Starting phenix.real_space_refine (version: 1.21rc1) on Sat Jul 15 01:49:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aoz_11848/07_2023/7aoz_11848_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aoz_11848/07_2023/7aoz_11848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aoz_11848/07_2023/7aoz_11848.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aoz_11848/07_2023/7aoz_11848.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aoz_11848/07_2023/7aoz_11848_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aoz_11848/07_2023/7aoz_11848_neut.pdb" } resolution = 2.85 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= 0.005 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: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 41 5.49 5 Mg 1 5.21 5 S 142 5.16 5 C 20102 2.51 5 N 5254 2.21 5 O 5968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 99": "NH1" <-> "NH2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A ARG 386": "NH1" <-> "NH2" Residue "A ARG 395": "NH1" <-> "NH2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A ARG 537": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 687": "NH1" <-> "NH2" Residue "A GLU 694": "OE1" <-> "OE2" Residue "A ARG 696": "NH1" <-> "NH2" Residue "A ARG 715": "NH1" <-> "NH2" Residue "A GLU 764": "OE1" <-> "OE2" Residue "A ARG 872": "NH1" <-> "NH2" Residue "A ARG 897": "NH1" <-> "NH2" Residue "A ARG 899": "NH1" <-> "NH2" Residue "A GLU 914": "OE1" <-> "OE2" Residue "A PHE 964": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 976": "OE1" <-> "OE2" Residue "A GLU 1034": "OE1" <-> "OE2" Residue "A ARG 1043": "NH1" <-> "NH2" Residue "A PHE 1136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1211": "NH1" <-> "NH2" Residue "A ARG 1263": "NH1" <-> "NH2" Residue "B ARG 29": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ARG 204": "NH1" <-> "NH2" Residue "B ARG 206": "NH1" <-> "NH2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "B ARG 250": "NH1" <-> "NH2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B ARG 351": "NH1" <-> "NH2" Residue "B ARG 358": "NH1" <-> "NH2" Residue "B GLU 375": "OE1" <-> "OE2" Residue "B ARG 382": "NH1" <-> "NH2" Residue "B ARG 392": "NH1" <-> "NH2" Residue "B ARG 442": "NH1" <-> "NH2" Residue "B ARG 478": "NH1" <-> "NH2" Residue "B GLU 533": "OE1" <-> "OE2" Residue "B ARG 553": "NH1" <-> "NH2" Residue "B ARG 554": "NH1" <-> "NH2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "B ARG 572": "NH1" <-> "NH2" Residue "B ARG 589": "NH1" <-> "NH2" Residue "B ARG 648": "NH1" <-> "NH2" Residue "B ARG 668": "NH1" <-> "NH2" Residue "B ARG 706": "NH1" <-> "NH2" Residue "B ARG 792": "NH1" <-> "NH2" Residue "B ARG 794": "NH1" <-> "NH2" Residue "B ARG 808": "NH1" <-> "NH2" Residue "B ARG 821": "NH1" <-> "NH2" Residue "B ARG 856": "NH1" <-> "NH2" Residue "B ARG 876": "NH1" <-> "NH2" Residue "B ARG 923": "NH1" <-> "NH2" Residue "B GLU 931": "OE1" <-> "OE2" Residue "B GLU 974": "OE1" <-> "OE2" Residue "B GLU 992": "OE1" <-> "OE2" Residue "B ARG 1047": "NH1" <-> "NH2" Residue "B ARG 1058": "NH1" <-> "NH2" Residue "B ARG 1105": "NH1" <-> "NH2" Residue "B ARG 1134": "NH1" <-> "NH2" Residue "C ARG 5": "NH1" <-> "NH2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 270": "NH1" <-> "NH2" Residue "E ARG 34": "NH1" <-> "NH2" Residue "E ARG 51": "NH1" <-> "NH2" Residue "E ARG 138": "NH1" <-> "NH2" Residue "E ARG 154": "NH1" <-> "NH2" Residue "E ARG 166": "NH1" <-> "NH2" Residue "F ARG 75": "NH1" <-> "NH2" Residue "F GLU 122": "OE1" <-> "OE2" Residue "F GLU 131": "OE1" <-> "OE2" Residue "G ARG 28": "NH1" <-> "NH2" Residue "I PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 210": "NH1" <-> "NH2" Residue "I ARG 317": "NH1" <-> "NH2" Residue "I GLU 352": "OE1" <-> "OE2" Residue "I ARG 583": "NH1" <-> "NH2" Residue "I ARG 595": "NH1" <-> "NH2" Residue "I ARG 659": "NH1" <-> "NH2" Residue "I ARG 710": "NH1" <-> "NH2" Residue "I ARG 784": "NH1" <-> "NH2" Residue "J ARG 24": "NH1" <-> "NH2" Residue "S ARG 119": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 31512 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 10188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1268, 10188 Classifications: {'peptide': 1268} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 1223} Chain: "B" Number of atoms: 9091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 9091 Classifications: {'peptide': 1129} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1076} Chain breaks: 2 Chain: "C" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2484 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 9, 'TRANS': 294} Chain: "E" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1495 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 8, 'TRANS': 175} Chain: "F" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 849 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "G" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1192 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 3, 'TRANS': 149} Chain breaks: 1 Chain: "I" Number of atoms: 3903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3903 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 443} Chain breaks: 3 Chain: "J" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 490 Classifications: {'peptide': 61} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 58} Chain: "N" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 327 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "P" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 108 Classifications: {'RNA': 5} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4} Chain: "S" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 952 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 114} 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: "T" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 428 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain breaks: 1 Chain: "A" 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} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 360 SG CYS A 49 88.906 103.054 62.445 1.00 93.69 S ATOM 382 SG CYS A 52 92.632 103.229 61.685 1.00 87.66 S ATOM 434 SG CYS A 59 91.146 99.994 63.072 1.00 85.61 S ATOM 694 SG CYS A 90 75.431 100.324 109.399 1.00113.59 S ATOM 718 SG CYS A 93 76.899 