Starting phenix.real_space_refine (version: dev) on Tue Feb 21 08:22:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb8_24399/02_2023/7rb8_24399_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb8_24399/02_2023/7rb8_24399.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb8_24399/02_2023/7rb8_24399.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb8_24399/02_2023/7rb8_24399.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb8_24399/02_2023/7rb8_24399_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb8_24399/02_2023/7rb8_24399_updated.pdb" } resolution = 3.63 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= 0.003 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 Process input model Symmetric amino acids flipped Residue "A ASP 25": "OD1" <-> "OD2" Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 56": "OD1" <-> "OD2" Residue "A GLU 72": "OE1" <-> "OE2" Residue "A ASP 80": "OD1" <-> "OD2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "A ASP 154": "OD1" <-> "OD2" Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "D TYR 1420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1537": "OD1" <-> "OD2" Residue "D TYR 1639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1869": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 56": "OD1" <-> "OD2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 364": "OE1" <-> "OE2" Residue "C ASP 25": "OD1" <-> "OD2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 56": "OD1" <-> "OD2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C ASP 80": "OD1" <-> "OD2" Residue "C GLU 107": "OE1" <-> "OE2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 364": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 14226 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 5363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5363 Classifications: {'peptide': 667} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 643} Chain breaks: 2 Chain: "B" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.23, per 1000 atoms: 0.58 Number of scatterers: 14226 At special positions: 0 Unit cell: (110.21, 151.41, 139.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 91 16.00 P 8 15.00 Mg 4 11.99 O 2705 8.00 N 2418 7.00 C 9000 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: 6.01 Conformation dependent library (CDL) restraints added in 2.1 seconds 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3346 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 90 helices and 15 sheets defined 45.3% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 196 removed outlier: 3.954A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.627A pdb=" N PHE A 255 " --> pdb=" O ASN A 252 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 256' Processing helix chain 'A' and resid 258 through 261 removed outlier: 3.555A pdb=" N LEU A 261 " --> pdb=" O PRO A 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 258 through 261' Processing helix chain 'A' and resid 274 through 284 Processing helix chain 'A' and resid 287 through 296 removed outlier: 4.040A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.506A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'D' and resid 1211 through 1213 No H-bonds generated for 'chain 'D' and resid 1211 through 1213' Processing helix chain 'D' and resid 1219 through 1231 Processing helix chain 'D' and resid 1257 through 1262 Processing helix chain 'D' and resid 1265 through 1267 No H-bonds generated for 'chain 'D' and resid 1265 through 1267' Processing helix chain 'D' and resid 1275 through 1289 removed outlier: 3.623A pdb=" N ILE D1278 " --> pdb=" O LEU D1275 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA D1282 " --> pdb=" O ALA D1279 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU D1287 " --> pdb=" O ALA D1284 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA D1289 " --> pdb=" O MET D1286 " (cutoff:3.500A) Processing helix chain 'D' and resid 1305 through 1319 Processing helix chain 'D' and resid 1332 through 1342 Proline residue: D1336 - end of helix removed outlier: 3.545A pdb=" N PHE D1341 " --> pdb=" O LEU D1338 " (cutoff:3.500A) Processing helix chain 'D' and resid 1380 through 1384 removed outlier: 3.543A pdb=" N ILE D1383 " --> pdb=" O LYS D1380 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL D1384 " --> pdb=" O SER D1381 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1380 through 1384' Processing helix chain 'D' and resid 1394 through 1401 Processing helix chain 'D' and resid 1405 through 1410 Processing helix chain 'D' and resid 1420 through 1425 removed outlier: 3.780A pdb=" N GLN D1424 " --> pdb=" O TYR D1420 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY D1425 " --> pdb=" O TYR D1421 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1420 through 1425' Processing helix