Starting phenix.real_space_refine (version: 1.21rc1) on Sun Aug 20 14:38:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8s_14562/08_2023/7z8s_14562.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8s_14562/08_2023/7z8s_14562.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8s_14562/08_2023/7z8s_14562.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8s_14562/08_2023/7z8s_14562.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8s_14562/08_2023/7z8s_14562.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8s_14562/08_2023/7z8s_14562.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 72 5.49 5 S 70 5.16 5 C 9171 2.51 5 N 2614 2.21 5 O 2871 1.98 5 H 14473 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 1071": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 1274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 1881": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 29271 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 1144 Classifications: {'DNA': 36} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 35} Chain: "B" Number of atoms: 1135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 1135 Classifications: {'DNA': 36} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 35} Chain: "D" Number of atoms: 2907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 2907 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 169} Chain: "E" Number of atoms: 24085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1514, 24085 Classifications: {'peptide': 1514} Link IDs: {'PTRANS': 76, 'TRANS': 1437} Chain breaks: 7 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 12.03, per 1000 atoms: 0.41 Number of scatterers: 29271 At special positions: 0 Unit cell: (142.965, 136.611, 140.847, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 70 16.00 P 72 15.00 O 2871 8.00 N 2614 7.00 C 9171 6.00 H 14473 1.00 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: 22.72 Conformation dependent library (CDL) restraints added in 2.4 seconds 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3212 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 3 sheets defined 68.0% alpha, 5.0% beta 35 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 13.74 Creating SS restraints... Processing helix chain 'D' and resid 97 through 104 removed outlier: 3.653A pdb=" N ALA D 104 " --> pdb=" O ILE D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 161 Processing helix chain 'D' and resid 187 through 193 Processing helix chain 'D' and resid 234 through 250 removed outlier: 4.200A pdb=" N ILE D 238 " --> pdb=" O VAL D 234 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N TYR D 239 " --> pdb=" O ARG D 235 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET D 244 " --> pdb=" O GLN D 240 " (cutoff:3.500A) Proline residue: D 247 - end of helix Processing helix chain 'D' and resid 251 through 253 No H-bonds generated for 'chain 'D' and resid 251 through 253' Processing helix chain 'E' and resid 3 through 11 removed outlier: 3.789A pdb=" N ILE E 11 " --> pdb=" O ARG E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 35 removed outlier: 3.708A pdb=" N THR E 23 " --> pdb=" O LEU E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 47 removed outlier: 3.731A pdb=" N LEU E 42 " --> pdb=" O GLU E 38 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG E 45 " --> pdb=" O ASN E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 52 Processing helix chain 'E' and resid 54 through 70 removed outlier: 3.809A pdb=" N THR E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE E 69 " --> pdb=" O ILE E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 324 removed outlier: 3.688A pdb=" N VAL E 322 " --> pdb=" O GLU E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 347 Processing helix chain 'E' and resid 348 through 350 No H-bonds generated for 'chain 'E' and resid 348 through 350' Processing helix chain 'E' and resid 357 through 383 removed outlier: 4.691A pdb=" N ASP E 363 " --> pdb=" O LYS E 359 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU E 364 " --> pdb=" O GLU E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 409 Processing helix chain 'E' and resid 413 through 428 removed outlier: 4.012A pdb=" N ALA E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 457 removed outlier: 3.542A pdb=" N ARG E 451 " --> pdb=" O MET