103.755 110.294 1.00116.72 S ATOM 1016 SG CYS A 130 76.654 101.059 112.924 1.00119.32 S ATOM 1059 SG CYS A 135 73.507 102.695 111.733 1.00122.90 S ATOM 18688 SG CYS B1087 99.163 104.548 76.572 1.00 74.24 S ATOM 18711 SG CYS B1090 95.648 103.339 77.448 1.00 75.71 S ATOM 18800 SG CYS B1103 96.039 105.895 74.870 1.00 76.68 S ATOM 18825 SG CYS B1106 96.715 106.919 78.411 1.00 78.28 S ATOM 27059 SG CYS I 326 101.623 96.083 38.599 1.00153.19 S ATOM 27372 SG CYS I 363 99.580 92.819 39.498 1.00135.23 S ATOM 27396 SG CYS I 366 102.989 93.435 41.068 1.00134.35 S Time building chain proxies: 14.32, per 1000 atoms: 0.45 Number of scatterers: 31512 At special positions: 0 Unit cell: (162.716, 152.081, 154.208, 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 4 29.99 S 142 16.00 P 41 15.00 Mg 1 11.99 O 5968 8.00 N 5254 7.00 C 20102 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS J 7 " - pdb=" SG CYS J 39 " distance=2.04 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: 11.56 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1302 " pdb="ZN ZN A1302 " - pdb=" NE2 HIS A 62 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 52 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 59 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 49 " pdb=" ZN A1303 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 135 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 93 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 90 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1103 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1090 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1106 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1087 " pdb=" ZN I 801 " pdb="ZN ZN I 801 " - pdb=" ND1 HIS I 328 " pdb="ZN ZN I 801 " - pdb=" SG CYS I 366 " pdb="ZN ZN I 801 " - pdb=" SG CYS I 363 " pdb="ZN ZN I 801 " - pdb=" SG CYS I 326 " Number of angles added : 18 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7228 Finding SS restraints... Secondary structure from input PDB file: 151 helices and 46 sheets defined 41.6% alpha, 15.3% beta 16 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 8.76 Creating SS restraints... Processing helix chain 'A' and resid 13 through 19 Processing helix chain 'A' and resid 78 through 87 Processing helix chain 'A' and resid 113 through 126 Processing helix chain 'A' and resid 161 through 171 removed outlier: 3.691A pdb=" N ILE A 165 " --> pdb=" O PRO A 161 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER A 171 " --> pdb=" O GLN A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 176 through 181 Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 218 through 233 Processing helix chain 'A' and resid 236 through 249 removed outlier: 3.874A pdb=" N ILE A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 253 Processing helix chain 'A' and resid 261 through 267 removed outlier: 3.853A pdb=" N ILE A 265 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 304 through 311 Processing helix chain 'A' and resid 321 through 331 Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 428 through 438 Processing helix chain 'A' and resid 460 through 471 Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'A' and resid 485 through 488 removed outlier: 4.053A pdb=" N ARG A 488 " --> pdb=" O LYS A 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 485 through 488' Processing helix chain 'A' and resid 499 through 508 removed outlier: 3.574A pdb=" N ILE A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.884A pdb=" N VAL A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 549 Processing helix chain 'A' and resid 550 through 573 Processing helix chain 'A' and resid 577 through 582 removed outlier: 3.715A pdb=" N LEU A 581 " --> pdb=" O THR A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 615 Processing helix chain 'A' and resid 622 through 656 Processing helix chain 'A' and resid 659 through 668 Processing helix chain 'A' and resid 672 through 681 Processing helix chain 'A' and resid 711 through 715 Processing helix chain 'A' and resid 727 through 764 Processing helix chain 'A' and resid 809 through 821 Processing helix chain 'A' and resid 841 through 846 removed outlier: 3.806A pdb=" N VAL A 844 " --> pdb=" O ASN A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 877 Processing helix chain 'A' and resid 882 through 893 removed outlier: 3.588A pdb=" N GLU A 886 " --> pdb=" O ILE A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 919 removed outlier: 3.620A pdb=" N THR A 919 " --> pdb=" O LYS A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 943 Processing helix chain 'A' and resid 944 through 946 No H-bonds generated for 'chain 'A' and resid 944 through 946' Processing helix chain 'A' and resid 960 through 970 Processing helix chain 'A' and resid 984 through 996 removed outlier: 4.071A pdb=" N LEU A 988 " --> pdb=" O ASP A 984 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 991 " --> pdb=" O LYS A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1004 Processing helix chain 'A' and resid 1024 through 1030 Processing helix chain 'A' and resid 1033 through 1048 removed outlier: 3.660A pdb=" N PHE A1047 " --> pdb=" O ARG A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1093 removed outlier: 3.555A pdb=" N ASN A1081 " --> pdb=" O PRO A1077 " (cutoff:3.500A) Proline residue: A1090 - end of helix Processing helix chain 'A' and resid 1131 through 1136 removed outlier: 4.089A pdb=" N SER A1135 " --> pdb=" O GLU A1132 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE A1136 " --> pdb=" O LEU A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1155 Processing helix chain 'A' and resid 1155 through 1170 Processing helix chain 'A' and resid 1175 through 1177 No H-bonds generated for 'chain 'A' and resid 1175 through 1177' Processing helix chain 'A' and resid 1178 through 1190 Processing helix chain 'A' and resid 1207 through 1215 Processing helix chain 'A' and resid 1218 through 1227 Processing helix chain 'A' and resid 1234 through 1241 Processing helix chain 'A' and resid 1247 through 1252 removed outlier: 3.705A pdb=" N TYR A1252 " --> pdb=" O THR A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1258 through 1263 Processing helix chain 'B' and resid 9 through 17 