Starting phenix.real_space_refine (version: dev) on Sun Dec 18 15:30:04 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a1d_11606/12_2022/7a1d_11606.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a1d_11606/12_2022/7a1d_11606.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a1d_11606/12_2022/7a1d_11606.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a1d_11606/12_2022/7a1d_11606.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a1d_11606/12_2022/7a1d_11606.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a1d_11606/12_2022/7a1d_11606.pdb" } resolution = 4.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 527": "NH1" <-> "NH2" Residue "A ARG 560": "NH1" <-> "NH2" Residue "A ARG 636": "NH1" <-> "NH2" Residue "A ARG 666": "NH1" <-> "NH2" Residue "A ARG 685": "NH1" <-> "NH2" Residue "A ARG 709": "NH1" <-> "NH2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "A ARG 723": "NH1" <-> "NH2" Residue "A ARG 780": "NH1" <-> "NH2" Residue "A ARG 1123": "NH1" <-> "NH2" Residue "A PHE 1126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1291": "NH1" <-> "NH2" Residue "A ARG 1299": "NH1" <-> "NH2" Residue "A ARG 1304": "NH1" <-> "NH2" Residue "A ARG 1341": "NH1" <-> "NH2" Residue "A ARG 1358": "NH1" <-> "NH2" Residue "A ARG 1360": "NH1" <-> "NH2" Residue "A ARG 1380": "NH1" <-> "NH2" Residue "A ARG 1381": "NH1" <-> "NH2" Residue "A ARG 1385": "NH1" <-> "NH2" Residue "A ARG 1388": "NH1" <-> "NH2" Residue "A ARG 1406": "NH1" <-> "NH2" Residue "A TYR 1457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1471": "NH1" <-> "NH2" Residue "A ARG 1501": "NH1" <-> "NH2" Residue "A ARG 1504": "NH1" <-> "NH2" Residue "A ARG 1510": "NH1" <-> "NH2" Residue "A ARG 1552": "NH1" <-> "NH2" Residue "A ARG 1558": "NH1" <-> "NH2" Residue "A ARG 1579": "NH1" <-> "NH2" Residue "A ARG 1582": "NH1" <-> "NH2" Residue "A ARG 1586": "NH1" <-> "NH2" Residue "B ARG 527": "NH1" <-> "NH2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B ARG 636": "NH1" <-> "NH2" Residue "B ARG 666": "NH1" <-> "NH2" Residue "B ARG 685": "NH1" <-> "NH2" Residue "B ARG 709": "NH1" <-> "NH2" Residue "B ARG 712": "NH1" <-> "NH2" Residue "B ARG 723": "NH1" <-> "NH2" Residue "B ARG 780": "NH1" <-> "NH2" Residue "B ARG 1123": "NH1" <-> "NH2" Residue "B PHE 1126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1291": "NH1" <-> "NH2" Residue "B ARG 1299": "NH1" <-> "NH2" Residue "B ARG 1304": "NH1" <-> "NH2" Residue "B ARG 1341": "NH1" <-> "NH2" Residue "B ARG 1358": "NH1" <-> "NH2" Residue "B ARG 1360": "NH1" <-> "NH2" Residue "B ARG 1380": "NH1" <-> "NH2" Residue "B ARG 1381": "NH1" <-> "NH2" Residue "B ARG 1385": "NH1" <-> "NH2" Residue "B ARG 1388": "NH1" <-> "NH2" Residue "B ARG 1406": "NH1" <-> "NH2" Residue "B TYR 1457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1471": "NH1" <-> "NH2" Residue "B ARG 1501": "NH1" <-> "NH2" Residue "B ARG 1504": "NH1" <-> "NH2" Residue "B ARG 1510": "NH1" <-> "NH2" Residue "B ARG 1552": "NH1" <-> "NH2" Residue "B ARG 1558": "NH1" <-> "NH2" Residue "B ARG 1579": "NH1" <-> "NH2" Residue "B ARG 1582": "NH1" <-> "NH2" Residue "B ARG 1586": "NH1" <-> "NH2" Residue "C ARG 527": "NH1" <-> "NH2" Residue "C ARG 560": "NH1" <-> "NH2" Residue "C ARG 636": "NH1" <-> "NH2" Residue "C ARG 666": "NH1" <-> "NH2" Residue "C ARG 685": "NH1" <-> "NH2" Residue "C ARG 709": "NH1" <-> "NH2" Residue "C ARG 712": "NH1" <-> "NH2" Residue "C ARG 723": "NH1" <-> "NH2" Residue "C ARG 780": "NH1" <-> "NH2" Residue "C ARG 1123": "NH1" <-> "NH2" Residue "C PHE 1126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1291": "NH1" <-> "NH2" Residue "C ARG 1299": "NH1" <-> "NH2" Residue "C ARG 1304": "NH1" <-> "NH2" Residue "C ARG 1341": "NH1" <-> "NH2" Residue "C ARG 1358": "NH1" <-> "NH2" Residue "C ARG 1360": "NH1" <-> "NH2" Residue "C ARG 1380": "NH1" <-> "NH2" Residue "C ARG 1381": "NH1" <-> "NH2" Residue "C ARG 1385": "NH1" <-> "NH2" Residue "C ARG 1388": "NH1" <-> "NH2" Residue "C ARG 1406": "NH1" <-> "NH2" Residue "C TYR 1457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1471": "NH1" <-> "NH2" Residue "C ARG 1501": "NH1" <-> "NH2" Residue "C ARG 1504": "NH1" <-> "NH2" Residue "C ARG 1510": "NH1" <-> "NH2" Residue "C ARG 1552": "NH1" <-> "NH2" Residue "C ARG 1558": "NH1" <-> "NH2" Residue "C ARG 1579": "NH1" <-> "NH2" Residue "C ARG 1582": "NH1" <-> "NH2" Residue "C ARG 1586": "NH1" <-> "NH2" Residue "D ARG 527": "NH1" <-> "NH2" Residue "D ARG 560": "NH1" <-> "NH2" Residue "D ARG 636": "NH1" <-> "NH2" Residue "D ARG 666": "NH1" <-> "NH2" Residue "D ARG 685": "NH1" <-> "NH2" Residue "D ARG 709": "NH1" <-> "NH2" Residue "D ARG 712": "NH1" <-> "NH2" Residue "D ARG 723": "NH1" <-> "NH2" Residue "D ARG 780": "NH1" <-> "NH2" Residue "D ARG 1123": "NH1" <-> "NH2" Residue "D PHE 1126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1291": "NH1" <-> "NH2" Residue "D ARG 1299": "NH1" <-> "NH2" Residue "D ARG 1304": "NH1" <-> "NH2" Residue "D ARG 1341": "NH1" <-> "NH2" Residue "D ARG 1358": "NH1" <-> "NH2" Residue "D ARG 1360": "NH1" <-> "NH2" Residue "D ARG 1380": "NH1" <-> "NH2" Residue "D ARG 1381": "NH1" <-> "NH2" Residue "D ARG 1385": "NH1" <-> "NH2" Residue "D ARG 1388": "NH1" <-> "NH2" Residue "D ARG 1406": "NH1" <-> "NH2" Residue "D TYR 1457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1471": "NH1" <-> "NH2" Residue "D ARG 1501": "NH1" <-> "NH2" Residue "D ARG 1504": "NH1" <-> "NH2" Residue "D ARG 1510": "NH1" <-> "NH2" Residue "D ARG 1552": "NH1" <-> "NH2" Residue "D ARG 1558": "NH1" <-> "NH2" Residue "D ARG 1579": "NH1" <-> "NH2" Residue "D ARG 1582": "NH1" <-> "NH2" Residue "D ARG 1586": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 33032 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8258 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 42, 'TRANS': 1020} Chain breaks: 3 Chain: "B" Number of atoms: 8258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8258 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 42, 'TRANS': 1020} Chain breaks: 3 Chain: "C" Number of atoms: 8258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8258 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 42, 'TRANS': 1020} Chain breaks: 3 Chain: "D" Number of atoms: 8258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8258 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 42, 'TRANS': 1020} Chain breaks: 3 Time building chain proxies: 17.81, per 1000 atoms: 0.54 Number of scatterers: 33032 At special positions: 0 Unit cell: (233.2, 136.74, 126.