Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 00:01:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw7_13677/04_2023/7pw7_13677_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw7_13677/04_2023/7pw7_13677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw7_13677/04_2023/7pw7_13677.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw7_13677/04_2023/7pw7_13677.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw7_13677/04_2023/7pw7_13677_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw7_13677/04_2023/7pw7_13677_updated.pdb" } resolution = 3.59 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= 0.003 sd= 0.065 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 P 9 5.49 5 Mg 1 5.21 5 S 81 5.16 5 Cl 1 4.86 5 C 10404 2.51 5 N 2870 2.21 5 O 2861 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1827": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 323": "OD1" <-> "OD2" Residue "C TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 492": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 16227 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 13724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1944, 13724 Classifications: {'peptide': 1944} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 542} Link IDs: {'PTRANS': 61, 'TRANS': 1882} Chain breaks: 39 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1531 Unresolved non-hydrogen angles: 2011 Unresolved non-hydrogen dihedrals: 1110 Unresolved non-hydrogen chiralities: 70 Planarities with less than four sites: {'GLN:plan1': 20, 'HIS:plan': 3, 'ASN:plan1': 17, 'TYR:plan': 4, 'UNK:plan-1': 195, 'TRP:plan': 4, 'ASP:plan': 47, 'PHE:plan': 6, 'GLU:plan': 70, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 912 Chain: "C" Number of atoms: 2396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2396 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 16, 'TRANS': 290} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 70 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'88C': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="MG MG C 602 " occ=0.00 Time building chain proxies: 9.18, per 1000 atoms: 0.57 Number of scatterers: 16227 At special positions: 0 Unit cell: (121.722, 108.102, 183.008, 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) Cl 1 17.00 S 81 16.00 P 9 15.00 Mg 1 11.99 O 2861 8.00 N 2870 7.00 C 10404 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.30 Conformation dependent library (CDL) restraints added in 2.4 seconds 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4342 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 119 helices and 4 sheets defined 68.6% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.07 Creating SS restraints... Processing helix chain 'A' and resid 148 through 155 removed outlier: 3.853A pdb=" N UNK A 154 " --> pdb=" O UNK A 150 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N UNK A 155 " --> pdb=" O UNK A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 169 No H-bonds generated for 'chain 'A' and resid 166 through 169' Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 208 through 220 removed outlier: 4.193A pdb=" N UNK A 220 " --> pdb=" O UNK A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 243 removed outlier: 3.594A pdb=" N UNK A 234 " --> pdb=" O UNK A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 264 Processing helix chain 'A' and resid 271 through 284 removed outlier: 3.930A pdb=" N UNK A 284 " --> pdb=" O UNK A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 303 removed outlier: 3.989A pdb=" N UNK A 303 " --> pdb=" O UNK A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 322 removed outlier: 3.876A pdb=" N THR A 318 " --> pdb=" O ASN A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 356 through 375 removed outlier: 3.988A pdb=" N GLY A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 410 Processing helix chain 'A' and resid 429 through 443 Processing helix chain 'A' and resid 450 through 466 Processing helix chain 'A' and resid 476 through 488 removed outlier: 3.850A pdb=" N ASN A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 510 removed outlier: 3.744A pdb=" N SER A 499 " --> pdb=" O ASP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 521 Processing helix chain 'A' and resid 530 through 532 No H-bonds generated for 'chain 'A' and resid 530 through 532' Processing helix chain 'A' and resid 539 through 553 Processing helix chain 'A' and resid 558 through 583 removed outlier: 3.974A pdb=" N THR A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA A 564 " --> pdb=" O VAL A 560 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 592 No H-bonds generated for 'chain 'A' and resid 