Processing helix chain 'B' and resid 28 through 43 removed outlier: 4.603A pdb=" N PHE B 33 " --> pdb=" O ARG B 29 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLN B 34 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 51 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 233 through 241 Processing helix chain 'B' and resid 244 through 253 removed outlier: 3.712A pdb=" N ILE B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 278 removed outlier: 3.861A pdb=" N LEU B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 298 Processing helix chain 'B' and resid 307 through 314 removed outlier: 3.763A pdb=" N ASN B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 344 removed outlier: 3.509A pdb=" N LYS B 327 " --> pdb=" O PRO B 323 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 348 removed outlier: 3.524A pdb=" N TYR B 348 " --> pdb=" O THR B 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 345 through 348' Processing helix chain 'B' and resid 353 through 357 removed outlier: 3.545A pdb=" N CYS B 356 " --> pdb=" O SER B 353 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS B 357 " --> pdb=" O MET B 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 353 through 357' Processing helix chain 'B' and resid 361 through 391 removed outlier: 3.570A pdb=" N TYR B 365 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 416 Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 463 through 467 Processing helix chain 'B' and resid 498 through 515 Processing helix chain 'B' and resid 518 through 522 Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 544 through 558 removed outlier: 3.657A pdb=" N ASP B 551 " --> pdb=" O ASP B 547 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET B 558 " --> pdb=" O ARG B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 611 removed outlier: 4.150A pdb=" N SER B 609 " --> pdb=" O PRO B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 614 No H-bonds generated for 'chain 'B' and resid 612 through 614' Processing helix chain 'B' and resid 615 through 623 Processing helix chain 'B' and resid 632 through 637 removed outlier: 3.653A pdb=" N PHE B 637 " --> pdb=" O GLU B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 649 removed outlier: 3.660A pdb=" N MET B 649 " --> pdb=" O GLN B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 656 removed outlier: 3.666A pdb=" N LYS B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 669 removed outlier: 3.890A pdb=" N ASP B 669 " --> pdb=" O GLU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 676 Processing helix chain 'B' and resid 678 through 682 Processing helix chain 'B' and resid 683 through 695 removed outlier: 3.946A pdb=" N LYS B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 731 Processing helix chain 'B' and resid 762 through 767 Processing helix chain 'B' and resid 795 through 799 Processing helix chain 'B' and resid 898 through 902 removed outlier: 3.822A pdb=" N LEU B 902 " --> pdb=" O GLU B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 923 removed outlier: 3.728A pdb=" N PHE B 921 " --> pdb=" O SER B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 941 removed outlier: 4.043A pdb=" N LEU B 929 " --> pdb=" O THR B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 977 removed outlier: 3.565A pdb=" N TYR B 965 " --> pdb=" O SER B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 990 Processing helix chain 'B' and resid 1054 through 1065 removed outlier: 3.521A pdb=" N GLY B1065 " --> pdb=" O LEU B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1074 Processing helix chain 'B' and resid 1077 through 1081 removed outlier: 3.660A pdb=" N TYR B1081 " --> pdb=" O GLU B1078 " (cutoff:3.500A) Processing helix chain 'B' and resid 1103 through 1109 Processing helix chain 'B' and resid 1121 through 1134 Processing helix chain 'C' and resid 15 through 30 Processing helix chain 'C' and resid 48 through 58 removed outlier: 4.152A pdb=" N HIS C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 64 removed outlier: 5.353A pdb=" N MET C 62 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS C 63 " --> pdb=" O PRO C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 68 through 74 Processing helix chain 'C' and resid 95 through 99 Processing helix chain 'C' and resid 117 through 123 Processing helix chain 'C' and resid 152 through 157 removed outlier: 3.641A pdb=" N SER C 156 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS C 157 " --> pdb=" O ASP C 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 152 through 157' Processing helix chain 'C' and resid 162 through 177 Processing helix chain 'C' and resid 191 through 193 No H-bonds generated for 'chain 'C' and resid 191 through 193' Processing helix chain 'C' and resid 207 through 229 removed outlier: 3.909A pdb=" N CYS C 211 " --> pdb=" O ASP C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 265 Processing helix chain 'C' and resid 278 through 282 Processing helix chain 'C' and resid 283 through 304 Processing helix chain 'E' and resid 4 through 22 removed outlier: 3.963A pdb=" N TYR E 8 " --> pdb=" O TYR E 4 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU E 15 " --> pdb=" O LYS E 11 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR E 17 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 33 removed outlier: 3.625A pdb=" N LEU E 32 " --> pdb=" O ASN E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 101 removed outlier: 4.039A pdb=" N TYR E 101 " --> pdb=" O ASN E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 98 through 101' Processing helix chain 'E' and resid 117 through 129 Processing helix chain 'E' and resid 146 through 153 Processing helix chain 'F' and resid 63 through 75 removed outlier: 3.778A pdb=" N ARG F 75 " --> pdb=" O ARG F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 95 removed outlier: 3.543A pdb=" N ILE F 82 " --> pdb=" O SER F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 123 Processing helix chain 'F' and resid 140 through 142 No H-bonds generated for 'chain 'F' and resid 140 through 142' Processing helix chain 'F' and resid 143 through 161 Processing helix chain 'G' and resid 15 through 19 Processing helix chain 'G' and resid 22 through 36 Processing helix chain 'G' and resid 109 