Starting phenix.real_space_refine on Wed Sep 25 23:10:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9f44_50183/09_2024/9f44_50183.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9f44_50183/09_2024/9f44_50183.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9f44_50183/09_2024/9f44_50183.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9f44_50183/09_2024/9f44_50183.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9f44_50183/09_2024/9f44_50183.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9f44_50183/09_2024/9f44_50183.cif" } resolution = 3.68 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 374 5.16 5 C 36206 2.51 5 N 9916 2.21 5 O 10340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 56848 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 17467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2192, 17467 Classifications: {'peptide': 2192} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 87, 'TRANS': 2104} Chain breaks: 20 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 236 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 110 Chain: "C" Number of atoms: 2456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2456 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain: "E" Number of atoms: 8385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1052, 8385 Classifications: {'peptide': 1052} Link IDs: {'PTRANS': 56, 'TRANS': 995} Chain breaks: 5 Chain: "G" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 80 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: D, F, H, B Time building chain proxies: 65.43, per 1000 atoms: 1.15 Number of scatterers: 56848 At special positions: 0 Unit cell: (226.63, 310.47, 153.27, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 374 16.00 P 12 15.00 O 10340 8.00 N 9916 7.00 C 36206 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 - 3.00 Amino acid : True - 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: 11.08 Conformation dependent library (CDL) restraints added in 5.6 seconds 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13628 Finding SS restraints... Secondary structure from input PDB file: 352 helices and 38 sheets defined 65.8% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.31 Creating SS restraints... Processing helix chain 'A' and resid 18 through 30 Processing helix chain 'A' and resid 38 through 53 removed outlier: 3.664A pdb=" N LEU A 52 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 74 Processing helix chain 'A' and resid 83 through 98 Processing helix chain 'A' and resid 100 through 115 removed outlier: 4.039A pdb=" N ASN A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 135 Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 139 through 156 removed outlier: 4.505A pdb=" N GLU A 143 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 179 Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 187 through 198 removed outlier: 3.762A pdb=" N VAL A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 223 removed outlier: 3.663A pdb=" N ALA A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 246 Processing helix chain 'A' and resid 261 through 276 removed outlier: 3.524A pdb=" N LEU A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 289 removed outlier: 4.487A pdb=" N GLU A 280 " --> pdb=" O SER A 276 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 371 removed outlier: 3.695A pdb=" N ASP A 371 " --> pdb=" O GLU A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 376 Processing helix chain 'A' and resid 387 through 404 Proline residue: A 397 - end of helix Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 411 through 426 removed outlier: 3.711A pdb=" N HIS A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 444 Processing helix chain 'A' and resid 446 through 450 removed outlier: 3.512A pdb=" N VAL A 450 " --> pdb=" O GLU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 463 Processing helix chain 'A' and resid 479 through 491 Processing helix chain 'A' and resid 499 through 512 removed outlier: 4.121A pdb=" N GLU A 503 " --> pdb=" O GLN A 499 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Proline residue: A 507 - end of helix removed outlier: 4.066A pdb=" N GLY A 512 " --> pdb=" O MET A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 528 Processing helix chain 'A' and resid 531 through 549 removed outlier: 4.247A pdb=" N HIS A 549 " --> pdb=" O LEU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 592 removed outlier: 4.156A pdb=" N PHE A 592 " --> pdb=" O THR A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 612 removed outlier: 3.611A pdb=" N ASP A 608 " --> pdb=" O ARG A 604 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 611 " --> pdb=" O ALA A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 630 Processing helix chain 'A' and resid 645 through 666 Processing helix chain 'A' and resid 668 through 679 Processing helix chain 'A' and resid 680 through 682 No H-bonds generated for 'chain 'A' and resid 680 through 682' Processing helix chain 'A' and resid 683 through 688 Processing helix chain 'A' and resid 689 through 701 removed outlier: 4.041A pdb=" N ASN A 701 " --> pdb=" O PHE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 718 Processing helix chain 'A' and resid 722 through 744 Proline residue: A 728 - end of helix Processing helix chain 'A' and resid 746 through 764 Processing helix chain 'A' and resid 764 through 769 Processing helix chain 'A' and resid 771 through 784 Processing helix chain 'A' and resid 792 through 810 removed outlier: 3.761A pdb=" N GLY A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 815 No H-bonds generated for 'chain 'A' and resid 813 through 815' Processing helix chain 'A' and resid 816 through 829 Processing helix chain 'A' and resid 836 through 852 Processing helix chain 'A' and resid 855 through 861 Processing helix chain 'A' and resid 863 through 875 removed outlier: 3.663A pdb=" N LEU A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS A 873 " --> pdb=" O LEU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 892 Processing helix chain 'A' and resid 895 through 903 Processing helix chain 'A' and resid 934 through 941 Processing helix chain 'A' and resid 942 through 960 Proline residue: A 948 - end of helix Processing helix chain 'A' and resid 963 through 983 removed outlier: 6.944A pdb=" N THR A 969 " --> pdb=" O SER A 965 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N MET A 970 " --> pdb=" O HIS A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 988 removed outlier: 3.822A pdb=" N VAL A 987 " --> pdb=" O LEU A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1004 Proline residue: A 995 - end of helix Processing helix chain 'A' and resid 1007 through 1024 removed outlier: 3.837A pdb=" N PHE A1011 " --> pdb=" O ALA A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1042 removed outlier: 4.353A pdb=" N ASP A1032 " --> pdb=" O ARG A1028 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLU A1033 " --> pdb=" O PRO A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1064 Processing helix chain 'A' and resid 1066 through 1084 removed outlier: 4.229A pdb=" N TYR A1070 " --> pdb=" O GLU A1066 " (cutoff:3.500A) Proline residue: A1072 - end of helix Proline residue: A1076 - end of helix Processing helix chain 'A' and resid 1087 through 1089 No H-bonds generated for 'chain 'A' and resid 1087 through 1089' Processing helix chain 'A' and resid 1090 through 1104 removed outlier: 3.984A pdb=" N GLY A1104 " --> pdb=" O ILE A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1108 Processing helix chain 'A' and resid 1110 through 1124 Proline residue: A1116 - end of helix Processing helix chain 'A' and resid 1128 through 1146 removed outlier: 3.742A pdb=" N GLU A1144 " --> pdb=" O ASP A1140 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER A1145 " --> pdb=" O ARG A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1166 Proline residue: A1158 - end of helix Processing helix chain 'A' and resid 1169 through 1185 Processing helix chain 'A' and resid 1186 through 1190 removed outlier: 3.989A pdb=" N ILE A1190 " --> pdb=" O LYS A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1203 Processing helix chain 'A' and resid 1206 through 1219 Processing helix chain 'A' and resid 1262 through 1270 Processing helix chain 'A' and resid 1276 through 1295 Processing helix chain 'A' and resid 1297 through 1302 Processing helix chain 'A' and resid 1303 through 1310 removed outlier: 3.618A pdb=" N ALA A1309 " --> pdb=" O ALA A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1310 through 1317 removed outlier: 3.780A pdb=" N ALA A1314 " --> pdb=" O TYR A1310 " (cutoff:3.500A) Processing helix chain 'A' and resid 1317 through 1329 Processing helix chain 'A' and resid 1331 through 1347 Processing helix chain 'A' and resid 1350 through 1367 Processing helix chain 'A' and resid 1376 through 1378 No H-bonds generated for 'chain 'A' and resid 1376 through 1378' Processing helix chain 'A' and resid 1379 through 1390 Processing helix chain 'A' and resid 1392 through 1407 Processing helix chain 'A' and resid 1409 through 1423 Processing helix chain 'A' and resid 1425 through 1441 Processing helix chain 'A' and resid 1446 through 1454 removed outlier: 4.076A pdb=" N TYR A1450 " --> pdb=" O GLN A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1455 through 1470 Processing helix chain 'A' and resid 1473 through 1488 Processing helix chain 'A' and resid 1489 through 1500 Processing helix chain 'A' and resid 1505 through 1524 removed outlier: 4.263A pdb=" N ARG A1514 " --> pdb=" O ALA A1510 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N MET A1515 " --> pdb=" O LYS A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1536 removed outlier: 3.550A pdb=" N MET A1535 " --> pdb=" O GLU A1531 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1554 Processing helix chain 'A' and resid 1556 through 1581 removed outlier: 4.632A pdb=" N ALA A1573 " --> pdb=" O ASP A1569 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLU A1574 " --> pdb=" O LEU A1570 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU A1581 " --> pdb=" O ALA A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1582 through 1608 removed outlier: 3.983A pdb=" N ALA A1586 " --> pdb=" O SER A1582 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLY A1588 " --> pdb=" O SER A1584 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ALA A1589 " --> pdb=" O ARG A1585 " (cutoff:3.500A) Processing helix chain 'A' and resid 1611 through 1626 Processing helix chain 'A' and resid 1629 through 1641 Processing helix chain 'A' and resid 1645 through 1648 Processing helix chain 'A' and resid 1649 through 1663 removed outlier: 3.990A pdb=" N TRP A1653 " --> pdb=" O ASP A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1665 through 1678 Processing helix chain 'A' and resid 1693 through 1707 Processing helix chain 'A' and resid 1709 through 1732 Processing helix chain 'A' and resid 1737 through 1762 Processing helix chain 'A' and resid 1767 through 1783 removed outlier: 4.075A pdb=" N LYS A1771 " --> pdb=" O SER A1767 " (cutoff:3.500A) Processing helix chain 'A' and resid 1786 through 1812 removed outlier: 3.681A pdb=" N TRP A1790 " --> pdb=" O TRP A1786 " (cutoff:3.500A) Processing helix chain 'A' and resid 1868 through 1896 removed outlier: 3.592A pdb=" N VAL A1882 " --> pdb=" O LEU A1878 " (cutoff:3.500A) Proline residue: A1883 - end of helix Processing helix chain 'A' and resid 1899 through 1914 Processing helix chain 'A' and resid 1916 through 1930 Processing helix chain 'A' and resid 1932 through 1937 Processing helix chain 'A' and resid 1938 through 1945 removed outlier: 3.784A pdb=" N ARG A1945 " --> pdb=" O GLN A1941 " (cutoff:3.500A) Processing helix chain 'A' and resid 1950 through 1967 removed outlier: 3.530A pdb=" N LEU A1956 " --> pdb=" O LEU A1952 " (cutoff:3.500A) Processing helix chain 'A' and resid 1968 through 1971 Processing helix chain 'A' and resid 1972 through 1981 removed outlier: 3.662A pdb=" N LYS A1981 " --> pdb=" O THR A1977 " (cutoff:3.500A) Processing helix chain 'A' and resid 1984 through 2002 removed outlier: 3.620A pdb=" N HIS A1988 " --> pdb=" O THR A1984 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN A1997 " --> pdb=" O LYS A1993 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A2000 " --> pdb=" O LYS A1996 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS A2001 " --> pdb=" O ASN A1997 " (cutoff:3.500A) Processing helix chain 'A' and resid 2003 through 2021 Processing helix chain 'A' and resid 2022 through 2040 Processing helix chain 'A' and resid 2043 through 2059 Proline residue: A2053 - end of helix Processing helix chain 'A' and resid 2064 through 2074 Processing helix chain 'A' and resid 2074 through 2092 Processing helix chain 'A' and resid 2093 through 2115 removed outlier: 3.756A pdb=" N GLN A2099 " --> pdb=" O LYS A2095 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA A2100 " --> pdb=" O ASP A2096 " (cutoff:3.500A) Processing helix chain 'A' and resid 2116 through 2118 No H-bonds generated for 'chain 'A' and resid 2116 through 2118' Processing helix chain 'A' and resid 2123 through 2127 Processing helix chain 'A' and resid 2127 through 2133 removed outlier: 3.689A pdb=" N LEU A2131 " --> pdb=" O SER A2127 " (cutoff:3.500A) Processing helix chain 'A' and resid 2192 through 2212 Processing helix chain 'A' and resid 2212 through 2219 Processing helix chain 'A' and resid 2246 through 2257 Processing helix chain 'A' and resid 2262 through 2272 Processing helix chain 'A' and resid 2274 through 2278 Processing helix chain 'A' and resid 2279 through 2293 Processing helix chain 'A' and resid 2297 through 2307 Processing helix chain 'A' and resid 2309 through 2335 Processing helix chain 'A' and resid 2340 through 2342 No H-bonds generated for 'chain 'A' and resid 2340 through 2342' Processing helix chain 'A' and resid 2363 through 2368 Processing helix chain 'A' and resid 2380 through 2387 Processing helix chain 'A' and resid 2394 through 2410 Processing helix chain 'A' and resid 2410 through 2423 removed outlier: 3.692A