590 through 592' Processing helix chain 'A' and resid 595 through 597 No H-bonds generated for 'chain 'A' and resid 595 through 597' Processing helix chain 'A' and resid 604 through 622 removed outlier: 3.642A pdb=" N THR A 619 " --> pdb=" O LEU A 615 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N THR A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 643 Processing helix chain 'A' and resid 648 through 650 No H-bonds generated for 'chain 'A' and resid 648 through 650' Processing helix chain 'A' and resid 653 through 656 No H-bonds generated for 'chain 'A' and resid 653 through 656' Processing helix chain 'A' and resid 658 through 678 removed outlier: 3.689A pdb=" N ARG A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N HIS A 675 " --> pdb=" O HIS A 671 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP A 676 " --> pdb=" O CYS A 672 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N HIS A 677 " --> pdb=" O THR A 673 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N PHE A 678 " --> pdb=" O ARG A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 702 No H-bonds generated for 'chain 'A' and resid 699 through 702' Processing helix chain 'A' and resid 707 through 719 Processing helix chain 'A' and resid 725 through 743 removed outlier: 3.538A pdb=" N ARG A 743 " --> pdb=" O ALA A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 752 removed outlier: 3.739A pdb=" N ALA A 749 " --> pdb=" O GLU A 746 " (cutoff:3.500A) Proline residue: A 750 - end of helix No H-bonds generated for 'chain 'A' and resid 746 through 752' Processing helix chain 'A' and resid 755 through 767 Processing helix chain 'A' and resid 773 through 785 Processing helix chain 'A' and resid 792 through 805 removed outlier: 3.611A pdb=" N ARG A 797 " --> pdb=" O ASP A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 822 Processing helix chain 'A' and resid 826 through 829 No H-bonds generated for 'chain 'A' and resid 826 through 829' Processing helix chain 'A' and resid 836 through 850 Processing helix chain 'A' and resid 859 through 870 Processing helix chain 'A' and resid 882 through 889 Processing helix chain 'A' and resid 903 through 905 No H-bonds generated for 'chain 'A' and resid 903 through 905' Processing helix chain 'A' and resid 909 through 926 Processing helix chain 'A' and resid 936 through 955 removed outlier: 3.969A pdb=" N PHE A 940 " --> pdb=" O ALA A 936 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU A 955 " --> pdb=" O ALA A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 998 removed outlier: 3.790A pdb=" N GLY A 974 " --> pdb=" O ASP A 970 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN A 977 " --> pdb=" O HIS A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1018 removed outlier: 3.859A pdb=" N THR A1018 " --> pdb=" O THR A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1040 removed outlier: 4.534A pdb=" N LEU A1032 " --> pdb=" O THR A1028 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N SER A1033 " --> pdb=" O ARG A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1057 Processing helix chain 'A' and resid 1070 through 1083 Processing helix chain 'A' and resid 1086 through 1098 removed outlier: 4.126A pdb=" N SER A1098 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1115 removed outlier: 3.841A pdb=" N ASN A1108 " --> pdb=" O LEU A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1133 Processing helix chain 'A' and resid 1144 through 1150 Processing helix chain 'A' and resid 1180 through 1196 Processing helix chain 'A' and resid 1200 through 1217 Processing helix chain 'A' and resid 1228 through 1239 Processing helix chain 'A' and resid 1242 through 1251 removed outlier: 3.636A pdb=" N GLU A1247 " --> pdb=" O VAL A1243 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A1251 " --> pdb=" O GLU A1247 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1304 Processing helix chain 'A' and resid 1318 through 1340 removed outlier: 4.020A pdb=" N LYS A1322 " --> pdb=" O GLU A1318 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLY A1333 " --> pdb=" O ARG A1329 " (cutoff:3.500A) Proline residue: A1334 - end of helix Processing helix chain 'A' and resid 1348 through 1366 Processing helix chain 'A' and resid 1371 through 1373 No H-bonds generated for 'chain 'A' and resid 1371 through 1373' Processing helix chain 'A' and resid 1379 through 1382 Processing helix chain 'A' and resid 1391 through 1409 removed outlier: 3.863A pdb=" N GLN A1395 " --> pdb=" O ARG A1391 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A1396 " --> pdb=" O PRO A1392 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR A1402 " --> pdb=" O ARG A1398 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN