Starting phenix.real_space_refine (version: dev) on Sun Dec 18 16:32:42 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k4y_9916/12_2022/6k4y_9916.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k4y_9916/12_2022/6k4y_9916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k4y_9916/12_2022/6k4y_9916.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k4y_9916/12_2022/6k4y_9916.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k4y_9916/12_2022/6k4y_9916.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k4y_9916/12_2022/6k4y_9916.pdb" } resolution = 3.79 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= 0.000 sd= 0.008 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C ARG 903": "NH1" <-> "NH2" Residue "D TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 47": "NH1" <-> "NH2" Residue "D PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 297": "NH1" <-> "NH2" Residue "D ARG 1345": "NH1" <-> "NH2" Residue "F ARG 599": "NH1" <-> "NH2" Residue "F ARG 603": "NH1" <-> "NH2" Residue "I ARG 23": "NH1" <-> "NH2" Residue "I ARG 47": "NH1" <-> "NH2" Residue "M ARG 98": "NH1" <-> "NH2" Residue "M ARG 101": "NH1" <-> "NH2" Residue "M ARG 104": "NH1" <-> "NH2" Residue "M ARG 145": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 33247 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1686 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1673 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1282} Chain: "D" Number of atoms: 10384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10384 Classifications: {'peptide': 1335} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1279} Chain breaks: 2 Chain: "E" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 3781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3781 Classifications: {'peptide': 463} Link IDs: {'PTRANS': 14, 'TRANS': 448} Chain breaks: 3 Chain: "I" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 729 Classifications: {'peptide': 88} Link IDs: {'TRANS': 87} Chain: "M" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1638 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 205} Chain: "N" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1223 Classifications: {'DNA': 59} Link IDs: {'rna3p': 58} Chain: "T" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 936 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain breaks: 1 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14375 SG CYS D 70 112.221 80.164 69.021 1.00246.10 S ATOM 14521 SG CYS D 88 113.627 83.179 67.558 1.00234.97 S ATOM 20209 SG CYS D 814 80.053 100.736 127.254 1.00129.78 S ATOM 20774 SG CYS D 888 80.127 100.167 122.633 1.00124.84 S ATOM 20825 SG CYS D 895 79.376 97.507 124.881 1.00118.99 S ATOM 20846 SG CYS D 898 77.013 100.142 125.450 1.00116.34 S Time building chain proxies: 18.16, per 1000 atoms: 0.55 Number of scatterers: 33247 At special positions: 0 Unit cell: (171.217, 190.822, 160.761, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 137 16.00 P 105 15.00 Mg 1 11.99 O 6582 8.00 N 5884 7.00 C 20536 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=0, symmetry=0 Time building additional restraints: 14.33 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " Number of angles added : 6 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7340 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 55 sheets defined 43.3% alpha, 13.4% beta 45 base pairs and 88 stacking pairs defined. Time for finding SS restraints: 10.83 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.608A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.727A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.975A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA B 42 " --> pdb=" O THR B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.756A pdb=" N LEU B 82 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 158 Processing helix chain 'B' and resid 212 through 227 removed outlier: 3.620A pdb=" N ALA B 220 " --> pdb=" O ALA B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 232 removed outlier: 3.647A pdb=" N PHE B 231 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL B 232 " --> pdb=" O GLU B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 228 through 232' Processing helix chain 'C' and resid 28 through 39 Processing helix chain 'C' and resid 48 through 55 removed outlier: 3.584A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.642A pdb=" N CYS C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 213 Processing helix chain 'C' and resid 216 through 223 Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.622A pdb=" N ILE C 274 " --> pdb=" O THR C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 294 removed outlier: 3.788A pdb=" N ILE C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 removed outlier: 3.635A pdb=" N GLY C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 354 removed outlier: 3.629A pdb=" N THR C 350 " --> pdb=" O TYR C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 removed outlier: 3.676A pdb=" N ALA C 362 " --> pdb=" O ASP C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 387 Processing helix chain 'C' and resid 398 through 409 removed outlier: 3.547A pdb=" N LEU C 409 " --> pdb=" O PHE C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.801A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 482 removed outlier: 4.193A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 507 removed outlier: 3.592A pdb=" N SER C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 