pdb=" N PHE A2421 " --> pdb=" O VAL A2417 " (cutoff:3.500A) Processing helix chain 'A' and resid 2424 through 2426 No H-bonds generated for 'chain 'A' and resid 2424 through 2426' Processing helix chain 'A' and resid 2427 through 2435 removed outlier: 4.465A pdb=" N LEU A2431 " --> pdb=" O LEU A2427 " (cutoff:3.500A) Processing helix chain 'A' and resid 2493 through 2510 Processing helix chain 'A' and resid 2520 through 2534 Processing helix chain 'A' and resid 2534 through 2539 Processing helix chain 'A' and resid 2542 through 2546 Processing helix chain 'B' and resid 18 through 30 Processing helix chain 'B' and resid 38 through 53 removed outlier: 3.664A pdb=" N LEU B 52 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 74 Processing helix chain 'B' and resid 83 through 98 Processing helix chain 'B' and resid 100 through 115 removed outlier: 4.040A pdb=" N ASN B 109 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR B 110 " --> pdb=" O ARG B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 135 Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 139 through 156 removed outlier: 4.505A pdb=" N GLU B 143 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 179 Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 187 through 198 removed outlier: 3.762A pdb=" N VAL B 196 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 223 removed outlier: 3.663A pdb=" N ALA B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 246 Processing helix chain 'B' and resid 261 through 276 removed outlier: 3.524A pdb=" N LEU B 271 " --> pdb=" O ILE B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 289 removed outlier: 4.487A pdb=" N GLU B 280 " --> pdb=" O SER B 276 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG B 283 " --> pdb=" O GLY B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 371 removed outlier: 3.695A pdb=" N ASP B 371 " --> pdb=" O GLU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 376 Processing helix chain 'B' and resid 387 through 404 Proline residue: B 397 - end of helix Proline residue: B 404 - end of helix Processing helix chain 'B' and resid 411 through 426 removed outlier: 3.710A pdb=" N HIS B 419 " --> pdb=" O ASP B 415 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS B 426 " --> pdb=" O SER B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 444 Processing helix chain 'B' and resid 446 through 450 removed outlier: 3.512A pdb=" N VAL B 450 " --> pdb=" O GLU B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 463 Processing helix chain 'B' and resid 479 through 491 Processing helix chain 'B' and resid 499 through 512 removed outlier: 4.121A pdb=" N GLU B 503 " --> pdb=" O GLN B 499 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) Proline residue: B 507 - end of helix removed outlier: 4.066A pdb=" N GLY B 512 " --> pdb=" O MET B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 528 Processing helix chain 'B' and resid 531 through 549 removed outlier: 4.247A pdb=" N HIS B 549 " --> pdb=" O LEU B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 592 removed outlier: 4.155A pdb=" N PHE B 592 " --> pdb=" O THR B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 612 removed outlier: 3.611A pdb=" N ASP B 608 " --> pdb=" O ARG B 604 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 611 " --> pdb=" O ALA B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 630 Processing helix chain 'B' and resid 645 through 666 Processing helix chain 'B' and resid 668 through 679 Processing helix chain 'B' and resid 680 through 682 No H-bonds generated for 'chain 'B' and resid 680 through 682' Processing helix chain 'B' and resid 683 through 688 Processing helix chain 'B' and resid 689 through 701 removed outlier: 4.042A pdb=" N ASN B 701 " --> pdb=" O PHE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 718 Processing helix chain 'B' and resid 722 through 744 Proline residue: B 728 - end of helix Processing helix chain 'B' and resid 746 through 764 Processing helix chain 'B' and resid 764 through 769 Processing helix chain 'B' and resid 771 through 784 Processing helix chain 'B' and resid 792 through 810 removed outlier: 3.761A pdb=" N GLY B 810 " --> pdb=" O ALA B 806 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 815 No H-bonds generated for 'chain 'B' and resid 813 through 815' Processing helix chain 'B' and resid 816 through 829 Processing helix chain 'B' and resid 836 through 852 Processing helix chain 'B' and resid 855 through 861 Processing helix chain 'B' and resid 863 through 875 removed outlier: 3.662A pdb=" N LEU B 872 " --> pdb=" O LEU B 868 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS B 873 " --> pdb=" O LEU B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 877 through 892 Processing helix chain 'B' and resid 895 through 903 Processing helix chain 'B' and resid 934 through 941 Processing helix chain 'B' and resid 942 through 960 Proline residue: B 948 - end of helix Processing helix chain 'B' and resid 963 through 983 removed outlier: 6.944A pdb=" N THR B 969 " --> pdb=" O SER B 965 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N MET B 970 " --> pdb=" O HIS B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 988 removed outlier: 3.823A pdb=" N VAL B 987 " --> pdb=" O LEU B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1004 Proline residue: B 995 - end of helix Processing helix chain 'B' and resid 1007 through 1024 removed outlier: 3.837A pdb=" N PHE B1011 " --> pdb=" O ALA B1007 " (cutoff:3.500A) Processing helix chain 'B' and resid 1027 through 1042 removed outlier: 4.354A pdb=" N ASP B1032 " --> pdb=" O ARG B1028 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N GLU B1033 " --> pdb=" O PRO B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1064 Processing helix chain 'B' and resid 1066 through 1084 removed outlier: 4.231A pdb=" N TYR B1070 " --> pdb=" O GLU B1066 " (cutoff:3.500A) Proline residue: B1072 - end of helix Proline residue: B1076 - end of helix Processing helix chain 'B' and resid 1087 through 1089 No H-bonds generated for 'chain 'B' and resid 1087 through 1089' Processing helix chain 'B' and resid 1090 through 1104 removed outlier: 3.985A pdb=" N GLY B1104 " --> pdb=" O ILE B1100 " (cutoff:3.500A) Processing helix chain 'B' and resid 1105 through 1108 Processing helix chain 'B' and resid 1110 through 1124 Proline residue: B1116 - end of helix Processing helix chain 'B' and resid 1128 through 1146 removed outlier: 3.742A pdb=" N GLU B1144 " --> pdb=" O ASP B1140 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER B1145 " --> pdb=" O ARG B1141 " (cutoff:3.500A) Processing helix chain 'B' and resid 1151 through 1166 Proline residue: B1158 - end of helix Processing helix chain 'B' and resid 1169 through 1185 Processing helix chain 'B' and resid 1186 through 1190 removed outlier: 3.990A pdb=" N ILE B1190 " --> pdb=" O LYS B1187 " (cutoff:3.500A) Processing helix chain 'B' and resid 1191 through 1203 Processing helix chain 'B' and resid 1206 through 1219 Processing helix chain 'B' and resid 1262 through 1270 Processing helix chain 'B' and resid 1276 through 1295 Processing helix chain 'B' and resid 1297 through 1302 Processing helix chain 'B' and resid 1303 through 1310 removed outlier: 3.618A pdb=" N ALA B1309 " --> pdb=" O ALA B1305 " (cutoff:3.500A) Processing helix chain 'B' and resid 1310 through 1317 removed outlier: 3.779A pdb=" N ALA B1314 " --> pdb=" O TYR B1310 " (cutoff:3.500A) Processing helix chain 'B' and resid 1317 through 1329 Processing helix chain 'B' and resid 1331 through 1347 Processing helix chain 'B' and resid 1350 through 1367 Processing helix chain 'B' and resid 1376 through 1378 No H-bonds generated for 'chain 'B' and resid 1376 through 1378' Processing helix chain 'B' and resid 1379 through 1390 Processing helix chain 'B' and resid 1392 through 1407 Processing helix chain 'B' and resid 1409 through 1423 Processing helix chain 'B' and resid 1425 through 1441 Processing helix chain 'B' and resid 1446 through 1454 removed outlier: 4.076A pdb=" N TYR B1450 " --> pdb=" O GLN B1446 " (cutoff:3.500A) Processing helix chain 'B' and resid 1455 through 1470 Processing helix chain 'B' and resid 1473 through 1488 Processing helix chain 'B' and resid 1489 through 1500 Processing helix chain 'B' and resid 1505 through 1524 removed outlier: 4.263A pdb=" N ARG B1514 " --> pdb=" O ALA B1510 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N MET B1515 " --> pdb=" O LYS B1511 " (cutoff:3.500A) Processing helix chain 'B' and resid 1525 through 1536 removed outlier: 3.550A pdb=" N MET B1535 " --> pdb=" O GLU B1531 " (cutoff:3.500A) Processing helix chain 'B' and resid 1540 through 1554 Processing helix chain 'B' and resid 1556 through 1581 removed outlier: 4.632A pdb=" N ALA B1573 " --> pdb=" O ASP B1569 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLU B1574 " --> pdb=" O LEU B1570 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLU B1581 " --> pdb=" O ALA B1577 " (cutoff:3.500A) Processing helix chain 'B' and resid 1582 through 1608 removed outlier: 3.983A pdb=" N ALA B1586 " --> pdb=" O SER B1582 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLY B1588 " --> pdb=" O SER B1584 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ALA B1589 " --> pdb=" O ARG B1585 " (cutoff:3.500A) Processing helix chain 'B' and resid 1611 through 1626 Processing helix chain 'B' and resid 1629 through 1641 Processing helix chain 'B' and resid 1645 through 1648 Processing helix chain 'B' and resid 1649 through 1663 removed outlier: 3.990A pdb=" N TRP B1653 " --> pdb=" O ASP B1649 " (cutoff:3.500A) Processing helix chain 'B' and resid 1665 through 1678 Processing helix chain 'B' and resid 1693 through 1707 Processing helix chain 'B' and resid 1709 through 1732 Processing helix chain 'B' and resid 1737 through 1762 Processing helix chain 'B' and resid 1767 through 1783 removed outlier: 4.074A pdb=" N LYS B1771 " --> pdb=" O SER B1767 " (cutoff:3.500A) Processing helix chain 'B' and resid 1786 through 1812 removed outlier: 3.681A pdb=" N TRP B1790 " --> pdb=" O TRP B1786 " (cutoff:3.500A) Processing helix chain 'B' and resid 1868 through 1896 removed outlier: 3.592A pdb=" N VAL B1882 " --> pdb=" O LEU B1878 " (cutoff:3.500A) Proline residue: B1883 - end of helix Processing helix chain 'B' and resid 1899 through 1914 Processing helix chain 'B' and resid 1916 through 1930 Processing helix chain 'B' and resid 1932 through 1937 Processing helix chain 'B' and resid 1938 through 1945 removed outlier: 3.785A pdb=" N ARG B1945 " --> pdb=" O GLN B1941 " (cutoff:3.500A) Processing helix chain 'B' and resid 1950 through 1967 removed outlier: 3.530A pdb=" N LEU B1956 " --> pdb=" O LEU B1952 " (cutoff:3.500A) Processing helix chain 'B' and resid 1968 through 1971 Processing helix chain 'B' and resid 1972 through 1981 removed outlier: 3.662A pdb=" N LYS B1981 " --> pdb=" O THR B1977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1984 through 2002 removed outlier: 3.620A pdb=" N HIS B1988 " --> pdb=" O THR B1984 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN B1997 " --> pdb=" O LYS B1993 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU B2000 " --> pdb=" O LYS B1996 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS B2001 " --> pdb=" O ASN B1997 " (cutoff:3.500A) Processing helix chain 'B' and resid 2003 through 2021 Processing helix chain 'B' and resid 2022 through 2040 Processing helix chain 'B' and resid 2043 through 2059 Proline residue: B2053 - end of helix Processing helix chain 'B' and resid 2064 through 2074 Processing helix chain 'B' and resid 2074 through 2092 Processing helix chain 'B' and resid 2093 through 2115 removed outlier: 3.756A pdb=" N GLN B2099 " --> pdb=" O LYS B2095 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA B2100 " --> pdb=" O ASP B2096 " (cutoff:3.500A) Processing helix chain 'B' and resid 2116 through 2118 No H-bonds generated for 'chain 'B' and resid 2116 through 2118' Processing helix chain 'B' and resid 2123 through 2127 Processing helix chain 'B' and resid 2127 through 2133 removed outlier: 3.688A pdb=" N LEU B2131 " --> pdb=" O SER B2127 " (cutoff:3.500A) Processing helix chain 'B' and resid 2192 through 2212 Processing helix chain 'B' and resid 2212 through 2219 Processing helix chain 'B' and resid 2246 through 2257 Processing helix chain 'B' and resid 2262 through 2272 Processing helix chain 'B' and resid 2274 through 2278 Processing helix chain 'B' and resid 2279 through 2293 Processing helix chain 'B' and resid 2297 through 2307 Processing helix chain 'B' and resid 2309 through 2335 Processing helix chain 'B' and resid 2340 through 2342 No H-bonds generated for 'chain 'B' and resid 2340 through 2342' Processing helix chain 'B' and resid 2363 through 2368 Processing helix chain 'B' and resid 2380 through 2387 Processing helix chain 'B' and resid 2394 through 2410 Processing helix chain 'B' and resid 2410 through 2423 removed outlier: 3.692A pdb=" N PHE B2421 " --> pdb=" O VAL B2417 " (cutoff:3.500A) Processing helix chain 'B' and resid 2424 through 2426 No H-bonds generated for 'chain 'B' and resid 2424 through 2426' Processing helix chain 'B' and resid 2427 through 2435 removed outlier: 4.465A pdb=" N LEU B2431 " --> pdb=" O LEU B2427 " (cutoff:3.500A) Processing helix chain 'B' and resid 2493 through 2510 Processing helix chain 'B' and resid 2520 through 2534 Processing helix chain 'B' and resid 2534 through 2539 Processing helix chain 'B' and resid 2542 through 2546 Processing helix chain 'E' and resid 19 through 25 removed outlier: 3.861A pdb=" N ASP E 23 " --> pdb=" O ALA E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 37 Processing helix chain 'E' and resid 94 through 114 removed outlier: 3.932A pdb=" N TRP E 113 " --> pdb=" O GLN E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 141 Processing helix chain 'E' and resid 178 through 186 Processing helix chain 'E' and resid 198 through 219 removed outlier: 3.661A pdb=" N ILE E 202 " --> pdb=" O ASN E 198 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU E 218 " --> pdb=" O GLU E 214 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL E 219 " --> pdb=" O GLN E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 269 Processing helix chain 'E' and resid 269 through 279 Processing helix chain 'E' and resid 280 through 287 removed outlier: 6.021A pdb=" N CYS E 283 " --> pdb=" O MET E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 297 Processing helix chain 'E' and resid 307 through 328 Processing helix chain 'E' and resid 329 through 338 removed outlier: 3.597A pdb=" N ARG E 338 " --> pdb=" O GLN E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 359 removed outlier: 3.904A pdb=" N LEU E 352 " --> pdb=" O ARG E 348 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER E 359 " --> pdb=" O ARG E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 391 removed outlier: 3.591A pdb=" N ALA E 381 " --> pdb=" O ALA E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 398 Processing helix chain 'E' and resid 407 through 422 removed outlier: 3.857A pdb=" N MET E 422 " --> pdb=" O VAL E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 441 removed outlier: 3.883A pdb=" N LEU E 441 " --> pdb=" O LEU E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 458 Processing helix chain 'E' and resid 460 through 470 Processing helix chain 'E' and resid 472 through 479 Processing helix chain 'E' and resid 480 through 482 No H-bonds generated for 'chain 'E' and resid 480 through 482' Processing helix chain 'E' and resid 486 through 502 removed outlier: 4.698A pdb=" N LEU E 490 " --> pdb=" O GLU E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 504 through 513 removed outlier: 4.477A pdb=" N ASP E 508 " --> pdb=" O SER E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 514 through 523 Processing helix chain 'E' and resid 528 through 543 Processing helix chain 'E' and resid 546 through 556 Processing helix chain 'E' and resid 557 through 565 Processing helix chain 'E' and resid 570 through 585 removed outlier: 3.650A pdb=" N TRP E 585 " --> pdb=" O LEU E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 598 Processing helix chain 'E' and resid 599 through 605 Processing helix chain 'E' and resid 606 through 610 Processing helix chain 'E' and resid 612 through 629 removed outlier: 3.755A pdb=" N ASN E 629 " --> pdb=" O THR E 625 " (cutoff:3.500A) Processing helix chain 'E' and resid 634 through 650 removed outlier: 3.805A pdb=" N GLN E 650 " --> pdb=" O MET E 646 " (cutoff:3.500A) Processing helix chain 'E' and resid 656 through 674 Processing helix chain 'E' and resid 674 through 686 removed outlier: 3.579A pdb=" N PHE E 685 " --> pdb=" O VAL E 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 807 through 820 Processing helix chain 'E' and resid 823 through 839 removed outlier: 3.550A pdb=" N ILE E 837 " --> pdb=" O VAL E 833 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA E 838 " --> pdb=" O LEU E 834 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR E 839 " --> pdb=" O ASN E 835 " (cutoff:3.500A) Processing helix chain 'E' and resid 950 through 954 Processing helix chain 'E' and resid 958 through 969 removed outlier: 3.914A pdb=" N TYR E 966 " --> pdb=" O TRP E 962 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N PHE E 967 " --> pdb=" O SER E 963 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA E 968 " --> pdb=" O ALA E 964 " (cutoff:3.500A) Processing helix chain 'E' and resid 982 through 1008 Processing helix chain 'E' and resid 1198 through 1201 Processing helix chain 'F' and resid 19 through 25 removed outlier: 3.861A pdb=" N ASP F 23 " --> pdb=" O ALA F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 37 Processing helix chain 'F' and resid 94 through 114 removed outlier: 3.933A pdb=" N TRP F 113 " --> pdb=" O GLN F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 141 Processing helix chain 'F' and resid 178 through 186 Processing helix chain 'F' and resid 198 through 219 removed outlier: 3.661A pdb=" N ILE F 202 " --> pdb=" O ASN F 198 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU F 218 " --> pdb=" O GLU F 214 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL F 219 " --> pdb=" O GLN F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 269 Processing helix chain 'F' and resid 269 through 279 Processing helix chain 'F' and resid 280 through 287 removed outlier: 6.022A pdb=" N CYS F 283 " --> pdb=" O MET F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 297 Processing helix chain 'F' and resid 307 through 328 Processing helix chain 'F' and resid 329 through 338 removed outlier: 3.598A pdb=" N ARG F 338 " --> pdb=" O GLN F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 359 removed outlier: 3.905A pdb=" N LEU F 352 " --> pdb=" O ARG F 348 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER F 359 " --> pdb=" O ARG F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 391 removed outlier: 3.590A pdb=" N ALA F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 398 Processing helix chain 'F' and resid 407 through 422 removed outlier: 3.857A pdb=" N MET F 422 " --> pdb=" O VAL F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 441 removed outlier: 3.883A pdb=" N LEU F 441 " --> pdb=" O LEU F 437 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 458 Processing helix chain 'F' and resid 460 through 470 Processing helix chain 'F' and resid 472 through 479 Processing helix chain 'F' and resid 480 through 482 No H-bonds generated for 'chain 'F' and resid 480 through 482' Processing helix chain 'F' and resid 486 through 502 removed outlier: 4.697A pdb=" N LEU F 490 " --> pdb=" O GLU F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 504 through 513 removed outlier: 4.476A pdb=" N ASP F 508 " --> pdb=" O SER F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 523 Processing helix chain 'F' and resid 528 through 543 Processing helix chain 'F' and resid 546 through 556 Processing helix chain 'F' and resid 557 through 565 Processing helix chain 'F' and resid 570 through 585 removed outlier: 3.650A pdb=" N TRP F 585 " --> pdb=" O LEU F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 598 Processing helix chain 'F' and resid 599 through 605 Processing helix chain 'F' and resid 606 through 610 Processing helix chain 'F' and resid 612 through 629 removed outlier: 3.756A pdb=" N ASN F 629 " --> pdb=" O THR F 625 " (cutoff:3.500A) Processing helix chain 'F' and resid 634 through 650 removed outlier: 3.805A pdb=" N GLN F 650 " --> pdb=" O MET F 646 " (cutoff:3.500A) Processing helix chain 'F' and resid 656 through 674 Processing helix chain 'F' and resid 674 through 686 removed outlier: 3.578A pdb=" N PHE F 685 " --> pdb=" O VAL F 681 " (cutoff:3.500A) Processing helix chain 'F' and resid 807 through 820 Processing helix chain 'F' and resid 823 through 839 removed outlier: 3.549A pdb=" N ILE F 837 " --> pdb=" O VAL F 833 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA F 838 " --> pdb=" O LEU F 834 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR F 839 " --> pdb=" O ASN F 835 " (cutoff:3.500A) Processing helix chain 'F' and resid 950 through 954 Processing helix chain 'F' and resid 958 through 969 removed outlier: 3.914A pdb=" N TYR F 966 " --> pdb=" O TRP F 962 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N PHE F 967 " --> pdb=" O SER F 963 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA F 968 " --> pdb=" O ALA F 964 " (cutoff:3.500A) Processing helix chain 'F' and resid 982 through 1008 Processing helix chain 'F' and resid 1198 through 1201 Processing sheet with id=AA1, first strand: chain 'A' and resid 2120 through 2122 Processing sheet with id=AA2, first strand: chain 'A' and resid 2153 through 2156 removed outlier: 6.919A pdb=" N MET A2175 " --> pdb=" O GLN A2154 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ILE A2156 " --> pdb=" O THR A2173 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N THR A2173 " --> pdb=" O ILE A2156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2243 through 2245 Processing sheet with id=AA4, first strand: chain 'B' and resid 2120 through 2122 Processing sheet with id=AA5, first strand: chain 'B' and resid 2153 through 2156 removed outlier: 6.920A pdb=" N MET B2175 " --> pdb=" O GLN B2154 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ILE B2156 " --> pdb=" O THR B2173 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N THR B2173 " --> pdb=" O ILE B2156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 2243 through 2245 Processing sheet with id=AA7, first strand: chain 'C' and resid 15 through 18 removed outlier: 3.918A pdb=" N LEU C 15 " --> pdb=" O TRP C 27 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 47 through 50 removed outlier: 3.780A pdb=" N ILE C 79 " --> pdb=" O MET C 67 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 88 through 91 removed outlier: 7.105A pdb=" N GLY C 103 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL C 91 " --> pdb=" O TYR C 101 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TYR C 101 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLY C 104 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N THR C 108 " --> pdb=" O GLY C 104 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG C 123 " --> pdb=" O ILE C 111 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 134 through 136 Processing sheet with id=AB2, first strand: chain 'C' and resid 173 through 178 removed outlier: 3.550A pdb=" N SER C 175 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N CYS C 194 " --> pdb=" O LYS C 215 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LYS C 215 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL C 196 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 226 through 228 removed outlier: 3.828A pdb=" N THR C 256 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG C 248 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU C 254 " --> pdb=" O ARG C 248 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 277 through 278 removed outlier: 3.653A pdb=" N ARG C 306 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N CYS C 298 " --> pdb=" O ILE C 304 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE C 304 " --> pdb=" O CYS C 298 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 15 through 18 removed outlier: 3.919A pdb=" N LEU D 15 " --> pdb=" O TRP D 27 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 47 through 50 removed outlier: 3.779A pdb=" N ILE D 79 " --> pdb=" O MET D 67 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 88 through 91 removed outlier: 7.105A pdb=" N GLY D 103 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL D 91 " --> pdb=" O TYR D 101 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TYR D 101 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLY D 104 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N THR D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG D 123 " --> pdb=" O ILE D 111 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 134 through 136 Processing sheet with id=AB9, first strand: chain 'D' and resid 173 through 178 removed outlier: 3.550A pdb=" N SER D 175 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N CYS D 194 " --> pdb=" O LYS D 215 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N LYS D 215 " --> pdb=" O CYS D 194 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL D 196 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 226 through 228 removed outlier: 3.827A pdb=" N THR D 256 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG D 248 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU D 254 " --> pdb=" O ARG D 248 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 277 through 278 removed outlier: 3.653A pdb=" N ARG D 306 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N CYS D 298 " --> pdb=" O ILE D 304 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE D 304 " --> pdb=" O CYS D 298 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 118 through 123 removed outlier: 6.888A pdb=" N SER E 59 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N HIS E 149 " --> pdb=" O SER E 59 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ALA E 61 " --> pdb=" O HIS E 149 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ASN E 151 " --> pdb=" O ALA E 61 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N VAL E 63 " --> pdb=" O ASN E 151 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL E 146 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL E 193 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N PHE E 148 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ASP E 195 " --> pdb=" O PHE E 148 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N TYR E 150 " --> pdb=" O ASP E 195 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 166 through 167 Processing sheet with id=AC5, first strand: chain 'E' and resid 1015 through 1021 removed outlier: 4.096A pdb=" N ASP E1015 " --> pdb=" O SER E1329 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER E1329 " --> pdb=" O ASP E1015 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL E1327 " --> pdb=" O ILE E1017 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU E1019 " --> pdb=" O ILE E1325 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE E1325 " --> pdb=" O LEU E1019 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER E1326 " --> pdb=" O VAL E1318 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N CYS E1306 " --> pdb=" O GLY E1319 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 1028 through 1031 removed outlier: 3.706A pdb=" N VAL E1028 " --> pdb=" O ALA E1041 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE E1048 " --> pdb=" O ASP E1058 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASP E1058 " --> pdb=" O PHE E1048 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 1070 through 1074 removed outlier: 3.933A pdb=" N ALA E1072 " --> pdb=" O ALA E1087 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA E1087 " --> pdb=" O ALA E1072 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA E1092 " --> pdb=" O THR E1088 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE E1093 " --> pdb=" O ALA E1111 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA E1111 " --> pdb=" O ILE E1093 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL E1095 " --> pdb=" O VAL E1109 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 1127 through 1129 removed outlier: 3.525A pdb=" N ARG E1148 " --> pdb=" O SER E1140 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY E1142 " --> pdb=" O ILE E1146 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE E1146 " --> pdb=" O GLY E1142 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N VAL E1147 " --> pdb=" O ASP E1160 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP E1160 " --> pdb=" O VAL E1147 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE E1149 " --> pdb=" O VAL E1158 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET E1156 " --> pdb=" O ASP E1151 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 1169 through 1173 removed outlier: 3.691A pdb=" N SER E1171 " --> pdb=" O GLY E1184 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ILE E1190 " --> pdb=" O THR E1206 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N THR E1206 " --> pdb=" O ILE E1190 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N VAL E1192 " --> pdb=" O VAL E1204 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 1214 through 1219 removed outlier: 7.222A pdb=" N VAL E1230 " --> pdb=" O VAL E1215 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ALA E1217 " --> pdb=" O VAL E1228 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N VAL E1228 " --> pdb=" O ALA E1217 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER E1231 " --> pdb=" O ASP E1235 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ASP E1235 " --> pdb=" O SER E1231 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN E1248 " --> pdb=" O ILE E1238 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 1259 through 1261 removed outlier: 6.924A pdb=" N ASN E1281 " --> pdb=" O LEU E1286 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU E1286 " --> pdb=" O ASN E1281 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 118 through 123 removed outlier: 6.888A pdb=" N SER F 59 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N HIS F 149 " --> pdb=" O SER F 59 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ALA F 61 " --> pdb=" O HIS F 149 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ASN F 151 " --> pdb=" O ALA F 61 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N VAL F 63 " --> pdb=" O ASN F 151 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL F 146 " --> pdb=" O ILE F 191 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N VAL F 193 " --> pdb=" O VAL F 146 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N PHE F 148 " --> pdb=" O VAL F 193 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ASP F 195 " --> pdb=" O PHE F 148 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N TYR F 150 " --> pdb=" O ASP F 195 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 166 through 167 Processing sheet with id=AD5, first strand: chain 'F' and resid 1015 through 1021 removed outlier: 4.095A pdb=" N ASP F1015 " --> pdb=" O SER F1329 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER F1329 " --> pdb=" O ASP F1015 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL F1327 " --> pdb=" O ILE F1017 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU F1019 " --> pdb=" O ILE F1325 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE F1325 " --> pdb=" O LEU F1019 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER F1326 " --> pdb=" O VAL F1318 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N CYS F1306 " --> pdb=" O GLY F1319 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 1028 through 1031 removed outlier: 3.705A pdb=" N VAL F1028 " --> pdb=" O ALA F1041 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE F1048 " --> pdb=" O ASP F1058 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASP F1058 " --> pdb=" O PHE F1048 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 1070 through 1074 removed outlier: 3.933A pdb=" N ALA F1072 " --> pdb=" O ALA F1087 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA F1087 " --> pdb=" O ALA F1072 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA F1092 " --> pdb=" O THR F1088 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE F1093 " --> pdb=" O ALA F1111 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA F1111 " --> pdb=" O ILE F1093 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL F1095 " --> pdb=" O VAL F1109 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 1127 through 1129 removed outlier: 3.526A pdb=" N ARG F1148 " --> pdb=" O SER F1140 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY F1142 " --> pdb=" O ILE F1146 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE F1146 " --> pdb=" O GLY F1142 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N VAL F1147 " --> pdb=" O ASP F1160 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASP F1160 " --> pdb=" O VAL F1147 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE F1149 " --> pdb=" O VAL F1158 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET F1156 " --> pdb=" O ASP F1151 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 1169 through 1173 removed outlier: 3.692A pdb=" N SER F1171 " --> pdb=" O GLY F1184 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ILE F1190 " --> pdb=" O THR F1206 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N THR F1206 " --> pdb=" O ILE F1190 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL F1192 " --> pdb=" O VAL F1204 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 1214 through 1219 removed outlier: 7.222A pdb=" N VAL F1230 " --> pdb=" O VAL F1215 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ALA F1217 " --> pdb=" O VAL F1228 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL F1228 " --> pdb=" O ALA F1217 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER F1231 " --> pdb=" O ASP F1235 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ASP F1235 " --> pdb=" O SER F1231 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN F1248 " --> pdb=" O ILE F1238 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 1259 through 1261 removed outlier: 6.924A pdb=" N ASN F1281 " --> pdb=" O LEU F1286 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LEU F1286 " --> pdb=" O ASN F1281 " (cutoff:3.500A) 3390 hydrogen bonds defined for protein. 9942 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: 28.32 Time building geometry restraints manager: 13.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 18708 1.34 - 1.46: 12553 1.46 - 1.58: 26183 1.58 - 1.70: 12 1.70 - 1.81: 604 Bond restraints: 58060 Sorted by residual: bond pdb=" O12 IHP B2601 " pdb=" P2 IHP B2601 " ideal model delta sigma weight residual 1.675 1.596 0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" O12 IHP A2601 " pdb=" P2 IHP A2601 " ideal model delta sigma weight residual 1.675 1.597 0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" O14 IHP A2601 " pdb=" P4 IHP A2601 " ideal model delta sigma weight residual 1.671 1.601 0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" O14 IHP B2601 " pdb=" P4 IHP B2601 " ideal model delta sigma weight residual 1.671 1.601 0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" O15 IHP B2601 " pdb=" P5 IHP B2601 " ideal model delta sigma weight residual 1.675 1.621 0.054 2.00e-02 2.50e+03 7.24e+00 ... (remaining 58055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 77343 1.53 - 3.05: 1145 3.05 - 4.58: 192 4.58 - 6.11: 86 6.11 - 7.63: 12 Bond angle restraints: 78778 Sorted by residual: angle pdb=" N ILE C 260 " pdb=" CA ILE C 260 " pdb=" C ILE C 260 " ideal model delta sigma weight residual 111.88 108.49 3.39 1.06e+00 8.90e-01 1.02e+01 angle pdb=" N ILE D 260 " pdb=" CA ILE D 260 " pdb=" C ILE D 260 " ideal model delta sigma weight residual 111.88 108.50 3.38 1.06e+00 8.90e-01 1.01e+01 angle pdb=" C ASN A1330 " pdb=" N GLU A1331 " pdb=" CA GLU A1331 " ideal model delta sigma weight residual 121.54 127.44 -5.90 1.91e+00 2.74e-01 9.55e+00 angle pdb=" C ASN B1330 " pdb=" N GLU B1331 " pdb=" CA GLU B1331 " ideal model delta sigma weight residual 121.54 127.43 -5.89 1.91e+00 2.74e-01 9.52e+00 angle pdb=" C VAL A1882 " pdb=" CA VAL A1882 " pdb=" CB VAL A1882 " ideal model delta sigma weight residual 113.70 111.28 2.42 9.50e-01 1.11e+00 6.50e+00 ... (remaining 78773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 32210 17.92 - 35.84: 2202 35.84 - 53.76: 531 53.76 - 71.68: 103 71.68 - 89.61: 44 Dihedral angle restraints: 35090 sinusoidal: 14186 harmonic: 20904 Sorted by residual: dihedral pdb=" CA ASP A1332 " pdb=" C ASP A1332 " pdb=" N GLN A1333 " pdb=" CA GLN A1333 " ideal model delta harmonic sigma weight residual 180.00 163.72 16.28 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA ASP B1332 " pdb=" C ASP B1332 " pdb=" N GLN B1333 " pdb=" CA GLN B1333 " ideal model delta harmonic sigma weight residual 180.00 163.73 16.27 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA VAL B 993 " pdb=" C VAL B 993 " pdb=" N MET B 994 " pdb=" CA MET B 994 " ideal model delta harmonic sigma weight residual -180.00 -163.98 -16.02 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 35087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 7996 0.061 - 0.123: 901 0.123 - 0.184: 43 0.184 - 0.246: 0 0.246 - 0.307: 4 Chirality restraints: 8944 Sorted by residual: chirality pdb=" C1 IHP B2601 " pdb=" C2 IHP B2601 " pdb=" C6 IHP B2601 " pdb=" O11 IHP B2601 " both_signs ideal model delta sigma weight residual False 2.32 2.62 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C1 IHP A2601 " pdb=" C2 IHP A2601 " pdb=" C6 IHP A2601 " pdb=" O11 IHP A2601 " both_signs ideal model delta sigma weight residual False 2.32 2.62 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" C3 IHP B2601 " pdb=" C2 IHP B2601 " pdb=" C4 IHP B2601 " pdb=" O13 IHP B2601 " both_signs ideal model delta sigma weight residual False -2.34 -2.59 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 8941 not shown) Planarity restraints: 10028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B2003 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.07e+00 pdb=" C ASN B2003 " 0.043 2.00e-02 2.50e+03 pdb=" O ASN B2003 " -0.016 2.00e-02 2.50e+03 pdb=" N THR B2004 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A2003 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.03e+00 pdb=" C ASN A2003 " -0.042 2.00e-02 2.50e+03 pdb=" O ASN A2003 " 0.016 2.00e-02 2.50e+03 pdb=" N THR A2004 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A1116 " 0.037 5.00e-02 4.00e+02 5.65e-02 5.10e+00 pdb=" N PRO A1117 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A1117 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A1117 " 0.032 5.00e-02 4.00e+02 ... (remaining 10025 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1241 2.71 - 3.26: 59694 3.26 - 3.80: 95484 3.80 - 4.35: 116319 4.35 - 4.90: 194912 Nonbonded interactions: 467650 Sorted by model distance: nonbonded pdb=" NH2 ARG F 660 " pdb=" O ALA F1111 " model vdw 2.161 3.120 nonbonded pdb=" NH2 ARG E 660 " pdb=" O ALA E1111 " model vdw 2.162 3.120 nonbonded pdb=" OG SER C 229 " pdb=" OD1 ASP C 231 " model vdw 2.183 3.040 nonbonded pdb=" OG SER D 229 " pdb=" OD1 ASP D 231 " model vdw 2.184 3.040 nonbonded pdb=" OG1 THR F 126 " pdb=" OD1 ASP F 128 " model vdw 2.202 3.040 ... (remaining 467645 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } 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: 8.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 1.800 Check model and map are aligned: 0.330 Set scattering table: 0.440 Process input model: 150.160 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.210 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:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 164.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 58060 Z= 0.177 Angle : 0.513 7.632 78778 Z= 0.265 Chirality : 0.039 0.307 8944 Planarity : 0.004 0.056 10028 Dihedral : 13.418 89.606 21462 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.68 % Favored : 97.29 % Rotamer: Outliers : 1.65 % Allowed : 8.66 % Favored : 89.68 % 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: 2.01 (0.10), residues: 7024 helix: 2.47 (0.08), residues: 4306 sheet: -0.85 (0.21), residues: 654 loop : -0.38 (0.15), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 816 HIS 0.003 0.001 HIS F 601 PHE 0.019 0.001 PHE A 610 TYR 0.013 0.001 TYR E 517 ARG 0.004 0.000 ARG E 532 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 6270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 509 time to evaluate : 4.989 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: A 671 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.7992 (tp) REVERT: A 727 MET cc_start: 0.8626 (tpp) cc_final: 0.8078 (mmt) REVERT: A 756 MET cc_start: 0.8797 (mmt) cc_final: 0.8486 (mmt) REVERT: A 824 ILE cc_start: 0.9385 (tp) cc_final: 0.9158 (tp) REVERT: A 826 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.8050 (m-30) REVERT: A 883 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8085 (mm-30) REVERT: A 1031 MET cc_start: 0.9309 (tpt) cc_final: 0.9046 (tpt) REVERT: A 1174 MET cc_start: 0.7408 (tpp) cc_final: 0.6819 (tpp) REVERT: A 1437 MET cc_start: 0.8684 (mtt) cc_final: 0.8298 (mmm) REVERT: A 1590 MET cc_start: 0.8891 (mmm) cc_final: 0.8504 (mmm) REVERT: A 1624 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7961 (mp10) REVERT: A 1747 MET cc_start: 0.8325 (tpp) cc_final: 0.7685 (tpp) REVERT: A 1796 MET cc_start: 0.8780 (mmm) cc_final: 0.8569 (tpp) REVERT: A 2010 MET cc_start: 0.9123 (mmm) cc_final: 0.8800 (mmm) REVERT: A 2387 MET cc_start: 0.7707 (mtp) cc_final: 0.7444 (mtp) REVERT: A 2498 ILE cc_start: 0.7218 (mm) cc_final: 0.6887 (pt) REVERT: A 2540 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7172 (mp-120) REVERT: B 123 MET cc_start: 0.0702 (tpp) cc_final: 0.0207 (tmm) REVERT: B 671 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7955 (tp) REVERT: B 727 MET cc_start: 0.8605 (tpp) cc_final: 0.8053 (mmt) REVERT: B 756 MET cc_start: 0.8802 (mmt) cc_final: 0.8519 (mmt) REVERT: B 824 ILE cc_start: 0.9387 (tp) cc_final: 0.9138 (tp) REVERT: B 826 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8067 (m-30) REVERT: B 883 GLU cc_start: 0.8307 (mm-30) cc_final: 0.8057 (mm-30) REVERT: B 1031 MET cc_start: 0.9313 (tpt) cc_final: 0.9052 (tpt) REVERT: B 1174 MET cc_start: 0.7408 (tpp) cc_final: 0.6815 (tpp) REVERT: B 1437 MET cc_start: 0.8680 (mtt) cc_final: 0.8293 (mmm) REVERT: B 1484 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8954 (mm) REVERT: B 1590 MET cc_start: 0.8902 (mmm) cc_final: 0.8513 (mmm) REVERT: B 1624 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7953 (mp10) REVERT: B 1747 MET cc_start: 0.8257 (tpp) cc_final: 0.7620 (tpp) REVERT: B 1796 MET cc_start: 0.8790 (mmm) cc_final: 0.8589 (tpp) REVERT: B 2010 MET cc_start: 0.9121 (mmm) cc_final: 0.8797 (mmm) REVERT: B 2387 MET cc_start: 0.7696 (mtp) cc_final: 0.7431 (mtp) REVERT: B 2498 ILE cc_start: 0.7309 (mm) cc_final: 0.6996 (pt) REVERT: B 2540 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7167 (mp-120) REVERT: C 170 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8703 (mp0) REVERT: C 211 ILE cc_start: 0.9631 (mp) cc_final: 0.9245 (mp) REVERT: C 274 TRP cc_start: 0.6702 (OUTLIER) cc_final: 0.6097 (p90) REVERT: C 292 ASN cc_start: 0.8059 (OUTLIER) cc_final: 0.7668 (m-40) REVERT: C 305 LYS cc_start: 0.8631 (mmmm) cc_final: 0.8212 (mmmm) REVERT: D 170 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8699 (mp0) REVERT: D 211 ILE cc_start: 0.9636 (mp) cc_final: 0.9234 (mp) REVERT: D 274 TRP cc_start: 0.6541 (OUTLIER) cc_final: 0.6098 (p90) REVERT: D 292 ASN cc_start: 0.8041 (OUTLIER) cc_final: 0.7646 (m-40) REVERT: D 305 LYS cc_start: 0.8633 (mmmm) cc_final: 0.8150 (mmmm) REVERT: E 59 SER cc_start: 0.6652 (t) cc_final: 0.6446 (m) REVERT: E 170 ASN cc_start: 0.8232 (p0) cc_final: 0.8021 (p0) REVERT: E 502 ASP cc_start: 0.7230 (t0) cc_final: 0.6899 (t0) REVERT: E 534 MET cc_start: 0.8614 (mtm) cc_final: 0.7925 (ptm) REVERT: E 646 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7155 (mmp) REVERT: E 1064 ASN cc_start: 0.3378 (OUTLIER) cc_final: 0.1632 (p0) REVERT: E 1073 MET cc_start: 0.8349 (mtm) cc_final: 0.7550 (mtm) REVERT: E 1108 MET cc_start: 0.8988 (tmm) cc_final: 0.8726 (tpp) REVERT: E 1127 MET cc_start: 0.5563 (tpp) cc_final: 0.4042 (tmm) REVERT: E 1323 TYR cc_start: 0.8689 (OUTLIER) cc_final: 0.8302 (m-80) REVERT: E 1330 VAL cc_start: 0.7180 (OUTLIER) cc_final: 0.6741 (t) REVERT: F 502 ASP cc_start: 0.7241 (t0) cc_final: 0.6904 (t0) REVERT: F 534 MET cc_start: 0.8616 (mtm) cc_final: 0.7928 (ptm) REVERT: F 646 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7167 (mmp) REVERT: F 1064 ASN cc_start: 0.3393 (OUTLIER) cc_final: 0.1642 (p0) REVERT: F 1073 MET cc_start: 0.8348 (mtm) cc_final: 0.7552 (mtm) REVERT: F 1108 MET cc_start: 0.8991 (tmm) cc_final: 0.8727 (tpp) REVERT: F 1127 MET cc_start: 0.5657 (tpp) cc_final: 0.3963 (tmm) REVERT: F 1323 TYR cc_start: 0.8688 (OUTLIER) cc_final: 0.8301 (m-80) REVERT: F 1330 VAL cc_start: 0.7170 (OUTLIER) cc_final: 0.6731 (t) outliers start: 102 outliers final: 17 residues processed: 577 average time/residue: 0.5581 time to fit residues: 546.6104 Evaluate side-chains 430 residues out of total 6270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 392 time to evaluate : 4.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 825 MET Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1220 TYR Chi-restraints excluded: chain A residue 1311 ASN Chi-restraints excluded: chain A residue 1372 LEU Chi-restraints excluded: chain A residue 1624 GLN Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2540 GLN Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain B residue 826 ASP Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1220 TYR Chi-restraints excluded: chain B residue 1311 ASN Chi-restraints excluded: chain B residue 1372 LEU Chi-restraints excluded: chain B residue 1484 LEU Chi-restraints excluded: chain B residue 1624 GLN Chi-restraints excluded: chain B residue 2303 LEU Chi-restraints excluded: chain B residue 2540 GLN Chi-restraints excluded: chain C residue 274 TRP Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain D residue 274 TRP Chi-restraints excluded: chain D residue 292 ASN Chi-restraints excluded: chain E residue 257 ASP Chi-restraints excluded: chain E residue 551 GLU Chi-restraints excluded: chain E residue 646 MET Chi-restraints excluded: chain E residue 1064 ASN Chi-restraints excluded: chain E residue 1323 TYR Chi-restraints excluded: chain E residue 1330 VAL Chi-restraints excluded: chain F residue 257 ASP Chi-restraints excluded: chain F residue 551 GLU Chi-restraints excluded: chain F residue 646 MET Chi-restraints excluded: chain F residue 1064 ASN Chi-restraints excluded: chain F residue 1323 TYR Chi-restraints excluded: chain F residue 1330 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 599 optimal weight: 5.9990 chunk 538 optimal weight: 1.9990 chunk 298 optimal weight: 0.0070 chunk 183 optimal weight: 3.9990 chunk 363 optimal weight: 0.3980 chunk 287 optimal weight: 0.8980 chunk 556 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 338 optimal weight: 2.9990 chunk 414 optimal weight: 0.9990 chunk 644 optimal weight: 0.8980 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 HIS A 703 GLN ** A 968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2194 GLN ** A2428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 HIS B 703 GLN ** B 968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2194 GLN ** B2428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1022 ASN ** E1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1064 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1064 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 58060 Z= 0.187 Angle : 0.560 9.831 78778 Z= 0.279 Chirality : 0.040 0.192 8944 Planarity : 0.004 0.054 10028 Dihedral : 5.016 65.605 7869 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.82 % Favored : 97.15 % Rotamer: Outliers : 1.44 % Allowed : 12.09 % Favored : 86.47 % 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: 1.87 (0.10), residues: 7024 helix: 2.32 (0.08), residues: 4302 sheet: -0.87 (0.21), residues: 686 loop : -0.33 (0.14), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 576 HIS 0.011 0.001 HIS F 978 PHE 0.021 0.001 PHE A1122 TYR 0.017 0.001 TYR D 184 ARG 0.009 0.000 ARG F 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 6270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 408 time to evaluate : 4.993 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: A 615 HIS cc_start: 0.7525 (t-170) cc_final: 0.7310 (t-170) REVERT: A 671 ILE cc_start: 0.8243 (tt) cc_final: 0.8001 (tp) REVERT: A 727 MET cc_start: 0.8621 (tpp) cc_final: 0.8059 (mmt) REVERT: A 756 MET cc_start: 0.8863 (mmt) cc_final: 0.8365 (mmt) REVERT: A 994 MET cc_start: 0.9269 (mmm) cc_final: 0.9018 (mmm) REVERT: A 1174 MET cc_start: 0.7356 (tpp) cc_final: 0.6697 (tpp) REVERT: A 1200 VAL cc_start: 0.8862 (t) cc_final: 0.8596 (p) REVERT: A 1437 MET cc_start: 0.8569 (mtt) cc_final: 0.8325 (mmm) REVERT: A 1578 MET cc_start: 0.9093 (tpp) cc_final: 0.8865 (tpp) REVERT: A 1624 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7995 (mp10) REVERT: A 1638 MET cc_start: 0.7999 (tpp) cc_final: 0.7389 (tpp) REVERT: A 1747 MET cc_start: 0.8156 (tpp) cc_final: 0.7404 (tpp) REVERT: A 2010 MET cc_start: 0.9241 (mmm) cc_final: 0.8888 (mmm) REVERT: A 2387 MET cc_start: 0.7437 (mtp) cc_final: 0.7019 (mtp) REVERT: A 2432 MET cc_start: 0.6974 (mmp) cc_final: 0.6184 (ptt) REVERT: A 2498 ILE cc_start: 0.7402 (mm) cc_final: 0.6986 (pt) REVERT: A 2540 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7219 (mp-120) REVERT: B 123 MET cc_start: 0.1186 (tpp) cc_final: 0.0973 (tmm) REVERT: B 615 HIS cc_start: 0.7517 (t-170) cc_final: 0.7306 (t-170) REVERT: B 671 ILE cc_start: 0.8195 (tt) cc_final: 0.7960 (tp) REVERT: B 727 MET cc_start: 0.8598 (tpp) cc_final: 0.8037 (mmt) REVERT: B 756 MET cc_start: 0.8866 (mmt) cc_final: 0.8365 (mmt) REVERT: B 994 MET cc_start: 0.9296 (mmm) cc_final: 0.9057 (mmm) REVERT: B 1174 MET cc_start: 0.7360 (tpp) cc_final: 0.6695 (tpp) REVERT: B 1437 MET cc_start: 0.8586 (mtt) cc_final: 0.8320 (mmm) REVERT: B 1578 MET cc_start: 0.9067 (tpp) cc_final: 0.8846 (tpp) REVERT: B 1624 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7968 (mp10) REVERT: B 1638 MET cc_start: 0.8064 (tpp) cc_final: 0.7493 (tpp) REVERT: B 1747 MET cc_start: 0.8159 (tpp) cc_final: 0.7388 (tpp) REVERT: B 2010 MET cc_start: 0.9239 (mmm) cc_final: 0.8884 (mmm) REVERT: B 2387 MET cc_start: 0.7428 (mtp) cc_final: 0.7009 (mtp) REVERT: B 2432 MET cc_start: 0.6961 (mmp) cc_final: 0.6172 (ptt) REVERT: B 2498 ILE cc_start: 0.7454 (mm) cc_final: 0.7053 (pt) REVERT: B 2540 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7227 (mp-120) REVERT: C 170 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8685 (mp0) REVERT: C 274 TRP cc_start: 0.6241 (OUTLIER) cc_final: 0.5711 (p90) REVERT: C 292 ASN cc_start: 0.7888 (OUTLIER) cc_final: 0.7468 (m-40) REVERT: D 170 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8685 (mp0) REVERT: D 274 TRP cc_start: 0.6361 (OUTLIER) cc_final: 0.5812 (p90) REVERT: D 292 ASN cc_start: 0.7949 (OUTLIER) cc_final: 0.7605 (m-40) REVERT: E 170 ASN cc_start: 0.8109 (p0) cc_final: 0.7822 (p0) REVERT: E 172 THR cc_start: 0.7406 (p) cc_final: 0.7004 (p) REVERT: E 211 LEU cc_start: 0.8307 (mt) cc_final: 0.7715 (tp) REVERT: E 502 ASP cc_start: 0.7467 (t0) cc_final: 0.7123 (t0) REVERT: E 534 MET cc_start: 0.8629 (mtm) cc_final: 0.8284 (ttm) REVERT: E 646 MET cc_start: 0.8073 (mmm) cc_final: 0.7393 (mmp) REVERT: E 1073 MET cc_start: 0.8469 (mtm) cc_final: 0.7803 (mtm) REVERT: E 1127 MET cc_start: 0.4853 (tpp) cc_final: 0.4101 (tmm) REVERT: E 1197 MET cc_start: 0.8104 (pmm) cc_final: 0.7854 (pmm) REVERT: E 1323 TYR cc_start: 0.8740 (OUTLIER) cc_final: 0.8360 (m-80) REVERT: F 211 LEU cc_start: 0.8310 (mt) cc_final: 0.7719 (tp) REVERT: F 502 ASP cc_start: 0.7476 (t0) cc_final: 0.7131 (t0) REVERT: F 534 MET cc_start: 0.8630 (mtm) cc_final: 0.8282 (ttm) REVERT: F 646 MET cc_start: 0.8021 (mmm) cc_final: 0.7347 (mmp) REVERT: F 1073 MET cc_start: 0.8486 (mtm) cc_final: 0.7816 (mtm) REVERT: F 1127 MET cc_start: 0.4860 (tpp) cc_final: 0.4086 (tmm) REVERT: F 1197 MET cc_start: 0.8111 (pmm) cc_final: 0.7844 (pmm) REVERT: F 1323 TYR cc_start: 0.8735 (OUTLIER) cc_final: 0.8420 (m-80) outliers start: 89 outliers final: 29 residues processed: 476 average time/residue: 0.5963 time to fit residues: 488.9286 Evaluate side-chains 408 residues out of total 6270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 369 time to evaluate : 4.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 609 HIS Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1311 ASN Chi-restraints excluded: chain A residue 1372 LEU Chi-restraints excluded: chain A residue 1624 GLN Chi-restraints excluded: chain A residue 1946 ILE Chi-restraints excluded: chain A residue 2280 LEU Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2540 GLN Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 609 HIS Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 826 ASP Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1311 ASN Chi-restraints excluded: chain B residue 1372 LEU Chi-restraints excluded: chain B residue 1484 LEU Chi-restraints excluded: chain B residue 1624 GLN Chi-restraints excluded: chain B residue 1946 ILE Chi-restraints excluded: chain B residue 2280 LEU Chi-restraints excluded: chain B residue 2303 LEU Chi-restraints excluded: chain B residue 2540 GLN Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 274 TRP Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 274 TRP Chi-restraints excluded: chain D residue 292 ASN Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 551 GLU Chi-restraints excluded: chain E residue 1011 THR Chi-restraints excluded: chain E residue 1323 TYR Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 266 CYS Chi-restraints excluded: chain F residue 551 GLU Chi-restraints excluded: chain F residue 1011 THR Chi-restraints excluded: chain F residue 1323 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 358 optimal weight: 0.0370 chunk 200 optimal weight: 0.4980 chunk 536 optimal weight: 1.9990 chunk 439 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 645 optimal weight: 0.8980 chunk 697 optimal weight: 3.9990 chunk 575 optimal weight: 20.0000 chunk 640 optimal weight: 1.9990 chunk 220 optimal weight: 50.0000 chunk 518 optimal weight: 0.9990 overall best weight: 0.