chain 'D' and resid 1436 through 1448 Processing helix chain 'D' and resid 1453 through 1471 removed outlier: 3.589A pdb=" N ASN D1471 " --> pdb=" O LEU D1467 " (cutoff:3.500A) Processing helix chain 'D' and resid 1490 through 1498 Processing helix chain 'D' and resid 1504 through 1511 Processing helix chain 'D' and resid 1529 through 1558 Processing helix chain 'D' and resid 1584 through 1615 Processing helix chain 'D' and resid 1617 through 1619 No H-bonds generated for 'chain 'D' and resid 1617 through 1619' Processing helix chain 'D' and resid 1628 through 1635 Processing helix chain 'D' and resid 1641 through 1650 removed outlier: 3.664A pdb=" N CYS D1650 " --> pdb=" O ASP D1646 " (cutoff:3.500A) Processing helix chain 'D' and resid 1656 through 1666 Processing helix chain 'D' and resid 1700 through 1702 No H-bonds generated for 'chain 'D' and resid 1700 through 1702' Processing helix chain 'D' and resid 1709 through 1716 Processing helix chain 'D' and resid 1721 through 1733 Processing helix chain 'D' and resid 1754 through 1771 Processing helix chain 'D' and resid 1793 through 1803 Processing helix chain 'D' and resid 1805 through 1812 Processing helix chain 'D' and resid 1822 through 1828 Processing helix chain 'D' and resid 1847 through 1853 Processing helix chain 'D' and resid 1872 through 1885 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.954A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.628A pdb=" N PHE B 255 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 252 through 256' Processing helix chain 'B' and resid 258 through 261 removed outlier: 3.555A pdb=" N LEU B 261 " --> pdb=" O PRO B 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 258 through 261' Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 287 through 296 removed outlier: 4.040A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 338 through 348 Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.506A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 144 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.954A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 252 through 256 removed outlier: 3.627A pdb=" N PHE C 255 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 252 through 256' Processing helix chain 'C' and resid 258 through 261 removed outlier: 3.555A pdb=" N LEU C 261 " --> pdb=" O PRO C 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 258 through 261' Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 287 through 296 removed outlier: 4.040A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.505A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 371 Processing sheet with id= A, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.973A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 35 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 298 through 300 removed outlier: 3.917A pdb=" N SER A 155 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= E, first strand: chain 'D' and resid 1237 through 1239 removed outlier: 7.989A pdb=" N VAL D1295 " --> pdb=" O SER D1567 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ALA D1569 " --> pdb=" O VAL D1295 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE D1297 " --> pdb=" O ALA D1569 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU D1571 " --> pdb=" O ILE D1297 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N GLY D1299 " --> pdb=" O LEU D1571 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 1513 through 1517 Processing sheet with id= G, first strand: chain 'D' and resid 1682 through 1687 Processing sheet with id= H, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.973A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 35 through 38 Processing sheet with id= J, first strand: chain 'B' and resid 298 through 300 removed outlier: 3.917A pdb=" N SER B 155 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= L, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.973A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= N, first strand: chain 'C' and resid 298 through 300 removed outlier: 3.917A pdb=" N SER C 155 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 238 through 241 558 hydrogen bonds defined for protein. 