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 76 16.00 O 6324 8.00 N 5888 7.00 C 20744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.13 Conformation dependent library (CDL) restraints added in 4.8 seconds 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7896 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 16 sheets defined 60.0% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 500 through 509 Processing helix chain 'A' and resid 545 through 551 removed outlier: 3.843A pdb=" N LEU A 549 " --> pdb=" O LEU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 610 removed outlier: 3.508A pdb=" N TRP A 609 " --> pdb=" O VAL A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 627 removed outlier: 3.665A pdb=" N ALA A 625 " --> pdb=" O LEU A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 645 removed outlier: 3.830A pdb=" N LEU A 635 " --> pdb=" O GLN A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 661 removed outlier: 3.663A pdb=" N ILE A 654 " --> pdb=" O SER A 650 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN A 661 " --> pdb=" O VAL A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 673 removed outlier: 3.593A pdb=" N THR A 665 " --> pdb=" O ASN A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 702 removed outlier: 4.170A pdb=" N ASP A 700 " --> pdb=" O ALA A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 720 Processing helix chain 'A' and resid 791 through 806 removed outlier: 3.706A pdb=" N LEU A 797 " --> pdb=" O ARG A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 856 removed outlier: 3.617A pdb=" N VAL A 856 " --> pdb=" O GLY A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 906 Processing helix chain 'A' and resid 929 through 943 removed outlier: 3.912A pdb=" N ALA A 933 " --> pdb=" O THR A 929 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU A 943 " --> pdb=" O ARG A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 972 removed outlier: 3.686A pdb=" N VAL A 965 " --> pdb=" O MET A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1008 Processing helix chain 'A' and resid 1012 through 1023 removed outlier: 3.843A pdb=" N TYR A1016 " --> pdb=" O SER A1012 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU A1023 " --> pdb=" O SER A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1044 removed outlier: 3.772A pdb=" N ARG A1042 " --> pdb=" O SER A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1066 removed outlier: 5.032A pdb=" N LYS A1061 " --> pdb=" O PRO A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1128 Processing helix chain 'A' and resid 1137 through 1164 Processing helix chain 'A' and resid 1167 through 1178 removed outlier: 3.975A pdb=" N ARG A1171 " --> pdb=" O THR A1167 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A1176 " --> pdb=" O THR A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1182 through 1203 removed outlier: 3.625A pdb=" N VAL A1186 " --> pdb=" O VAL A1182 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN A1203 " --> pdb=" O THR A1199 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1220 Processing helix chain 'A' and resid 1224 through 1229 Processing helix chain 'A' and resid 1236 through 1242 Processing helix chain 'A' and resid 1248 through 1268 removed outlier: 3.963A pdb=" N LEU A1255 " --> pdb=" O GLU A1251 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU A1268 " --> pdb=" O LYS A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1275 through 1282 removed outlier: 3.696A pdb=" N ALA A1279 " --> pdb=" O GLN A1275 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1299 removed outlier: 3.528A pdb=" N ARG A1291 " --> pdb=" O PRO A1287 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU A1293 " --> pdb=" O ARG A1289 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N GLY A1296 " --> pdb=" O GLU A1292 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLU A1297 " --> pdb=" O GLU A1293 " (cutoff:3.500A) Processing helix chain 'A' and resid 1303 through 1319 removed outlier: 3.848A pdb=" N THR A1319 " --> pdb=" O ASP A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1322 through 1330 removed outlier: 4.254A pdb=" N TYR A1326 " --> pdb=" O ILE A1322 " (cutoff:3.500A) Processing helix chain 'A' and resid 1335 through 1351 Processing helix chain 'A' and resid 1351 through 1361 Processing helix chain 'A' and resid 1368 through 1394 removed outlier: 3.829A pdb=" N THR A1372 " --> pdb=" O PRO A1368 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG A1394 " --> pdb=" O LEU A1390 " (cutoff:3.500A) Processing helix chain 'A' and resid 1399 through 1412 removed outlier: 3.976A pdb=" N GLU A1403 " --> pdb=" O ALA A1399 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LYS A1410 " --> pdb=" O ARG A1406 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA A1412 " --> pdb=" O GLY A1408 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 removed outlier: 3.705A pdb=" N MET A1418 " --> pdb=" O THR A1415 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU A1420 " --> pdb=" O ARG A1417 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1439 Processing helix chain 'A' and resid 1443 through 1470 removed outlier: 3.923A pdb=" N ALA A1447 " --> pdb=" O PRO A1443 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ALA A1451 " --> pdb=" O ALA A1447 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N SER A1458 " --> pdb=" O LEU A1454 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL A1469 " --> pdb=" O ILE A1465 " (cutoff:3.500A) Processing helix chain 'A' and resid 1472 through 1488 removed outlier: 3.563A pdb=" N VAL A1476 " --> pdb=" O GLU A1472 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1497 Processing helix chain 'A' and resid 1503 through 1532 removed outlier: 3.948A pdb=" N GLY A1532 " --> pdb=" O VAL A1528 " (cutoff:3.500A) Processing helix chain 'A' and resid 1537 through 1548 removed outlier: 3.868A pdb=" N THR A1548 " --> pdb=" O GLU A1544 " (cutoff:3.500A) Processing helix chain 'A' and resid 1549 through 1566 removed outlier: 5.072A pdb=" N ARG A1555 " --> pdb=" O SER A1551 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASP A1566 " --> pdb=" O GLU A1562 " (cutoff:3.500A) Processing helix chain 'A' and resid 1570 through 1587 removed outlier: 3.569A pdb=" N LEU A1574 " --> pdb=" O ASP A1570 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR A1587 " --> pdb=" O SER A1583 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 509 Processing helix chain 'B' and resid 545 through 551 removed outlier: 3.843A pdb=" N LEU B 549 " --> pdb=" O LEU B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 610 removed outlier: 3.509A pdb=" N TRP B 609 " --> pdb=" O VAL B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 627 removed outlier: 3.664A pdb=" N ALA B 625 " --> pdb=" O LEU B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 645 removed outlier: 3.832A pdb=" N LEU B 635 " --> pdb=" O GLN B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 661 removed outlier: 3.664A pdb=" N ILE B 654 " --> pdb=" O SER B 650 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN B 661 " --> pdb=" O VAL B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 673 removed outlier: 3.593A pdb=" N THR B 665 " --> pdb=" O ASN B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 702 removed outlier: 4.171A pdb=" N ASP B 700 " --> pdb=" O ALA B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 720 Processing helix chain 'B' and resid 791 through 806 removed outlier: 3.706A pdb=" N LEU B 797 " --> pdb=" O ARG B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 856 removed outlier: 3.616A pdb=" N VAL B 856 " --> pdb=" O GLY B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 906 Processing helix chain 'B' and resid 929 through 943 removed outlier: 3.913A pdb=" N ALA B 933 " --> pdb=" O THR B 929 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU B 943 " --> pdb=" O ARG B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 972 removed outlier: 3.686A pdb=" N VAL B 965 " --> pdb=" O