Starting phenix.real_space_refine on Fri Mar 15 07:21:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6s_33026/03_2024/7x6s_33026.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6s_33026/03_2024/7x6s_33026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6s_33026/03_2024/7x6s_33026.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6s_33026/03_2024/7x6s_33026.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6s_33026/03_2024/7x6s_33026.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6s_33026/03_2024/7x6s_33026.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.005 sd= 0.075 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: 5 Type Number sf(0) Gaussians Mn 1 7.51 5 S 66 5.16 5 C 6987 2.51 5 N 1854 2.21 5 O 2079 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 75": "OE1" <-> "OE2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 106": "NH1" <-> "NH2" Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 571": "NH1" <-> "NH2" Residue "A PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 580": "OE1" <-> "OE2" Residue "A ARG 594": "NH1" <-> "NH2" Residue "A ARG 611": "NH1" <-> "NH2" Residue "A PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 653": "NH1" <-> "NH2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A PHE 690": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 741": "OE1" <-> "OE2" Residue "A PHE 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 750": "NH1" <-> "NH2" Residue "A PHE 844": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 858": "OE1" <-> "OE2" Residue "A TYR 859": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 876": "OE1" <-> "OE2" Residue "A GLU 881": "OE1" <-> "OE2" Residue "A ASP 882": "OD1" <-> "OD2" Residue "A ASP 890": "OD1" <-> "OD2" Residue "A PHE 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 903": "OE1" <-> "OE2" Residue "A GLU 1093": "OE1" <-> "OE2" Residue "A TYR 1099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1105": "OD1" <-> "OD2" Residue "A TYR 1115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1123": "NH1" <-> "NH2" Residue "A ARG 1131": "NH1" <-> "NH2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "A PHE 1146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1158": "OD1" <-> "OD2" Residue "A PHE 1161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1162": "OE1" <-> "OE2" Residue "A ARG 1173": "NH1" <-> "NH2" Residue "A TYR 1209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1264": "NH1" <-> "NH2" Residue "A GLU 1312": "OE1" <-> "OE2" Residue "A ARG 1313": "NH1" <-> "NH2" Residue "A ASP 1328": "OD1" <-> "OD2" Residue "A ARG 1329": "NH1" <-> "NH2" Residue "A ARG 1330": "NH1" <-> "NH2" Residue "A PHE 1369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1432": "NH1" <-> "NH2" Residue "A PHE 1443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1464": "NH1" <-> "NH2" Residue "A TYR 1466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1527": "OE1" <-> "OE2" Residue "A ASP 1534": "OD1" <-> "OD2" Residue "A PHE 1544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1624": "NH1" <-> "NH2" Residue "A GLU 1625": "OE1" <-> "OE2" Residue "A TYR 1628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1697": "OE1" <-> "OE2" Residue "A PHE 1774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1807": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10987 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10986 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1453, 10980 Classifications: {'peptide': 1453} Incomplete info: {'truncation_to_alanine': 237} Link IDs: {'PTRANS': 47, 'TRANS': 1405} Chain breaks: 16 Unresolved non-hydrogen bonds: 795 Unresolved non-hydrogen angles: 991 Unresolved non-hydrogen dihedrals: 615 Unresolved non-hydrogen chiralities: 102 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 1, 'GLU:plan': 21, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 357 Conformer: "B" Number of residues, atoms: 1453, 10980 Classifications: {'peptide': 1453} Incomplete info: {'truncation_to_alanine': 237} Link IDs: {'PTRANS': 47, 'TRANS': 1405} Chain breaks: 16 Unresolved non-hydrogen bonds: 795 Unresolved non-hydrogen angles: 991 Unresolved non-hydrogen dihedrals: 615 Unresolved non-hydrogen chiralities: 102 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 1, 'GLU:plan': 21, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 357 bond proxies already assigned to first conformer: 11179 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.15, per 1000 atoms: 1.01 Number of scatterers: 10987 At special positions: 0 Unit cell: (108, 109.08, 122.