1515 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.96 Time building geometry restraints manager: 6.47 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: 2958 1.33 - 1.45: 3299 1.45 - 1.57: 8101 1.57 - 1.69: 12 1.69 - 1.82: 153 Bond restraints: 14523 Sorted by residual: bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.405 -0.058 2.00e-02 2.50e+03 8.35e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.405 -0.058 2.00e-02 2.50e+03 8.34e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.405 -0.058 2.00e-02 2.50e+03 8.32e+00 bond pdb=" C GLY D1256 " pdb=" N PRO D1257 " ideal model delta sigma weight residual 1.336 1.367 -0.031 1.25e-02 6.40e+03 6.19e+00 bond pdb=" CG HIC A 73 " pdb=" CD2 HIC A 73 " ideal model delta sigma weight residual 1.369 1.413 -0.044 2.00e-02 2.50e+03 4.90e+00 ... (remaining 14518 not shown) Histogram of bond angle deviations from ideal: 99.19 - 106.60: 474 106.60 - 114.00: 8260 114.00 - 121.41: 7470 121.41 - 128.81: 3398 128.81 - 136.22: 85 Bond angle restraints: 19687 Sorted by residual: angle pdb=" N ILE D1865 " pdb=" CA ILE D1865 " pdb=" C ILE D1865 " ideal model delta sigma weight residual 111.56 104.82 6.74 8.60e-01 1.35e+00 6.15e+01 angle pdb=" C GLY D1256 " pdb=" N PRO D1257 " pdb=" CA PRO D1257 " ideal model delta sigma weight residual 119.56 113.04 6.52 1.01e+00 9.80e-01 4.17e+01 angle pdb=" N ASN D1320 " pdb=" CA ASN D1320 " pdb=" C ASN D1320 " ideal model delta sigma weight residual 109.76 101.09 8.67 1.64e+00 3.72e-01 2.80e+01 angle pdb=" N ILE D1242 " pdb=" CA ILE D1242 " pdb=" C ILE D1242 " ideal model delta sigma weight residual 109.55 116.54 -6.99 1.38e+00 5.25e-01 2.57e+01 angle pdb=" C ILE D1239 " pdb=" CA ILE D1239 " pdb=" CB ILE D1239 " ideal model delta sigma weight residual 113.22 108.32 4.90 1.12e+00 7.97e-01 1.92e+01 ... (remaining 19682 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.36: 8235 23.36 - 46.72: 462 46.72 - 70.07: 51 70.07 - 93.43: 12 93.43 - 116.79: 4 Dihedral angle restraints: 8764 sinusoidal: 3564 harmonic: 5200 Sorted by residual: dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 -176.79 116.79 1 2.00e+01 2.50e-03 3.48e+01 dihedral pdb=" O1B ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PB ADP A 401 " pdb=" PA ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 -176.79 116.79 1 2.00e+01 2.50e-03 3.48e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 -176.78 116.78 1 2.00e+01 2.50e-03 3.48e+01 ... (remaining 8761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1649 0.049 - 0.097: 416 0.097 - 0.146: 117 0.146 - 0.195: 7 0.195 - 0.244: 5 Chirality restraints: 2194 Sorted by residual: chirality pdb=" CA ILE D1242 " pdb=" N ILE D1242 " pdb=" C ILE D1242 " pdb=" CB ILE D1242 " both_signs ideal model delta sigma weight residual False 2.43 2.19 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB ILE D1297 " pdb=" CA ILE D1297 " pdb=" CG1 ILE D1297 " pdb=" CG2 ILE D1297 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA LYS D1867 " pdb=" N LYS D1867 " pdb=" C LYS D1867 " pdb=" CB LYS D1867 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 2191 not shown) Planarity restraints: 2528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET D1251 " 0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C MET D1251 " -0.056 2.00e-02 2.50e+03 pdb=" O MET D1251 " 0.021 2.00e-02 2.50e+03 pdb=" N PHE D1252 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D1318 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.95e+00 pdb=" C ALA D1318 " -0.049 2.00e-02 2.50e+03 pdb=" O ALA D1318 " 0.018 2.00e-02 2.50e+03 pdb=" N MET D1319 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 242 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO A 243 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " 0.023 5.00e-02 4.00e+02 ... (remaining 2525 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 50 2.52 - 3.11: 10510 3.11 - 3.71: 21643 3.71 - 4.30: 29653 4.30 - 4.90: 50375 Nonbonded interactions: 112231 Sorted by model distance: nonbonded pdb=" O LEU D1837 " pdb=" CD1 LEU D1837 " model vdw 1.921 3.460 nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 402 " model vdw 2.186 2.170 nonbonded pdb=" O3B ADP A 401 " pdb="MG MG A 402 " model vdw 2.186 2.170 nonbonded pdb=" O3B ADP B 401 " pdb="MG MG B 402 " model vdw 2.186 2.170 nonbonded pdb=" O LEU D1377 " pdb=" OH TYR D1574 " model vdw 2.256 2.440 ... (remaining 112226 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 4 5.21 5 S 91 5.16 5 C 9000 2.51 5 N 2418 2.21 5 O 2705 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: 10.330 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: 29.520 Check model and map are aligned: 0.210 Process input model: 39.170 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.160 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 14523 Z= 0.241 Angle : 0.676 9.614 19687 Z= 0.376 Chirality : 0.046 0.244 2194 Planarity : 0.004 0.041 2528 Dihedral : 14.222 116.791 5418 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.21), residues: 1765 helix: 0.73 (0.19), residues: 823 sheet: -1.06 (0.30), residues: 288 loop : -0.59 (0.26), residues: 654 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 1.785 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.2696 time to fit residues: 72.6202 Evaluate side-chains 110 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.806 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 84 optimal