A1403 " --> pdb=" O TYR A1399 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLU A1408 " --> pdb=" O ASN A1404 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LYS A1409 " --> pdb=" O GLN A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1435 removed outlier: 3.714A pdb=" N ARG A1435 " --> pdb=" O PHE A1431 " (cutoff:3.500A) Processing helix chain 'A' and resid 1438 through 1449 Processing helix chain 'A' and resid 1459 through 1466 removed outlier: 3.550A pdb=" N VAL A1463 " --> pdb=" O ALA A1459 " (cutoff:3.500A) Processing helix chain 'A' and resid 1480 through 1493 Processing helix chain 'A' and resid 1497 through 1513 removed outlier: 3.943A pdb=" N LYS A1513 " --> pdb=" O ILE A1509 " (cutoff:3.500A) Processing helix chain 'A' and resid 1521 through 1534 Processing helix chain 'A' and resid 1536 through 1550 removed outlier: 5.509A pdb=" N GLY A1541 " --> pdb=" O LYS A1537 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N GLN A1542 " --> pdb=" O GLU A1538 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A1543 " --> pdb=" O ILE A1539 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS A1544 " --> pdb=" O SER A1540 " (cutoff:3.500A) Processing helix chain 'A' and resid 1560 through 1569 Processing helix chain 'A' and resid 1589 through 1591 No H-bonds generated for 'chain 'A' and resid 1589 through 1591' Processing helix chain 'A' and resid 1597 through 1611 Processing helix chain 'A' and resid 1616 through 1636 Processing helix chain 'A' and resid 1647 through 1655 Processing helix chain 'A' and resid 1664 through 1674 removed outlier: 3.755A pdb=" N UNK A1674 " --> pdb=" O UNK A1670 " (cutoff:3.500A) Processing helix chain 'A' and resid 1704 through 1716 Processing helix chain 'A' and resid 1729 through 1739 Processing helix chain 'A' and resid 1743 through 1758 removed outlier: 3.761A pdb=" N ASN A1758 " --> pdb=" O PHE A1754 " (cutoff:3.500A) Processing helix chain 'A' and resid 1782 through 1798 Processing helix chain 'A' and resid 1804 through 1810 removed outlier: 4.792A pdb=" N HIS A1809 " --> pdb=" O GLN A1805 " (cutoff:3.500A) Processing helix chain 'A' and resid 1823 through 1828 Processing helix chain 'A' and resid 1836 through 1849 Processing helix chain 'A' and resid 1857 through 1864 Processing helix chain 'A' and resid 1925 through 1939 removed outlier: 3.969A pdb=" N CYS A1929 " --> pdb=" O MET A1925 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N TYR A1930 " --> pdb=" O MET A1926 " (cutoff:3.500A) Processing helix chain 'A' and resid 1942 through 1957 Processing helix chain 'A' and resid 1963 through 1977 Processing helix chain 'A' and resid 2007 through 2019 Processing helix chain 'A' and resid 2036 through 2043 Processing helix chain 'A' and resid 2047 through 2055 Processing helix chain 'A' and resid 2069 through 2082 Processing helix chain 'A' and resid 2161 through 2177 removed outlier: 3.509A pdb=" N ARG A2165 " --> pdb=" O HIS A2161 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET A2176 " --> pdb=" O ILE A2172 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE A2177 " --> pdb=" O VAL A2173 " (cutoff:3.500A) Processing helix chain 'A' and resid 2180 through 2182 No H-bonds generated for 'chain 'A' and resid 2180 through 2182' Processing helix chain 'A' and resid 2214 through 2231 removed outlier: 3.775A pdb=" N TYR A2218 " --> pdb=" O LEU A2214 " (cutoff:3.500A) Processing helix chain 'A' and resid 2249 through 2264 removed outlier: 3.557A pdb=" N LYS A2256 " --> pdb=" O LEU A2252 " (cutoff:3.500A) Proline residue: A2259 - end of helix Processing helix chain 'A' and resid 2277 through 2288 Processing helix chain 'A' and resid 2294 through 2303 removed outlier: 3.899A pdb=" N GLU A2299 " --> pdb=" O LEU A2295 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A2300 " --> pdb=" O LEU A2296 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TRP A2301 " --> pdb=" O ALA A2297 " (cutoff:3.500A) Processing helix chain 'A' and resid 2307 through 2331 Processing helix chain 'A' and resid 2338 through 2340 No H-bonds generated for 'chain 'A' and resid 2338 through 2340' Processing helix chain 'A' and resid 2362 through 2364 No H-bonds generated for 'chain 'A' and resid 2362 through 2364' Processing helix chain 'A' and resid 2377 through 2383 removed outlier: 3.702A pdb=" N LEU A2383 " --> pdb=" O ILE A2379 " (cutoff:3.500A) Processing helix chain 'A' and resid 2391 through 2405 Processing helix chain 'A' and resid 2407 through 2418 Processing helix chain 'A' and resid 3608 through 3621 Processing helix chain 'A' and resid 3633 through 3645 Processing helix chain 'A' and resid 3647 through 3650 No H-bonds generated for 'chain 'A' and