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 1 24.99 S 66 16.00 O 2079 8.00 N 1854 7.00 C 6987 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: 4.25 Conformation dependent library (CDL) restraints added in 4.0 seconds 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2790 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 10 sheets defined 52.4% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 1 through 16 removed outlier: 4.363A pdb=" N LEU A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN A 14 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 16 " --> pdb=" O CYS A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 31 removed outlier: 4.028A pdb=" N ARG A 24 " --> pdb=" O GLU A 20 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 59 removed outlier: 3.746A pdb=" N ILE A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 75 Processing helix chain 'A' and resid 108 through 126 removed outlier: 4.052A pdb=" N ILE A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 153 through 174 Processing helix chain 'A' and resid 180 through 187 Processing helix chain 'A' and resid 216 through 221 removed outlier: 3.725A pdb=" N CYS A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 242 removed outlier: 3.625A pdb=" N SER A 240 " --> pdb=" O PHE A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 262 through 272 Processing helix chain 'A' and resid 283 through 292 Processing helix chain 'A' and resid 297 through 302 removed outlier: 3.700A pdb=" N ALA A 302 " --> pdb=" O ARG A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 327 removed outlier: 3.628A pdb=" N MET A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 346 removed outlier: 3.996A pdb=" N LEU A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASP A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 430 removed outlier: 3.780A pdb=" N CYS A 424 " --> pdb=" O LYS A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 447 removed outlier: 4.574A pdb=" N GLU A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU A 444 " --> pdb=" O HIS A 440 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N HIS A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'A' and resid 493 through 498 Processing helix chain 'A' and resid 568 through 572 Processing helix chain 'A' and resid 581 through 590 removed outlier: 3.614A pdb=" N ASP A 587 " --> pdb=" O TYR A 583 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE A 590 " --> pdb=" O ILE A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 599 Processing helix chain 'A' and resid 602 through 620 removed outlier: 3.608A pdb=" N LEU A 616 " --> pdb=" O THR A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 641 removed outlier: 3.831A pdb=" N VAL A 629 " --> pdb=" O ASN A 625 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ARG A 633 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N TYR A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A 636 " --> pdb=" O VAL A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 651 removed outlier: 3.572A pdb=" N ASP A 650 " --> pdb=" O SER A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 676 Processing helix chain 'A' and resid 683 through 697 Processing helix chain 'A' and resid 698 through 701 Processing helix chain 'A' and resid 708 through 727 removed outlier: 4.355A pdb=" N LYS A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N CYS A 715 " --> pdb=" O ASP A 711 " (cutoff:3.500A) Proline residue: A 722 - end of helix removed outlier: 3.580A pdb=" N GLN A 725 " --> pdb=" O GLU A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 752 Processing helix chain 'A' and resid 769 through 779 Processing helix chain 'A' and resid 834 through 844 removed outlier: 3.695A pdb=" N GLU A 842 " --> pdb=" O SER A 838 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE A 844 " --> pdb=" O ILE A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 867 Processing helix chain 'A' and resid 889 through 898 removed outlier: 3.838A pdb=" N GLU A 894 " --> pdb=" O ASP A 890 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 898 " --> pdb=" O GLU A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 918 removed outlier: 4.099A pdb=" N ARG A 917 " --> pdb=" O ARG A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 954 Processing helix chain 'A' and resid 1084 through 1088 removed outlier: 3.688A pdb=" N LEU A1088 " --> pdb=" O LEU A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1148 removed outlier: 3.674A pdb=" N ARG A1137 " --> pdb=" O LYS A1133 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A1138 " --> pdb=" O MET A1134 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A1139 " --> pdb=" O PHE A1135 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU A1144 " --> pdb=" O GLU A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1173 removed outlier: 3.769A pdb=" N PHE A1161 " --> pdb=" O ASN A1157 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU A1162 " --> pdb=" O ASP A1158 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN A1163 " --> pdb=" O LYS A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1200 