MET B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1008 Processing helix chain 'B' and resid 1012 through 1023 removed outlier: 3.843A pdb=" N TYR B1016 " --> pdb=" O SER B1012 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU B1023 " --> pdb=" O SER B1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 1038 through 1044 removed outlier: 3.772A pdb=" N ARG B1042 " --> pdb=" O SER B1038 " (cutoff:3.500A) Processing helix chain 'B' and resid 1055 through 1066 removed outlier: 5.032A pdb=" N LYS B1061 " --> pdb=" O PRO B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1120 through 1128 Processing helix chain 'B' and resid 1137 through 1164 Processing helix chain 'B' and resid 1167 through 1178 removed outlier: 3.976A pdb=" N ARG B1171 " --> pdb=" O THR B1167 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU B1176 " --> pdb=" O THR B1172 " (cutoff:3.500A) Processing helix chain 'B' and resid 1182 through 1203 removed outlier: 3.624A pdb=" N VAL B1186 " --> pdb=" O VAL B1182 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN B1203 " --> pdb=" O THR B1199 " (cutoff:3.500A) Processing helix chain 'B' and resid 1208 through 1220 Processing helix chain 'B' and resid 1224 through 1229 Processing helix chain 'B' and resid 1236 through 1242 Processing helix chain 'B' and resid 1248 through 1268 removed outlier: 3.963A pdb=" N LEU B1255 " --> pdb=" O GLU B1251 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU B1268 " --> pdb=" O LYS B1264 " (cutoff:3.500A) Processing helix chain 'B' and resid 1275 through 1282 removed outlier: 3.696A pdb=" N ALA B1279 " --> pdb=" O GLN B1275 " (cutoff:3.500A) Processing helix chain 'B' and resid 1287 through 1299 removed outlier: 3.529A pdb=" N ARG B1291 " --> pdb=" O PRO B1287 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU B1293 " --> pdb=" O ARG B1289 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N GLY B1296 " --> pdb=" O GLU B1292 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLU B1297 " --> pdb=" O GLU B1293 " (cutoff:3.500A) Processing helix chain 'B' and resid 1303 through 1319 removed outlier: 3.848A pdb=" N THR B1319 " --> pdb=" O ASP B1315 " (cutoff:3.500A) Processing helix chain 'B' and resid 1322 through 1330 removed outlier: 4.253A pdb=" N TYR B1326 " --> pdb=" O ILE B1322 " (cutoff:3.500A) Processing helix chain 'B' and resid 1335 through 1351 Processing helix chain 'B' and resid 1351 through 1361 Processing helix chain 'B' and resid 1368 through 1394 removed outlier: 3.830A pdb=" N THR B1372 " --> pdb=" O PRO B1368 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG B1394 " --> pdb=" O LEU B1390 " (cutoff:3.500A) Processing helix chain 'B' and resid 1399 through 1412 removed outlier: 3.976A pdb=" N GLU B1403 " --> pdb=" O ALA B1399 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LYS B1410 " --> pdb=" O ARG B1406 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA B1412 " --> pdb=" O GLY B1408 " (cutoff:3.500A) Processing helix chain 'B' and resid 1415 through 1420 removed outlier: 3.705A pdb=" N MET B1418 " --> pdb=" O THR B1415 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU B1420 " --> pdb=" O ARG B1417 " (cutoff:3.500A) Processing helix chain 'B' and resid 1423 through 1439 Processing helix chain 'B' and resid 1443 through 1470 removed outlier: 3.923A pdb=" N ALA B1447 " --> pdb=" O PRO B1443 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ALA B1451 " --> pdb=" O ALA B1447 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N SER B1458 " --> pdb=" O LEU B1454 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL B1469 " --> pdb=" O ILE B1465 " (cutoff:3.500A) Processing helix chain 'B' and resid 1472 through 1488 removed outlier: 3.563A pdb=" N VAL B1476 " --> pdb=" O GLU B1472 " (cutoff:3.500A) Processing helix chain 'B' and resid 1489 through 1497 Processing helix chain 'B' and resid 1503 through 1532 removed outlier: 3.949A pdb=" N GLY B1532 " --> pdb=" O VAL B1528 " (cutoff:3.500A) Processing helix chain 'B' and resid 1537 through 1548 removed outlier: 3.868A pdb=" N THR B1548 " --> pdb=" O GLU B1544 " (cutoff:3.500A) Processing helix chain 'B' and resid 1549 through 1566 removed outlier: 5.071A pdb=" N ARG B1555 " --> pdb=" O SER B1551 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASP B1566 " --> pdb=" O GLU B1562 " (cutoff:3.500A) Processing helix chain 'B' and resid 1570 through 1587 removed outlier: 3.569A pdb=" N LEU B1574 " --> pdb=" O ASP B1570 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR B1587 " --> pdb=" O SER B1583 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 509 Processing helix chain 'C' and resid 545 through 551 removed outlier: 3.843A pdb=" N LEU C 549 " --> pdb=" O LEU C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 610 removed outlier: 3.508A pdb=" N TRP C 609 " --> pdb=" O VAL C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 627 removed outlier: 3.665A pdb=" N ALA C 625 " --> pdb=" O LEU C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 645 removed outlier: 3.831A pdb=" N LEU C 635 " --> pdb=" O GLN C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 661 removed outlier: 3.663A pdb=" N ILE C 654 " --> pdb=" O SER C 650 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN C 661 " --> pdb=" O VAL C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 673 removed outlier: 3.593A pdb=" N THR C 665 " --> pdb=" O ASN C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 702 removed outlier: 4.171A pdb=" N ASP C 700 " --> pdb=" O ALA C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 720 Processing helix chain 'C' and resid 791 through 806 removed outlier: 3.706A pdb=" N LEU C 797 " --> pdb=" O ARG C 793 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 856 removed outlier: 3.617A pdb=" N VAL C 856 " --> pdb=" O GLY C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 906 Processing helix chain 'C' and resid 929 through 943 removed outlier: 3.913A pdb=" N ALA C 933 " --> pdb=" O THR C 929 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU C 943 " --> pdb=" O ARG C 939 " (cutoff:3.500A) Processing helix chain 'C' and resid 961 through 972 removed outlier: 3.687A pdb=" N VAL C 965 " --> pdb=" O MET C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 995 through 1008 Processing helix chain 'C' and resid 1012 through 1023 removed outlier: 3.843A pdb=" N TYR C1016 " --> pdb=" O SER C1012 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU C1023 " --> pdb=" O SER C1019 " (cutoff:3.500A) Processing helix chain 'C' and resid 1038 through 1044 removed outlier: 3.772A pdb=" N ARG C1042 " --> pdb=" O SER C1038 " (cutoff:3.500A) Processing helix chain 'C' and resid 1055 through 1066 removed outlier: 5.032A pdb=" N LYS C1061 " --> pdb=" O PRO C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1120 through 1128 Processing helix chain 'C' and resid 1137 through 1164 Processing helix chain 'C' and resid 1167 through 1178 removed outlier: 3.975A pdb=" N ARG C1171 " --> pdb=" O THR C1167 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU C1176 " --> pdb=" O THR C1172 " (cutoff:3.500A) Processing helix chain 'C' and resid 1182 through 1203 removed outlier: 3.625A pdb=" N VAL C1186 " --> pdb=" O VAL C1182 