weight: 0.0060 chunk 103 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.078 14523 Z= 0.422 Angle : 0.679 9.008 19687 Z= 0.335 Chirality : 0.048 0.219 2194 Planarity : 0.004 0.043 2528 Dihedral : 7.307 105.210 1997 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.21), residues: 1765 helix: 0.61 (0.19), residues: 820 sheet: -1.03 (0.30), residues: 279 loop : -0.69 (0.25), residues: 666 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 114 time to evaluate : 1.754 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 122 average time/residue: 0.2464 time to fit residues: 46.9155 Evaluate side-chains 107 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 1.763 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1402 time to fit residues: 3.7623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 0.0270 chunk 133 optimal weight: 0.9990 chunk 109 optimal weight: 0.0970 chunk 44 optimal weight: 7.9990 chunk 161 optimal weight: 0.8980 chunk 173 optimal weight: 0.0770 chunk 143 optimal weight: 0.0570 chunk 159 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 129 optimal weight: 0.2980 overall best weight: 0.1112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1616 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.050 14523 Z= 0.130 Angle : 0.549 7.184 19687 Z= 0.265 Chirality : 0.042 0.171 2194 Planarity : 0.004 0.037 2528 Dihedral : 6.577 92.889 1997 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.21), residues: 1765 helix: 0.87 (0.19), residues: 813 sheet: -0.60 (0.30), residues: 286 loop : -0.31 (0.27), residues: 666 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 122 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 131 average time/residue: 0.3092 time to fit residues: 64.4823 Evaluate side-chains 109 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 104 time to evaluate : 1.893 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1407 time to fit residues: 3.6577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 153 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1760 GLN B 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.101 14523 Z= 0.486 Angle : 0.700 7.403 19687 Z= 0.346 Chirality : 0.049 0.310 2194 Planarity : 0.004 0.046 2528 Dihedral : 6.955 97.899 1997 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.21), residues: 1765 helix: 0.66 (0.19), residues: 817 sheet: -0.81 (0.30), residues: 279 loop : -0.55 (0.26), residues: 669 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 1.645 Fit side-chains outliers start: 20 outliers final: 3 residues processed: 122 average time/residue: 0.2330 time to fit residues: 44.9662 Evaluate side-chains 104 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 1.612 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1392 time to fit residues: 2.9351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 0.9980 chunk 97 optimal weight: 20.0000 chunk 2 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 118 optimal weight: 0.0870 chunk 0 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 153 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 14523 Z= 0.168 Angle : 0.566 7.564 19687 Z= 0.272 Chirality : 0.043 0.139 2194 Planarity : 0.004 0.037 2528 Dihedral : 6.587 90.846 1997 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.21), residues: 1765 helix: 0.85 (0.19), residues: 812 sheet: -0.60 (0.29), residues: 291 loop : -0.29 (0.26), residues: 662 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 1.643 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 1 residues processed: 119 average time/residue: 0.2449 time to fit residues: 46.2139 Evaluate side-chains 103 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 1.806 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1642 time to fit residues: 2.4575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 7.9990 chunk 154 optimal weight: 0.6980 chunk 33 optimal weight: 0.0370 chunk 100 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 56 optimal weight: 0.0020 chunk 89 optimal weight: 6.9990 overall best weight: 0.5468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 14523 Z= 0.152 Angle : 0.553 6.949 19687 Z= 0.265 Chirality : 0.043 0.140 2194 Planarity : 0.003 0.036 2528 Dihedral : 6.282 83.941 1997 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.21), residues: 1765 helix: 0.94 (0.19), residues: 810 sheet: -0.54 (0.29), residues: 291 loop : -0.18 (0.27), residues: 664 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 106 time to evaluate : 1.760 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 112 average time/residue: 0.2593 time to fit residues: 45.6508 Evaluate side-chains 102 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 1.835 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1298 time to fit residues: 