=" O ALA F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 317 removed outlier: 3.509A pdb=" N VAL F 315 " --> pdb=" O SER F 311 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU F 316 " --> pdb=" O LEU F 312 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS F 317 " --> pdb=" O ILE F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 334 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) Processing helix chain 'F' and resid 346 through 352 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) Processing helix chain 'F' and resid 360 through 362 No H-bonds generated for 'chain 'F' and resid 360 through 362' Processing helix chain 'F' and resid 364 through 367 No H-bonds generated for 'chain 'F' and resid 364 through 367' Processing helix chain 'F' and resid 370 through 376 removed outlier: 3.750A pdb=" N THR F 375 " --> pdb=" O ALA F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 401 Processing helix chain 'F' and resid 404 through 413 Processing helix chain 'F' and resid 417 through 437 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 440 through 443 No H-bonds generated for 'chain 'F' and resid 440 through 443' Processing helix chain 'F' and resid 450 through 456 removed outlier: 3.775A pdb=" N MET F 455 " --> pdb=" O THR F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 485 Processing helix chain 'F' and resid 493 through 508 Processing helix chain 'F' and resid 526 through 534 Processing helix chain 'F' and resid 548 through 556 Processing helix chain 'F' and resid 568 through 581 Processing helix chain 'F' and resid 599 through 614 removed outlier: 3.597A pdb=" N LEU F 613 " --> pdb=" O THR F 609 " (cutoff:3.500A) Processing helix chain 'F' and resid 620 through 638 removed outlier: 3.789A pdb=" N ASP F 625 " --> pdb=" O GLY F 621 " (cutoff:3.500A) Processing helix chain 'F' and resid 648 through 651 No H-bonds generated for 'chain 'F' and resid 648 through 651' Processing helix chain 'F' and resid 655 through 667 removed outlier: 3.821A pdb=" N TYR F 659 " --> pdb=" O SER F 656 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE F 660 " --> pdb=" O GLN F 657 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE F 662 " --> pdb=" O TYR F 659 " (cutoff:3.500A) Processing helix chain 'F' and resid 670 through 678 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) Processing helix chain 'F' and resid 682 through 690 removed outlier: 4.152A pdb=" N SER F 690 " --> pdb=" O LEU F 686 " (cutoff:3.500A) Processing helix chain 'F' and resid 696 through 702 Processing helix chain 'F' and resid 712 through 722 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 726 through 740 removed outlier: 4.171A pdb=" N LEU F 736 " --> pdb=" O ALA F 732 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ARG F 737 " --> pdb=" O THR F 733 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N VAL F 738 " --> pdb=" O LYS F 734 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU F 739 " --> pdb=" O HIS F 735 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 760 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) removed outlier: 4.028A pdb=" N HIS F 760 " --> pdb=" O VAL F 756 " (cutoff:3.500A) Processing helix chain 'F' and resid 764 through 779 removed outlier: 4.383A pdb=" N GLU F 779 " --> pdb=" O ASP F 775 " (cutoff:3.500A) Processing helix chain 'F' and resid 781 through 788 removed outlier: 3.543A pdb=" N ALA F 786 " --> pdb=" O ALA F 782 " (cutoff:3.500A) Processing helix chain 'F' and resid 799 through 810 removed outlier: 3.813A pdb=" N ARG F 807 " --> pdb=" O LEU F 803 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE F 808 " --> pdb=" O LEU F 804 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU F 809 " --> pdb=" O LEU F 805 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER F 810 " --> pdb=" O LEU F 806 " (cutoff:3.500A) Processing helix chain 'F' and resid 812 through 820 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) Processing helix chain 'F' and resid 824 through 833 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 836 through 851 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 882 through 886 Processing helix chain 'F' and resid 891 through 899 removed outlier: 3.805A pdb=" N GLN F 899 " --> pdb=" O LEU F 895 " (cutoff:3.500A) Processing helix chain 'F' and resid 902 through 910 Processing helix chain 'F' and resid 918 through 935 removed outlier: 3.924A pdb=" N SER F 935 " --> pdb=" O GLY F 931 " (cutoff:3.500A) Processing helix chain 'F' and resid 