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN C1203 " --> pdb=" O THR C1199 " (cutoff:3.500A) Processing helix chain 'C' and resid 1208 through 1220 Processing helix chain 'C' and resid 1224 through 1229 Processing helix chain 'C' and resid 1236 through 1242 Processing helix chain 'C' and resid 1248 through 1268 removed outlier: 3.963A pdb=" N LEU C1255 " --> pdb=" O GLU C1251 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU C1268 " --> pdb=" O LYS C1264 " (cutoff:3.500A) Processing helix chain 'C' and resid 1275 through 1282 removed outlier: 3.697A pdb=" N ALA C1279 " --> pdb=" O GLN C1275 " (cutoff:3.500A) Processing helix chain 'C' and resid 1287 through 1299 removed outlier: 3.528A pdb=" N ARG C1291 " --> pdb=" O PRO C1287 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU C1293 " --> pdb=" O ARG C1289 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N GLY C1296 " --> pdb=" O GLU C1292 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLU C1297 " --> pdb=" O GLU C1293 " (cutoff:3.500A) Processing helix chain 'C' and resid 1303 through 1319 removed outlier: 3.848A pdb=" N THR C1319 " --> pdb=" O ASP C1315 " (cutoff:3.500A) Processing helix chain 'C' and resid 1322 through 1330 removed outlier: 4.254A pdb=" N TYR C1326 " --> pdb=" O ILE C1322 " (cutoff:3.500A) Processing helix chain 'C' and resid 1335 through 1351 Processing helix chain 'C' and resid 1351 through 1361 Processing helix chain 'C' and resid 1368 through 1394 removed outlier: 3.830A pdb=" N THR C1372 " --> pdb=" O PRO C1368 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG C1394 " --> pdb=" O LEU C1390 " (cutoff:3.500A) Processing helix chain 'C' and resid 1399 through 1412 removed outlier: 3.977A pdb=" N GLU C1403 " --> pdb=" O ALA C1399 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LYS C1410 " --> pdb=" O ARG C1406 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA C1412 " --> pdb=" O GLY C1408 " (cutoff:3.500A) Processing helix chain 'C' and resid 1415 through 1420 removed outlier: 3.705A pdb=" N MET C1418 " --> pdb=" O THR C1415 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU C1420 " --> pdb=" O ARG C1417 " (cutoff:3.500A) Processing helix chain 'C' and resid 1423 through 1439 Processing helix chain 'C' and resid 1443 through 1470 removed outlier: 3.924A pdb=" N ALA C1447 " --> pdb=" O PRO C1443 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ALA C1451 " --> pdb=" O ALA C1447 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N SER C1458 " --> pdb=" O LEU C1454 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL C1469 " --> pdb=" O ILE C1465 " (cutoff:3.500A) Processing helix chain 'C' and resid 1472 through 1488 removed outlier: 3.563A pdb=" N VAL C1476 " --> pdb=" O GLU C1472 " (cutoff:3.500A) Processing helix chain 'C' and resid 1489 through 1497 Processing helix chain 'C' and resid 1503 through 1532 removed outlier: 3.948A pdb=" N GLY C1532 " --> pdb=" O VAL C1528 " (cutoff:3.500A) Processing helix chain 'C' and resid 1537 through 1548 removed outlier: 3.868A pdb=" N THR C1548 " --> pdb=" O GLU C1544 " (cutoff:3.500A) Processing helix chain 'C' and resid 1549 through 1566 removed outlier: 5.072A pdb=" N ARG C1555 " --> pdb=" O SER C1551 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASP C1566 " --> pdb=" O GLU C1562 " (cutoff:3.500A) Processing helix chain 'C' and resid 1570 through 1587 removed outlier: 3.570A pdb=" N LEU C1574 " --> pdb=" O ASP C1570 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR C1587 " --> pdb=" O SER C1583 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 509 Processing helix chain 'D' and resid 545 through 551 removed outlier: 3.843A pdb=" N LEU D 549 " --> pdb=" O LEU D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 610 removed outlier: 3.508A pdb=" N TRP D 609 " --> pdb=" O VAL D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 627 removed outlier: 3.665A pdb=" N ALA D 625 " --> pdb=" O LEU D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 645 removed outlier: 3.831A pdb=" N LEU D 635 " --> pdb=" O GLN D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 661 removed outlier: 3.663A pdb=" N ILE D 654 " --> pdb=" O SER D 650 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN D 661 " --> pdb=" O VAL D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 661 through 673 removed outlier: 3.593A pdb=" N THR D 665 " --> pdb=" O ASN D 661 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 702 removed outlier: 4.171A pdb=" N ASP D 700 " --> pdb=" O ALA D 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 720 Processing helix chain 'D' and resid 791 through 806 removed outlier: 3.707A pdb=" N LEU D 797 " --> pdb=" O ARG D 793 " (cutoff:3.500A) Processing helix chain 'D' and resid 830 through 856 removed outlier: 3.617A pdb=" N VAL D 856 " --> pdb=" O GLY D 852 " (cutoff:3.500A) Processing helix chain 'D' and resid 894 through 906 Processing helix chain 'D' and resid 929 through 943 removed outlier: 3.913A pdb=" N ALA D 933 " --> pdb=" O THR D 929 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU D 943 " --> pdb=" O ARG D 939 " (cutoff:3.500A) Processing helix chain 'D' and resid 961 through 972 removed outlier: 3.686A pdb=" N VAL D 965 " --> pdb=" O MET D 961 " (cutoff:3.500A) Processing helix chain 'D' and resid 995 through 1008 Processing helix chain 'D' and resid 1012 through 1023 removed outlier: 3.843A pdb=" N TYR D1016 " --> pdb=" O SER D1012 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU D1023 " --> pdb=" O SER D1019 " (cutoff:3.500A) Processing helix chain 'D' and resid 1038 through 1044 removed outlier: 3.772A pdb=" N ARG D1042 " --> pdb=" O SER D1038 " (cutoff:3.500A) Processing helix chain 'D' and resid 1055 through 1066 removed outlier: 5.032A pdb=" N LYS D1061 " --> pdb=" O PRO D1057 " (cutoff:3.500A) Processing helix chain 'D' and resid 1120 through 1128 Processing helix chain 'D' and resid 1137 through 1164 Processing helix chain 'D' and resid 1167 through 1178 removed outlier: 3.976A pdb=" N ARG D1171 " --> pdb=" O THR D1167 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU D1176 " --> pdb=" O THR D1172 " (cutoff:3.500A) Processing helix chain 'D' and resid 1182 through 1203 removed outlier: 3.625A pdb=" N VAL D1186 " --> pdb=" O VAL D1182 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN D1203 " --> pdb=" O THR D1199 " (cutoff:3.500A) Processing helix chain 'D' and resid 1208 through 1220 Processing helix chain 'D' and resid 1224 through 1229 Processing helix chain 'D' and resid 1236 through 1242 Processing helix chain 'D' and resid 1248 through 1268 removed outlier: 3.964A pdb=" N LEU D1255 " --> pdb=" O GLU D1251 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU D1268 " --> pdb=" O LYS D1264 " (cutoff:3.500A) Processing helix chain 'D' and resid 1275 through 1282 removed outlier: 3.696A pdb=" N ALA D1279 " --> pdb=" O GLN D1275 " (cutoff:3.500A) Processing helix chain 'D' and resid 1287 through 1299 removed outlier: 3.528A pdb=" N ARG D1291 " --> pdb=" O PRO D1287 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLU D1293 " --> pdb=" O ARG D1289 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLY D1296 " --> pdb=" O GLU D1292 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLU D1297 " --> pdb=" O