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 HIS ** A1808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2071 ASN A2223 GLN ** A2428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2071 ASN B2223 GLN ** B2428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1248 ASN ** F 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1248 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 58060 Z= 0.205 Angle : 0.549 8.003 78778 Z= 0.276 Chirality : 0.040 0.179 8944 Planarity : 0.004 0.055 10028 Dihedral : 4.798 65.182 7838 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.86 % Favored : 97.11 % Rotamer: Outliers : 2.00 % Allowed : 11.71 % Favored : 86.29 % 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: 1.75 (0.10), residues: 7024 helix: 2.20 (0.08), residues: 4314 sheet: -0.81 (0.20), residues: 674 loop : -0.36 (0.14), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B2084 HIS 0.012 0.001 HIS F 978 PHE 0.021 0.001 PHE A1122 TYR 0.016 0.001 TYR D 20 ARG 0.012 0.000 ARG E1012 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 6270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 401 time to evaluate : 5.011 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 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: A 727 MET cc_start: 0.8619 (tpp) cc_final: 0.7897 (mmt) REVERT: A 767 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8445 (tm) REVERT: A 826 ASP cc_start: 0.8636 (OUTLIER) cc_final: 0.8359 (m-30) REVERT: A 956 MET cc_start: 0.9027 (mmt) cc_final: 0.8640 (mmm) REVERT: A 994 MET cc_start: 0.9264 (mmm) cc_final: 0.8791 (mmm) REVERT: A 1109 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.8171 (t0) REVERT: A 1174 MET cc_start: 0.7399 (tpp) cc_final: 0.6943 (tpp) REVERT: A 1194 MET cc_start: 0.7122 (ppp) cc_final: 0.6564 (ppp) REVERT: A 1196 ASN cc_start: 0.8483 (m-40) cc_final: 0.8225 (t0) REVERT: A 1200 VAL cc_start: 0.8871 (t) cc_final: 0.8627 (p) REVERT: A 1437 MET cc_start: 0.8614 (mtt) cc_final: 0.8376 (mmm) REVERT: A 1442 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7608 (tm-30) REVERT: A 1581 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.7825 (pm20) REVERT: A 1595 MET cc_start: 0.8605 (mmm) cc_final: 0.8057 (mmt) REVERT: A 1624 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7929 (mp10) REVERT: A 1638 MET cc_start: 0.8353 (tpp) cc_final: 0.7670 (tpp) REVERT: A 1704 MET cc_start: 0.8638 (ttt) cc_final: 0.8268 (tmm) REVERT: A 1712 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.8203 (p0) REVERT: A 1747 MET cc_start: 0.8089 (tpp) cc_final: 0.7366 (tpp) REVERT: A 2010 MET cc_start: 0.9207 (mmm) cc_final: 0.8794 (mmm) REVERT: A 2048 PHE cc_start: 0.9245 (m-80) cc_final: 0.9036 (m-80) REVERT: A 2387 MET cc_start: 0.7515 (mtp) cc_final: 0.6980 (mtp) REVERT: A 2498 ILE cc_start: 0.7480 (mm) cc_final: 0.7002 (pt) REVERT: A 2540 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7640 (mp-120) REVERT: B 123 MET cc_start: 0.1276 (tpp) cc_final: 0.1057 (tmm) REVERT: B 727 MET cc_start: 0.8616 (tpp) cc_final: 0.7898 (mmt) REVERT: B 767 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8433 (tm) REVERT: B 826 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8370 (m-30) REVERT: B 956 MET cc_start: 0.9030 (mmt) cc_final: 0.8642 (mmm) REVERT: B 994 MET cc_start: 0.9265 (mmm) cc_final: 0.8790 (mmm) REVERT: B 1109 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8173 (t0) REVERT: B 1174 MET cc_start: 0.7397 (tpp) cc_final: 0.6923 (tpp) REVERT: B 1437 MET cc_start: 0.8608 (mtt) cc_final: 0.8372 (mmm) REVERT: B 1442 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7612 (tm-30) REVERT: B 1477 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7785 (tpp) REVERT: B 1578 MET cc_start: 0.9043 (tpp) cc_final: 0.8839 (tpp) REVERT: B 1581 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7823 (pm20) REVERT: B 1590 MET cc_start: 0.8961 (mmm) cc_final: 0.8588 (mmm) REVERT: B 1595 MET cc_start: 0.8608 (mmm) cc_final: 0.8057 (mmt) REVERT: B 1624 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7922 (mp10) REVERT: B 1638 MET cc_start: 0.8387 (tpp) cc_final: 0.7688 (tpp) REVERT: B 1704 MET cc_start: 0.8651 (ttt) cc_final: 0.8279 (tmm) REVERT: B 1712 ASP cc_start: 0.8502 (OUTLIER) cc_final: 0.8200 (p0) REVERT: B 1747 MET cc_start: 0.8071 (tpp) cc_final: 0.7342 (tpp) REVERT: B 2010 MET cc_start: 0.9203 (mmm) cc_final: 0.8789 (mmm) REVERT: B 2048 PHE cc_start: 0.9249 (m-80) cc_final: 0.9043 (m-80) REVERT: B 2387 MET cc_start: 0.7492 (mtp) cc_final: 0.6953 (mtp) REVERT: B 2498 ILE cc_start: 0.7471 (mm) cc_final: 0.7012 (pt) REVERT: B 2540 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8142 (mm110) REVERT: C 170 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8696 (mp0) REVERT: C 274 TRP cc_start: 0.6416 (OUTLIER) cc_final: 0.5712 (p90) REVERT: C 292 ASN cc_start: 0.7770 (OUTLIER) cc_final: 0.7321 (m-40) REVERT: D 170 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8677 (mp0) REVERT: D 274 TRP cc_start: 0.6420 (OUTLIER) cc_final: 0.5863 (p90) REVERT: D 292 ASN cc_start: 0.7825 (OUTLIER) cc_final: 0.7467 (m-40) REVERT: E 502 ASP cc_start: 0.7559 (t0) cc_final: 0.7295 (t0) REVERT: E 646 MET cc_start: 0.8088 (mmm) cc_final: 0.7457 (mmp) REVERT: E 1073 MET cc_start: 0.8444 (mtm) cc_final: 0.7774 (mtm) REVERT: E 1127 MET cc_start: 0.4865 (tpp) cc_final: 0.4096 (tmm) REVERT: E 1197 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7931 (pmm) REVERT: E 1323 TYR cc_start: 0.8758 (OUTLIER) cc_final: 0.8434 (m-80) REVERT: F 502 ASP cc_start: 0.7571 (t0) cc_final: 0.7307 (t0) REVERT: F 646 MET cc_start: 0.8081 (mmm) cc_final: 0.7452 (mmp) REVERT: F 1073 MET cc_start: 0.8453 (mtm) cc_final: 0.7781 (mtm) REVERT: F 1127 MET cc_start: 0.5051 (tpp) cc_final: 0.4326 (tmm) REVERT: F 1197 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7908 (pmm) REVERT: F 1323 TYR cc_start: 0.8771 (OUTLIER) cc_final: 0.8446 (m-80) outliers start: 123 outliers final: 40 residues processed: 506 average time/residue: 0.5257 time to fit residues: 461.3936 Evaluate side-chains 440 residues out of total 6270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 377 time to evaluate : 4.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 609 HIS Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 1004 CYS Chi-restraints excluded: chain A residue 1109 ASP Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1220 TYR Chi-restraints excluded: chain A residue 1372 LEU Chi-restraints excluded: chain A residue 1465 LYS Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1581 GLU Chi-restraints excluded: chain A residue 1624 GLN Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1712 ASP Chi-restraints excluded: chain A residue 1946 ILE Chi-restraints excluded: chain A residue 2000 GLU Chi-restraints excluded: chain A residue 2007 GLN Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2329 MET Chi-restraints excluded: chain A residue 2540 GLN Chi-restraints excluded: chain B residue 609 HIS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 826 ASP Chi-restraints excluded: chain B residue 1004 CYS Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1220 TYR Chi-restraints excluded: chain B residue 1372 LEU Chi-restraints excluded: chain B residue 1465 LYS Chi-restraints excluded: chain B residue 1477 MET Chi-restraints excluded: chain B residue 1484 LEU Chi-restraints excluded: chain B residue 1581 GLU Chi-restraints excluded: chain B residue 1624 GLN Chi-restraints excluded: chain B residue 1637 LEU Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1712 ASP Chi-restraints excluded: chain B residue 1946 ILE Chi-restraints excluded: chain B residue 2007 GLN Chi-restraints excluded: chain B residue 2303 LEU Chi-restraints excluded: chain B residue 2329 MET Chi-restraints excluded: chain B residue 2540 GLN Chi-restraints excluded: chain C residue 274 TRP Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain D residue 274 TRP Chi-restraints excluded: chain D residue 292 ASN Chi-restraints excluded: chain E residue 279 CYS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 1011 THR Chi-restraints excluded: chain E residue 1197 MET Chi-restraints excluded: chain E residue 1323 TYR Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 279 CYS Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 1011 THR Chi-restraints excluded: chain F residue 1197 MET Chi-restraints excluded: chain F residue 1323 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 638 optimal weight: 1.9990 chunk 485 optimal weight: 3.9990 chunk 335 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 308 optimal weight: 0.9990 chunk 433 optimal weight: 0.8980 chunk 648 optimal weight: 0.7980 chunk 686 optimal weight: 0.8980 chunk 338 optimal weight: 0.7980 chunk 614 optimal weight: 0.9990 chunk 184 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 937 ASN ** A1808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2428 ASN B 937 ASN ** B1808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2428 ASN ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 58060 Z= 0.196 Angle : 0.548 9.982 78778 Z= 0.275 Chirality : 0.040 0.214 8944 Planarity : 0.004 0.057 10028 Dihedral : 4.710 63.125 7828 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.78 % Favored : 97.20 % Rotamer: Outliers : 2.08 % Allowed : 12.82 % Favored : 85.11 % 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: 1.76 (0.10), residues: 7024 helix: 2.20 (0.08), residues: 4296 sheet: -0.75 (0.20), residues: 666 loop : -0.34 (0.14), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B2084 HIS 0.007 0.001 HIS B 968 PHE 0.022 0.001 PHE B 610 TYR 0.021 0.001 TYR D 184 ARG 0.004 0.000 ARG E 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 6270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 383 time to evaluate : 4.974 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 revert: symmetry clash REVERT: A 727 MET cc_start: 0.8611 (tpp) cc_final: 0.7761 (mmt) REVERT: A 756 MET cc_start: 0.9101 (mmt) cc_final: 0.8850 (mmm) REVERT: A 767 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.8454 (tm) REVERT: A 994 MET cc_start: 0.9294 (mmm) cc_final: 0.8846 (mmm) REVERT: A 1004 CYS cc_start: 0.7345 (OUTLIER) cc_final: 0.5833 (p) REVERT: A 1109 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.8234 (t0) REVERT: A 1119 VAL cc_start: 0.7902 (OUTLIER) cc_final: 0.7665 (p) REVERT: A 1194 MET cc_start: 0.7389 (ppp) cc_final: 0.6788 (ppp) REVERT: A 1364 MET cc_start: 0.9197 (mmm) cc_final: 0.8923 (mmm) REVERT: A 1437 MET cc_start: 0.8576 (mtt) cc_final: 0.8340 (mmm) REVERT: A 1515 MET cc_start: 0.9003 (mtt) cc_final: 0.8606 (mtt) REVERT: A 1525 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.8640 (mp10) REVERT: A 1581 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7828 (pm20) REVERT: A 1590 MET cc_start: 0.8991 (mmm) cc_final: 0.8341 (mmm) REVERT: A 1624 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7990 (mp10) REVERT: A 1638 MET cc_start: 0.8516 (tpp) cc_final: 0.7822 (tpp) REVERT: A 1666 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8231 (mt) REVERT: A 1704 MET cc_start: 0.8658 (ttt) cc_final: 0.8280 (tmm) REVERT: A 1712 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8260 (p0) REVERT: A 1730 HIS cc_start: 0.8819 (p-80) cc_final: 0.8563 (p90) REVERT: A 1747 MET cc_start: 0.8070 (tpp) cc_final: 0.7309 (tpp) REVERT: A 2010 MET cc_start: 0.9243 (mmm) cc_final: 0.8806 (mmm) REVERT: A 2387 MET cc_start: 0.7495 (mtp) cc_final: 0.6959 (mtp) REVERT: A 2392 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7445 (mt) REVERT: A 2432 MET cc_start: 0.6799 (mmp) cc_final: 0.6128 (ptt) REVERT: A 2498 ILE cc_start: 0.7603 (mm) cc_final: 0.7115 (pt) REVERT: A 2540 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7752 (mp-120) REVERT: B 123 MET cc_start: 0.1585 (tpp) cc_final: 0.1322 (tmm) REVERT: B 727 MET cc_start: 0.8614 (tpp) cc_final: 0.7769 (mmt) REVERT: B 756 MET cc_start: 0.9104 (mmt) cc_final: 0.8850 (mmm) REVERT: B 767 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8452 (tm) REVERT: B 994 MET cc_start: 0.9298 (mmm) cc_final: 0.8844 (mmm) REVERT: B 1004 CYS cc_start: 0.7353 (OUTLIER) cc_final: 0.5850 (p) REVERT: B 1109 ASP cc_start: 0.8612 (OUTLIER) cc_final: 0.8233 (t0) REVERT: B 1119 VAL cc_start: 0.7909 (OUTLIER) cc_final: 0.7671 (p) REVERT: B 1174 MET cc_start: 0.7325 (tpp) cc_final: 0.6933 (tpp) REVERT: B 1196 ASN cc_start: 0.8564 (m-40) cc_final: 0.8151 (t0) REVERT: B 1364 MET cc_start: 0.9191 (mmm) cc_final: 0.8892 (mmm) REVERT: B 1437 MET cc_start: 0.8571 (mtt) cc_final: 0.8335 (mmm) REVERT: B 1477 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7860 (tpp) REVERT: B 1515 MET cc_start: 0.9003 (mtt) cc_final: 0.8613 (mtt) REVERT: B 1525 GLN cc_start: 0.9184 (OUTLIER) cc_final: 0.8635 (mp10) REVERT: B 1581 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.7821 (pm20) REVERT: B 1590 MET cc_start: 0.9003 (mmm) cc_final: 0.8709 (mmm) REVERT: B 1624 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7982 (mp10) REVERT: B 1638 MET cc_start: 0.8524 (tpp) cc_final: 0.7826 (tpp) REVERT: B 1666 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8173 (mt) REVERT: B 1704 MET cc_start: 0.8666 (ttt) cc_final: 0.8289 (tmm) REVERT: B 1712 ASP cc_start: 0.8556 (OUTLIER) cc_final: 0.8255 (p0) REVERT: B 1730 HIS cc_start: 0.8824 (p-80) cc_final: 0.8519 (p90) REVERT: B 1747 MET cc_start: 0.8067 (tpp) cc_final: 0.7304 (tpp) REVERT: B 2010 MET cc_start: 0.9239 (mmm) cc_final: 0.8800 (mmm) REVERT: B 2387 MET cc_start: 0.7486 (mtp) cc_final: 0.6950 (mtp) REVERT: B 2392 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7441 (mt) REVERT: B 2432 MET cc_start: 0.6783 (mmp) cc_final: 0.6118 (ptt) REVERT: B 2498 ILE cc_start: 0.7591 (mm) cc_final: 0.7106 (pt) REVERT: B 2540 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.7780 (mp-120) REVERT: C 170 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8707 (mp0) REVERT: C 178 ILE cc_start: 0.5510 (OUTLIER) cc_final: 0.5286 (tt) REVERT: D 170 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8716 (mp0) REVERT: D 178 ILE cc_start: 0.5528 (OUTLIER) cc_final: 0.5304 (tt) REVERT: E 534 MET cc_start: 0.8717 (mtm) cc_final: 0.8325 (ttm) REVERT: E 646 MET cc_start: 0.8172 (mmm) cc_final: 0.7588 (mmp) REVERT: E 1073 MET cc_start: 0.8406 (mtm) cc_final: 0.7774 (mtm) REVERT: E 1127 MET cc_start: 0.5007 (tpp) cc_final: 0.4541 (tmm) REVERT: E 1197 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7893 (pmm) REVERT: E 1243 MET cc_start: 0.8006 (ptm) cc_final: 0.7436 (ptp) REVERT: F 534 MET cc_start: 0.8716 (mtm) cc_final: 0.8324 (ttm) REVERT: F 646 MET cc_start: 0.8129 (mmm) cc_final: 0.7509 (mmp) REVERT: F 1073 MET cc_start: 0.8410 (mtm) cc_final: 0.7776 (mtm) REVERT: F 1127 MET cc_start: 0.5000 (tpp) cc_final: 0.4519 (tmm) REVERT: F 1197 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7865 (pmm) REVERT: F 1243 MET cc_start: 0.7997 (ptm) cc_final: 0.7428 (ptp) REVERT: F 1323 TYR cc_start: 0.8718 (OUTLIER) cc_final: 0.8359 (m-80) outliers start: 128 outliers final: 57 residues processed: 495 average time/residue: 0.5218 time to fit residues: 450.3077 Evaluate side-chains 448 residues out of total 6270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 363 time to evaluate : 4.