608 through 612 removed outlier: 3.771A pdb=" N GLY C 612 " --> pdb=" O ILE C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 661 removed outlier: 3.595A pdb=" N GLN C 659 " --> pdb=" O SER C 656 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL C 661 " --> pdb=" O GLN C 658 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 656 through 661' Processing helix chain 'C' and resid 662 through 667 removed outlier: 3.596A pdb=" N LEU C 667 " --> pdb=" O VAL C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 863 Processing helix chain 'C' and resid 896 through 905 Processing helix chain 'C' and resid 943 through 979 Processing helix chain 'C' and resid 993 through 998 removed outlier: 3.654A pdb=" N LEU C 998 " --> pdb=" O ASP C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1099 through 1103 removed outlier: 3.883A pdb=" N GLY C1102 " --> pdb=" O ASN C1099 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.658A pdb=" N THR C1115 " --> pdb=" O GLN C1111 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS C1127 " --> pdb=" O GLY C1123 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.886A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU C1151 " --> pdb=" O ARG C1147 " (cutoff:3.500A) Processing helix chain 'C' and resid 1167 through 1176 Processing helix chain 'C' and resid 1177 through 1179 No H-bonds generated for 'chain 'C' and resid 1177 through 1179' Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.534A pdb=" N GLY C1202 " --> pdb=" O LEU C1198 " (cutoff:3.500A) Processing helix chain 'C' and resid 1238 through 1243 removed outlier: 3.557A pdb=" N LYS C1242 " --> pdb=" O LEU C1238 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.580A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1290 removed outlier: 3.844A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1310 Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 3.534A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 removed outlier: 3.609A pdb=" N SER D 34 " --> pdb=" O ILE D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 95 through 100 removed outlier: 3.724A pdb=" N ARG D 98 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU D 100 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 180 through 192 removed outlier: 3.571A pdb=" N ALA D 184 " --> pdb=" O MET D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 208 Processing helix chain 'D' and resid 210 through 230 Processing helix chain 'D' and resid 233 through 236 removed outlier: 3.672A pdb=" N TRP D 236 " --> pdb=" O LYS D 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 233 through 236' Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 285 removed outlier: 4.079A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 327 through 331 removed outlier: 3.564A pdb=" N MET D 330 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 342 removed outlier: 3.757A pdb=" N LEU D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 376 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 407 through 415 removed outlier: 3.677A pdb=" N ILE D 411 " --> pdb=" O VAL D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 505 through 514 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 581 removed outlier: 4.059A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 593 removed outlier: 3.562A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 613 removed outlier: 3.656A pdb=" N GLY D 613 " --> pdb=" O TYR D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.678A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 669 Processing helix chain 'D' and resid 675 through 702 Processing helix chain 'D' and resid 720 through 729 Processing helix chain 'D' and resid 733 through 741 removed outlier: 4.018A pdb=" N ILE D 737 " --> pdb=" O SER D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.838A pdb=" N TYR D 772 " --> pdb=" O ASN D 768 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TYR D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP D 802 " --> pdb=" O ARG D 798 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL D 803 " --> pdb=" O ARG D 799 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN D 805 " --> pdb=" O VAL D 801 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 839 removed outlier: 3.833A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 876 Processing helix chain 'D' and resid 884 through 888 removed outlier: 3.674A pdb=" N SER D 887 " --> pdb=" O SER D 884 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 899 No H-bonds generated for 'chain 'D' and resid 897 through 899' Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.807A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 930 removed outlier: 3.574A pdb=" N LEU D 930 " --> pdb=" O GLY D 927 " (cutoff:3.500A) Processing helix chain 'D' and resid 1069 through 1074 removed outlier: 3.880A pdb=" N ASP D1073 " --> pdb=" O ALA D1069 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU D1074 " --> pdb=" O GLY D1070 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1069 through 1074' Processing helix chain 'D' and resid 1137 through 1147 removed outlier: 3.648A pdb=" N VAL D1141 " --> pdb=" O GLY D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1225 removed outlier: 3.692A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1226 through 1244 removed outlier: 3.970A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1251 through 1261 removed outlier: 3.646A pdb=" N LEU D1261 " --> pdb=" O VAL D1257 " (cutoff:3.500A) Processing helix chain 'D' and resid 1281 through 1292 Processing helix chain 'D' and resid 1310 through 1315 removed outlier: 4.021A pdb=" N LEU D1314 " --> pdb=" O THR D1310 " (cutoff:3.500A) Processing helix chain 'D' and resid 1318 through 1325 Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.776A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) Processing helix chain 'D' and resid 1347 through 1354 Processing helix chain 'D' and resid 1360 through 1372 removed outlier: 4.185A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 removed outlier: 3.539A pdb=" N VAL E 10 " --> pdb=" O VAL E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 32 removed outlier: 3.505A pdb=" N VAL E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 80 removed outlier: 4.561A pdb=" N LEU E 80 " --> pdb=" O GLU E 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 Processing helix chain 'F' and resid 112 through 136 Processing helix chain 'F' and resid 137 through 153 removed outlier: 3.733A pdb=" N ILE F 141 " --> pdb=" O TYR F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 234 removed outlier: 4.174A pdb=" N THR F 234 " --> pdb=" O VAL F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 257 Processing helix chain 'F' and resid 262 through 293 Processing helix chain 'F' and resid 299 through 304 Processing helix chain 'F' and resid 313 through 321 Processing helix chain 'F' and resid 324 through 329 Processing helix chain 'F' and resid 330 through 332 No H-bonds generated for 'chain 'F' and resid 330 through 332' Processing helix chain 'F' and resid 333 through 352 removed outlier: 4.222A pdb=" N LYS F 343 " --> pdb=" O ARG F 339 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 392 removed outlier: 5.481A pdb=" N ARG F 385 " --> pdb=" O GLU F 381 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N LEU F 386 " --> pdb=" O ALA F 382 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS F 392 " --> pdb=" O ILE F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 395 No H-bonds generated for 'chain 'F' and resid 393 through 395' Processing helix chain 'F' and resid 400 through 417 removed outlier: 3.765A pdb=" N LEU F 404 " --> pdb=" O GLN F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 447 removed outlier: 4.330A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 475 Processing helix chain 'F' and resid 479 through 487 Processing helix chain 'F' and resid 491 through 500 removed outlier: 3.569A pdb=" N ARG F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS F 496 " --> pdb=" O ASP F 492 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 515 removed outlier: 3.820A pdb=" N GLU F 515 " --> pdb=" O GLY F 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 522 Processing helix chain 'F' and resid 541 through 551 removed outlier: 3.529A pdb=" N VAL F 547 " --> pdb=" O ALA F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 554 through 561 Processing helix chain 'F' and resid 572 through 597 removed outlier: 4.128A pdb=" N ARG F 596 " --> pdb=" O ALA F 592 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS F 597 " --> pdb=" O LYS F 593 " (cutoff:3.500A) Processing helix chain 'F' and resid 603 through 608 removed outlier: 3.874A pdb=" N LEU F 607 " --> pdb=" O ARG F 603 " (cutoff:3.500A) Processing helix chain 'F' and resid 609 through 611 No H-bonds generated for 'chain 'F' and resid 609 through 611' Processing helix chain 'I' and resid 4 through 21 Processing helix chain 'I' and resid 24 through 29 removed outlier: 4.245A pdb=" N GLU I 28 " --> pdb=" O GLU I 24 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN I 29 " --> pdb=" O ASP I 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 24 through 29' Processing helix chain 'I' and resid 30 through 41 Processing helix chain 'I' and resid 50 through 60 Processing helix chain 'I' and resid 62 through 74 Processing helix chain 'I' and resid 77 through 87 removed outlier: 3.633A pdb=" N TYR I 81 " --> pdb=" O PHE I 77 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR I 83 " --> pdb=" O GLY I 79 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N TYR I 87 " --> pdb=" O TYR I 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 11 Processing helix chain 'M' and resid 16 through 29 Processing helix chain 'M' and resid 33 through 40 Processing helix chain 'M' and resid 45 through 59 Processing helix chain 'M' and resid 72 through 90 Processing helix chain 'M' and resid 107 through 124 Processing helix chain 'M' and resid 168 through 178 removed outlier: 3.952A pdb=" N ILE M 178 " --> pdb=" O LYS M 174 " (cutoff:3.500A) Processing helix chain 'M' and resid 197 through 209 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 17 removed outlier: 6.710A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE A 16 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LYS A 25 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 104 removed outlier: 6.060A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 91 Processing sheet with id=AA5, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.936A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 15 through 17 removed outlier: 4.367A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR B 27 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL B 202 " --> pdb=" O TYR B 185 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TYR B 185 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLU B 204 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE B 183 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLU B 206 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 15 through 17 removed outlier: 4.367A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR B 27 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AB1, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AB2, first strand: chain 'B' and resid 104 through 105 Processing sheet with id=AB3, first strand: chain 'B' and resid 108 through 111 removed outlier: 6.548A pdb=" N GLY B 108 " --> pdb=" O HIS B 132 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N HIS B 132 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.865A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.671A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB7, first strand: chain 'C' and resid 451 through 453 removed outlier: 6.462A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB9, first strand: chain 'C' and resid 226 through 231 removed outlier: 4.774A pdb=" N GLU C 226 " --> pdb=" O PHE C 337 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 239 through 240 Processing sheet with id=AC2, first strand: chain 'C' and resid 249 through 250 removed outlier: 4.166A pdb=" N GLU C 249 " --> pdb=" O ILE C 269 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.747A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 296 through 297 removed outlier: 4.237A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 301 through 302 removed outlier: 7.163A pdb=" N TYR C 301 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.598A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.598A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 716 through 718 removed outlier: 6.654A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP C 781 " --> pdb=" O ALA C 718 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 722 through 727 removed outlier: 5.383A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.694A pdb=" N THR C 757 " --> pdb=" O ILE C 765 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE C 765 " --> pdb=" O THR C 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AD3, first strand: chain 'C' and resid 1079 through 1080 removed outlier: 7.019A pdb=" N VAL C 818 " --> pdb=" O ASN C1080 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 830 through 838 removed outlier: 3.938A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 876 through 877 Processing sheet with id=AD6, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.791A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 887 through 889 Processing sheet with id=AD8, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 6.200A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 7.815A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 1268 through 1270 removed outlier: 3.544A pdb=" N GLN C1268 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 1335 through 1339 removed outlier: 3.780A pdb=" N LYS D 21 " --> pdb=" O GLU C1338 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP D1342 " --> pdb=" O ILE D 20 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 103 through 112 removed outlier: 10.430A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.496A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AE5, first strand: chain 'D' and resid 253 through 254 Processing sheet with id=AE6, first strand: chain 'D' and resid 526 through 527 removed outlier: 7.583A pdb=" N LEU D 527 " --> pdb=" O ARG D 551 " (cutoff:3.500A) removed outlier: 9.690A pdb=" N THR D 553 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 809 through 811 removed outlier: 6.317A pdb=" N VAL D 894 " --> pdb=" O VAL D 809 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE9, first strand: chain 'D' and resid 825 through 826 removed outlier: 6.738A pdb=" N VAL D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 848 through 849 removed outlier: 6.451A pdb=" N VAL D 848 " --> pdb=" O LEU D 857 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 949 through 952 removed outlier: 6.763A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 957 through 959 Processing sheet with id=AF4, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AF5, first strand: chain 'D' and resid 1025 through 1026 Processing sheet with id=AF6, first strand: chain 'D' and resid 1098 through 1100 removed outlier: 3.636A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG D1036 " --> pdb=" O LYS D1079 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 1046 through 1050 removed outlier: 3.787A pdb=" N ALA D1105 " --> pdb=" O VAL D1061 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 1190 through 1191 removed outlier: 6.784A pdb=" N LYS D1172 " --> pdb=" O GLU D1168 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLU D1168 " --> pdb=" O LYS D1172 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ARG D1174 " --> pdb=" O GLY D1166 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL D1204 " --> pdb=" O GLY D1161 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 1264 through 1268 removed outlier: 6.848A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 128 through 133 removed outlier: 7.248A pdb=" N ILE M 141 " --> pdb=" O LYS M 129 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL M 131 " --> pdb=" O LEU M 139 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU M 139 " --> pdb=" O VAL M 131 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ARG M 150 " --> pdb=" O LEU M 142 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ILE M 149 " --> pdb=" O TYR M 165 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N TYR M 165 " --> pdb=" O ILE M 149 " (cutoff:3.500A) 1369 hydrogen bonds defined for protein. 