removed outlier: 3.640A pdb=" N PHE A1195 " --> pdb=" O CYS A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1226 removed outlier: 3.540A pdb=" N LYS A1214 " --> pdb=" O VAL A1210 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP A1215 " --> pdb=" O ARG A1211 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N HIS A1216 " --> pdb=" O SER A1212 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THR A1219 " --> pdb=" O ASP A1215 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N THR A1222 " --> pdb=" O SER A1218 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TRP A1223 " --> pdb=" O THR A1219 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N HIS A1226 " --> pdb=" O THR A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1232 through 1249 Processing helix chain 'A' and resid 1258 through 1261 Processing helix chain 'A' and resid 1262 through 1271 Processing helix chain 'A' and resid 1289 through 1311 removed outlier: 3.993A pdb=" N TYR A1304 " --> pdb=" O ARG A1300 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY A1307 " --> pdb=" O ASN A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1331 removed outlier: 3.515A pdb=" N LEU A1331 " --> pdb=" O ASP A1328 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1328 through 1331' Processing helix chain 'A' and resid 1332 through 1338 removed outlier: 4.115A pdb=" N VAL A1336 " --> pdb=" O SER A1332 " (cutoff:3.500A) Processing helix chain 'A' and resid 1341 through 1356 removed outlier: 3.569A pdb=" N SER A1350 " --> pdb=" O LEU A1346 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A1353 " --> pdb=" O GLN A1349 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY A1354 " --> pdb=" O SER A1350 " (cutoff:3.500A) Processing helix chain 'A' and resid 1386 through 1395 removed outlier: 3.508A pdb=" N PHE A1390 " --> pdb=" O LEU A1386 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A1393 " --> pdb=" O LYS A1389 " (cutoff:3.500A) Processing helix chain 'A' and resid 1402 through 1420 removed outlier: 4.296A pdb=" N GLU A1408 " --> pdb=" O HIS A1404 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A1410 " --> pdb=" O LEU A1406 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP A1411 " --> pdb=" O CYS A1407 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP A1415 " --> pdb=" O ASP A1411 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN A1420 " --> pdb=" O GLN A1416 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1441 Processing helix chain 'A' and resid 1463 through 1476 removed outlier: 3.553A pdb=" N ARG A1467 " --> pdb=" O SER A1463 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS A1476 " --> pdb=" O ILE A1472 " (cutoff:3.500A) Processing helix chain 'A' and resid 1484 through 1493 Processing helix chain 'A' and resid 1501 through 1508 removed outlier: 3.525A pdb=" N PHE A1508 " --> pdb=" O PHE A1504 " (cutoff:3.500A) Processing helix chain 'A' and resid 1514 through 1524 removed outlier: 3.937A pdb=" N LEU A1523 " --> pdb=" O LEU A1519 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1534 Processing helix chain 'A' and resid 1568 through 1577 removed outlier: 3.605A pdb=" N LYS A1572 " --> pdb=" O PRO A1568 " (cutoff:3.500A) Processing helix chain 'A' and resid 1606 through 1614 removed outlier: 4.433A pdb=" N LYS A1612 " --> pdb=" O ILE A1608 " (cutoff:3.500A) Processing helix chain 'A' and resid 1628 through 1639 removed outlier: 4.016A pdb=" N LEU A1632 " --> pdb=" O TYR A1628 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A1636 " --> pdb=" O LEU A1632 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR A1637 " --> pdb=" O LEU A1633 " (cutoff:3.500A) Processing helix chain 'A' and resid 1656 through 1660 Processing helix chain 'A' and resid 1677 through 1689 removed outlier: 3.722A pdb=" N ILE A1682 " --> pdb=" O ASP A1678 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N SER A1687 " --> pdb=" O SER A1683 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A1688 " --> pdb=" O LEU A1684 " (cutoff:3.500A) Processing helix chain 'A' and resid 1692 through 1696 Processing helix chain 'A' and resid 1733 through 1743 Processing helix chain 'A' and resid 1747 through 1752 Processing helix chain 'A' and resid 1774 through 1785 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 removed outlier: 7.312A pdb=" N LEU A 98 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE A 140 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LEU A 100 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASP A 142 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLU A 102 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ARG A 144 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N PHE A 104 " --> pdb=" O ARG A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AA3, first strand: chain 'A' and resid 531 