resid 3647 through 3650' Processing helix chain 'A' and resid 3655 through 3657 No H-bonds generated for 'chain 'A' and resid 3655 through 3657' Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 243 through 248 removed outlier: 4.016A pdb=" N GLU C 247 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG C 248 " --> pdb=" O GLU C 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 243 through 248' Processing helix chain 'C' and resid 276 through 283 Processing helix chain 'C' and resid 296 through 313 Processing helix chain 'C' and resid 330 through 339 removed outlier: 3.552A pdb=" N MET C 339 " --> pdb=" O GLN C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 378 No H-bonds generated for 'chain 'C' and resid 376 through 378' Processing helix chain 'C' and resid 381 through 394 removed outlier: 3.524A pdb=" N GLN C 386 " --> pdb=" O ARG C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 411 Processing helix chain 'C' and resid 419 through 421 No H-bonds generated for 'chain 'C' and resid 419 through 421' Processing helix chain 'C' and resid 466 through 478 Processing helix chain 'C' and resid 492 through 507 Processing helix chain 'C' and resid 511 through 517 Processing sheet with id= A, first strand: chain 'A' and resid 2129 through 2131 removed outlier: 3.521A pdb=" N TYR A2152 " --> pdb=" O LEU A2140 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 2341 through 2343 Processing sheet with id= C, first strand: chain 'A' and resid 2121 through 2124 removed outlier: 7.035A pdb=" N LEU A2143 " --> pdb=" O HIS A2122 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 428 through 430 removed outlier: 8.859A pdb=" N PHE C 429 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N PHE C 369 " --> pdb=" O PHE C 429 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL C 209 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE C 256 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N PHE C 258 " --> pdb=" O LYS C 182 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N LYS C 182 " --> pdb=" O PHE C 258 " (cutoff:3.500A) 910 hydrogen bonds defined for protein. 2658 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: 6.32 Time building geometry restraints manager: 7.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2544 1.31 - 1.44: 4312 1.44 - 1.57: 9517 1.57 - 1.69: 12 1.69 - 1.82: 128 Bond restraints: 16513 Sorted by residual: bond pdb=" C28 88C A3702 " pdb=" N30 88C A3702 " ideal model delta sigma weight residual 1.352 1.453 -0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" C13 88C A3702 " pdb=" N12 88C A3702 " ideal model delta sigma weight residual 1.364 1.455 -0.091 2.00e-02 2.50e+03 2.09e+01 bond pdb=" C22 88C A3702 " pdb=" C23 88C A3702 " ideal model delta sigma weight residual 1.476 1.387 0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" C17 88C A3702 " pdb=" C18 88C A3702 " ideal model delta sigma weight residual 1.480 1.391 0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C28 88C A3702 " pdb=" N27 88C A3702 " ideal model delta sigma weight residual 1.376 1.457 -0.081 2.00e-02 2.50e+03 1.63e+01 ... (remaining 16508 not shown) Histogram of bond angle deviations from ideal: 96.78 - 105.37: 276 105.37 - 113.96: 9988 113.96 - 122.54: 10901 122.54 - 131.13: 1312 131.13 - 139.72: 83 Bond angle restraints: 22560 Sorted by residual: angle pdb=" N VAL A 393 " pdb=" CA VAL A 393 " pdb=" C VAL A 393 " ideal model delta sigma weight residual 113.20 107.58 5.62 9.60e-01 1.09e+00 3.42e+01 angle pdb=" O07 88C A3702 " pdb=" S06 88C A3702 " pdb=" O08 88C A3702 " ideal model delta sigma weight residual 117.67 100.87 16.80 3.00e+00 1.11e-01 3.14e+01 angle pdb=" CA PRO C 272 " pdb=" N PRO C 272 " pdb=" CD PRO C 272 " ideal model delta sigma weight residual 112.00 105.58 6.42 1.40e+00 5.10e-01 2.10e+01 angle pdb=" N PRO C 272 " pdb=" CD PRO C 272 " pdb=" CG PRO C 272 " ideal model delta sigma weight residual 103.20 96.78 6.42 1.50e+00 4.44e-01 1.83e+01 angle pdb=" C ALA A 997 " pdb=" N TYR A 998 " pdb=" CA TYR A 998 " ideal model delta sigma weight residual 121.66 116.36 5.30 1.76e+00 3.23e-01 9.06e+00 ... (remaining 22555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 8987 17.70 - 35.39: 630 35.39 - 53.09: 117 53.09 - 70.78: 34 70.78 - 88.48: 10 Dihedral angle restraints: 9778 sinusoidal: 3169 harmonic: 6609 Sorted by residual: dihedral pdb=" CA ASP A1136 " pdb=" CB ASP A1136 " pdb=" CG ASP A1136 " pdb=" OD1 ASP A1136 " ideal model delta sinusoidal sigma weight residual -30.00 -87.94 57.94 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP C 327 " pdb=" CB ASP C 327 " pdb=" CG ASP C 327 " pdb=" OD1 ASP C 327 " ideal model delta sinusoidal sigma weight residual -30.00 -86.49 56.49 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CB GLU A2380 " pdb=" CG GLU A2380 " pdb=" CD GLU A2380 " pdb=" OE1 GLU A2380 " ideal model delta sinusoidal sigma weight residual 0.00 88.48 -88.48 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 9775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.008: 2780 1.008 - 2.016: 0 2.016 - 3.024: 0 3.024 - 4.031: 0 4.031 - 5.039: 3 Chirality restraints: 2783 Sorted by residual: chirality pdb=" C2 IHP A3701 " pdb=" C1 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" O12 IHP A3701 " both_signs ideal model delta sigma weight residual False -2.52 2.52 -5.04 2.00e-01 2.50e+01 6.35e+02 chirality pdb=" C4 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" C5 IHP A3701 " pdb=" O14 IHP A3701 " both_signs ideal model delta sigma weight residual False 2.48 -2.54 5.02 2.00e-01 2.50e+01 6.29e+02 chirality pdb=" C1 IHP A3701 " pdb=" C2 IHP A3701 " pdb=" C6 IHP A3701 " pdb=" O11 IHP A3701 " both_signs ideal model delta sigma weight residual False 2.32 -2.48 4.79 2.00e-01 2.50e+01 5.74e+02 ... (remaining 2780 not shown) Planarity restraints: 2806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 271 " 0.056 5.00e-02 4.00e+02 8.22e-02 1.08e+01 pdb=" N PRO C 272 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO C 272 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 272 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A2417 " -0.021 2.00e-02 2.50e+03 1.89e-02 6.24e+00 pdb=" CG PHE A2417 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE A2417 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A2417 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A2417 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A2417 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE A2417 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 421 " -0.013 2.00e-02 2.50e+03 1.39e-02 3.40e+00 pdb=" CG PHE C 421 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE C 421 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE C 421 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE C 421 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE C 421 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 421 " -0.000 2.00e-02 2.50e+03 ... (remaining 2803 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 70 2.60 - 3.17: 13710 3.17 - 3.75: 24772 3.75 - 4.32: 30978 4.32 - 4.90: 53329 Nonbonded interactions: 122859 Sorted by model distance: nonbonded pdb=" O3B ATP C 601 " pdb="MG MG C 602 " model vdw 2.020 2.170 nonbonded pdb=" O2B ATP C 601 " pdb="MG MG C 602 " model vdw 2.172 2.170 nonbonded pdb=" O LEU C 367 " pdb=" ND2 ASN C 427 " model vdw 2.201 2.520 nonbonded pdb=" OG SER A1328 " pdb=" OG SER A1357 " model vdw 2.203 2.440 nonbonded pdb=" OH TYR A 669 " pdb=" OE1 GLU A 737 " model vdw 2.254 2.440 ... (remaining 122854 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=0.00 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: 2.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 13.090 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 45.270 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 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 : 0.003 0.101 16513 Z= 0.219 Angle : 0.626 16.805 22560 Z= 0.327 Chirality : 0.167 5.039 2783 Planarity : 0.003 0.082 2806 Dihedral : 13.250 88.480 5436 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.20), residues: 1994 helix: 2.57 (0.15), residues: 1258 sheet: 0.33 (0.60), residues: 75 loop : -1.22 (0.25), residues: 661 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.870 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2470 time to fit residues: 60.3578 Evaluate side-chains 114 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.888 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 106 optimal weight: 0.2980 chunk 130 optimal weight: 40.0000 chunk 203 optimal weight: 1.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1019 ASN C 213 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 16513 Z= 0.235 Angle : 0.526 13.014 22560 Z= 0.249 Chirality : 0.038 0.360 2783 Planarity : 0.004 0.040 2806 Dihedral : 3.537 52.361 2382 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.20), residues: 1994 helix: 2.39 (0.15), residues: 1267 sheet: 0.67 (0.57), residues: 80 loop : -1.23 (0.25), residues: 647 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 121 time to evaluate : 2.016 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 123 average time/residue: 0.2529 time to fit residues: 53.0458 Evaluate side-chains 115 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 110 time to evaluate : 2.628 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1616 time to fit