3870 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 106 hydrogen bonds 204 hydrogen bond angles 0 basepair planarities 45 basepair parallelities 88 stacking parallelities Total time for adding SS restraints: 16.00 Time building geometry restraints manager: 15.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8774 1.33 - 1.45: 6151 1.45 - 1.57: 18573 1.57 - 1.69: 207 1.69 - 1.81: 242 Bond restraints: 33947 Sorted by residual: bond pdb=" N ARG D 47 " pdb=" CA ARG D 47 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.29e-02 6.01e+03 8.83e+00 bond pdb=" N ILE I 26 " pdb=" CA ILE I 26 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.23e+00 bond pdb=" N TYR D 46 " pdb=" CA TYR D 46 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.97e+00 bond pdb=" N LEU D 376 " pdb=" CA LEU D 376 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.42e-02 4.96e+03 6.42e+00 bond pdb=" N ARG D 709 " pdb=" CA ARG D 709 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.23e-02 6.61e+03 6.25e+00 ... (remaining 33942 not shown) Histogram of bond angle deviations from ideal: 96.65 - 104.32: 836 104.32 - 111.99: 16481 111.99 - 119.66: 13072 119.66 - 127.33: 15497 127.33 - 135.00: 372 Bond angle restraints: 46258 Sorted by residual: angle pdb=" C ILE I 26 " pdb=" N VAL I 27 " pdb=" CA VAL I 27 " ideal model delta sigma weight residual 122.66 115.35 7.31 9.70e-01 1.06e+00 5.69e+01 angle pdb=" N VAL I 27 " pdb=" CA VAL I 27 " pdb=" C VAL I 27 " ideal model delta sigma weight residual 111.90 106.47 5.43 8.10e-01 1.52e+00 4.50e+01 angle pdb=" C ARG D 709 " pdb=" N ASP D 710 " pdb=" CA ASP D 710 " ideal model delta sigma weight residual 121.54 133.25 -11.71 1.91e+00 2.74e-01 3.76e+01 angle pdb=" C SER B 20 " pdb=" N SER B 21 " pdb=" CA SER B 21 " ideal model delta sigma weight residual 121.54 132.11 -10.57 1.91e+00 2.74e-01 3.06e+01 angle pdb=" N ASP D 710 " pdb=" CA ASP D 710 " pdb=" C ASP D 710 " ideal model delta sigma weight residual 110.80 99.29 11.51 2.13e+00 2.20e-01 2.92e+01 ... (remaining 46253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.61: 19532 28.61 - 57.21: 915 57.21 - 85.82: 87 85.82 - 114.42: 3 114.42 - 143.03: 2 Dihedral angle restraints: 20539 sinusoidal: 9159 harmonic: 11380 Sorted by residual: dihedral pdb=" CA VAL A 192 " pdb=" C VAL A 192 " pdb=" N GLU A 193 " pdb=" CA GLU A 193 " ideal model delta harmonic sigma weight residual -180.00 -150.79 -29.21 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA LYS C1133 " pdb=" C LYS C1133 " pdb=" N GLN C1134 " pdb=" CA GLN C1134 " ideal model delta harmonic sigma weight residual 180.00 151.55 28.45 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA SER C1295 " pdb=" C SER C1295 " pdb=" N ASP C1296 " pdb=" CA ASP C1296 " ideal model delta harmonic sigma weight residual -180.00 -151.84 -28.16 0 5.00e+00 4.00e-02 3.17e+01 ... (remaining 20536 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 4015 0.063 - 0.126: 1069 0.126 - 0.190: 165 0.190 - 0.253: 25 0.253 - 0.316: 8 Chirality restraints: 5282 Sorted by residual: chirality pdb=" CB ILE C 39 " pdb=" CA ILE C 39 " pdb=" CG1 ILE C 39 " pdb=" CG2 ILE C 39 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CB ILE C 854 " pdb=" CA ILE C 854 " pdb=" CG1 ILE C 854 " pdb=" CG2 ILE C 854 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA ASP D 710 " pdb=" N ASP D 710 " pdb=" C ASP D 710 " pdb=" CB ASP D 710 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 5279 not shown) Planarity restraints: 5664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 20 " -0.016 2.00e-02 2.50e+03 3.47e-02 1.21e+01 pdb=" C SER B 20 " 0.060 2.00e-02 2.50e+03 pdb=" O SER B 20 " -0.024 2.00e-02 2.50e+03 pdb=" N SER B 21 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 708 " 0.018 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C ASN D 708 " -0.059 2.00e-02 2.50e+03 pdb=" O ASN D 708 " 0.022 2.00e-02 2.50e+03 pdb=" N ARG D 709 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP I 25 " -0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C ASP I 25 " 0.059 2.00e-02 2.50e+03 pdb=" O ASP I 25 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE I 26 " -0.020 2.00e-02 2.50e+03 ... (remaining 5661 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 7164 2.77 - 3.31: 30662 3.31 - 3.84: 56281 3.84 - 4.37: 64373 4.37 - 4.90: 105190 Nonbonded interactions: 263670 Sorted by model distance: nonbonded pdb=" OG1 THR D1029 " pdb=" O SER D1116 " model vdw 2.242 2.440 nonbonded pdb=" O2 DC N 27 " pdb=" N2 DG T 35 " model vdw 2.245 2.496 nonbonded pdb=" O ARG C1033 " pdb=" OG1 THR C1037 " model vdw 2.256 2.440 nonbonded pdb=" OG1 THR D 514 " pdb=" O GLN D 594 " model vdw 2.261 2.440 nonbonded pdb=" O ASP F 278 " pdb=" OG1 THR F 282 " model vdw 2.267 2.440 ... (remaining 263665 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 135 or (resid 136 and (name N or name CA or name \ C or name O or name CB )) or resid 137 through 158 or resid 170 through 232)) selection = (chain 'B' and (resid 8 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 232)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 105 5.49 5 Mg 1 5.21 5 S 137 5.16 5 C 20536 2.51 5 N 5884 2.21 5 O 6582 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.290 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: 0.020 Extract box with map and model: 5.070 Check model and map are aligned: 0.560 Convert atoms to be neutral: 0.340 Process input model: 100.480 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.098 33947 Z= 0.494 Angle : 0.984 11.709 46258 Z= 0.546 Chirality : 0.058 0.316 5282 Planarity : 0.007 0.073 5664 Dihedral : 14.868 143.028 13199 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.60 % Favored : 92.30 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.05 % 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: -4.54 (0.10), residues: 3920 helix: -3.13 (0.09), residues: 1530 sheet: -2.52 (0.22), residues: 432 loop : -3.02 (0.11), residues: 1958 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 3387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 835 time to evaluate : 3.