E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 464 removed outlier: 3.845A pdb=" N LEU E 462 " --> pdb=" O LYS E 458 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP E 464 " --> pdb=" O LEU E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 480 removed outlier: 4.484A pdb=" N ILE E 468 " --> pdb=" O ASP E 464 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY E 480 " --> pdb=" O MET E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 483 through 495 removed outlier: 3.572A pdb=" N THR E 493 " --> pdb=" O VAL E 489 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU E 494 " --> pdb=" O SER E 490 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE E 495 " --> pdb=" O ALA E 491 " (cutoff:3.500A) Processing helix chain 'E' and resid 497 through 502 Processing helix chain 'E' and resid 505 through 522 removed outlier: 3.780A pdb=" N LEU E 509 " --> pdb=" O ARG E 505 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASN E 514 " --> pdb=" O ASP E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 542 removed outlier: 4.071A pdb=" N LYS E 533 " --> pdb=" O ALA E 529 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 558 Processing helix chain 'E' and resid 559 through 561 No H-bonds generated for 'chain 'E' and resid 559 through 561' Processing helix chain 'E' and resid 562 through 567 Processing helix chain 'E' and resid 568 through 576 Proline residue: E 572 - end of helix removed outlier: 4.228A pdb=" N ARG E 575 " --> pdb=" O PRO E 572 " (cutoff:3.500A) Processing helix chain 'E' and resid 578 through 594 removed outlier: 3.805A pdb=" N LEU E 586 " --> pdb=" O ARG E 582 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN E 594 " --> pdb=" O MET E 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 619 removed outlier: 3.619A pdb=" N LEU E 609 " --> pdb=" O ASN E 605 " (cutoff:3.500A) Processing helix chain 'E' and resid 621 through 643 removed outlier: 3.982A pdb=" N ASP E 643 " --> pdb=" O LEU E 639 " (cutoff:3.500A) Processing helix chain 'E' and resid 643 through 652 removed outlier: 3.610A pdb=" N LEU E 647 " --> pdb=" O ASP E 643 " (cutoff:3.500A) Processing helix chain 'E' and resid 654 through 663 Processing helix chain 'E' and resid 676 through 680 Processing helix chain 'E' and resid 732 through 736 removed outlier: 3.593A pdb=" N MET E 735 " --> pdb=" O ASP E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 744 through 766 removed outlier: 4.181A pdb=" N LEU E 761 " --> pdb=" O LYS E 757 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE E 762 " --> pdb=" O ALA E 758 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER E 764 " --> pdb=" O GLY E 760 " (cutoff:3.500A) Processing helix chain 'E' and resid 767 through 770 Processing helix chain 'E' and resid 771 through 782 removed outlier: 3.601A pdb=" N ALA E 777 " --> pdb=" O SER E 773 " (cutoff:3.500A) Processing helix chain 'E' and resid 786 through 804 Processing helix chain 'E' and resid 806 through 812 removed outlier: 4.661A pdb=" N ARG E 812 " --> pdb=" O VAL E 809 " (cutoff:3.500A) Processing helix chain 'E' and resid 813 through 823 removed outlier: 3.678A pdb=" N ILE E 820 " --> pdb=" O PRO E 816 " (cutoff:3.500A) Processing helix chain 'E' and resid 829 through 831 No H-bonds generated for 'chain 'E' and resid 829 through 831' Processing helix chain 'E' and resid 832 through 853 removed outlier: 3.809A pdb=" N VAL E 836 " --> pdb=" O LEU E 832 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG E 851 " --> pdb=" O ILE E 847 " (cutoff:3.500A) Processing helix chain 'E' and resid 880 through 899 removed outlier: 3.553A pdb=" N ASN E 889 " --> pdb=" O GLU E 885 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP E 891 " --> pdb=" O VAL E 887 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N PHE E 892 " --> pdb=" O VAL E 888 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU E 898 " --> pdb=" O ARG E 894 " (cutoff:3.500A) Processing helix chain 'E' and resid 903 through 947 Proline residue: E 909 - end of helix removed outlier: 3.517A pdb=" N GLU E 924 " --> pdb=" O GLU E 920 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA E 943 " --> pdb=" O ALA E 939 " (cutoff:3.500A) Processing helix chain 'E' and resid 954 through 968 removed outlier: 3.593A pdb=" N SER E 964 " --> pdb=" O ALA E 960 " (cutoff:3.500A) Processing helix chain 'E' and resid 970 through 991 removed