2.7107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 170 optimal weight: 0.0570 chunk 106 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 78 optimal weight: 0.4980 overall best weight: 0.8902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1218 GLN ** D1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 14523 Z= 0.184 Angle : 0.559 7.445 19687 Z= 0.267 Chirality : 0.043 0.136 2194 Planarity : 0.003 0.036 2528 Dihedral : 6.049 78.635 1997 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.21), residues: 1765 helix: 1.01 (0.19), residues: 809 sheet: -0.47 (0.30), residues: 291 loop : -0.14 (0.26), residues: 665 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 105 time to evaluate : 1.808 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 108 average time/residue: 0.2701 time to fit residues: 45.8630 Evaluate side-chains 103 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 1.884 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1373 time to fit residues: 3.0236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 108 optimal weight: 0.1980 chunk 116 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 155 optimal weight: 0.0470 overall best weight: 0.8482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 14523 Z= 0.180 Angle : 0.556 6.999 19687 Z= 0.266 Chirality : 0.043 0.137 2194 Planarity : 0.003 0.034 2528 Dihedral : 5.855 72.265 1997 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.21), residues: 1765 helix: 1.04 (0.19), residues: 805 sheet: -0.42 (0.30), residues: 291 loop : -0.13 (0.26), residues: 669 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 106 time to evaluate : 1.828 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 110 average time/residue: 0.2687 time to fit residues: 46.6728 Evaluate side-chains 103 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 2.057 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1469 time to fit residues: 2.9390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 6.9990 chunk 149 optimal weight: 0.7980 chunk 158 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 143 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 14523 Z= 0.271 Angle : 0.611 9.213 19687 Z= 0.295 Chirality : 0.044 0.167 2194 Planarity : 0.004 0.037 2528 Dihedral : 5.891 69.498 1997 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.21), residues: 1765 helix: 1.00 (0.19), residues: 805 sheet: -0.39 (0.30), residues: 291 loop : -0.21 (0.26), residues: 669 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 1.597 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 103 average time/residue: 0.2592 time to fit residues: 41.8143 Evaluate side-chains 99 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 1.735 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1408 time to fit residues: 2.6031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 102 optimal weight: 20.0000 chunk 79 optimal weight: 0.2980 chunk 116 optimal weight: 3.9990 chunk 176 optimal weight: 0.6980 chunk 162 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 108 optimal weight: 0.0570 chunk 86 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.059 14523 Z= 0.162 Angle : 0.571 9.090 19687 Z= 0.272 Chirality : 0.043 0.137 2194 Planarity : 0.003 0.035 2528 Dihedral : 5.617 61.980 1997 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.21), residues: 1765 helix: 1.06 (0.20), residues: 803 sheet: -0.36 (0.30), residues: 291 loop : -0.11 (0.26), residues: 671 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 1.827 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 105 average time/residue: 0.2658 time to fit residues: 44.0149 Evaluate side-chains 99 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.765 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 43 optimal weight: 0.0570 chunk 129 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 144 optimal weight: 0.2980 chunk 17 optimal weight: 0.2980 chunk 25 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.119153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.084908 restraints weight = 26935.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.084368 restraints weight = 14478.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.085259 restraints weight = 10882.339| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 14523 Z= 0.151 Angle : 0.573 9.582 19687 Z= 0.271 Chirality : 0.042 0.138 2194 Planarity : 0.003 0.034 2528 Dihedral : 5.367 55.080 1997 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.21), residues: 1765 helix: 1.12 (0.20), residues: 804 sheet: -0.35 (0.30), residues: 291 loop : -0.05 (0.26), residues: 670 =============================================================================== Job complete usr+sys time: 2559.08 seconds wall clock time: 48 minutes 28.99 seconds (2908.99 seconds total)