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 6 residues processed: 849 average time/residue: 0.5245 time to fit residues: 685.7451 Evaluate side-chains 425 residues out of total 3387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 419 time to evaluate : 3.807 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2950 time to fit residues: 8.7143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 336 optimal weight: 9.9990 chunk 302 optimal weight: 8.9990 chunk 167 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 203 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 chunk 312 optimal weight: 0.0770 chunk 121 optimal weight: 0.9990 chunk 190 optimal weight: 3.9990 chunk 232 optimal weight: 2.9990 chunk 362 optimal weight: 2.9990 overall best weight: 1.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN B 66 HIS B 147 GLN C 69 GLN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS C 406 ASN C 447 HIS C 551 HIS ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C1157 GLN C1264 GLN C1268 GLN C1313 HIS D 157 GLN D 320 ASN D 489 ASN D 739 GLN D 792 ASN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 907 HIS D1195 GLN D1197 ASN E 31 GLN E 72 GLN F 147 GLN F 446 GLN F 600 HIS M 52 ASN M 124 ASN M 156 ASN M 200 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 33947 Z= 0.204 Angle : 0.657 11.351 46258 Z= 0.349 Chirality : 0.044 0.204 5282 Planarity : 0.005 0.059 5664 Dihedral : 17.482 143.269 5366 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.95 % Favored : 95.00 % Rotamer Outliers : 2.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.05 % 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: -3.01 (0.12), residues: 3920 helix: -1.28 (0.11), residues: 1590 sheet: -2.08 (0.24), residues: 399 loop : -2.62 (0.12), residues: 1931 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 486 time to evaluate : 3.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 94 outliers final: 46 residues processed: 549 average time/residue: 0.4796 time to fit residues: 421.7502 Evaluate side-chains 411 residues out of total 3387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 365 time to evaluate : 3.873 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.3211 time to fit residues: 32.9305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 201 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 301 optimal weight: 6.9990 chunk 246 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 chunk 362 optimal weight: 9.9990 chunk 392 optimal weight: 10.0000 chunk 323 optimal weight: 10.0000 chunk 359 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 291 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS B 103 ASN C 604 HIS C 808 ASN C1220 GLN D 739 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 907 HIS ** D1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 200 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.064 33947 Z= 0.421 Angle : 0.743 11.411 46258 Z= 0.395 Chirality : 0.048 0.182 5282 Planarity : 0.005 0.056 5664 Dihedral : 17.380 145.017 5366 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.12 % Favored : 92.86 % Rotamer Outliers : 2.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.05 % 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: -2.49 (0.12), residues: 3920 helix: -0.60 (0.12), residues: 1587 sheet: -1.77 (0.24), residues: 395 loop : -2.58 (0.12), residues: 1938 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 392 time to evaluate : 4.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 41 residues processed: 465 average time/residue: 0.4473 time to fit residues: 340.6161 Evaluate side-chains 355 residues out of total 3387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 314 time to evaluate : 3.865 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.3034 time to fit residues: 28.3652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 358 optimal weight: 4.9990 chunk 272 optimal weight: 7.9990 chunk 188 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 chunk 173 optimal weight: 6.9990 chunk 243 optimal weight: 30.0000 chunk 364 optimal weight: 10.0000 chunk 385 optimal weight: 9.9990 chunk 190 optimal weight: 10.0000 chunk 345 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 HIS C1136 GLN C1264 GLN D 80 HIS ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 865 HIS D1195 GLN F 129 GLN M 41 HIS M 200 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 33947 Z= 0.268 Angle : 0.636 11.365 46258 Z= 0.337 Chirality : 0.044 0.197 5282 Planarity : 0.004 0.050 5664 Dihedral : 17.206 143.755 5366 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.59 % Favored : 94.39 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.05 % 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: -2.01 (0.13), residues: 3920 helix: -0.11 (0.13), residues: 1596 sheet: -1.56 (0.24), residues: 413 loop : -2.40 (0.13), residues: 1911 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 379 time to evaluate : 3.