GLU D1293 " (cutoff:3.500A) Processing helix chain 'D' and resid 1303 through 1319 removed outlier: 3.849A pdb=" N THR D1319 " --> pdb=" O ASP D1315 " (cutoff:3.500A) Processing helix chain 'D' and resid 1322 through 1330 removed outlier: 4.254A pdb=" N TYR D1326 " --> pdb=" O ILE D1322 " (cutoff:3.500A) Processing helix chain 'D' and resid 1335 through 1351 Processing helix chain 'D' and resid 1351 through 1361 Processing helix chain 'D' and resid 1368 through 1394 removed outlier: 3.830A pdb=" N THR D1372 " --> pdb=" O PRO D1368 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG D1394 " --> pdb=" O LEU D1390 " (cutoff:3.500A) Processing helix chain 'D' and resid 1399 through 1412 removed outlier: 3.976A pdb=" N GLU D1403 " --> pdb=" O ALA D1399 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LYS D1410 " --> pdb=" O ARG D1406 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA D1412 " --> pdb=" O GLY D1408 " (cutoff:3.500A) Processing helix chain 'D' and resid 1415 through 1420 removed outlier: 3.705A pdb=" N MET D1418 " --> pdb=" O THR D1415 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU D1420 " --> pdb=" O ARG D1417 " (cutoff:3.500A) Processing helix chain 'D' and resid 1423 through 1439 Processing helix chain 'D' and resid 1443 through 1470 removed outlier: 3.924A pdb=" N ALA D1447 " --> pdb=" O PRO D1443 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ALA D1451 " --> pdb=" O ALA D1447 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N SER D1458 " --> pdb=" O LEU D1454 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL D1469 " --> pdb=" O ILE D1465 " (cutoff:3.500A) Processing helix chain 'D' and resid 1472 through 1488 removed outlier: 3.563A pdb=" N VAL D1476 " --> pdb=" O GLU D1472 " (cutoff:3.500A) Processing helix chain 'D' and resid 1489 through 1497 Processing helix chain 'D' and resid 1503 through 1532 removed outlier: 3.948A pdb=" N GLY D1532 " --> pdb=" O VAL D1528 " (cutoff:3.500A) Processing helix chain 'D' and resid 1537 through 1548 removed outlier: 3.868A pdb=" N THR D1548 " --> pdb=" O GLU D1544 " (cutoff:3.500A) Processing helix chain 'D' and resid 1549 through 1566 removed outlier: 5.072A pdb=" N ARG D1555 " --> pdb=" O SER D1551 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASP D1566 " --> pdb=" O GLU D1562 " (cutoff:3.500A) Processing helix chain 'D' and resid 1570 through 1587 removed outlier: 3.569A pdb=" N LEU D1574 " --> pdb=" O ASP D1570 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR D1587 " --> pdb=" O SER D1583 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 518 through 522 removed outlier: 6.308A pdb=" N LEU A 570 " --> pdb=" O ARG A 565 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ARG A 565 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL A 572 " --> pdb=" O THR A 563 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR A 563 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE A 574 " --> pdb=" O PRO A 561 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLN A 576 " --> pdb=" O GLU A 559 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLU A 559 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LYS A 578 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A 557 " --> pdb=" O LYS A 578 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 721 through 727 removed outlier: 4.172A pdb=" N ARG A 723 " --> pdb=" O LYS A 743 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A 743 " --> pdb=" O ARG A 723 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN A 725 " --> pdb=" O ALA A 741 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA A 741 " --> pdb=" O ASN A 725 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 780 through 783 removed outlier: 3.913A pdb=" N LEU A 783 " --> pdb=" O ALA A 886 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 988 through 989 removed outlier: 3.595A pdb=" N PHE A 988 " --> pdb=" O ALA A 981 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 518 through 522 removed outlier: 6.308A pdb=" N LEU B 570 " --> pdb=" O ARG B 565 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ARG B 565 " --> pdb=" O LEU B 570 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL B 572 " --> pdb=" O THR B 563 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N THR B 563 " --> pdb=" O VAL B 572 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE B 574 " --> pdb=" O PRO B 561 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLN B 576 " --> pdb=" O GLU B 559 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLU B 559 " --> pdb=" O GLN B 576 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LYS B 578 " --> pdb=" O LEU B 557 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU B 557 " --> pdb=" O LYS B 578 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 721 through 727 removed outlier: 4.173A pdb=" N ARG B 723 " --> pdb=" O LYS B 743 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS B 743 " --> pdb=" O ARG B 723 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN B 725 " --> pdb=" O ALA B 741 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA B 741 " --> pdb=" O ASN B 725 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 780 through 783 removed outlier: 3.914A pdb=" N LEU B 783 " --> pdb=" O ALA B 886 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 988 through 989 removed outlier: 3.595A pdb=" N PHE B 988 " --> pdb=" O ALA B 981 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 518 through 522 removed outlier: 6.308A pdb=" N LEU C 570 " --> pdb=" O ARG C 565 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ARG C 565 " --> pdb=" O LEU C 570 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL C 572 " --> pdb=" O THR C 563 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR C 563 " --> pdb=" O VAL C 572 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE C 574 " --> pdb=" O PRO C 561 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLN C 576 " --> pdb=" O GLU C 559 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLU C 559 " --> pdb=" O GLN C 576 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LYS C 578 " --> pdb=" O LEU C 557 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU C 557 " --> pdb=" O LYS C 578 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 721 through 727 removed outlier: 4.174A pdb=" N ARG C 723 " --> pdb=" O LYS C 743 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS C 743 " --> pdb=" O ARG C 723 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN C 725 " --> pdb=" O ALA C 741 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA C 741 " --> pdb=" O ASN C 725 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 780 through 783 removed outlier: 3.913A pdb=" N LEU C 783 " --> pdb=" O ALA C 886 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 988 through 989 removed outlier: 3.594A pdb=" N PHE C 988 " --> pdb=" O ALA C 981 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 518 through 522 removed outlier: 6.308A pdb=" N LEU D 570 " --> pdb=" O ARG D 565 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ARG D 565 " --> pdb=" O LEU D 570 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL D 572 " --> pdb=" O THR D 563 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR D 563 " --> pdb=" O VAL D 572 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE D 574 " --> pdb=" O PRO D 561 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLN D 576 " --> pdb=" O GLU D 559 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLU D 559 " --> pdb=" O GLN D 576 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LYS D 578 " --> pdb=" O LEU D 557 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU D 557 " --> pdb=" O LYS D 578 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 721 through 727 removed outlier: 4.173A pdb=" N ARG D 723 " --> pdb=" O LYS D 743 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS D 743 " --> pdb=" O ARG D 723 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN D 725 " --> pdb=" O ALA D 741 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA D 741 " --> pdb=" O ASN D 725 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 780 through 783 removed outlier: 3.914A pdb=" N LEU D 783 " --> pdb=" O ALA D 886 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 988 through 989 removed outlier: 3.595A pdb=" N PHE D 988 " --> pdb=" O ALA D 981 " (cutoff:3.500A) 1837 hydrogen bonds defined for protein. 5439 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: 12.48 Time building geometry restraints manager: 15.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10766 1.34 - 1.46: 5085 1.46 - 1.57: 17637 1.57 - 1.69: 0 1.69 - 1.81: 136 Bond restraints: 33624 Sorted by residual: bond pdb=" C PRO A1056 " pdb=" N PRO A1057 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.31e+00 bond pdb=" C PRO B1056 " pdb=" N PRO B1057 " ideal model delta sigma weight residual 1.334 1.387 -0.053 2.34e-02 1.83e+03 5.22e+00 bond pdb=" C PRO D1056 " pdb=" N PRO D1057 " ideal model delta sigma weight residual 1.334 1.387 -0.053 2.34e-02 1.83e+03 5.17e+00 bond pdb=" C PRO C1056 " pdb=" N PRO C1057 " ideal model delta sigma weight residual 1.334 1.387 -0.053 2.34e-02 1.83e+03 5.15e+00 bond pdb=" CB TRP D 629 " pdb=" CG TRP D 629 " ideal model delta sigma weight residual 1.498 1.444 0.054 3.10e-02 1.04e+03 3.00e+00 ... (remaining 33619 not shown) Histogram of bond angle deviations from ideal: 97.27 - 104.77: 536 104.77 - 112.27: 16333 112.27 - 119.77: 13072 119.77 - 127.27: 15394 127.27 - 134.77: 321 Bond angle restraints: 45656 Sorted by residual: angle pdb=" C PRO D 766 " pdb=" N ARG D 767 " pdb=" CA ARG D 767 " ideal model delta sigma weight residual 126.45 133.80 -7.35 1.77e+00 3.19e-01 1.72e+01 angle pdb=" C PRO B 766 " pdb=" N ARG B 767 " pdb=" CA ARG B 767 " ideal model delta sigma weight residual 126.45 133.79 -7.34 1.77e+00 3.19e-01 1.72e+01 angle pdb=" C PRO C 766 " pdb=" N ARG C 767 " pdb=" CA ARG C 767 " ideal model delta sigma weight residual 126.45 133.75 -7.30 1.77e+00 3.19e-01 1.70e+01 angle pdb=" C PRO A 766 " pdb=" N ARG A 767 " pdb=" CA ARG A 767 " ideal model delta sigma weight residual 126.45 133.75 -7.30 1.77e+00 3.19e-01 1.70e+01 angle pdb=" N GLY A 626 " pdb=" CA GLY A 626 " pdb=" C GLY A 626 " ideal model delta sigma weight residual 113.18 122.46 -9.28 2.37e+00 1.78e-01 1.53e+01 ... (remaining 45651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.78: 19026 15.78 - 31.56: 1002 31.56 - 47.35: 212 47.35 - 63.13: 16 63.13 - 78.91: 16 Dihedral angle restraints: 20272 sinusoidal: 8040 harmonic: 12232 Sorted by residual: dihedral pdb=" CA ASP B 952 " pdb=" C ASP B 952 " pdb=" N PHE B 953 " pdb=" CA PHE B 953 " ideal model delta harmonic sigma weight residual -180.00 -150.13 -29.87 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA ASP C 952 " pdb=" C ASP C 952 " pdb=" N PHE C 953 " pdb=" CA PHE C 953 " ideal model delta harmonic sigma weight residual -180.00 -150.17 -29.83 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA ASP A 952 " pdb=" C ASP A 952 " pdb=" N PHE A 953 " pdb=" CA PHE A 953 " ideal model delta harmonic sigma weight residual 180.00 -150.21 -29.79 0 5.00e+00 4.00e-02 3.55e+01 ... (remaining 20269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3859 0.061 - 0.121: 1081 0.121 - 0.182: 236 0.182 - 0.243: 22 0.243 - 0.304: 18 Chirality restraints: 5216 Sorted by residual: chirality pdb=" CB VAL A 703 " pdb=" CA VAL A 703 " pdb=" CG1 VAL A 703 " pdb=" CG2 VAL A 703 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CB VAL D 703 " pdb=" CA VAL D 703 " pdb=" CG1 VAL D 703 " pdb=" CG2 VAL D 703 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CB VAL C 703 " pdb=" CA VAL C 703 " pdb=" CG1 VAL C 703 " pdb=" CG2 VAL C 703 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 5213 not shown) Planarity restraints: 5996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A1305 " -0.015 2.00e-02 2.50e+03 3.07e-02 9.45e+00 pdb=" C ARG A1305 " 0.053 2.00e-02 2.50e+03 pdb=" O ARG A1305 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU A1306 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B1305 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.38e+00 pdb=" C ARG B1305 " -0.053 2.00e-02 2.50e+03 pdb=" O ARG B1305 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU B1306 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C1305 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.21e+00 pdb=" C ARG C1305 " 0.052 2.00e-02 2.50e+03 pdb=" O ARG C1305 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU C1306 " -0.018 2.00e-02 2.50e+03 ... (remaining 5993 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 7233 2.78 - 3.31: 32071 3.31 - 3.84: 54040 3.84 - 4.37: 60176 4.37 - 4.90: 101228 Nonbonded interactions: 254748 Sorted by model distance: nonbonded pdb=" OD1 ASP C 855 " pdb=" OH TYR C 905 " model vdw 2.253 2.440 nonbonded pdb=" OD1 ASP B 855 " pdb=" OH TYR B 905 " model vdw 2.253 2.440 nonbonded pdb=" OD1 ASP A 855 " pdb=" OH TYR A 905 " model vdw 2.253 2.440 nonbonded pdb=" OD1 ASP D 855 " pdb=" OH TYR D 905 " model vdw 2.253 2.440 nonbonded pdb=" O PRO D 662 " pdb=" OG1 THR D 665 " model vdw 2.258 2.440 ... (remaining 254743 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 76 5.16 5 C 20744 2.51 5 N 5888 2.21 5 O 6324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 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: 0.030 Extract box with map and model: 13.480 Check model and map are aligned: 0.520 Convert atoms to be neutral: 0.300 Process input model: 83.860 Find NCS groups from input model: 2.110 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 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 : 0.006 0.082 33624 Z= 0.387 Angle : 1.037 10.435 45656 Z= 0.569 Chirality : 0.060 0.304 5216 Planarity : 0.008 0.067 5996 Dihedral : 10.620 78.910 12376 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer Outliers : 0.35 % 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: -4.40 (0.10), residues: 4220 helix: -2.58 (0.08), residues: 2420 sheet: -1.77 (0.26), residues: 348 loop : -3.55 (0.13), residues: 1452 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 887 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 875 time to evaluate : 3.