through 113 removed outlier: 3.529A pdb=" N SER G 112 " --> pdb=" O SER G 109 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY G 113 " --> pdb=" O ARG G 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 109 through 113' Processing helix chain 'I' and resid 105 through 119 Processing helix chain 'I' and resid 170 through 186 removed outlier: 6.075A pdb=" N ASP I 180 " --> pdb=" O GLU I 176 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N GLN I 181 " --> pdb=" O LYS I 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 254 through 264 removed outlier: 3.711A pdb=" N ASP I 258 " --> pdb=" O ASN I 254 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LYS I 261 " --> pdb=" O SER I 257 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL I 262 " --> pdb=" O ASP I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 267 No H-bonds generated for 'chain 'I' and resid 265 through 267' Processing helix chain 'I' and resid 269 through 272 Processing helix chain 'I' and resid 273 through 279 Processing helix chain 'I' and resid 283 through 285 No H-bonds generated for 'chain 'I' and resid 283 through 285' Processing helix chain 'I' and resid 286 through 291 Processing helix chain 'I' and resid 326 through 336 removed outlier: 3.887A pdb=" N ILE I 330 " --> pdb=" O CYS I 326 " (cutoff:3.500A) Processing helix chain 'I' and resid 341 through 353 Processing helix chain 'I' and resid 638 through 649 Processing helix chain 'I' and resid 688 through 694 removed outlier: 4.159A pdb=" N TYR I 692 " --> pdb=" O LEU I 688 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE I 693 " --> pdb=" O LYS I 689 " (cutoff:3.500A) Processing helix chain 'I' and resid 705 through 710 Processing helix chain 'I' and resid 723 through 742 Processing helix chain 'I' and resid 756 through 770 removed outlier: 3.571A pdb=" N LYS I 770 " --> pdb=" O ILE I 766 " (cutoff:3.500A) Processing helix chain 'I' and resid 773 through 793 removed outlier: 5.524A pdb=" N THR I 783 " --> pdb=" O ASP I 779 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ARG I 784 " --> pdb=" O GLU I 780 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 20 removed outlier: 3.631A pdb=" N LYS J 20 " --> pdb=" O HIS J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 36 removed outlier: 3.791A pdb=" N SER J 34 " --> pdb=" O ASP J 30 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS J 36 " --> pdb=" O LEU J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 47 Processing helix chain 'S' and resid 37 through 51 Processing helix chain 'S' and resid 59 through 63 Processing helix chain 'S' and resid 72 through 81 Processing helix chain 'S' and resid 82 through 85 Processing helix chain 'S' and resid 102 through 109 Processing helix chain 'S' and resid 112 through 131 removed outlier: 3.542A pdb=" N GLU S 116 " --> pdb=" O GLY S 112 " (cutoff:3.500A) Processing helix chain 'S' and resid 144 through 149 removed outlier: 3.562A pdb=" N PHE S 148 " --> pdb=" O TYR S 144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1229 through 1231 Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 24 removed outlier: 4.397A pdb=" N SER A 67 " --> pdb=" O ILE A 24 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 74 Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 144 removed outlier: 4.295A pdb=" N PHE A 151 " --> pdb=" O VAL A 160 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1027 through 1029 removed outlier: 7.351A pdb=" N ILE A 402 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL A 289 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ILE A 404 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N GLY A 291 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 312 through 316 removed outlier: 7.341A pdb=" N ALA A 369 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N VAL A 334 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 518 through 519 Processing sheet with id=AA8, first strand: chain 'A' and resid 684 through 685 Processing sheet with id=AA9, first strand: chain 'A' and resid 767 through 768 removed outlier: 6.456A pdb=" N VAL A 774 " --> pdb=" O ILE A 781 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 796 through 799 Processing sheet with id=AB2, first strand: chain 'A' and resid 825 through 826 Processing sheet with id=AB3, first strand: chain 'A' and resid 1106 through 1107 Processing sheet with id=AB4, first strand: chain 'A' and resid 998 through 999 Processing sheet with id=AB5, first strand: chain 'A' and resid 1008 through 1012 Processing sheet with id=AB6, first strand: chain 'F' and resid 137 through 138 removed outlier: 3.685A pdb=" N LYS A1253 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N TYR A1254 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 137 through 138 removed outlier: 3.685A pdb=" N LYS A1253 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N TYR A1254 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS G 47 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ALA G 77 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ALA G 45 " --> pdb=" O ALA G 77 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1264 through 1265 Processing sheet with id=AB9, first strand: chain 'B' and resid 54 through 59 removed outlier: 5.602A pdb=" N ILE B 68 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 57 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LYS B 104 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LYS B 116 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL B 106 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ILE B 114 " --> pdb=" O VAL B 106 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 74 through 76 Processing sheet with id=AC2, first strand: chain 'B' and resid 157 through 158 Processing sheet with id=AC3, first strand: chain 'B' and resid 359 through 360 removed outlier: 6.553A pdb=" N ASN B 169 " --> pdb=" O GLY B 445 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 179 through 184 removed outlier: 6.479A pdb=" N SER B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 493 through 494 Processing sheet with id=AC6, first strand: chain 'B' and resid 598 through 599 Processing sheet with id=AC7, first strand: chain 'B' and resid 535 through 540 removed outlier: 