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 28 residues processed: 423 average time/residue: 0.4577 time to fit residues: 316.2255 Evaluate side-chains 359 residues out of total 3387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 331 time to evaluate : 3.617 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3022 time to fit residues: 21.2382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 321 optimal weight: 30.0000 chunk 218 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 287 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 329 optimal weight: 7.9990 chunk 266 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 196 optimal weight: 2.9990 chunk 346 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN B 227 GLN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN C 761 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 301 ASN F 409 ASN M 200 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 33947 Z= 0.251 Angle : 0.616 11.444 46258 Z= 0.325 Chirality : 0.043 0.182 5282 Planarity : 0.004 0.049 5664 Dihedral : 17.079 143.109 5366 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.45 % Favored : 93.52 % Rotamer Outliers : 1.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.05 % 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: -1.71 (0.13), residues: 3920 helix: 0.20 (0.13), residues: 1585 sheet: -1.38 (0.25), residues: 406 loop : -2.29 (0.13), residues: 1929 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 365 time to evaluate : 4.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 28 residues processed: 408 average time/residue: 0.4551 time to fit residues: 304.7937 Evaluate side-chains 356 residues out of total 3387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 328 time to evaluate : 3.975 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3035 time to fit residues: 21.5036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 129 optimal weight: 5.9990 chunk 347 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 226 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 386 optimal weight: 20.0000 chunk 320 optimal weight: 30.0000 chunk 178 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 127 optimal weight: 8.9990 chunk 202 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN D 489 ASN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1289 ASN D1366 HIS ** M 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 200 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 33947 Z= 0.355 Angle : 0.675 11.373 46258 Z= 0.356 Chirality : 0.045 0.258 5282 Planarity : 0.005 0.051 5664 Dihedral : 17.057 142.808 5366 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.14 % Favored : 92.83 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.05 % 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: -1.67 (0.13), residues: 3920 helix: 0.21 (0.13), residues: 1583 sheet: -1.26 (0.25), residues: 393 loop : -2.27 (0.13), residues: 1944 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 352 time to evaluate : 4.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 36 residues processed: 396 average time/residue: 0.4690 time to fit residues: 305.4627 Evaluate side-chains 350 residues out of total 3387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 314 time to evaluate : 4.171 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.3057 time to fit residues: 26.7049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 372 optimal weight: 20.0000 chunk 43 optimal weight: 0.8980 chunk 219 optimal weight: 0.9990 chunk 281 optimal weight: 7.9990 chunk 218 optimal weight: 0.7980 chunk 324 optimal weight: 9.9990 chunk 215 optimal weight: 0.2980 chunk 384 optimal weight: 5.9990 chunk 240 optimal weight: 20.0000 chunk 234 optimal weight: 2.9990 chunk 177 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN B 147 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN C 327 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 33947 Z= 0.163 Angle : 0.579 14.260 46258 Z= 0.305 Chirality : 0.042 0.235 5282 Planarity : 0.004 0.051 5664 Dihedral : 16.826 141.090 5366 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.80 % Favored : 95.18 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.05 % 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: -1.23 (0.13), residues: 3920 helix: 0.63 (0.13), residues: 1604 sheet: -1.26 (0.24), residues: 426 loop : -2.05 (0.13), residues: 1890 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 386 time to evaluate : 3.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 11 residues processed: 410 average time/residue: 0.4601 time to fit residues: 309.8736 Evaluate side-chains 353 residues out of total 3387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 342 time to evaluate : 3.846 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3712 time to fit residues: 12.4033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 237 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 229 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 75 optimal weight: 20.0000 chunk 74 optimal weight: 7.9990 chunk 244 optimal weight: 20.0000 chunk 262 optimal weight: 6.9990 chunk 190 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 302 optimal weight: 6.