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 883 average time/residue: 0.5161 time to fit residues: 697.3710 Evaluate side-chains 432 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 424 time to evaluate : 3.817 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2841 time to fit residues: 9.6038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 358 optimal weight: 5.9990 chunk 321 optimal weight: 9.9990 chunk 178 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 216 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 332 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 202 optimal weight: 0.7980 chunk 247 optimal weight: 0.7980 chunk 385 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 803 GLN A1097 GLN ** A1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1449 HIS B1097 GLN ** B1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1449 HIS C 803 GLN C1032 GLN C1097 GLN ** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1449 HIS D 803 GLN D1097 GLN ** D1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1449 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 33624 Z= 0.220 Angle : 0.683 9.779 45656 Z= 0.358 Chirality : 0.044 0.177 5216 Planarity : 0.005 0.054 5996 Dihedral : 5.968 26.676 4688 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % 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: -2.75 (0.11), residues: 4220 helix: -0.96 (0.09), residues: 2420 sheet: -1.33 (0.27), residues: 344 loop : -3.36 (0.13), residues: 1456 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 603 time to evaluate : 3.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 608 average time/residue: 0.4630 time to fit residues: 441.7780 Evaluate side-chains 346 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 3.846 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 213 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 320 optimal weight: 0.8980 chunk 262 optimal weight: 8.9990 chunk 106 optimal weight: 9.9990 chunk 385 optimal weight: 2.9990 chunk 416 optimal weight: 5.9990 chunk 343 optimal weight: 0.8980 chunk 382 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 309 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1486 HIS C1032 GLN C1221 ASN C1486 HIS D1149 HIS ** D1190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1221 ASN D1486 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 33624 Z= 0.308 Angle : 0.738 8.602 45656 Z= 0.391 Chirality : 0.045 0.196 5216 Planarity : 0.005 0.041 5996 Dihedral : 5.796 25.969 4688 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer Outliers : 0.06 % 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: -2.15 (0.12), residues: 4220 helix: -0.30 (0.10), residues: 2428 sheet: -1.29 (0.27), residues: 396 loop : -3.49 (0.14), residues: 1396 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 499 time to evaluate : 3.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 501 average time/residue: 0.4672 time to fit residues: 373.8096 Evaluate side-chains 319 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 3.994 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 381 optimal weight: 0.7980 chunk 290 optimal weight: 2.9990 chunk 200 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 184 optimal weight: 0.9990 chunk 259 optimal weight: 9.9990 chunk 387 optimal weight: 0.8980 chunk 409 optimal weight: 0.8980 chunk 202 optimal weight: 7.9990 chunk 366 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 975 HIS A1097 GLN ** A1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1486 HIS B 550 GLN ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 975 HIS B1097 GLN ** B1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1149 HIS C 975 HIS C1032 GLN ** C1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 975 HIS D1097 GLN ** D1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 33624 Z= 0.196 Angle : 0.659 7.192 45656 Z= 0.339 Chirality : 0.044 0.211 5216 Planarity : 0.004 0.046 5996 Dihedral : 5.416 24.709 4688 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % 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: -1.69 (0.12), residues: 4220 helix: 0.10 (0.10), residues: 2456 sheet: -0.84 (0.28), residues: 340 loop : -3.42 (0.14), residues: 1424 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 516 time to evaluate : 4.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 516 average time/residue: 0.4672 time to fit residues: 384.3552 Evaluate side-chains 323 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 323 time to evaluate : 4.099 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 341 optimal weight: 0.8980 chunk 232 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 305 optimal weight: 0.7980 chunk 169 optimal weight: 10.0000 chunk 349 optimal weight: 5.9990 chunk 283 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 209 optimal weight: 3.9990 chunk 367 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 738 ASN A 940 HIS ** A1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1258 HIS ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 940 HIS ** B1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 940 HIS C1032 GLN ** C1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 738 ASN D 940 HIS ** D1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1190 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.5353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 33624 Z= 0.363 Angle : 0.787 7.832 45656 Z= 0.412 Chirality : 0.047 0.229 5216 Planarity : 0.005 0.050 5996 Dihedral : 5.797 25.114 4688 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 22.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.58 % Favored : 91.40 % Rotamer Outliers : 0.06 % 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: -2.08 (0.12), residues: 4220 helix: -0.27 (0.10), residues: 2464 sheet: -1.15 (0.28), residues: 352 loop : -3.45 (0.14), residues: 1404 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 424 time to evaluate : 4.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 426 average time/residue: 0.4688 time to fit residues: 321.3548 Evaluate side-chains 292 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 3.804 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 137 optimal weight: 4.9990 chunk 369 optimal weight: 0.0770 chunk 81 optimal weight: 3.9990 chunk 240 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 410 optimal weight: 5.9990 chunk 340 optimal weight: 1.9990 chunk 189 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 135 optimal weight: 0.1980 chunk 215 optimal weight: 5.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 738 ASN ** A1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1258 HIS B 550 GLN ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 738 ASN B1032 GLN B1104 GLN ** B1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 738 ASN C1032 GLN ** C1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 33624 Z= 0.187 Angle : 0.667 7.082 45656 Z= 0.340 Chirality : 0.043 0.188 5216 Planarity : 0.004 0.044 5996 Dihedral : 5.270 23.470 4688 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer Outliers : 0.09 % 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: -1.51 (0.13), residues: 4220 helix: 0.25 (0.10), residues: 2456 sheet: -0.65 (0.28), residues: 344 loop : -3.38 (0.14), residues: 1420 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 482 time to evaluate : 3.