6.783A pdb=" N ILE B 530 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SER B 539 " --> pdb=" O PHE B 528 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N PHE B 528 " --> pdb=" O SER B 539 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE B 580 " --> pdb=" O PRO B 529 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N THR B 531 " --> pdb=" O ILE B 580 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.771A pdb=" N ILE B 772 " --> pdb=" O ARG B 875 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LYS B 864 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LEU B 861 " --> pdb=" O LYS B 864 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYS B 866 " --> pdb=" O VAL B 859 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL B 859 " --> pdb=" O LYS B 866 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARG B 868 " --> pdb=" O VAL B 857 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL B 857 " --> pdb=" O ARG B 868 " (cutoff:3.500A) removed outlier: 9.183A pdb=" N ASP J 61 " --> pdb=" O GLU B 855 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL B 857 " --> pdb=" O ASP J 61 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 723 through 724 Processing sheet with id=AD1, first strand: chain 'B' and resid 992 through 993 removed outlier: 6.528A pdb=" N ILE B 758 " --> pdb=" O ALA B 894 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N VAL B 896 " --> pdb=" O ILE B 758 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE B 760 " --> pdb=" O VAL B 896 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE B1009 " --> pdb=" O LEU B 746 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1086 through 1087 Processing sheet with id=AD3, first strand: chain 'B' and resid 1095 through 1097 Processing sheet with id=AD4, first strand: chain 'C' and resid 5 through 13 Processing sheet with id=AD5, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AD6, first strand: chain 'C' and resid 37 through 43 removed outlier: 5.418A pdb=" N GLY C 38 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N PHE C 144 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N VAL C 40 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE C 142 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 93 through 94 Processing sheet with id=AD8, first strand: chain 'C' and resid 251 through 253 Processing sheet with id=AD9, first strand: chain 'E' and resid 35 through 38 Processing sheet with id=AE1, first strand: chain 'E' and resid 63 through 65 removed outlier: 6.439A pdb=" N ILE E 83 " --> pdb=" O PHE E 95 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 113 through 115 removed outlier: 6.319A pdb=" N MET E 142 " --> pdb=" O ILE E 181 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 84 through 91 removed outlier: 4.411A pdb=" N VAL G 97 " --> pdb=" O LEU G 108 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL G 153 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ALA G 144 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU G 155 " --> pdb=" O MET G 142 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 114 through 116 Processing sheet with id=AE5, first strand: chain 'I' and resid 121 through 124 removed outlier: 4.447A pdb=" N TYR I 234 " --> pdb=" O ARG I 124 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 161 through 166 removed outlier: 6.400A pdb=" N ILE I 128 " --> pdb=" O LYS I 162 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE I 164 " --> pdb=" O ILE I 128 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ILE I 130 " --> pdb=" O ILE I 164 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N PHE I 166 " --> pdb=" O ILE I 130 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N VAL I 132 " --> pdb=" O PHE I 166 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 209 through 217 Processing sheet with id=AE8, first strand: chain 'I' and resid 355 through 357 Processing sheet with id=AE9, first strand: chain 'I' and resid 657 through 659 Processing sheet with id=AF1, first strand: chain 'I' and resid 667 through 670 removed outlier: 4.209A pdb=" N LYS I 667 " --> pdb=" O GLU I 678 " (cutoff:3.500A) 1295 hydrogen bonds defined for protein. 3558 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 13.40 Time building geometry restraints manager: 12.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9880 1.34 - 1.46: 7559 1.46 - 1.59: 14494 1.59 - 1.71: 79 1.71 - 1.83: 223 Bond restraints: 32235 Sorted by residual: bond pdb=" C3' DT N 55 " pdb=" O3' DT N 55 " ideal model delta sigma weight residual 1.422 1.515 -0.093 3.00e-02 1.11e+03 9.62e+00 bond pdb=" C3' DA N 53 " pdb=" O3' DA N 53 " ideal model delta sigma weight residual 1.422 1.514 -0.092 3.00e-02 1.11e+03 9.50e+00 bond pdb=" C3' DC N 54 " pdb=" O3' DC N 54 " ideal model delta sigma weight residual 1.422 1.512 -0.090 3.00e-02 1.11e+03 9.09e+00 bond pdb=" C3' DG N 57 " pdb=" O3' DG N 57 " ideal model delta sigma weight residual 1.422 1.512 -0.090 3.00e-02 1.11e+03 8.96e+00 bond pdb=" C3' DA N 48 " pdb=" O3' DA N 48 " ideal model delta sigma weight residual 1.422 1.512 -0.090 3.00e-02 1.11e+03 8.93e+00 ... (remaining 32230 not shown) Histogram of bond angle deviations from ideal: 99.69 - 106.57: 1015 106.57 - 113.44: 17600 113.44 - 120.32: 12109 120.32 - 127.19: 12659 127.19 - 134.07: 364 Bond angle restraints: 43747 Sorted by residual: angle pdb=" C5' DC N 51 " pdb=" C4' DC N 51 " pdb=" O4' DC N 51 " ideal model delta sigma weight residual 109.40 103.02 6.38 1.50e+00 4.44e-01 1.81e+01 angle pdb=" C5' DC N 52 " pdb=" C4' DC N 52 " pdb=" O4' DC N 52 " ideal model delta sigma weight residual 109.40 103.18 6.22 1.50e+00 4.44e-01 1.72e+01 angle pdb=" C5' DG N 57 " pdb=" C4' DG N 57 " pdb=" O4' DG N 57 " ideal model delta sigma weight residual 109.40 103.18 6.22 1.50e+00 4.44e-01 1.72e+01 angle pdb=" C5' DA N 49 " pdb=" C4' DA N 49 " pdb=" O4' DA N 49 " ideal model delta sigma weight residual 109.40 103.48 5.92 1.50e+00 4.44e-01 1.56e+01 angle pdb=" C5' DC N 50 " pdb=" C4' DC N 50 " pdb=" O4' DC N 50 " ideal model delta sigma weight residual 109.40 103.56 5.84 1.50e+00 4.44e-01 1.51e+01 ... (remaining 43742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 18136 17.98 - 35.96: 935 35.96 - 53.93: 271 53.93 - 71.91: 76 71.91 - 89.89: 8 Dihedral angle restraints: 19426 sinusoidal: 8232 harmonic: 11194 Sorted by residual: dihedral pdb=" CB CYS J 7 " pdb=" SG CYS J 7 " pdb=" SG CYS J 39 " pdb=" CB CYS J 39 " ideal model delta sinusoidal sigma weight residual -86.00 -159.60 73.60 1 1.00e+01 1.00e-02 6.89e+01 dihedral pdb=" CA VAL I 660 " pdb=" C VAL I 660 " pdb=" N HIS I 661 " pdb=" CA HIS I 661 " ideal model delta harmonic sigma weight residual 180.00 -143.67 -36.33 0 5.00e+00 4.00e-02 5.28e+01 dihedral pdb=" CA ILE A 458 " pdb=" C ILE A 458 " pdb=" N GLN A 459 " pdb=" CA GLN A 459 " ideal model delta harmonic sigma weight residual 180.00 147.71 32.29 0 5.00e+00 4.00e-02 4.17e+01 ... (remaining 19423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3700 0.046 - 0.093: 902 0.093 - 0.139: 306 0.139 - 0.186: 33 0.186 - 0.232: 11 Chirality restraints: 4952 Sorted by residual: chirality pdb=" C3' DT N 55 " pdb=" C4' DT N 55 " pdb=" O3' DT N 55 " pdb=" C2' DT N 55 " both_signs ideal model delta sigma weight residual False -2.66 -2.89 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" C3' DT N 56 " pdb=" C4' DT N 56 " pdb=" O3' DT N 56 " pdb=" C2' DT N 56 " both_signs ideal model delta sigma weight residual False -2.66 -2.88 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C3' DA N 53 " pdb=" C4' DA N 53 " pdb=" O3' DA N 53 " pdb=" C2' DA N 53 " both_signs ideal model delta sigma weight residual False -2.66 -2.88 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 4949 not shown) Planarity restraints: 5392 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 856 " 0.012 2.00e-02 2.50e+03 2.52e-02 6.35e+00 pdb=" C ARG B 856 " -0.044 2.00e-02 2.50e+03 pdb=" O ARG B 856 " 0.017 2.00e-02 2.50e+03 pdb=" N VAL B 857 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 938 " 0.021 2.00e-02 2.50e+03 1.84e-02 5.94e+00 pdb=" CG PHE A 938 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 938 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 938 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 938 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 938 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 938 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 316 " -0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO B 317 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 317 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 317 " -0.028 5.00e-02 4.00e+02 ... (remaining 5389 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 335 2.62 - 3.19: 28079 3.19 - 3.76: 47599 3.76 - 4.33: 70895 4.33 - 4.90: 115641 Nonbonded interactions: 262549 Sorted by model distance: nonbonded pdb=" OD1 ASP A 415 " pdb="MG MG A1301 " model vdw 2.045 2.170 nonbonded pdb=" OD1 ASP A 417 " pdb="MG MG A1301 " model vdw 2.071 2.170 nonbonded pdb=" OG SER A 98 " pdb=" OE1 GLU A 100 " model vdw 2.076 2.440 nonbonded pdb=" OH TYR A 783 " pdb=" OD2 ASP E 177 " model vdw 2.086 2.440 nonbonded pdb=" OG SER A 145 " pdb=" O LYS A 148 " model vdw 2.095 2.440 ... (remaining 262544 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: 2.260 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: 9.750 Check model and map are aligned: 0.500 Set scattering table: 0.270 Process input model: 86.240 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.110 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:10.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 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 : 0.005 0.093 32235 Z= 0.303 Angle : 0.651 8.844 43747 Z= 0.353 Chirality : 0.047 0.232 4952 Planarity : 0.003 0.050 5392 Dihedral : 12.750 89.890 12195 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer Outliers : 2.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.31 (0.14), residues: 3752 helix: 0.94 (0.14), residues: 1365 sheet: -0.75 (0.21), residues: 536 loop : -0.87 (0.15), residues: 1851 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 446 time to evaluate : 3.698 Fit side-chains revert: symmetry clash outliers start: 84 outliers final: 18 residues processed: 515 average time/residue: 1.6349 time to fit residues: 978.2248 Evaluate side-chains 277 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 259 time to evaluate : 3.654 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 17 residues processed: 1 average time/residue: 0.2783 time to fit residues: 5.4653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 318 optimal weight: 9.9990 chunk 285 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 192 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 chunk 295 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 219 optimal weight: 4.9990 chunk 342 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS A 184 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 GLN A 853 ASN ** G 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 GLN I 181 GLN I 626 GLN I 776 GLN S 90 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 32235 Z= 0.280 Angle : 0.585 10.917 43747 Z= 0.311 Chirality : 0.045 0.312 4952 Planarity : 0.004 0.046 5392 Dihedral : 10.675 61.586 4551 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer Outliers : 2.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.10 (0.14), residues: 3752 helix: 1.12 (0.14), residues: 1386 sheet: -0.61 (0.22), residues: 553 loop : -0.79 (0.15), residues: 1813 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 272 time to evaluate : 3.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 32 residues processed: 350 average time/residue: 1.5922 time to fit residues: 653.2685 Evaluate side-chains 279 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 247 time to evaluate : 3.620 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 30 residues processed: 2 average time/residue: 1.0324 time to fit residues: 7.5198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 190 optimal weight: 0.5980 chunk 106 optimal weight: 6.9990 chunk 284 optimal weight: 0.8980 chunk 233 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 342 optimal weight: 5.9990 chunk 370 optimal weight: 4.9990 chunk 305 optimal weight: 0.0980 chunk 340 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 275 optimal weight: 5.