residues: 4.0398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 0.9980 chunk 63 optimal weight: 0.0870 chunk 169 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 203 optimal weight: 2.9990 chunk 220 optimal weight: 0.7980 chunk 181 optimal weight: 4.9990 chunk 202 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 163 optimal weight: 0.7980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 16513 Z= 0.136 Angle : 0.450 10.297 22560 Z= 0.216 Chirality : 0.035 0.187 2783 Planarity : 0.003 0.039 2806 Dihedral : 3.333 52.047 2382 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.20), residues: 1994 helix: 2.49 (0.15), residues: 1269 sheet: 0.77 (0.57), residues: 80 loop : -1.22 (0.25), residues: 645 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 1.947 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 120 average time/residue: 0.2264 time to fit residues: 46.7577 Evaluate side-chains 113 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 110 time to evaluate : 1.920 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1528 time to fit residues: 3.5082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 0.0570 chunk 153 optimal weight: 9.9990 chunk 105 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 chunk 97 optimal weight: 0.2980 chunk 136 optimal weight: 0.4980 chunk 204 optimal weight: 7.9990 chunk 216 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 193 optimal weight: 0.2980 chunk 58 optimal weight: 0.6980 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 16513 Z= 0.109 Angle : 0.426 9.319 22560 Z= 0.205 Chirality : 0.035 0.165 2783 Planarity : 0.003 0.038 2806 Dihedral : 3.354 53.487 2382 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer Outliers : 0.62 % 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: 2.03 (0.20), residues: 1994 helix: 2.51 (0.15), residues: 1283 sheet: 0.95 (0.59), residues: 80 loop : -1.17 (0.26), residues: 631 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 1.922 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 127 average time/residue: 0.2251 time to fit residues: 48.0813 Evaluate side-chains 114 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 111 time to evaluate : 1.710 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1474 time to fit residues: 3.3835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 0.1980 chunk 122 optimal weight: 9.9990 chunk 3 optimal weight: 50.0000 chunk 161 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 110 optimal weight: 0.9990 chunk 194 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 578 ASN A 645 ASN ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1050 HIS A3649 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.098 16513 Z= 0.343 Angle : 0.602 10.479 22560 Z= 0.297 Chirality : 0.040 0.188 2783 Planarity : 0.004 0.038 2806 Dihedral : 3.966 59.853 2382 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer Outliers : 1.65 % 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: 1.23 (0.19), residues: 1994 helix: 1.87 (0.15), residues: 1278 sheet: 0.70 (0.56), residues: 80 loop : -1.43 (0.25), residues: 636 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 115 time to evaluate : 1.943 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 19 residues processed: 131 average time/residue: 0.2369 time to fit residues: 54.2915 Evaluate side-chains 125 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 1.887 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1495 time to fit residues: 7.9373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 0.7980 chunk 194 optimal weight: 7.9990 chunk 42 optimal weight: 0.1980 chunk 127 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 216 optimal weight: 0.9990 chunk 179 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 71 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 427 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.078 16513 Z= 0.135 Angle : 0.462 9.574 22560 Z= 0.225 Chirality : 0.036 0.185 2783 Planarity : 0.003 0.039 2806 Dihedral : 3.689 58.436 2382 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.20), residues: 1994 helix: 2.27 (0.15), residues: 1276 sheet: 0.84 (0.57), residues: 80 loop : -1.30 (0.25), residues: 638 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 121 average time/residue: 0.2259 time to fit residues: 46.9490 Evaluate side-chains 114 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 111 time to evaluate : 1.899 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1501 time to fit residues: 3.4238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 215 optimal weight: 7.9990 chunk 135 optimal weight: 1.9990 chunk 131 optimal weight: 20.0000 chunk 99 