through 532 removed outlier: 3.576A pdb=" N ILE A 532 " --> pdb=" O TYR A 539 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 551 through 553 removed outlier: 3.993A pdb=" N ARG A 551 " --> pdb=" O ALA A 567 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA A 567 " --> pdb=" O ARG A 551 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE A 565 " --> pdb=" O TYR A 553 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1113 through 1115 Processing sheet with id=AA6, first strand: chain 'A' and resid 1183 through 1184 removed outlier: 4.562A pdb=" N PHE A1359 " --> pdb=" O SER A1184 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1229 through 1230 Processing sheet with id=AA8, first strand: chain 'A' and resid 1315 through 1318 removed outlier: 4.341A pdb=" N GLU A1315 " --> pdb=" O LEU A1326 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR A1317 " --> pdb=" O ILE A1324 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE A1324 " --> pdb=" O TYR A1317 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1536 through 1538 removed outlier: 3.593A pdb=" N ARG A1673 " --> pdb=" O TRP A1537 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1619 through 1620 443 hydrogen bonds defined for protein. 1269 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: 3.44 Time building geometry restraints manager: 4.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.26: 1869 1.26 - 1.40: 2738 1.40 - 1.54: 6396 1.54 - 1.67: 96 1.67 - 1.81: 96 Bond restraints: 11195 Sorted by residual: bond pdb=" C PHE A 474 " pdb=" O PHE A 474 " ideal model delta sigma weight residual 1.235 1.127 0.108 1.26e-02 6.30e+03 7.37e+01 bond pdb=" CA GLN A 475 " pdb=" CB GLN A 475 " ideal model delta sigma weight residual 1.530 1.651 -0.122 1.58e-02 4.01e+03 5.91e+01 bond pdb=" N GLU A 876 " pdb=" CA GLU A 876 " ideal model delta sigma weight residual 1.457 1.362 0.095 1.29e-02 6.01e+03 5.45e+01 bond pdb=" C ILE A1603 " pdb=" O ILE A1603 " ideal model delta sigma weight residual 1.242 1.156 0.086 1.17e-02 7.31e+03 5.39e+01 bond pdb=" CA GLN A 475 " pdb=" C GLN A 475 " ideal model delta sigma weight residual 1.524 1.597 -0.073 1.26e-02 6.30e+03 3.39e+01 ... (remaining 11190 not shown) Histogram of bond angle deviations from ideal: 81.56 - 93.12: 4 93.12 - 104.69: 200 104.69 - 116.25: 7024 116.25 - 127.81: 7838 127.81 - 139.38: 88 Bond angle restraints: 15154 Sorted by residual: angle pdb=" N THR A 877 " pdb=" CA THR A 877 " pdb=" C THR A 877 " ideal model delta sigma weight residual 107.73 81.56 26.17 1.34e+00 5.57e-01 3.81e+02 angle pdb=" N TRP A1459 " pdb=" CA TRP A1459 " pdb=" C TRP A1459 " ideal model delta sigma weight residual 114.56 90.05 24.51 1.27e+00 6.20e-01 3.72e+02 angle pdb=" N GLU A 188 " pdb=" CA GLU A 188 " pdb=" C GLU A 188 " ideal model delta sigma weight residual 109.15 88.25 20.90 1.44e+00 4.82e-01 2.11e+02 angle pdb=" N CYS A1154 " pdb=" CA CYS A1154 " pdb=" C CYS A1154 " ideal model delta sigma weight residual 112.30 131.88 -19.58 1.36e+00 5.41e-01 2.07e+02 angle pdb=" O GLU A 875 " pdb=" C GLU A 875 " pdb=" N GLU A 876 " ideal model delta sigma weight residual 122.59 138.87 -16.28 1.33e+00 5.65e-01 1.50e+02 ... (remaining 15149 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 5892 16.59 - 33.18: 710 33.18 - 49.77: 111 49.77 - 66.37: 23 66.37 - 82.96: 9 Dihedral angle restraints: 6745 sinusoidal: 2473 harmonic: 4272 Sorted by residual: dihedral pdb=" C THR A 877 " pdb=" N THR A 877 " pdb=" CA THR A 877 " pdb=" CB THR A 877 " ideal model delta harmonic sigma weight residual -122.00 -95.02 -26.98 0 2.50e+00 1.60e-01 1.16e+02 dihedral pdb=" C PHE A 474 " pdb=" N PHE A 474 " pdb=" CA PHE A 474 " pdb=" CB PHE A 474 " ideal model delta harmonic sigma weight residual -122.60 -149.48 26.88 0 2.50e+00 1.60e-01 1.16e+02 dihedral pdb=" C GLU A 275 " pdb=" N GLU A 275 " pdb=" CA GLU A 275 " pdb=" CB GLU A 275 " ideal model delta harmonic sigma weight residual -122.60 -147.80 25.20 0 2.50e+00 1.60e-01 1.02e+02 ... (remaining 6742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.227: 1676 0.227 - 0.454: 34 0.454 - 0.681: 12 0.681 - 0.908: 3 0.908 - 1.135: 3 Chirality restraints: 1728 Sorted by residual: chirality pdb=" CA PHE A 474 " pdb=" N PHE A 474 " pdb=" C PHE A 474 " pdb=" CB PHE A 474 " both_signs ideal model delta sigma weight residual False 2.51 1.38 1.13 2.00e-01 2.50e+01 3.22e+01 chirality pdb=" CA CYS A1154 " pdb=" N CYS A1154 " pdb=" C CYS A1154 " pdb=" CB CYS A1154 " both_signs ideal model delta sigma weight residual False 2.51 1.49 1.02 2.00e-01 2.50e+01 2.62e+01 chirality pdb=" CA GLU A 275 " pdb=" N GLU A 275 " pdb=" C GLU A 275 " pdb=" CB GLU A 275 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.37e+01 ... (remaining 1725 not shown) Planarity restraints: 1962 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A1458 " -0.033 