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS A 184 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 GLN A 853 ASN A 947 HIS ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 GLN I 181 GLN I 626 GLN I 776 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 32235 Z= 0.315 Angle : 0.580 9.668 43747 Z= 0.308 Chirality : 0.045 0.300 4952 Planarity : 0.004 0.051 5392 Dihedral : 10.686 59.864 4551 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer Outliers : 2.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.05 (0.14), residues: 3752 helix: 1.16 (0.14), residues: 1394 sheet: -0.47 (0.22), residues: 540 loop : -0.80 (0.15), residues: 1818 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 255 time to evaluate : 3.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 103 outliers final: 50 residues processed: 341 average time/residue: 1.5789 time to fit residues: 633.6756 Evaluate side-chains 290 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 240 time to evaluate : 3.687 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 48 residues processed: 2 average time/residue: 0.3262 time to fit residues: 6.1438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 338 optimal weight: 0.9990 chunk 257 optimal weight: 0.7980 chunk 177 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 230 optimal weight: 5.9990 chunk 344 optimal weight: 4.9990 chunk 364 optimal weight: 0.4980 chunk 179 optimal weight: 0.7980 chunk 326 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 GLN A 853 ASN ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN E 168 ASN F 161 GLN ** G 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 GLN I 181 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 32235 Z= 0.167 Angle : 0.524 11.301 43747 Z= 0.277 Chirality : 0.043 0.319 4952 Planarity : 0.003 0.052 5392 Dihedral : 10.427 59.870 4551 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer Outliers : 2.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.17 (0.14), residues: 3752 helix: 1.40 (0.14), residues: 1390 sheet: -0.29 (0.22), residues: 538 loop : -0.75 (0.15), residues: 1824 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 264 time to evaluate : 3.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 55 residues processed: 343 average time/residue: 1.5953 time to fit residues: 640.7838 Evaluate side-chains 295 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 240 time to evaluate : 3.762 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 51 residues processed: 4 average time/residue: 0.2985 time to fit residues: 7.3377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 303 optimal weight: 2.9990 chunk 206 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 271 optimal weight: 0.0770 chunk 150 optimal weight: 1.9990 chunk 310 optimal weight: 2.9990 chunk 251 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 186 optimal weight: 3.9990 chunk 327 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 GLN A 853 ASN ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 181 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 32235 Z= 0.274 Angle : 0.554 10.404 43747 Z= 0.293 Chirality : 0.044 0.347 4952 Planarity : 0.004 0.063 5392 Dihedral : 10.406 59.933 4551 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer Outliers : 2.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.16 (0.14), residues: 3752 helix: 1.40 (0.14), residues: 1389 sheet: -0.29 (0.22), residues: 541 loop : -0.76 (0.15), residues: 1822 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 248 time to evaluate : 3.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 100 outliers final: 63 residues processed: 333 average time/residue: 1.5778 time to fit residues: 617.9909 Evaluate side-chains 306 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 243 time to evaluate : 3.752 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 59 residues processed: 4 average time/residue: 0.6335 time to fit residues: 8.6492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 122 optimal weight: 5.9990 chunk 328 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 213 optimal weight: 0.0060 chunk 89 optimal weight: 0.8980 chunk 364 optimal weight: 0.4980 chunk 302 optimal weight: 0.0670 chunk 168 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 191 optimal weight: 1.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 GLN A 853 ASN G 100 GLN ** G 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 GLN I 181 GLN I 626 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 32235 Z= 0.138 Angle : 0.505 9.892 43747 Z= 0.268 Chirality : 0.042 0.212 4952 Planarity : 0.003 0.053 5392 Dihedral : 10.204 59.582 4551 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer Outliers : 2.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.32 (0.14), residues: 3752 helix: 1.57 (0.14), residues: 1389 sheet: -0.16 (0.23), residues: 535 loop : -0.71 (0.15), residues: 1828 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 266 time to evaluate : 4.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 56 residues processed: 338 average time/residue: 1.5984 time to fit residues: 638.0256 Evaluate side-chains 305 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 249 time to evaluate : 3.681 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 53 residues processed: 4 average time/residue: 0.9690 time to fit residues: 9.8826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 351 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 266 optimal weight: 3.9990 chunk 206 optimal weight: 10.0000 chunk 307 optimal weight: 3.9990 chunk 203 optimal weight: 6.9990 chunk 363 optimal weight: 10.0000 chunk 227 optimal weight: 6.9990 chunk 221 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS A 184 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 GLN A 853 ASN ** E 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 GLN ** G 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 181 GLN I 626 GLN S 62 ASN S 97 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.136 32235 Z= 0.604 Angle : 0.693 13.491 43747 Z= 0.366 Chirality : 0.050 0.367 4952 Planarity : 0.005 0.088 5392 Dihedral : 10.563 59.946 4551 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.64 % Favored : 93.34 % Rotamer Outliers : 2.