937 through 944 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 949 through 958 removed outlier: 3.818A pdb=" N LYS F 957 " --> pdb=" O LEU F 953 " (cutoff:3.500A) Processing helix chain 'F' and resid 962 through 977 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) removed outlier: 4.232A pdb=" N LYS F 977 " --> pdb=" O GLY F 973 " (cutoff:3.500A) Processing helix chain 'F' and resid 979 through 987 removed outlier: 3.660A pdb=" N CYS F 987 " --> pdb=" O ASP F 983 " (cutoff:3.500A) Processing helix chain 'F' and resid 1433 through 1435 No H-bonds generated for 'chain 'F' and resid 1433 through 1435' Processing helix chain 'F' and resid 1480 through 1486 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 1489 through 1492 No H-bonds generated for 'chain 'F' and resid 1489 through 1492' Processing helix chain 'F' and resid 1523 through 1528 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) No H-bonds generated for 'chain 'F' and resid 1523 through 1528' Processing helix chain 'F' and resid 1610 through 1624 removed outlier: 3.552A pdb=" N LYS F1614 " --> pdb=" O ILE F1610 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER F1624 " --> pdb=" O VAL F1620 " (cutoff:3.500A) Processing helix chain 'F' and resid 1629 through 1642 Processing helix chain 'F' and resid 1650 through 1662 removed outlier: 3.861A pdb=" N GLU F1655 " --> pdb=" O CYS F1651 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS F1662 " --> pdb=" O HIS F1658 " (cutoff:3.500A) Processing helix chain 'F' and resid 1667 through 1676 Processing helix chain 'F' and resid 1683 through 1693 Processing helix chain 'H' and resid 7 through 20 Processing helix chain 'H' and resid 25 through 30 Processing helix chain 'H' and resid 85 through 100 removed outlier: 3.690A pdb=" N ASN H 99 " --> pdb=" O LYS H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 123 removed outlier: 4.040A pdb=" N SER H 122 " --> pdb=" O GLN H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 145 Processing sheet with id= A, first strand: chain 'B' and resid 2120 through 2122 Processing sheet with id= B, first strand: chain 'B' and resid 2181 through 2183 Processing sheet with id= C, first strand: chain 'B' and resid 2184 through 2188 removed outlier: 3.919A pdb=" N SER B2234 " --> pdb=" O SER B2231 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LEU B2236 " --> pdb=" O PRO B2229 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLY B2238 " --> pdb=" O VAL B2227 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL B2227 " --> pdb=" O GLY B2238 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 2243 through 2245 Processing sheet with id= E, first strand: chain 'D' and resid 315 through 321 removed outlier: 7.164A pdb=" N ALA D 18 " --> pdb=" O VAL D 316 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU D 318 " --> pdb=" O ALA D 16 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA D 16 " --> pdb=" O LEU D 318 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N PHE D 320 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE D 14 " --> pdb=" O PHE D 320 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU D 15 " --> pdb=" O TRP D 27 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY D 19 " --> pdb=" O THR D 23 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N THR D 23 " --> pdb=" O GLY D 19 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG D 36 " --> pdb=" O PHE D 26 " (cutoff:3.500A) Processing sheet with id= F, 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) Processing sheet with id= G, first strand: chain 'D' and resid 124 through 126 removed outlier: 4.263A pdb=" N THR D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER D 90 " --> pdb=" O GLY D 103 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 162 through 166 removed outlier: 4.731A pdb=" N ALA D 151 " --> pdb=" O ASP D 147 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP D 147 " --> pdb=" O ALA D 151 " (cutoff:3.500A) Processing sheet with id= I, 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: 3.559A pdb=" N CYS D 194 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR D 214 " --> pdb=" O VAL D 196 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASN D 198 " --> pdb=" O PRO D 212 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 223 through 228 removed outlier: 6.813A pdb=" N CYS D 238 " --> pdb=" O LEU D 224 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N CYS D 226 " --> pdb=" O ALA D 236 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA D 236 " --> pdb=" O CYS D 226 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N PHE D 228 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU D 234 " --> pdb=" O PHE D 228 " (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= K, first strand: chain 'D' and resid 273 through 277 removed outlier: 6.757A pdb=" N ALA D 288 " --> pdb=" O TRP D 274 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N CYS D 276 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL D 286 " --> pdb=" O CYS D 276 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N CYS D 298 " --> pdb=" O ILE D 304 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE D 304 " --> pdb=" O CYS D 298 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 990 through 992 1088 hydrogen bonds defined for protein. 3096 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: 9.13 Time building geometry restraints manager: 10.56 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: 14906 31.11 - 62.22: 448 62.22 - 93.33: 35 93.33 - 124.45: 1 124.45 - 155.56: 2 Dihedral angle restraints: 15392 sinusoidal: 6222 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 15389 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: 676 2.71 - 3.26: 25250 3.26 - 3.81: 38765 3.81 - 4.35: 50973 4.35 - 4.90: 85483 Nonbonded interactions: 201147 Sorted by model distance: nonbonded pdb=" O LEU B 894 " pdb=" OH TYR B1583 " model vdw 2.167 2.440 nonbonded pdb=" OD1 ASP D 53 " pdb=" OG SER D 55 " model vdw 2.207 2.440 nonbonded pdb=" OH TYR B2332 " pdb=" OD2 ASP B2512 " model vdw 2.251 2.440 nonbonded pdb=" OE2 GLU B2025 " pdb=" NH2 ARG B2170 " model vdw 2.270 2.520 nonbonded pdb=" NH2 ARG F 910 " pdb=" O GLU F 946 " model vdw 2.281 2.520 ... (remaining 201142 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.350 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 64.630 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.090 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:10.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.410 ------------------------------------------------------------------------------- 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= 0.245 Angle : 0.582 10.681 34594 Z= 0.362 Chirality : 0.040 0.226 3939 Planarity : 0.003 0.043 4391 Dihedral : 14.533 155.556 9424 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 % 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 *********************** 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 : 2.767 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 16 residues processed: 413 average time/residue: 1.5075 time to fit residues: 711.3124 Evaluate side-chains 259 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 243 time to evaluate : 2.899 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 0.8965 time to fit residues: 6.1782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 1.9990 chunk 234 optimal weight: 0.5980 chunk 130 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 242 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 147 optimal weight: 0.6980 chunk 180 optimal weight: 0.5980 chunk 281 optimal weight: 0.0010 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 791 ASN B 797 ASN B 838 GLN B 967 HIS B1014 GLN B1045 ASN B1106 ASN B1202 HIS B1617 GLN B1687 HIS B1715 GLN B1719 HIS B1722 GLN B1744 HIS B1809 GLN B2024 HIS 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 153 HIS 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 539 GLN F 540 HIS F 549 ASN F 848 ASN F 908 ASN F 958 GLN F1535 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 25505 Z= 0.153 Angle : 0.509 9.551 34594 Z= 0.257 Chirality : 0.039 0.231 3939 Planarity : 0.004 0.046 4391 Dihedral : 5.676 154.137 3405 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer Outliers : 3.26 % 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: -1.54 (0.15), residues: 3096 helix: -0.34 (0.12), residues: 1874 sheet: -1.36 (0.38), residues: 176 loop : -2.08 (0.18), residues: 1046 *********************** 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 356 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 268 time to evaluate : 3.118 Fit side-chains revert: symmetry clash outliers start: 88 outliers final: 40 residues processed: 325 average time/residue: 1.3500 time to fit residues: 514.8881 Evaluate side-chains 278 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 238 time to evaluate : 2.984 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 29 residues processed: 12 average time/residue: 1.0274 time to fit residues: 19.3168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 234 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 77 optimal weight: 0.0170 chunk 282 optimal weight: 3.9990 chunk 304 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 chunk 279 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 226 optimal weight: 2.9990 overall best weight: 1.