2.00e-02 2.50e+03 6.57e-02 4.31e+01 pdb=" CG ASP A1458 " 0.114 2.00e-02 2.50e+03 pdb=" OD1 ASP A1458 " -0.042 2.00e-02 2.50e+03 pdb=" OD2 ASP A1458 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 876 " 0.031 2.00e-02 2.50e+03 6.07e-02 3.68e+01 pdb=" C GLU A 876 " -0.105 2.00e-02 2.50e+03 pdb=" O GLU A 876 " 0.039 2.00e-02 2.50e+03 pdb=" N THR A 877 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1788 " -0.031 2.00e-02 2.50e+03 5.89e-02 3.47e+01 pdb=" C LEU A1788 " 0.102 2.00e-02 2.50e+03 pdb=" O LEU A1788 " -0.038 2.00e-02 2.50e+03 pdb=" N SER A1789 " -0.033 2.00e-02 2.50e+03 ... (remaining 1959 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 131 2.54 - 3.13: 9518 3.13 - 3.72: 15754 3.72 - 4.31: 21031 4.31 - 4.90: 34022 Nonbonded interactions: 80456 Sorted by model distance: nonbonded pdb=" O LEU A1334 " pdb=" O ASP A1338 " model vdw 1.947 3.040 nonbonded pdb=" OD1 ASN A 499 " pdb=" OH TYR A 543 " model vdw 1.970 2.440 nonbonded pdb=" OE2 GLU A1372 " pdb="MN MN A2301 " model vdw 1.987 2.320 nonbonded pdb=" OE1 GLU A1372 " pdb="MN MN A2301 " model vdw 2.017 2.320 nonbonded pdb=" N THR A 877 " pdb=" O THR A 877 " model vdw 2.027 2.496 ... (remaining 80451 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=0.11 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.350 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: 2.420 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 39.220 Find NCS groups from input model: 0.320 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: 0.010 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 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 : 0.010 0.122 11195 Z= 0.638 Angle : 1.438 26.172 15154 Z= 0.831 Chirality : 0.104 1.135 1728 Planarity : 0.007 0.096 1962 Dihedral : 14.712 82.957 3955 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.42 % Allowed : 15.79 % Favored : 83.79 % Rotamer: Outliers : 0.18 % Allowed : 1.17 % Favored : 98.65 % Cbeta Deviations : 2.22 % 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: -3.97 (0.20), residues: 1421 helix: -1.39 (0.19), residues: 687 sheet: -3.24 (0.71), residues: 51 loop : -4.07 (0.19), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A1459 HIS 0.015 0.002 HIS A 382 PHE 0.030 0.003 PHE A 299 TYR 0.023 0.003 TYR A1266 ARG 0.013 0.001 ARG A1467 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 1.706 Fit side-chains revert: symmetry clash REVERT: A 319 ARG cc_start: 0.7184 (mtm-85) cc_final: 0.6958 (ptt90) REVERT: A 1740 GLN cc_start: 0.8558 (mp10) cc_final: 0.8283 (mp10) outliers start: 1 outliers final: 1 residues processed: 135 average time/residue: 0.2263 time to fit residues: 44.6950 Evaluate side-chains 101 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 7.9990 chunk 109 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 74 optimal weight: 20.0000 chunk 58 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 HIS ** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 GLN A 935 HIS ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11195 Z= 0.217 Angle : 0.765 12.874 15154 Z= 0.385 Chirality : 0.045 0.204 1728 Planarity : 0.005 0.064 1962 Dihedral : 6.421 38.217 1537 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.91 % Favored : 87.95 % Rotamer: Outliers : 0.45 % Allowed : 7.46 % Favored : 92.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.21), residues: 1421 helix: -0.83 (0.19), residues: 746 sheet: -2.28 (0.80), residues: 46 loop : -3.85 (0.20), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1459 HIS 0.003 0.001 HIS A 382 PHE 0.028 0.002 PHE A 158 TYR 0.022 0.002 TYR A1294 ARG 0.006 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 119 time to evaluate : 1.324 Fit side-chains revert: symmetry clash REVERT: A 339 GLN cc_start: 0.6628 (tm-30) cc_final: 0.5645 (pm20) outliers start: 4 outliers final: 3 residues processed: 121 average time/residue: 0.1915 time to fit residues: 35.8236 Evaluate side-chains 105 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 102 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 1791 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 73 optimal weight: 7.9990 chunk 40 optimal weight: 0.0980 chunk 109 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 chunk 142 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 130 optimal weight: 0.1980 chunk 44 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 ASN ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 HIS ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11195 Z= 0.175 Angle : 0.687 10.492 15154 Z= 0.342 Chirality : 0.043 0.180 1728 Planarity : 0.004 0.068 1962 Dihedral : 5.599 27.094 1537 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.36 % Favored : 89.50 % Rotamer: Outliers : 1.44 % Allowed : 9.62 % Favored : 88.94 % 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: -2.73 (0.21), residues: 1421 helix: -0.44 (0.19), residues: 741 sheet: -1.28 (0.95), residues: 35 loop : -3.65 (0.21), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1459 HIS 0.003 0.001 HIS A 935 PHE 0.018 0.001 PHE A1508 TYR 0.019 0.002 TYR A1294 ARG 0.007 0.000 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 PHE cc_start: 0.8502 (m-80) cc_final: 0.8001 (m-80) REVERT: A 1508 PHE cc_start: 0.6856 (t80) cc_final: 0.6237 (t80) REVERT: A 1735 LEU cc_start: 0.8413 (mt) cc_final: 0.7949 (tp) outliers start: 15 outliers final: 7 residues processed: 126 average time/residue: 0.1921 time to fit residues: 36.8240 Evaluate side-chains 114 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 107 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 1418 ILE Chi-restraints excluded: chain A residue 1521 ASP Chi-restraints excluded: chain A residue 1523 LEU Chi-restraints excluded: chain A residue 1791 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 130 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 14 optimal weight: 0.0870 chunk 62 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 140 optimal weight: 0.1980 chunk 69 optimal weight: 0.4980 chunk 125 optimal weight: 9.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN A 382 HIS ** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 HIS ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11195 Z= 0.158 Angle : 0.654 14.936 15154 Z= 0.323 Chirality : 0.042 0.176 1728 Planarity : 0.004 0.069 1962 Dihedral : 5.211 26.212 1537 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.15 % Favored : 89.78 % Rotamer: Outliers : 1.44 % Allowed : 11.78 % Favored : 86.78 % 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: -2.38 (0.22), residues: 1421 helix: -0.21 (0.19), residues: 742 sheet: -1.15 (0.90), residues: 37 loop : -3.41 (0.21), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1459 HIS 0.003 0.000 HIS A 935 PHE 0.036 0.001 PHE A 158 TYR 0.023 0.002 TYR A1294 ARG 0.006 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 PHE cc_start: 0.8469 (m-80) cc_final: 0.7806 (m-10) REVERT: A 911 ARG cc_start: 0.8931 (tpp-160) cc_final: 0.8589 (tpm170) REVERT: A 944 MET cc_start: 0.6309 (mmm) cc_final: 0.6053 (mmm) REVERT: A 1508 PHE cc_start: 0.6680 (t80) cc_final: 0.6068 (t80) outliers start: 15 outliers final: 9 residues processed: 121 average time/residue: 0.1993 time to fit residues: 36.8804 Evaluate side-chains 111 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 1521 ASP Chi-restraints excluded: chain A residue 1523 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 116 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 57 optimal weight: 0.2980 chunk 119 optimal weight: 0.0470 chunk 96 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 71 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 chunk 35 optimal weight: 0.2980 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 HIS ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11195 Z= 0.178 Angle : 0.647 14.975 15154 Z= 0.319 Chirality : 0.042 0.159 1728 Planarity : 0.004 0.070 1962 Dihedral : 5.051 25.093 1537 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % Rotamer: Outliers : 1.89 % Allowed : 12.23 % Favored : 85.88 % 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: -2.21 (0.22), residues: 1421 helix: -0.05 (0.20), residues: 741 sheet: -0.66 (0.91), residues: 37 loop : -3.38 (0.22), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1459 HIS 0.003 0.001 HIS A 935 PHE 0.022 0.001 PHE A 245 TYR 0.033 0.002 TYR A 745 ARG 0.006 0.000 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 PHE cc_start: 0.8458 (m-80) cc_final: 0.7829 (m-10) REVERT: A 393 ARG cc_start: 0.6798 (mtp-110) cc_final: 0.6379 (mtp180) REVERT: A 944 MET cc_start: 0.6522 (mmm) cc_final: 0.6217 (mmm) REVERT: A 1508 PHE cc_start: 0.6601 (t80) cc_final: 0.5976 (t80) outliers start: 20 outliers final: 13 residues processed: 126 average time/residue: 0.2011 time to fit residues: 38.5664 Evaluate side-chains 115 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 102 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 696 TYR Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 1446 ASP Chi-restraints excluded: chain A residue 1486 LEU Chi-restraints excluded: chain A residue 1521 ASP Chi-restraints excluded: chain A residue 1543 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 47 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 140 optimal weight: 9.9990 chunk 116 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 46 optimal weight: 0.0670 chunk 73 optimal weight: 2.