outlier: 4.373A pdb=" N ARG E 976 " --> pdb=" O GLU E 972 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER E 977 " --> pdb=" O LEU E 973 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA E 982 " --> pdb=" O ALA E 978 " (cutoff:3.500A) Processing helix chain 'E' and resid 994 through 1009 removed outlier: 3.927A pdb=" N CYS E1009 " --> pdb=" O VAL E1005 " (cutoff:3.500A) Processing helix chain 'E' and resid 1010 through 1015 removed outlier: 5.739A pdb=" N ALA E1013 " --> pdb=" O VAL E1010 " (cutoff:3.500A) Processing helix chain 'E' and resid 1017 through 1022 Processing helix chain 'E' and resid 1028 through 1035 removed outlier: 4.563A pdb=" N LYS E1033 " --> pdb=" O SER E1030 " (cutoff:3.500A) Processing helix chain 'E' and resid 1044 through 1072 removed outlier: 3.850A pdb=" N ARG E1054 " --> pdb=" O ALA E1050 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY E1059 " --> pdb=" O ILE E1055 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU E1062 " --> pdb=" O ARG E1058 " (cutoff:3.500A) Processing helix chain 'E' and resid 1074 through 1079 removed outlier: 3.543A pdb=" N ARG E1078 " --> pdb=" O GLU E1074 " (cutoff:3.500A) Processing helix chain 'E' and resid 1080 through 1095 removed outlier: 3.880A pdb=" N MET E1086 " --> pdb=" O LEU E1082 " (cutoff:3.500A) Proline residue: E1089 - end of helix Processing helix chain 'E' and resid 1099 through 1104 removed outlier: 3.551A pdb=" N ASP E1104 " --> pdb=" O GLU E1101 " (cutoff:3.500A) Processing helix chain 'E' and resid 1107 through 1124 removed outlier: 4.349A pdb=" N GLN E1111 " --> pdb=" O ASN E1107 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE E1113 " --> pdb=" O PHE E1109 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL E1114 " --> pdb=" O GLY E1110 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N MET E1117 " --> pdb=" O ILE E1113 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER E1118 " --> pdb=" O VAL E1114 " (cutoff:3.500A) Processing helix chain 'E' and resid 1125 through 1127 No H-bonds generated for 'chain 'E' and resid 1125 through 1127' Processing helix chain 'E' and resid 1128 through 1130 No H-bonds generated for 'chain 'E' and resid 1128 through 1130' Processing helix chain 'E' and resid 1131 through 1147 removed outlier: 3.539A pdb=" N GLN E1138 " --> pdb=" O PHE E1134 " (cutoff:3.500A) Proline residue: E1140 - end of helix Processing helix chain 'E' and resid 1150 through 1168 removed outlier: 3.539A pdb=" N SER E1166 " --> pdb=" O ALA E1162 " (cutoff:3.500A) Processing helix chain 'E' and resid 1169 through 1180 Processing helix chain 'E' and resid 1181 through 1186 Processing helix chain 'E' and resid 1190 through 1208 removed outlier: 3.930A pdb=" N ILE E1200 " --> pdb=" O ALA E1196 " (cutoff:3.500A) Processing helix chain 'E' and resid 1209 through 1212 removed outlier: 4.148A pdb=" N LEU E1212 " --> pdb=" O ASP E1209 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1209 through 1212' Processing helix chain 'E' and resid 1214 through 1226 removed outlier: 3.880A pdb=" N LEU E1218 " --> pdb=" O TYR E1214 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N VAL E1220 " --> pdb=" O ILE E1216 " (cutoff:3.500A) Proline residue: E1221 - end of helix Processing helix chain 'E' and resid 1230 through 1248 removed outlier: 4.081A pdb=" N THR E1243 " --> pdb=" O THR E1239 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LYS E1246 " --> pdb=" O ALA E1242 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU E1247 " --> pdb=" O THR E1243 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL E1248 " --> pdb=" O LEU E1244 " (cutoff:3.500A) Processing helix chain 'E' and resid 1249 through 1251 No H-bonds generated for 'chain 'E' and resid 1249 through 1251' Processing helix chain 'E' and resid 1261 through 1280 removed outlier: 3.679A pdb=" N GLY E1267 " --> pdb=" O GLU E1263 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN E1277 " --> pdb=" O THR E1273 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU E1278 " --> pdb=" O PHE E1274 " (cutoff:3.500A) Processing helix chain 'E' and resid 1298 through 1315 removed outlier: 3.667A pdb=" N TYR E1314 " --> pdb=" O PHE E1310 " (cutoff:3.500A) Processing helix chain 'E' and resid 1327 through 1350 removed outlier: 3.582A pdb=" N GLU E1346 " --> pdb=" O GLN E1342 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE E1347 " --> pdb=" O ARG E1343 " (cutoff:3.500A) Processing helix chain 'E' and resid 1352 through 1356 Processing helix chain 'E' and resid 1365 through 1367 No H-bonds generated for 'chain 'E' and resid 1365 through 1367' Processing helix chain 'E' and resid 1368 through 1380 Processing helix chain 'E' and resid 1391 through 1396 Processing helix chain 'E' and resid 1397 through 1399 No H-bonds generated for 'chain 'E' and resid 1397 through 1399' Processing helix chain 'E' and resid 1400 through 1404 removed outlier: 3.748A pdb=" N ASP E1403 " --> pdb=" O ASP E1400 " (cutoff:3.500A) Processing helix chain 'E' and resid 1412 through 1416 Processing helix chain 'E' and resid 1418 through 1423 Processing helix chain 'E' and resid 1434 through 1439 removed outlier: 3.510A pdb=" N LEU E1437 " --> pdb=" O GLU E1434 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS E1439 " --> pdb=" O HIS E1436 " (cutoff:3.500A) Processing helix chain 'E' and resid 1443 through 1450 Processing helix chain 'E' and resid 1468 through 1480 removed outlier: 3.982A pdb=" N LEU E1472 " --> pdb=" O ASN E1468 " (cutoff:3.500A) Processing helix chain 'E' and resid 1486 through 1494 Processing helix chain 'E' and resid 1494 through 1501 removed outlier: 3.993A pdb=" N SER E1501 " --> pdb=" O PRO E1497 " (cutoff:3.500A) Processing helix chain 'E' and resid 1502 through 1504 No H-bonds generated for 'chain 'E' and resid 1502 through 1504' Processing helix chain 'E' and resid 1508 through 1526 removed outlier: 4.182A pdb=" N GLY E1514 " --> pdb=" O GLU E1510 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU E1519 " --> pdb=" O ALA E1515 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN E1524 " --> pdb=" O ALA E1520 " (cutoff:3.500A) Processing helix chain 'E' and resid 1527 through 1529 No H-bonds generated for 'chain 'E' and resid 1527 through 1529' Processing helix chain 'E' and resid 1533 through 1538 Processing helix chain 'E' and resid 1554 through 1566 Processing helix chain 'E' and resid 1587 through 1598 Processing helix chain 'E' and resid 1632 through 1643 Processing helix chain 'E' and resid 1645 through 1650 Processing helix chain 'E' and resid 1673 through 1685 removed outlier: 3.532A pdb=" N THR E1683 " --> pdb=" O MET E1679 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU E1685 " --> pdb=" O GLN E1681 " (cutoff:3.500A) Processing helix chain 'E' and resid 1705 through 1714 Processing helix chain 'E' and resid 1749 through 1758 Processing helix chain 'E' and resid 1779 through 1798 removed outlier: 4.174A pdb=" N LYS E1783 " --> pdb=" O THR E1779 " (cutoff:3.500A) Processing helix chain 'E' and resid 1811 through 1816 removed outlier: 3.754A pdb=" N ASP E1816 " --> pdb=" O ASP E1812 " (cutoff:3.500A) Processing helix chain 'E' and resid 1856 through 1861 removed outlier: 4.069A pdb=" N LEU E1860 " --> pdb=" O LYS E1856 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU E1861 " --> pdb=" O ALA E1857 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1856 through 1861' Processing helix chain 'E' and resid 1869 through 1877 removed outlier: 3.920A pdb=" N GLU E1873 " --> pdb=" O ASN E1869 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER E1875 " --> pdb=" O GLN E1871 " (cutoff:3.500A) Processing helix chain 'E' and resid 1877 through 1885 removed outlier: 3.625A pdb=" N PHE E1881 " --> pdb=" O ASP E1877 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 117 through 121 removed outlier: 6.781A pdb=" N VAL D 176 " --> pdb=" O GLN D 83 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ILE D 85 " --> pdb=" O ASN D 174 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASN D 174 " --> pdb=" O ILE D 85 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA D 87 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE D 172 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL D 89 " --> pdb=" O PHE D 170 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N PHE D 170 " --> pdb=" O VAL D 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 1318 through 1319 removed outlier: 7.000A pdb=" N GLY E1318 " --> pdb=" O ILE E1459 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU E1361 " --> pdb=" O TYR E1429 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 1544 through 1551 removed outlier: 6.166A pdb=" N VAL E1741 " --> pdb=" O TYR E1772 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ILE E1774 " --> pdb=" O VAL E1741 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N PHE E1743 " --> pdb=" O ILE E1774 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N THR E1776 " --> pdb=" O PHE E1743 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU E1695 " --> pdb=" O LEU E1723 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N THR E1725 " --> pdb=" O LEU E1695 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N LEU E1697 " --> pdb=" O THR E1725 " (cutoff:3.500A) 722 hydrogen bonds defined for protein. 