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.07 (0.14), residues: 3752 helix: 1.14 (0.14), residues: 1387 sheet: -0.44 (0.22), residues: 561 loop : -0.83 (0.15), residues: 1804 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 238 time to evaluate : 3.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 62 residues processed: 319 average time/residue: 1.5490 time to fit residues: 583.7979 Evaluate side-chains 299 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 237 time to evaluate : 3.739 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 60 residues processed: 2 average time/residue: 0.8401 time to fit residues: 7.2273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 224 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 217 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 231 optimal weight: 2.9990 chunk 247 optimal weight: 2.9990 chunk 179 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 285 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN A 284 GLN A 853 ASN A1081 ASN ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 ASN ** G 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 GLN I 589 ASN I 626 GLN S 62 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 32235 Z= 0.181 Angle : 0.541 11.844 43747 Z= 0.287 Chirality : 0.043 0.212 4952 Planarity : 0.004 0.075 5392 Dihedral : 10.362 59.122 4551 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.60 % Favored : 94.38 % Rotamer Outliers : 2.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.17 (0.14), residues: 3752 helix: 1.42 (0.14), residues: 1383 sheet: -0.24 (0.22), residues: 539 loop : -0.77 (0.15), residues: 1830 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 250 time to evaluate : 3.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 56 residues processed: 319 average time/residue: 1.6527 time to fit residues: 622.3304 Evaluate side-chains 293 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 237 time to evaluate : 3.806 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 53 residues processed: 3 average time/residue: 0.6784 time to fit residues: 7.9718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 330 optimal weight: 5.9990 chunk 348 optimal weight: 2.9990 chunk 317 optimal weight: 9.9990 chunk 338 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 265 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 305 optimal weight: 6.9990 chunk 320 optimal weight: 4.9990 chunk 337 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS A 284 GLN A 853 ASN ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 ASN E 65 ASN ** E 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 GLN I 181 GLN I 626 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.102 32235 Z= 0.398 Angle : 0.621 11.900 43747 Z= 0.326 Chirality : 0.047 0.391 4952 Planarity : 0.004 0.087 5392 Dihedral : 10.439 59.597 4551 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.32 % Favored : 93.66 % Rotamer Outliers : 2.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.05 (0.14), residues: 3752 helix: 1.31 (0.14), residues: 1381 sheet: -0.38 (0.22), residues: 548 loop : -0.80 (0.15), residues: 1823 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 236 time to evaluate : 3.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 57 residues processed: 304 average time/residue: 1.6379 time to fit residues: 587.3395 Evaluate side-chains 286 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 229 time to evaluate : 3.759 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 56 residues processed: 1 average time/residue: 1.4922 time to fit residues: 7.2625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 222 optimal weight: 3.9990 chunk 358 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 169 optimal weight: 0.6980 chunk 248 optimal weight: 0.7980 chunk 375 optimal weight: 10.0000 chunk 345 optimal weight: 0.3980 chunk 299 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 231 optimal weight: 7.9990 chunk 183 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS A 284 GLN A 853 ASN B 47 HIS B 305 ASN ** B1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 GLN ** G 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 GLN I 626 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 32235 Z= 0.172 Angle : 0.551 11.602 43747 Z= 0.289 Chirality : 0.043 0.244 4952 Planarity : 0.004 0.058 5392 Dihedral : 10.250 59.774 4551 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.24 (0.14), residues: 3752 helix: 1.50 (0.14), residues: 1383 sheet: -0.22 (0.23), residues: 540 loop : -0.75 (0.15), residues: 1829 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 242 time to evaluate : 3.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 56 residues processed: 303 average time/residue: 1.6295 time to fit residues: 584.1339 Evaluate side-chains 285 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 229 time to evaluate : 4.039 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 55 residues processed: 1 average time/residue: 0.5451 time to fit residues: 6.5847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 237 optimal weight: 3.9990 chunk 318 optimal weight: 0.0970 chunk 91 optimal weight: 3.9990 chunk 275 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 299 optimal weight: 4.9990 chunk 125 optimal weight: 0.0000 chunk 307 optimal weight: 0.0970 chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 GLN A 853 ASN B 958 ASN ** B1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 GLN I 181 GLN I 626 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.092934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.065681 restraints weight = 63560.303| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.45 r_work: 0.2795 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 32235 Z= 0.138 Angle : 0.524 11.569 43747 Z= 0.273 Chirality : 0.042 0.228 4952 Planarity : 0.004 0.107 5392 Dihedral : 10.010 59.903 4551 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.47 (0.14), residues: 3752 helix: 1.78 (0.14), residues: 1375 sheet: -0.12 (0.23), residues: 538 loop : -0.68 (0.15), residues: 1839 =============================================================================== Job complete usr+sys time: 10794.90 seconds wall clock time: 193 minutes 26.35 seconds (11606.35 seconds total)