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 ASN ** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 HIS ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1737 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11195 Z= 0.241 Angle : 0.690 14.325 15154 Z= 0.341 Chirality : 0.043 0.159 1728 Planarity : 0.004 0.071 1962 Dihedral : 5.253 27.073 1537 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.98 % Favored : 88.02 % Rotamer: Outliers : 1.53 % Allowed : 13.85 % Favored : 84.62 % 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: -2.24 (0.22), residues: 1421 helix: -0.06 (0.20), residues: 745 sheet: -2.04 (0.75), residues: 55 loop : -3.35 (0.22), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1459 HIS 0.005 0.001 HIS A 382 PHE 0.024 0.001 PHE A 245 TYR 0.028 0.002 TYR A1294 ARG 0.007 0.000 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 1.200 Fit side-chains revert: symmetry clash REVERT: A 151 PHE cc_start: 0.8447 (m-80) cc_final: 0.7822 (m-10) REVERT: A 393 ARG cc_start: 0.7009 (mtp-110) cc_final: 0.6675 (mtp180) REVERT: A 911 ARG cc_start: 0.8999 (tpp-160) cc_final: 0.8489 (tpm170) REVERT: A 944 MET cc_start: 0.6590 (mmm) cc_final: 0.6272 (mmm) REVERT: A 1508 PHE cc_start: 0.6659 (t80) cc_final: 0.6040 (t80) outliers start: 16 outliers final: 11 residues processed: 113 average time/residue: 0.2067 time to fit residues: 35.9757 Evaluate side-chains 111 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 696 TYR Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 1446 ASP Chi-restraints excluded: chain A residue 1521 ASP Chi-restraints excluded: chain A residue 1523 LEU Chi-restraints excluded: chain A residue 1643 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 135 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 79 optimal weight: 20.0000 chunk 102 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 139 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 HIS A 935 HIS ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11195 Z= 0.231 Angle : 0.677 13.730 15154 Z= 0.334 Chirality : 0.043 0.159 1728 Planarity : 0.004 0.070 1962 Dihedral : 5.179 27.069 1535 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.56 % Favored : 88.44 % Rotamer: Outliers : 1.71 % Allowed : 14.48 % Favored : 83.81 % 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: -2.18 (0.22), residues: 1421 helix: -0.00 (0.20), residues: 746 sheet: -2.06 (0.75), residues: 55 loop : -3.33 (0.22), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1459 HIS 0.005 0.001 HIS A 382 PHE 0.025 0.002 PHE A1503 TYR 0.024 0.001 TYR A1294 ARG 0.006 0.000 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 PHE cc_start: 0.8391 (m-80) cc_final: 0.7796 (m-10) REVERT: A 393 ARG cc_start: 0.7174 (mtp-110) cc_final: 0.6903 (mtp180) REVERT: A 944 MET cc_start: 0.6602 (mmm) cc_final: 0.6275 (mmm) REVERT: A 1508 PHE cc_start: 0.6571 (t80) cc_final: 0.5902 (t80) REVERT: A 1735 LEU cc_start: 0.8462 (mt) cc_final: 0.8001 (tp) outliers start: 18 outliers final: 12 residues processed: 119 average time/residue: 0.2008 time to fit residues: 36.6639 Evaluate side-chains 117 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 696 TYR Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 1446 ASP Chi-restraints excluded: chain A residue 1521 ASP Chi-restraints excluded: chain A residue 1643 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 55 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 27 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 69 optimal weight: 0.0370 chunk 13 optimal weight: 20.0000 chunk 109 optimal weight: 0.0980 chunk 127 optimal weight: 0.4980 chunk 133 optimal weight: 10.0000 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 HIS ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1686 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11195 Z= 0.151 Angle : 0.644 14.034 15154 Z= 0.311 Chirality : 0.041 0.190 1728 Planarity : 0.004 0.069 1962 Dihedral : 4.772 24.311 1535 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 1.08 % Allowed : 15.02 % Favored : 83.90 % 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: -1.89 (0.22), residues: 1421 helix: 0.22 (0.20), residues: 747 sheet: -1.22 (0.83), residues: 45 loop : -3.24 (0.22), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 592 HIS 0.003 0.000 HIS A 935 PHE 0.023 0.001 PHE A 158 TYR 0.020 0.001 TYR A1294 ARG 0.003 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 113 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 PHE cc_start: 0.8360 (m-80) cc_final: 0.7739 (m-10) REVERT: A 200 MET cc_start: 0.5616 (tpp) cc_final: 0.5190 (tpt) REVERT: A 325 ASN cc_start: 0.7971 (t0) cc_final: 0.7518 (t0) REVERT: A 393 ARG cc_start: 0.7078 (mtp-110) cc_final: 0.6833 (mtp180) REVERT: A 630 GLN cc_start: 0.7747 (tt0) cc_final: 0.7534 (tp-100) REVERT: A 911 ARG cc_start: 0.8992 (tpp-160) cc_final: 0.8439 (tpm170) REVERT: A 944 MET cc_start: 0.6636 (mmm) cc_final: 0.6304 (mmm) REVERT: A 1134 MET cc_start: 0.7537 (tpp) cc_final: 0.7336 (tpp) outliers start: 11 outliers final: 9 residues processed: 122 average time/residue: 0.2237 time