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 16513 Z= 0.236 Angle : 0.518 9.903 22560 Z= 0.252 Chirality : 0.038 0.196 2783 Planarity : 0.003 0.039 2806 Dihedral : 3.766 59.139 2382 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.20), residues: 1994 helix: 2.10 (0.15), residues: 1276 sheet: 0.72 (0.57), residues: 80 loop : -1.33 (0.25), residues: 638 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 1.954 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 123 average time/residue: 0.2326 time to fit residues: 49.1168 Evaluate side-chains 120 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 1.993 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1502 time to fit residues: 4.9616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 40.0000 chunk 86 optimal weight: 0.6980 chunk 128 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 20 optimal weight: 0.0470 chunk 169 optimal weight: 2.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 213 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.073 16513 Z= 0.138 Angle : 0.477 9.633 22560 Z= 0.230 Chirality : 0.036 0.286 2783 Planarity : 0.003 0.040 2806 Dihedral : 3.665 59.752 2382 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.20), residues: 1994 helix: 2.29 (0.15), residues: 1271 sheet: 0.83 (0.57), residues: 80 loop : -1.25 (0.26), residues: 643 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 118 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 122 average time/residue: 0.2220 time to fit residues: 46.5754 Evaluate side-chains 119 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 115 time to evaluate : 1.779 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1446 time to fit residues: 3.4838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 6.9990 chunk 206 optimal weight: 1.9990 chunk 188 optimal weight: 0.0040 chunk 201 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 157 optimal weight: 30.0000 chunk 61 optimal weight: 0.8980 chunk 181 optimal weight: 0.9980 chunk 190 optimal weight: 0.0170 chunk 200 optimal weight: 2.9990 overall best weight: 0.5832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.066 16513 Z= 0.130 Angle : 0.473 11.292 22560 Z= 0.226 Chirality : 0.036 0.208 2783 Planarity : 0.003 0.040 2806 Dihedral : 3.559 58.344 2382 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.20), residues: 1994 helix: 2.37 (0.15), residues: 1271 sheet: 0.89 (0.59), residues: 80 loop : -1.18 (0.26), residues: 643 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 118 average time/residue: 0.2373 time to fit residues: 47.5184 Evaluate side-chains 114 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 2.094 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1449 time to fit residues: 2.9951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 30.0000 chunk 212 optimal weight: 0.8980 chunk 129 optimal weight: 0.4980 chunk 100 optimal weight: 0.5980 chunk 147 optimal weight: 0.1980 chunk 223 optimal weight: 10.0000 chunk 205 optimal weight: 0.2980 chunk 177 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.069 16513 Z= 0.121 Angle : 0.469 10.514 22560 Z= 0.224 Chirality : 0.036 0.210 2783 Planarity : 0.003 0.042 2806 Dihedral : 3.490 56.687 2382 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.20), residues: 1994 helix: 2.45 (0.15), residues: 1273 sheet: 0.99 (0.60), residues: 80 loop : -1.08 (0.26), residues: 641 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 2.040 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.2312 time to fit residues: 46.5940 Evaluate side-chains 115 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.959 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 0.0370 chunk 189 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 163 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 177 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.125968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.097938 restraints weight = 34526.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.100367 restraints weight = 19636.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.102009 restraints weight = 13513.795| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 16513 Z= 0.179 Angle : 0.489 9.888 22560 Z= 0.237 Chirality : 0.037 0.208 2783 Planarity : 0.003 0.040 2806 Dihedral : 3.573 57.085 2382 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.20), residues: 1994 helix: 2.37 (0.15), residues: 1272 sheet: 0.85 (0.59), residues: 80 loop : -1.12 (0.26), residues: 642 =============================================================================== Job complete usr+sys time: 2555.85 seconds wall clock time: 47 minutes 47.85 seconds (2867.85 seconds total)