2073 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 95 hydrogen bonds 190 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 14.77 Time building geometry restraints manager: 23.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 14452 1.03 - 1.23: 42 1.23 - 1.42: 6150 1.42 - 1.62: 8926 1.62 - 1.81: 119 Bond restraints: 29689 Sorted by residual: bond pdb=" N SER D 76 " pdb=" CA SER D 76 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.14e+00 bond pdb=" C1' DC B 29 " pdb=" N1 DC B 29 " ideal model delta sigma weight residual 1.490 1.542 -0.052 3.00e-02 1.11e+03 3.05e+00 bond pdb=" N ALA E 2 " pdb=" CA ALA E 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.82e+00 bond pdb=" C1' DT B 10 " pdb=" N1 DT B 10 " ideal model delta sigma weight residual 1.490 1.539 -0.049 3.00e-02 1.11e+03 2.64e+00 bond pdb=" C1' DC B 34 " pdb=" N1 DC B 34 " ideal model delta sigma weight residual 1.490 1.538 -0.048 3.00e-02 1.11e+03 2.54e+00 ... (remaining 29684 not shown) Histogram of bond angle deviations from ideal: 99.61 - 106.49: 1039 106.49 - 113.36: 35045 113.36 - 120.24: 9671 120.24 - 127.12: 7856 127.12 - 134.00: 304 Bond angle restraints: 53915 Sorted by residual: angle pdb=" C VAL E 46 " pdb=" N VAL E 47 " pdb=" CA VAL E 47 " ideal model delta sigma weight residual 120.24 123.45 -3.21 6.30e-01 2.52e+00 2.60e+01 angle pdb=" C VAL E 47 " pdb=" CA VAL E 47 " pdb=" CB VAL E 47 " ideal model delta sigma weight residual 114.35 110.06 4.29 1.06e+00 8.90e-01 1.64e+01 angle pdb=" C VAL E1525 " pdb=" N LEU E1526 " pdb=" CA LEU E1526 " ideal model delta sigma weight residual 120.97 125.17 -4.20 1.48e+00 4.57e-01 8.06e+00 angle pdb=" N VAL E1248 " pdb=" CA VAL E1248 " pdb=" C VAL E1248 " ideal model delta sigma weight residual 108.88 114.87 -5.99 2.16e+00 2.14e-01 7.69e+00 angle pdb=" N LEU E 39 " pdb=" CA LEU E 39 " pdb=" C LEU E 39 " ideal model delta sigma weight residual 111.11 114.20 -3.09 1.20e+00 6.94e-01 6.64e+00 ... (remaining 53910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 10301 17.86 - 35.73: 970 35.73 - 53.59: 276 53.59 - 71.46: 78 71.46 - 89.32: 11 Dihedral angle restraints: 11636 sinusoidal: 6045 harmonic: 5591 Sorted by residual: dihedral pdb=" CA PHE E 501 " pdb=" C PHE E 501 " pdb=" N VAL E 502 " pdb=" CA VAL E 502 " ideal model delta harmonic sigma weight residual -180.00 -158.07 -21.93 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA ILE E1113 " pdb=" C ILE E1113 " pdb=" N VAL E1114 " pdb=" CA VAL E1114 " ideal model delta harmonic sigma weight residual 180.00 159.53 20.47 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA ILE D 121 " pdb=" C ILE D 121 " pdb=" N ARG D 122 " pdb=" CA ARG D 122 " ideal model delta harmonic sigma weight residual -180.00 -159.79 -20.21 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 11633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1628 0.038 - 0.075: 576 0.075 - 0.113: 174 0.113 - 0.150: 36 0.150 - 0.188: 4 Chirality restraints: 2418 Sorted by residual: chirality pdb=" CA THR E1124 " pdb=" N THR E1124 " pdb=" C THR E1124 " pdb=" CB THR E1124 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.81e-01 chirality pdb=" CA ILE E 766 " pdb=" N ILE E 766 " pdb=" C ILE E 766 " pdb=" CB ILE E 766 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.59e-01 chirality pdb=" CA ILE E 673 " pdb=" N ILE E 673 " pdb=" C ILE E 673 " pdb=" CB ILE E 673 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.43e-01 ... (remaining 2415 not shown) Planarity restraints: 4093 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E1083 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.87e+00 pdb=" C ARG E1083 " -0.029 2.00e-02 2.50e+03 pdb=" O ARG E1083 " 0.011 2.00e-02 2.50e+03 pdb=" N THR E1084 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E1491 