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 609 HIS Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 1004 CYS Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1109 ASP Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1220 TYR Chi-restraints excluded: chain A residue 1311 ASN Chi-restraints excluded: chain A residue 1372 LEU Chi-restraints excluded: chain A residue 1477 MET Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1525 GLN Chi-restraints excluded: chain A residue 1581 GLU Chi-restraints excluded: chain A residue 1624 GLN Chi-restraints excluded: chain A residue 1629 ILE Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1712 ASP Chi-restraints excluded: chain A residue 1946 ILE Chi-restraints excluded: chain A residue 2000 GLU Chi-restraints excluded: chain A residue 2007 GLN Chi-restraints excluded: chain A residue 2280 LEU Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2329 MET Chi-restraints excluded: chain A residue 2392 LEU Chi-restraints excluded: chain A residue 2533 THR Chi-restraints excluded: chain A residue 2540 GLN Chi-restraints excluded: chain B residue 609 HIS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 826 ASP Chi-restraints excluded: chain B residue 1004 CYS Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1220 TYR Chi-restraints excluded: chain B residue 1311 ASN Chi-restraints excluded: chain B residue 1372 LEU Chi-restraints excluded: chain B residue 1477 MET Chi-restraints excluded: chain B residue 1484 LEU Chi-restraints excluded: chain B residue 1525 GLN Chi-restraints excluded: chain B residue 1581 GLU Chi-restraints excluded: chain B residue 1624 GLN Chi-restraints excluded: chain B residue 1629 ILE Chi-restraints excluded: chain B residue 1637 LEU Chi-restraints excluded: chain B residue 1639 VAL Chi-restraints excluded: chain B residue 1666 LEU Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1712 ASP Chi-restraints excluded: chain B residue 1946 ILE Chi-restraints excluded: chain B residue 2000 GLU Chi-restraints excluded: chain B residue 2007 GLN Chi-restraints excluded: chain B residue 2280 LEU Chi-restraints excluded: chain B residue 2303 LEU Chi-restraints excluded: chain B residue 2329 MET Chi-restraints excluded: chain B residue 2392 LEU Chi-restraints excluded: chain B residue 2533 THR Chi-restraints excluded: chain B residue 2540 GLN Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 274 TRP Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 274 TRP Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 279 CYS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 551 GLU Chi-restraints excluded: chain E residue 1011 THR Chi-restraints excluded: chain E residue 1197 MET Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 266 CYS Chi-restraints excluded: chain F residue 279 CYS Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 551 GLU Chi-restraints excluded: chain F residue 1011 THR Chi-restraints excluded: chain F residue 1197 MET Chi-restraints excluded: chain F residue 1323 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 571 optimal weight: 4.9990 chunk 389 optimal weight: 0.9980 chunk 9 optimal weight: 30.0000 chunk 510 optimal weight: 7.9990 chunk 283 optimal weight: 0.8980 chunk 585 optimal weight: 0.0670 chunk 474 optimal weight: 6.9990 chunk 0 optimal weight: 70.0000 chunk 350 optimal weight: 0.7980 chunk 615 optimal weight: 7.9990 chunk 173 optimal weight: 2.9990 overall best weight: 1.1520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2515 HIS ** B1808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2189 HIS B2515 HIS C 161 HIS ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 HIS E 114 GLN E 149 HIS E 326 ASN ** E 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 GLN F 149 HIS ** F 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 58060 Z= 0.239 Angle : 0.581 9.872 78778 Z= 0.290 Chirality : 0.041 0.258 8944 Planarity : 0.004 0.057 10028 Dihedral : 4.720 62.402 7822 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.93 % Favored : 97.02 % Rotamer: Outliers : 2.53 % Allowed : 13.08 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.10), residues: 7024 helix: 2.12 (0.08), residues: 4302 sheet: -0.72 (0.20), residues: 680 loop : -0.29 (0.14), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2084 HIS 0.008 0.001 HIS B 968 PHE 0.022 0.001 PHE B1122 TYR 0.016 0.001 TYR B 897 ARG 0.007 0.000 ARG C 248 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 6270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 371 time to evaluate : 5.017 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: A 727 MET cc_start: 0.8640 (tpp) cc_final: 0.7790 (mmt) REVERT: A 767 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.8486 (tm) REVERT: A 956 MET cc_start: 0.9035 (mmt) cc_final: 0.8602 (mmm) REVERT: A 994 MET cc_start: 0.9338 (mmm) cc_final: 0.8777 (mmm) REVERT: A 1004 CYS cc_start: 0.7626 (OUTLIER) cc_final: 0.6128 (p) REVERT: A 1031 MET cc_start: 0.9359 (tpt) cc_final: 0.8889 (tpt) REVERT: A 1109 ASP cc_start: 0.8701 (OUTLIER) cc_final: 0.8392 (t0) REVERT: A 1119 VAL cc_start: 0.8028 (OUTLIER) cc_final: 0.7815 (p) REVERT: A 1174 MET cc_start: 0.7238 (tpp) cc_final: 0.6695 (tpp) REVERT: A 1194 MET cc_start: 0.7710 (ppp) cc_final: 0.7380 (ppp) REVERT: A 1364 MET cc_start: 0.9238 (mmm) cc_final: 0.8928 (mmm) REVERT: A 1437 MET cc_start: 0.8594 (mtt) cc_final: 0.8393 (mmm) REVERT: A 1467 MET cc_start: 0.8339 (mmm) cc_final: 0.8126 (mmt) REVERT: A 1581 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.7827 (pm20) REVERT: A 1624 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7902 (mp10) REVERT: A 1638 MET cc_start: 0.8638 (tpp) cc_final: 0.8168 (tpp) REVERT: A 1666 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8233 (mt) REVERT: A 1704 MET cc_start: 0.8619 (ttt) cc_final: 0.8287 (tmm) REVERT: A 1712 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.8292 (p0) REVERT: A 1747 MET cc_start: 0.8177 (tpp) cc_final: 0.7470 (tpp) REVERT: A 1796 MET cc_start: 0.8656 (mmm) cc_final: 0.8240 (tpp) REVERT: A 2010 MET cc_start: 0.9194 (mmm) cc_final: 0.8804 (mmm) REVERT: A 2387 MET cc_start: 0.7731 (mtp) cc_final: 0.7260 (mtp) REVERT: A 2392 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7451 (mt) REVERT: A 2432 MET cc_start: 0.6906 (mmp) cc_final: 0.6113 (ptt) REVERT: A 2540 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.7889 (mp10) REVERT: B 123 MET cc_start: 0.1754 (tpp) cc_final: 0.1463 (tmm) REVERT: B 727 MET cc_start: 0.8646 (tpp) cc_final: 0.7794 (mmt) REVERT: B 767 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.8483 (tm) REVERT: B 824 ILE cc_start: 0.9340 (tp) cc_final: 0.9139 (tp) REVERT: B 825 MET cc_start: 0.8629 (mtm) cc_final: 0.8384 (mtm) REVERT: B 956 MET cc_start: 0.9032 (mmt) cc_final: 0.8604 (mmm) REVERT: B 994 MET cc_start: 0.9339 (mmm) cc_final: 0.8788 (mmm) REVERT: B 1004 CYS cc_start: 0.7632 (OUTLIER) cc_final: 0.6136 (p) REVERT: B 1031 MET cc_start: 0.9368 (tpt) cc_final: 0.8706 (tpt) REVERT: B 1109 ASP cc_start: 0.8706 (OUTLIER) cc_final: 0.8394 (t0) REVERT: B 1119 VAL cc_start: 0.8030 (OUTLIER) cc_final: 0.7819 (p) REVERT: B 1364 MET cc_start: 0.9237 (mmm) cc_final: 0.8934 (mmm) REVERT: B 1467 MET cc_start: 0.8345 (mmm) cc_final: 0.8140 (mmt) REVERT: B 1477 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8146 (tpp) REVERT: B 1581 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.7809 (pm20) REVERT: B 1590 MET cc_start: 0.8998 (mmm) cc_final: 0.8781 (mmm) REVERT: B 1624 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7897 (mp10) REVERT: B 1638 MET cc_start: 0.8641 (tpp) cc_final: 0.8172 (tpp) REVERT: B 1666 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8310 (mt) REVERT: B 1704 MET cc_start: 0.8627 (ttt) cc_final: 0.8290 (tmm) REVERT: B 1712 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8389 (p0) REVERT: B 1747 MET cc_start: 0.8173 (tpp) cc_final: 0.7463 (tpp) REVERT: B 1796 MET cc_start: 0.8652 (mmm) cc_final: 0.8237 (tpp) REVERT: B 1996 LYS cc_start: 0.9012 (mmtt) cc_final: 0.8695 (mmtm) REVERT: B 2000 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8146 (pt0) REVERT: B 2010 MET cc_start: 0.9159 (mmm) cc_final: 0.8776 (mmm) REVERT: B 2387 MET cc_start: 0.7720 (mtp) cc_final: 0.7248 (mtp) REVERT: B 2392 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7450 (mt) REVERT: B 2432 MET cc_start: 0.6897 (mmp) cc_final: 0.6106 (ptt) REVERT: B 2540 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.7890 (mp10) REVERT: C 170 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8720 (mp0) REVERT: C 274 TRP cc_start: 0.6392 (OUTLIER) cc_final: 0.5803 (p90) REVERT: C 292 ASN cc_start: 0.8335 (OUTLIER) cc_final: 0.7861 (m-40) REVERT: D 170 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8724 (mp0) REVERT: D 274 TRP cc_start: 0.6384 (OUTLIER) cc_final: 0.5809 (p90) REVERT: D 292 ASN cc_start: 0.8311 (OUTLIER) cc_final: 0.7842 (m-40) REVERT: E 211 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.7940 (tp) REVERT: E 453 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9221 (tt) REVERT: E 646 MET cc_start: 0.8288 (mmm) cc_final: 0.7707 (mmp) REVERT: E 1073 MET cc_start: 0.8085 (mtm) cc_final: 0.7379 (mtm) REVERT: E 1127 MET cc_start: 0.4997 (tpp) cc_final: 0.4598 (tmm) REVERT: E 1197 MET cc_start: 0.8166 (pmm) cc_final: 0.7865 (pmm) REVERT: E 1243 MET cc_start: 0.7735 (ptm) cc_final: 0.7486 (ptp) REVERT: F 211 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.7997 (tp) REVERT: F 453 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9219 (tt) REVERT: F 646 MET cc_start: 0.8458 (mmm) cc_final: 0.7758 (mmp) REVERT: F 1073 MET cc_start: 0.8115 (mtm) cc_final: 0.7418 (mtm) REVERT: F 1127 MET cc_start: 0.5133 (tpp) cc_final: 0.4528 (tmm) REVERT: F 1197 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7901 (pmm) REVERT: F 1243 MET cc_start: 0.7736 (ptm) cc_final: 0.7488 (ptp) REVERT: F 1323 TYR cc_start: 0.8682 (OUTLIER) cc_final: 0.8307 (m-80) outliers start: 156 outliers final: 68 residues processed: 508 average time/residue: 0.5262 time to fit residues: 466.4542 Evaluate side-chains 449 residues out of total 6270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 349 time to evaluate : 4.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 609 HIS Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 1004 CYS Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1109 ASP Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1196 ASN Chi-restraints excluded: chain A residue 1220 TYR Chi-restraints excluded: chain A residue 1311 ASN Chi-restraints excluded: chain A residue 1372 LEU Chi-restraints excluded: chain A residue 1465 LYS Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1581 GLU Chi-restraints excluded: chain A residue 1624 GLN Chi-restraints excluded: chain A residue 1629 ILE Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1712 ASP Chi-restraints excluded: chain A residue 1946 ILE Chi-restraints excluded: chain A residue 1973 ILE Chi-restraints excluded: chain A residue 2000 GLU Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2280 LEU Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2329 MET Chi-restraints excluded: chain A residue 2392 LEU Chi-restraints excluded: chain A residue 2533 THR Chi-restraints excluded: chain A residue 2540 GLN Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 609 HIS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 826 ASP Chi-restraints excluded: chain B residue 1004 CYS Chi-restraints excluded: chain B residue 1075 ILE Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1220 TYR Chi-restraints excluded: chain B residue 1311 ASN Chi-restraints excluded: chain B residue 1372 LEU Chi-restraints excluded: chain B residue 1465 LYS Chi-restraints excluded: chain B residue 1477 MET Chi-restraints excluded: chain B residue 1484 LEU Chi-restraints excluded: chain B residue 1575 LEU Chi-restraints excluded: chain B residue 1581 GLU Chi-restraints excluded: chain B residue 1624 GLN Chi-restraints excluded: chain B residue 1629 ILE Chi-restraints excluded: chain B residue 1637 LEU Chi-restraints excluded: chain B residue 1639 VAL Chi-restraints excluded: chain B residue 1666 LEU Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1712 ASP Chi-restraints excluded: chain B residue 1946 ILE Chi-restraints excluded: chain B residue 1973 ILE Chi-restraints excluded: chain B residue 2000 GLU Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2280 LEU Chi-restraints excluded: chain B residue 2303 LEU Chi-restraints excluded: chain B residue 2329 MET Chi-restraints excluded: chain B residue 2333 ILE Chi-restraints excluded: chain B residue 2392 LEU Chi-restraints excluded: chain B residue 2533 THR Chi-restraints excluded: chain B residue 2540 GLN Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 274 TRP Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 274 TRP Chi-restraints excluded: chain D residue 292 ASN Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 279 CYS Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 551 GLU Chi-restraints excluded: chain E residue 1035 THR Chi-restraints excluded: chain E residue 1182 VAL Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 266 CYS Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 453 LEU Chi-restraints excluded: chain F residue 551 GLU Chi-restraints excluded: chain F residue 1035 THR Chi-restraints excluded: chain F residue 1182 VAL Chi-restraints excluded: chain F residue 1197 MET Chi-restraints excluded: chain F residue 1323 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 230 optimal weight: 7.9990 chunk 618 optimal weight: 0.9990 chunk 135 optimal weight: 0.5980 chunk 402 optimal weight: 10.0000 chunk 169 optimal weight: 0.9980 chunk 686 optimal weight: 3.9990 chunk 570 optimal weight: 0.9990 chunk 318 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 227 optimal weight: 20.0000 chunk 360 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1807 GLN A1989 ASN A1992 ASN A2024 HIS A2189 HIS A2515 HIS B1206 HIS ** B1725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1989 ASN B2515 HIS ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 326 ASN ** F 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1022 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 58060 Z= 0.199 Angle : 0.565 10.074 78778 Z= 0.280 Chirality : 0.040 0.236 8944 Planarity : 0.004 0.057 10028 Dihedral : 4.697 62.677 7822 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.89 % Favored : 97.07 % Rotamer: Outliers : 1.98 % Allowed : 14.02 % Favored : 84.00 % 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: 1.73 (0.10), residues: 7024 helix: 2.14 (0.08), residues: 4300 sheet: -0.66 (0.21), residues: 662 loop : -0.32 (0.14), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 