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2385 ASN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 846 GLN ** F 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 995 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 25505 Z= 0.215 Angle : 0.523 9.486 34594 Z= 0.263 Chirality : 0.041 0.198 3939 Planarity : 0.004 0.047 4391 Dihedral : 5.707 155.830 3405 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 3.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.15), residues: 3096 helix: -0.02 (0.12), residues: 1896 sheet: -1.34 (0.37), residues: 180 loop : -1.92 (0.19), residues: 1020 *********************** 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 345 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 256 time to evaluate : 3.122 Fit side-chains revert: symmetry clash outliers start: 89 outliers final: 53 residues processed: 313 average time/residue: 1.3206 time to fit residues: 486.3411 Evaluate side-chains 294 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 241 time to evaluate : 2.878 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 43 residues processed: 14 average time/residue: 0.8403 time to fit residues: 18.7532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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-1.21rc1-5013/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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-1.21rc1-5013/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/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: 69.4703 > 50: distance: 52 - 60: 31.828 distance: 60 - 61: 17.681 distance: 61 - 62: 25.716 distance: 61 - 64: 41.010 distance: 62 - 63: 15.558 distance: 62 - 69: 26.253 distance: 64 - 65: 46.678 distance: 65 - 66: 10.011 distance: 66 - 67: 27.778 distance: 66 - 68: 16.229 distance: 69 - 70: 46.806 distance: 70 - 71: 19.377 distance: 70 - 73: 19.069 distance: 71 - 72: 41.312 distance: 71 - 78: 41.843 distance: 73 - 74: 52.532 distance: 74 - 75: 14.537 distance: 75 - 76: 43.356 distance: 76 - 77: 30.637 distance: 78 - 79: 27.278 distance: 79 - 80: 15.277 distance: 79 - 82: 26.163 distance: 80 - 81: 24.133 distance: 80 - 89: 19.746 distance: 82 - 83: 19.429 distance: 83 - 84: 19.610 distance: 83 - 85: 29.865 distance: 84 - 86: 11.526 distance: 85 - 87: 34.996 distance: 86 - 88: 35.618 distance: 87 - 88: 9.008 distance: 89 - 90: 11.821 distance: 89 - 95: 7.471 distance: 90 - 91: 13.697 distance: 90 - 93: 11.958 distance: 91 - 92: 37.869 distance: 91 - 96: 10.182 distance: 93 - 94: 24.802 distance: 94 - 95: 10.002 distance: 96 - 97: 17.488 distance: 97 - 98: 44.643 distance: 97 - 100: 29.782 distance: 98 - 99: 28.371 distance: 98 - 105: 45.814 distance: 100 - 101: 37.695 distance: 101 - 102: 24.188 distance: 102 - 103: 50.696 distance: 102 - 104: 37.414 distance: 105 - 106: 26.845 distance: 106 - 107: 16.572 distance: 106 - 109: 22.857 distance: 107 - 108: 28.243 distance: 107 - 114: 53.085 distance: 109 - 110: 29.042 distance: 110 - 111: 10.673 distance: 111 - 112: 20.331 distance: 112 - 113: 26.789 distance: 114 - 115: 10.149 distance: 115 - 116: 26.387 distance: 115 - 118: 15.407 distance: 116 - 117: 48.060 distance: 116 - 122: 27.708 distance: 118 - 119: 28.497 distance: 118 - 120: 22.295 distance: 119 - 121: 69.470 distance: 122 - 123: 29.205 distance: 122 - 128: 34.568 distance: 123 - 124: 25.041 distance: 123 - 126: 23.589 distance: 124 - 125: 40.477 distance: 124 - 129: 31.485 distance: 127 - 128: 29.159 distance: 129 - 130: 42.716 distance: 130 - 131: 18.997 distance: 130 - 133: 54.522 distance: 131 - 132: 20.739 distance: 131 - 140: 25.929 distance: 133 - 134: 14.668 distance: 134 - 135: 25.177 distance: 134 - 136: 25.421 distance: 135 - 137: 28.045 distance: 136 - 138: 34.031 distance: 137 - 139: 11.017 distance: 138 - 139: 21.289 distance: 140 - 141: 3.780 distance: 141 - 142: 31.466 distance: 141 - 144: 56.611 distance: 142 - 143: 45.126 distance: 142 - 151: 16.124 distance: 144 - 145: 8.607 distance: 145 - 146: 23.588 distance: 146 - 147: 20.289 distance: 147 - 148: 10.729 distance: 148 - 149: 6.549 distance: 148 - 150: 5.527