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.85e+00 pdb=" C LEU E1491 " -0.029 2.00e-02 2.50e+03 pdb=" O LEU E1491 " 0.011 2.00e-02 2.50e+03 pdb=" N ASP E1492 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 332 " 0.144 9.50e-02 1.11e+02 4.80e-02 2.58e+00 pdb=" NE ARG E 332 " -0.005 2.00e-02 2.50e+03 pdb=" CZ ARG E 332 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG E 332 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG E 332 " -0.005 2.00e-02 2.50e+03 pdb="HH11 ARG E 332 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG E 332 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG E 332 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG E 332 " 0.007 2.00e-02 2.50e+03 ... (remaining 4090 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 3364 2.26 - 2.85: 64594 2.85 - 3.43: 75085 3.43 - 4.02: 100778 4.02 - 4.60: 154122 Nonbonded interactions: 397943 Sorted by model distance: nonbonded pdb=" OD1 ASP E1323 " pdb="HH12 ARG E1531 " model vdw 1.677 1.850 nonbonded pdb=" H ARG E1666 " pdb=" OD2 ASP E1739 " model vdw 1.686 1.850 nonbonded pdb=" O VAL E1684 " pdb=" H LEU E1689 " model vdw 1.688 1.850 nonbonded pdb="HD22 ASN D 106 " pdb=" O ARG D 120 " model vdw 1.692 1.850 nonbonded pdb=" O LEU E 761 " pdb=" HG SER E 764 " model vdw 1.695 1.850 ... (remaining 397938 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.280 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: 0.400 Extract box with map and model: 9.780 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 102.510 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 15216 Z= 0.267 Angle : 0.743 7.613 20906 Z= 0.415 Chirality : 0.042 0.188 2418 Planarity : 0.005 0.059 2430 Dihedral : 16.348 89.319 5854 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.20), residues: 1674 helix: -0.41 (0.16), residues: 972 sheet: -0.85 (0.47), residues: 114 loop : -0.57 (0.26), residues: 588 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Residue SER 1261 is missing expected H atoms. Skipping. Evaluate side-chains 373 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 358 time to evaluate : 2.189 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 outliers start: 15 outliers final: 4 residues processed: 370 average time/residue: 0.7354 time to fit residues: 377.7079 Evaluate side-chains 221 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 217 time to evaluate : 2.187 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.4346 time to fit residues: 5.7431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 136 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 ASN E 71 ASN E 418 HIS ** E 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1373 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 15216 Z= 0.197 Angle : 0.610 8.749 20906 Z= 0.335 Chirality : 0.039 0.164 2418 Planarity : 0.005 0.053 2430 Dihedral : 17.086 73.334 2547 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.20), residues: 1674 helix: 0.17 (0.16), residues: 981 sheet: -0.85 (0.49), residues: 102 loop : -0.72 (0.26), residues: 591 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Residue SER 1261 is missing expected H atoms. Skipping. Evaluate side-chains 265 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 234 time to evaluate : 2.522 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: 31 outliers final: 24 residues processed: 253 average time/residue: 0.5626 time to fit residues: 214.9897 Evaluate side-chains 232 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 208 time to evaluate : 2.009 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 24 outliers final: 1 residues processed: 24 average time/residue: 0.3271 time to fit residues: 16.9995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 chunk 171 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 15216 Z= 0.198 Angle : 0.571 6.595 20906 Z= 0.311 Chirality : 0.039 0.180 2418 Planarity : 0.004 0.043 2430 Dihedral : 17.130 65.508 2547 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.20), residues: 1674 helix: 0.49 (0.16), residues: 999 sheet: -0.96 (0.50), residues: 102 loop : -0.80 (0.26), residues: 573 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Residue SER 1261 is missing expected H atoms. Skipping. Evaluate side-chains 222 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 206 time to evaluate : 2.132 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 outliers start: 16 outliers final: 10 residues processed: 218 average time/residue: 0.5791 time to fit residues: 191.1548 Evaluate side-chains 208 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 198 time to evaluate : 2.078 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.3474 time to fit residues: 8.9300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 3.9990 chunk 119 optimal weight: 0.0470 chunk 82 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 158 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 overall best weight: 1.