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 320 ASN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 GLN D1367 GLN E 7 GLN ** F 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 579 GLN ** M 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 200 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.4973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.049 33947 Z= 0.370 Angle : 0.689 14.155 46258 Z= 0.360 Chirality : 0.045 0.251 5282 Planarity : 0.005 0.050 5664 Dihedral : 16.858 140.752 5366 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.09 % Favored : 92.88 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.05 % 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: -1.32 (0.13), residues: 3920 helix: 0.58 (0.13), residues: 1572 sheet: -1.07 (0.25), residues: 407 loop : -2.14 (0.13), residues: 1941 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 338 time to evaluate : 4.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 20 residues processed: 364 average time/residue: 0.4726 time to fit residues: 282.3277 Evaluate side-chains 347 residues out of total 3387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 327 time to evaluate : 3.574 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.3166 time to fit residues: 17.4733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 349 optimal weight: 9.9990 chunk 368 optimal weight: 6.9990 chunk 336 optimal weight: 20.0000 chunk 358 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 281 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 323 optimal weight: 9.9990 chunk 338 optimal weight: 20.0000 chunk 357 optimal weight: 0.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 GLN D 320 ASN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 HIS M 200 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 33947 Z= 0.254 Angle : 0.631 14.030 46258 Z= 0.330 Chirality : 0.043 0.242 5282 Planarity : 0.004 0.052 5664 Dihedral : 16.799 139.714 5366 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.35 % Favored : 93.62 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.05 % 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: -1.22 (0.13), residues: 3920 helix: 0.65 (0.13), residues: 1583 sheet: -0.99 (0.26), residues: 389 loop : -2.09 (0.13), residues: 1948 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 345 time to evaluate : 3.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 353 average time/residue: 0.4717 time to fit residues: 274.1538 Evaluate side-chains 327 residues out of total 3387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 319 time to evaluate : 4.292 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3196 time to fit residues: 10.0434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 235 optimal weight: 0.9990 chunk 378 optimal weight: 20.0000 chunk 231 optimal weight: 9.9990 chunk 179 optimal weight: 10.0000 chunk 263 optimal weight: 0.8980 chunk 397 optimal weight: 10.0000 chunk 365 optimal weight: 2.9990 chunk 316 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 244 optimal weight: 20.0000 chunk 194 optimal weight: 20.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 320 ASN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 33947 Z= 0.251 Angle : 0.627 13.169 46258 Z= 0.328 Chirality : 0.043 0.241 5282 Planarity : 0.004 0.062 5664 Dihedral : 16.763 138.284 5366 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.05 % 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: -1.17 (0.13), residues: 3920 helix: 0.66 (0.13), residues: 1590 sheet: -0.87 (0.26), residues: 389 loop : -2.06 (0.13), residues: 1941 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 333 time to evaluate : 4.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 338 average time/residue: 0.4731 time to fit residues: 263.7137 Evaluate side-chains 326 residues out of total 3387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 322 time to evaluate : 4.207 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3211 time to fit residues: 8.0563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 251 optimal weight: 1.9990 chunk 337 optimal weight: 20.0000 chunk 96 optimal weight: 3.9990 chunk 291 optimal weight: 8.9990 chunk 46 optimal weight: 0.0870 chunk 87 optimal weight: 5.9990 chunk 317 optimal weight: 0.7980 chunk 132 optimal weight: 7.9990 chunk 325 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 58 optimal weight: 0.0970 overall best weight: 1.3960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 320 ASN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.175551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.137834 restraints weight = 49519.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.129253 restraints weight = 79660.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.127875 restraints weight = 62212.943| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 33947 Z= 0.187 Angle : 0.600 12.543 46258 Z= 0.314 Chirality : 0.042 0.285 5282 Planarity : 0.004 0.052 5664 Dihedral : 16.682 136.781 5366 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.05 % 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: -0.94 (0.13), residues: 3920 helix: 0.87 (0.13), residues: 1589 sheet: -0.80 (0.25), residues: 415 loop : -1.94 (0.13), residues: 1916 =============================================================================== Job complete usr+sys time: 6673.47 seconds wall clock time: 120 minutes 58.30 seconds (7258.30 seconds total)