to fit residues: 42.4137 Evaluate side-chains 118 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 109 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 696 TYR Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 1446 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 8.9990 chunk 130 optimal weight: 0.7980 chunk 133 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 39 optimal weight: 20.0000 chunk 117 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 HIS ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1784 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11195 Z= 0.179 Angle : 0.652 15.991 15154 Z= 0.313 Chirality : 0.042 0.198 1728 Planarity : 0.004 0.071 1962 Dihedral : 4.729 24.127 1535 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 0.99 % Allowed : 15.65 % Favored : 83.36 % 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 (0.22), residues: 1421 helix: 0.26 (0.20), residues: 746 sheet: -1.18 (0.83), residues: 45 loop : -3.18 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1459 HIS 0.003 0.001 HIS A 935 PHE 0.023 0.001 PHE A1503 TYR 0.025 0.001 TYR A 745 ARG 0.003 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 PHE cc_start: 0.8320 (m-80) cc_final: 0.7700 (m-10) REVERT: A 325 ASN cc_start: 0.8060 (t0) cc_final: 0.7627 (t0) REVERT: A 393 ARG cc_start: 0.7127 (mtp-110) cc_final: 0.6883 (mtp180) REVERT: A 944 MET cc_start: 0.6652 (mmm) cc_final: 0.6322 (mmm) REVERT: A 1134 MET cc_start: 0.7539 (tpp) cc_final: 0.7322 (tpp) outliers start: 10 outliers final: 8 residues processed: 121 average time/residue: 0.2007 time to fit residues: 37.3742 Evaluate side-chains 117 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 696 TYR Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 1446 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 137 optimal weight: 0.0030 chunk 84 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 HIS ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11195 Z= 0.160 Angle : 0.652 16.422 15154 Z= 0.311 Chirality : 0.041 0.211 1728 Planarity : 0.004 0.069 1962 Dihedral : 4.629 29.538 1535 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer: Outliers : 1.17 % Allowed : 15.74 % Favored : 83.09 % 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: -1.73 (0.22), residues: 1421 helix: 0.35 (0.20), residues: 745 sheet: -1.14 (0.82), residues: 45 loop : -3.14 (0.22), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 592 HIS 0.003 0.000 HIS A 935 PHE 0.032 0.001 PHE A 104 TYR 0.020 0.001 TYR A1294 ARG 0.005 0.000 ARG A 48 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 111 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 PHE cc_start: 0.8344 (m-80) cc_final: 0.7805 (m-10) REVERT: A 325 ASN cc_start: 0.8056 (t0) cc_final: 0.7617 (t0) REVERT: A 393 ARG cc_start: 0.7109 (mtp-110) cc_final: 0.6874 (mtp180) REVERT: A 630 GLN cc_start: 0.7797 (tt0) cc_final: 0.7575 (tp-100) REVERT: A 944 MET cc_start: 0.6648 (mmm) cc_final: 0.6318 (mmm) REVERT: A 1485 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.6847 (ptpp) REVERT: A 1508 PHE cc_start: 0.6304 (m-80) cc_final: 0.6034 (m-80) outliers start: 12 outliers final: 9 residues processed: 121 average time/residue: 0.2032 time to fit residues: 37.4692 Evaluate side-chains 120 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 696 TYR Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 1446 ASP Chi-restraints excluded: chain A residue 1485 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 0.0370 chunk 35 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 48 optimal weight: 8.9990 chunk 118 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 101 optimal weight: 0.0770 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 HIS A1087 ASN ** A1661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.155133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.106735 restraints weight = 24033.912| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 4.11 r_work: 0.3379 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3392 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3392 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11195 Z= 0.149 Angle : 0.636 16.162 15154 Z= 0.302 Chirality : 0.040 0.174 1728 Planarity : 0.004 0.070 1962 Dihedral : 4.412 29.413 1535 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.99 % Allowed : 15.92 % Favored : 83.09 % 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: -1.55 (0.23), residues: 1421 helix: 0.56 (0.20), residues: 733 sheet: -1.28 (0.78), residues: 49 loop : -3.06 (0.22), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1537 HIS 0.003 0.000 HIS A 935 PHE 0.024 0.001 PHE A 104 TYR 0.018 0.001 TYR A1294 ARG 0.003 0.000 ARG A1264 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2400.47 seconds wall clock time: 43 minutes 52.89 seconds (2632.89 seconds total)