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 106 ASN ** E 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 15216 Z= 0.254 Angle : 0.580 6.590 20906 Z= 0.319 Chirality : 0.040 0.179 2418 Planarity : 0.004 0.036 2430 Dihedral : 17.078 59.863 2547 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.21), residues: 1674 helix: 0.58 (0.17), residues: 995 sheet: -0.98 (0.51), residues: 102 loop : -0.90 (0.26), residues: 577 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Residue SER 1261 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 211 time to evaluate : 2.179 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 outliers start: 14 outliers final: 10 residues processed: 216 average time/residue: 0.6082 time to fit residues: 197.6375 Evaluate side-chains 207 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 197 time to evaluate : 2.206 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.3819 time to fit residues: 9.4831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1665 HIS ** E1765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.074 15216 Z= 0.384 Angle : 0.643 7.373 20906 Z= 0.355 Chirality : 0.042 0.158 2418 Planarity : 0.005 0.056 2430 Dihedral : 17.115 59.893 2547 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.21), residues: 1674 helix: 0.31 (0.17), residues: 1003 sheet: -1.31 (0.50), residues: 104 loop : -1.19 (0.26), residues: 567 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Residue SER 1261 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 200 time to evaluate : 2.367 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 outliers start: 25 outliers final: 16 residues processed: 217 average time/residue: 0.5880 time to fit residues: 196.6952 Evaluate side-chains 205 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 189 time to evaluate : 2.341 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 16 outliers final: 1 residues processed: 16 average time/residue: 0.3787 time to fit residues: 14.0525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 55 optimal weight: 0.0870 chunk 88 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 15216 Z= 0.245 Angle : 0.582 6.487 20906 Z= 0.317 Chirality : 0.039 0.150 2418 Planarity : 0.004 0.039 2430 Dihedral : 17.063 59.860 2547 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.21), residues: 1674 helix: 0.51 (0.17), residues: 1001 sheet: -1.16 (0.51), residues: 104 loop : -1.10 (0.26), residues: 569 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Residue SER 1261 is missing expected H atoms. Skipping. Evaluate side-chains 206 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 193 time to evaluate : 2.122 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 outliers start: 13 outliers final: 7 residues processed: 202 average time/residue: 0.5687 time to fit residues: 173.4380 Evaluate side-chains 191 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 184 time to evaluate : 2.130 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.3825 time to fit residues: 7.3368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 15216 Z= 0.187 Angle : 0.554 8.502 20906 Z= 0.299 Chirality : 0.038 0.185 2418 Planarity : 0.003 0.038 2430 Dihedral : 17.001 59.682 2547 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.21), residues: 1674 helix: 0.73 (0.17), residues: 994 sheet: -1.05 (0.52), residues: 104 loop : -1.04 (0.26), residues: 576 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Residue SER 1261 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 186 time to evaluate : 2.280 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 outliers start: 8 outliers final: 5 residues processed: 191 average time/residue: 0.5761 time to fit residues: 167.4694 Evaluate side-chains 189 