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 482 average time/residue: 0.4635 time to fit residues: 358.0153 Evaluate side-chains 313 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 313 time to evaluate : 3.841 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 395 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 233 optimal weight: 2.9990 chunk 299 optimal weight: 0.9980 chunk 232 optimal weight: 1.9990 chunk 345 optimal weight: 0.0000 chunk 229 optimal weight: 0.9980 chunk 408 optimal weight: 4.9990 chunk 255 optimal weight: 0.0670 chunk 249 optimal weight: 5.9990 chunk 188 optimal weight: 0.5980 overall best weight: 0.5322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1032 GLN ** B1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1032 GLN ** C1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.5541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 33624 Z= 0.177 Angle : 0.648 7.276 45656 Z= 0.330 Chirality : 0.043 0.243 5216 Planarity : 0.004 0.044 5996 Dihedral : 5.048 22.528 4688 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % 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: -1.31 (0.13), residues: 4220 helix: 0.43 (0.10), residues: 2440 sheet: -1.11 (0.25), residues: 420 loop : -3.23 (0.15), residues: 1360 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 464 time to evaluate : 4.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 464 average time/residue: 0.4700 time to fit residues: 352.1639 Evaluate side-chains 320 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 320 time to evaluate : 3.837 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 252 optimal weight: 7.9990 chunk 163 optimal weight: 7.9990 chunk 244 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 259 optimal weight: 0.6980 chunk 278 optimal weight: 6.9990 chunk 202 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 321 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 GLN ** A1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1032 GLN ** B1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1032 GLN ** C1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.5715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 33624 Z= 0.192 Angle : 0.656 9.829 45656 Z= 0.335 Chirality : 0.044 0.270 5216 Planarity : 0.004 0.044 5996 Dihedral : 4.989 23.121 4688 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % 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: -1.22 (0.13), residues: 4220 helix: 0.51 (0.10), residues: 2436 sheet: -0.94 (0.25), residues: 412 loop : -3.23 (0.14), residues: 1372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 443 time to evaluate : 3.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 443 average time/residue: 0.4573 time to fit residues: 327.6460 Evaluate side-chains 297 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 3.756 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 371 optimal weight: 5.9990 chunk 391 optimal weight: 3.9990 chunk 357 optimal weight: 1.9990 chunk 380 optimal weight: 3.9990 chunk 229 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 299 optimal weight: 6.9990 chunk 116 optimal weight: 0.5980 chunk 344 optimal weight: 0.8980 chunk 360 optimal weight: 7.9990 chunk 379 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN A 738 ASN ** A1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1149 HIS B 653 HIS B 738 ASN B1032 GLN ** B1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 738 ASN C1032 GLN ** C1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 738 ASN ** D 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.6128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 33624 Z= 0.314 Angle : 0.743 10.159 45656 Z= 0.388 Chirality : 0.046 0.265 5216 Planarity : 0.005 0.104 5996 Dihedral : 5.340 24.649 4688 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer Outliers : 0.12 % 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 (0.12), residues: 4220 helix: 0.19 (0.10), residues: 2440 sheet: -1.05 (0.26), residues: 400 loop : -3.25 (0.14), residues: 1380 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 393 time to evaluate : 4.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 397 average time/residue: 0.4667 time to fit residues: 301.2151 Evaluate side-chains 279 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 276 time to evaluate : 3.894 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2945 time to fit residues: 7.1566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 250 optimal weight: 8.9990 chunk 402 optimal weight: 6.9990 chunk 245 optimal weight: 2.9990 chunk 191 optimal weight: 0.7980 chunk 279 optimal weight: 0.9990 chunk 422 optimal weight: 0.7980 chunk 388 optimal weight: 8.9990 chunk 336 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 259 optimal weight: 4.9990 chunk 206 optimal weight: 0.0870 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 GLN B 738 ASN B1032 GLN ** B1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1032 GLN ** C1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.6174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 33624 Z= 0.195 Angle : 0.677 9.133 45656 Z= 0.345 Chirality : 0.044 0.274 5216 Planarity : 0.004 0.049 5996 Dihedral : 5.043 22.892 4688 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer Outliers : 0.03 % 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: -1.20 (0.12), residues: 4220 helix: 0.50 (0.10), residues: 2448 sheet: -0.68 (0.26), residues: 368 loop : -3.24 (0.14), residues: 1404 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 432 time to evaluate : 4.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 433 average time/residue: 0.4637 time to fit residues: 325.3858 Evaluate side-chains 293 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 292 time to evaluate : 3.956 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2829 time to fit residues: 5.6645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 267 optimal weight: 7.9990 chunk 358 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 310 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 336 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 chunk 345 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 859 ASN B1032 GLN ** B1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1032 GLN ** C1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.086732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.071617 restraints weight = 148981.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.073049 restraints weight = 104069.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.074054 restraints weight = 80874.360| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.6369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 33624 Z= 0.247 Angle : 0.694 9.040 45656 Z= 0.357 Chirality : 0.045 0.265 5216 Planarity : 0.005 0.090 5996 Dihedral : 5.101 22.690 4688 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % 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: -1.30 (0.12), residues: 4220 helix: 0.43 (0.10), residues: 2440 sheet: -1.11 (0.26), residues: 404 loop : -3.18 (0.14), residues: 1376 =============================================================================== Job complete usr+sys time: 6867.57 seconds wall clock time: 124 minutes 34.01 seconds (7474.01 seconds total)