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 184 time to evaluate : 2.362 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.3823 time to fit residues: 6.3975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 82 optimal weight: 0.3980 chunk 15 optimal weight: 0.3980 chunk 131 optimal weight: 2.9990 chunk 152 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 146 optimal weight: 0.0170 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 664 HIS ** E 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 15216 Z= 0.158 Angle : 0.537 7.674 20906 Z= 0.288 Chirality : 0.038 0.147 2418 Planarity : 0.003 0.037 2430 Dihedral : 16.934 59.945 2547 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.21), residues: 1674 helix: 0.94 (0.17), residues: 996 sheet: -0.94 (0.52), residues: 104 loop : -0.92 (0.27), residues: 574 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Residue SER 1261 is missing expected H atoms. Skipping. Evaluate side-chains 201 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 195 time to evaluate : 2.486 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 outliers start: 6 outliers final: 4 residues processed: 198 average time/residue: 0.6007 time to fit residues: 180.9478 Evaluate side-chains 188 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 184 time to evaluate : 2.201 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.3772 time to fit residues: 5.4229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 147 optimal weight: 0.5980 chunk 155 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 165 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 106 ASN ** E 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 15216 Z= 0.174 Angle : 0.546 8.344 20906 Z= 0.292 Chirality : 0.038 0.146 2418 Planarity : 0.003 0.033 2430 Dihedral : 16.900 59.862 2547 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.21), residues: 1674 helix: 1.04 (0.17), residues: 995 sheet: -0.92 (0.52), residues: 104 loop : -0.91 (0.27), residues: 575 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Residue SER 1261 is missing expected H atoms. Skipping. Evaluate side-chains 198 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 189 time to evaluate : 2.171 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 outliers start: 9 outliers final: 7 residues processed: 192 average time/residue: 0.5859 time to fit residues: 170.9287 Evaluate side-chains 190 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 183 time to evaluate : 2.212 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.3855 time to fit residues: 7.3246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.076 15216 Z= 0.307 Angle : 0.607 7.389 20906 Z= 0.330 Chirality : 0.040 0.159 2418 Planarity : 0.004 0.045 2430 Dihedral : 16.946 59.859 2547 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.21), residues: 1674 helix: 0.84 (0.17), residues: 993 sheet: -1.00 (0.53), residues: 104 loop : -1.09 (0.27), residues: 577 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Residue SER 1261 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 174 time to evaluate : 2.942 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 outliers start: 8 outliers final: 5 residues processed: 179 average time/residue: 0.5581 time to fit residues: 154.3050 Evaluate side-chains 177 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 172 time to evaluate : 2.159 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.3599 time to fit residues: 5.8617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 138 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.129902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.096913 restraints weight = 79169.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.100496 restraints weight = 38721.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.102819 restraints weight = 23935.976| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 15216 Z= 0.253 Angle : 0.585 9.214 20906 Z= 0.316 Chirality : 0.039 0.145 2418 Planarity : 0.004 0.036 2430 Dihedral : 16.958 59.977 2547 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.21), residues: 1674 helix: 0.85 (0.17), residues: 997 sheet: -0.98 (0.53), residues: 104 loop : -1.22 (0.26), residues: 573 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6060.60 seconds wall clock time: 108 minutes 5.79 seconds (6485.79 seconds total)