576 HIS 0.017 0.001 HIS A1730 PHE 0.023 0.001 PHE A1122 TYR 0.022 0.001 TYR C 184 ARG 0.011 0.000 ARG A1811 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 6270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 360 time to evaluate : 4.978 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: A 727 MET cc_start: 0.8609 (tpp) cc_final: 0.7789 (mmt) REVERT: A 756 MET cc_start: 0.9248 (mmt) cc_final: 0.8997 (mmm) REVERT: A 767 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.8557 (tm) REVERT: A 994 MET cc_start: 0.9368 (mmm) cc_final: 0.8874 (mmm) REVERT: A 1097 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8343 (mp) REVERT: A 1109 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.8359 (t0) REVERT: A 1174 MET cc_start: 0.7249 (tpp) cc_final: 0.6731 (tpp) REVERT: A 1194 MET cc_start: 0.7722 (ppp) cc_final: 0.7422 (ppp) REVERT: A 1364 MET cc_start: 0.9258 (mmm) cc_final: 0.9039 (mmm) REVERT: A 1437 MET cc_start: 0.8583 (mtt) cc_final: 0.8383 (mmm) REVERT: A 1515 MET cc_start: 0.8942 (mtm) cc_final: 0.8521 (mtt) REVERT: A 1578 MET cc_start: 0.9079 (tpp) cc_final: 0.8833 (tpp) REVERT: A 1581 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.7844 (pm20) REVERT: A 1595 MET cc_start: 0.8544 (mmm) cc_final: 0.8116 (mmt) REVERT: A 1624 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7879 (mp10) REVERT: A 1638 MET cc_start: 0.8667 (tpp) cc_final: 0.8198 (tpp) REVERT: A 1666 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8315 (mt) REVERT: A 1704 MET cc_start: 0.8641 (ttt) cc_final: 0.8359 (tmm) REVERT: A 1712 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8393 (p0) REVERT: A 1747 MET cc_start: 0.8208 (tpp) cc_final: 0.7508 (tpp) REVERT: A 2010 MET cc_start: 0.9187 (mmm) cc_final: 0.8773 (mmm) REVERT: A 2047 MET cc_start: 0.7493 (mmm) cc_final: 0.7218 (mmt) REVERT: A 2432 MET cc_start: 0.6930 (mmp) cc_final: 0.6157 (ptt) REVERT: A 2540 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.7875 (mp10) REVERT: B 123 MET cc_start: 0.1992 (tpp) cc_final: 0.1789 (tmm) REVERT: B 727 MET cc_start: 0.8613 (tpp) cc_final: 0.7792 (mmt) REVERT: B 756 MET cc_start: 0.9248 (mmt) cc_final: 0.8994 (mmm) REVERT: B 767 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.8494 (tm) REVERT: B 994 MET cc_start: 0.9380 (mmm) cc_final: 0.8881 (mmm) REVERT: B 1031 MET cc_start: 0.9376 (tpt) cc_final: 0.8725 (tpt) REVERT: B 1097 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8244 (mp) REVERT: B 1109 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8353 (t0) REVERT: B 1364 MET cc_start: 0.9234 (mmm) cc_final: 0.8939 (mmm) REVERT: B 1477 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8084 (tpp) REVERT: B 1581 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.7830 (pm20) REVERT: B 1595 MET cc_start: 0.8551 (mmm) cc_final: 0.8115 (mmt) REVERT: B 1624 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7871 (mp10) REVERT: B 1638 MET cc_start: 0.8673 (tpp) cc_final: 0.8200 (tpp) REVERT: B 1666 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8315 (mt) REVERT: B 1704 MET cc_start: 0.8652 (ttt) cc_final: 0.8325 (tmm) REVERT: B 1712 ASP cc_start: 0.8636 (OUTLIER) cc_final: 0.8388 (p0) REVERT: B 1747 MET cc_start: 0.8206 (tpp) cc_final: 0.7504 (tpp) REVERT: B 2010 MET cc_start: 0.9219 (mmm) cc_final: 0.8794 (mmm) REVERT: B 2047 MET cc_start: 0.7481 (mmm) cc_final: 0.7207 (mmt) REVERT: B 2432 MET cc_start: 0.6917 (mmp) cc_final: 0.6150 (ptt) REVERT: B 2540 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.7867 (mp10) REVERT: C 170 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8694 (mp0) REVERT: C 255 MET cc_start: 0.9137 (pmm) cc_final: 0.8875 (pmm) REVERT: C 274 TRP cc_start: 0.6341 (OUTLIER) cc_final: 0.5721 (p90) REVERT: C 292 ASN cc_start: 0.8321 (OUTLIER) cc_final: 0.7856 (m-40) REVERT: D 170 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8731 (mp0) REVERT: D 274 TRP cc_start: 0.6329 (OUTLIER) cc_final: 0.5722 (p90) REVERT: D 292 ASN cc_start: 0.8354 (OUTLIER) cc_final: 0.7932 (m-40) REVERT: E 211 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.7917 (tp) REVERT: E 453 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9209 (tt) REVERT: E 534 MET cc_start: 0.8583 (mtm) cc_final: 0.8191 (ttm) REVERT: E 646 MET cc_start: 0.8485 (mmm) cc_final: 0.7899 (mmp) REVERT: E 1073 MET cc_start: 0.8074 (mtm) cc_final: 0.7394 (mtm) REVERT: E 1127 MET cc_start: 0.5059 (tpp) cc_final: 0.4544 (tmm) REVERT: E 1197 MET cc_start: 0.8205 (pmm) cc_final: 0.7916 (pmm) REVERT: E 1243 MET cc_start: 0.8036 (ptm) cc_final: 0.7811 (ptt) REVERT: F 211 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.7920 (tp) REVERT: F 453 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9211 (tt) REVERT: F 534 MET cc_start: 0.8583 (mtm) cc_final: 0.8191 (ttm) REVERT: F 646 MET cc_start: 0.8482 (mmm) cc_final: 0.7897 (mmp) REVERT: F 1073 MET cc_start: 0.8116 (mtm) cc_final: 0.7438 (mtm) REVERT: F 1127 MET cc_start: 0.5161 (tpp) cc_final: 0.4532 (tmm) REVERT: F 1197 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7894 (pmm) REVERT: F 1243 MET cc_start: 0.8033 (ptm) cc_final: 0.7807 (ptt) REVERT: F 1323 TYR cc_start: 0.8704 (OUTLIER) cc_final: 0.8489 (m-80) outliers start: 122 outliers final: 63 residues processed: 463 average time/residue: 0.5333 time to fit residues: 429.9871 Evaluate side-chains 436 residues out of total 6270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 346 time to evaluate : 4.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 609 HIS Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1109 ASP Chi-restraints excluded: chain A residue 1196 ASN Chi-restraints excluded: chain A residue 1220 TYR Chi-restraints excluded: chain A residue 1311 ASN Chi-restraints excluded: chain A residue 1372 LEU Chi-restraints excluded: chain A residue 1465 LYS Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1581 GLU Chi-restraints excluded: chain A residue 1624 GLN Chi-restraints excluded: chain A residue 1629 ILE Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1712 ASP Chi-restraints excluded: chain A residue 1946 ILE Chi-restraints excluded: chain A residue 2003 ASN Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2280 LEU Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2329 MET Chi-restraints excluded: chain A residue 2333 ILE Chi-restraints excluded: chain A residue 2533 THR Chi-restraints excluded: chain A residue 2540 GLN Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 609 HIS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 683 PHE Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 826 ASP Chi-restraints excluded: chain B residue 1075 ILE Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1220 TYR Chi-restraints excluded: chain B residue 1311 ASN Chi-restraints excluded: chain B residue 1372 LEU Chi-restraints excluded: chain B residue 1465 LYS Chi-restraints excluded: chain B residue 1477 MET Chi-restraints excluded: chain B residue 1484 LEU Chi-restraints excluded: chain B residue 1581 GLU Chi-restraints excluded: chain B residue 1624 GLN Chi-restraints excluded: chain B residue 1629 ILE Chi-restraints excluded: chain B residue 1637 LEU Chi-restraints excluded: chain B residue 1639 VAL Chi-restraints excluded: chain B residue 1666 LEU Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1712 ASP Chi-restraints excluded: chain B residue 1946 ILE Chi-restraints excluded: chain B residue 2000 GLU Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2280 LEU Chi-restraints excluded: chain B residue 2303 LEU Chi-restraints excluded: chain B residue 2329 MET Chi-restraints excluded: chain B residue 2533 THR Chi-restraints excluded: chain B residue 2540 GLN Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 274 TRP Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 274 TRP Chi-restraints excluded: chain D residue 292 ASN Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 279 CYS Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 551 GLU Chi-restraints excluded: chain E residue 1182 VAL Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 266 CYS Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 453 LEU Chi-restraints excluded: chain F residue 551 GLU Chi-restraints excluded: chain F residue 1182 VAL Chi-restraints excluded: chain F residue 1197 MET Chi-restraints excluded: chain F residue 1323 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 662 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 391 optimal weight: 0.9990 chunk 501 optimal weight: 0.8980 chunk 388 optimal weight: 0.6980 chunk 578 optimal weight: 20.0000 chunk 383 optimal weight: 0.9990 chunk 684 optimal weight: 2.9990 chunk 428 optimal weight: 0.9980 chunk 417 optimal weight: 0.7980 chunk 315 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1206 HIS ** A1725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2124 GLN A2515 HIS ** B1725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2024 HIS B2124 GLN B2515 HIS ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 58060 Z= 0.195 Angle : 0.570 10.977 78778 Z= 0.280 Chirality : 0.040 0.218 8944 Planarity : 0.004 0.066 10028 Dihedral : 4.668 62.612 7820 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.83 % Favored : 97.12 % Rotamer: Outliers : 2.29 % Allowed : 13.89 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.10), residues: 7024 helix: 2.14 (0.08), residues: 4300 sheet: -0.61 (0.21), residues: 662 loop : -0.34 (0.14), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 576 HIS 0.013 0.001 HIS A1730 PHE 0.027 0.001 PHE B1122 TYR 0.026 0.001 TYR D 184 ARG 0.004 0.000 ARG A1811 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 6270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 362 time to evaluate : 5.043 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: A 727 MET cc_start: 0.8600 (tpp) cc_final: 0.7792 (mmt) REVERT: A 756 MET cc_start: 0.9256 (mmt) cc_final: 0.9015 (mmm) REVERT: A 767 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.8560 (tm) REVERT: A 956 MET cc_start: 0.9020 (mmt) cc_final: 0.8539 (mmm) REVERT: A 994 MET cc_start: 0.9406 (mmm) cc_final: 0.9001 (mmm) REVERT: A 1004 CYS cc_start: 0.7920 (OUTLIER) cc_final: 0.6470 (p) REVERT: A 1031 MET cc_start: 0.9385 (tpt) cc_final: 0.9050 (tpp) REVERT: A 1097 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8415 (mp) REVERT: A 1109 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.8406 (t0) REVERT: A 1174 MET cc_start: 0.7179 (tpp) cc_final: 0.6735 (tpp) REVERT: A 1194 MET cc_start: 0.7811 (ppp) cc_final: 0.7546 (ppp) REVERT: A 1313 MET cc_start: 0.8354 (tpp) cc_final: 0.8112 (mtp) REVERT: A 1364 MET cc_start: 0.9282 (mmm) cc_final: 0.9015 (mmm) REVERT: A 1467 MET cc_start: 0.8294 (mmm) cc_final: 0.7516 (mpp) REVERT: A 1477 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7842 (tpt) REVERT: A 1481 MET cc_start: 0.7990 (mtt) cc_final: 0.7647 (mtt) REVERT: A 1515 MET cc_start: 0.8995 (mtm) cc_final: 0.8545 (mtt) REVERT: A 1578 MET cc_start: 0.9018 (tpp) cc_final: 0.8759 (tpp) REVERT: A 1581 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.7872 (pm20) REVERT: A 1624 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7872 (mp10) REVERT: A 1638 MET cc_start: 0.8653 (tpp) cc_final: 0.8152 (tpp) REVERT: A 1666 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8255 (mt) REVERT: A 1704 MET cc_start: 0.8642 (ttt) cc_final: 0.8362 (tmm) REVERT: A 1712 ASP cc_start: 0.8651 (OUTLIER) cc_final: 0.8396 (p0) REVERT: A 1747 MET cc_start: 0.8319 (tpp) cc_final: 0.7655 (tpp) REVERT: A 2010 MET cc_start: 0.9247 (mmm) cc_final: 0.8815 (mmm) REVERT: A 2047 MET cc_start: 0.7387 (mmm) cc_final: 0.7098 (mmt) REVERT: A 2498 ILE cc_start: 0.7811 (mm) cc_final: 0.7218 (pt) REVERT: A 2540 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.7787 (mp10) REVERT: B 123 MET cc_start: 0.2110 (tpp) cc_final: 0.1874 (tmm) REVERT: B 727 MET cc_start: 0.8602 (tpp) cc_final: 0.7793 (mmt) REVERT: B 756 MET cc_start: 0.9257 (mmt) cc_final: 0.9014 (mmm) REVERT: B 767 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.8562 (tm) REVERT: B 956 MET cc_start: 0.9017 (mmt) cc_final: 0.8540 (mmm) REVERT: B 994 MET cc_start: 0.9389 (mmm) cc_final: 0.8945 (mmm) REVERT: B 1004 CYS cc_start: 0.7923 (OUTLIER) cc_final: 0.6469 (p) REVERT: B 1031 MET cc_start: 0.9382 (tpt) cc_final: 0.8801 (tpt) REVERT: B 1097 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8426 (mp) REVERT: B 1109 ASP cc_start: 0.8693 (OUTLIER) cc_final: 0.8402 (t0) REVERT: B 1313 MET cc_start: 0.8347 (tpp) cc_final: 0.8099 (mtp) REVERT: B 1364 MET cc_start: 0.9232 (mmm) cc_final: 0.8970 (mmm) REVERT: B 1467 MET cc_start: 0.8366 (mmm) cc_final: 0.7575 (mpp) REVERT: B 1477 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7993 (tpp) REVERT: B 1515 MET cc_start: 0.8989 (mtm) cc_final: 0.8758 (mtt) REVERT: B 1581 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.7854 (pm20) REVERT: B 1595 MET cc_start: 0.8521 (mmm) cc_final: 0.8176 (mmt) REVERT: B 1624 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7822 (mp10) REVERT: B 1638 MET cc_start: 0.8657 (tpp) cc_final: 0.8162 (tpp) REVERT: B 1666 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8330 (mt) REVERT: B 1704 MET cc_start: 0.8652 (ttt) cc_final: 0.8326 (tmm) REVERT: B 1712 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8394 (p0) REVERT: B 1747 MET cc_start: 0.8219 (tpp) cc_final: 0.7546 (tpp) REVERT: B 1996 LYS cc_start: 0.9009 (mmtt) cc_final: 0.8772 (mmtt) REVERT: B 2000 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8155 (pt0) REVERT: B 2010 MET cc_start: 0.9236 (mmm) cc_final: 0.8801 (mmm) REVERT: B 2047 MET cc_start: 0.7383 (mmm) cc_final: 0.7088 (mmt) REVERT: B 2432 MET cc_start: 0.6927 (mmp) cc_final: 0.6142 (ptt) REVERT: B 2498 ILE cc_start: 0.7773 (mm) cc_final: 0.7164 (pt) REVERT: B 2540 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.7787 (mp10) REVERT: C 170 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8714 (mp0) REVERT: C 255 MET cc_start: 0.9283 (pmm) cc_final: 0.9068 (pmm) REVERT: C 274 TRP cc_start: 0.6439 (OUTLIER) cc_final: 0.5774 (p90) REVERT: C 292 ASN cc_start: 0.8351 (OUTLIER) cc_final: 0.7951 (m-40) REVERT: D 56 MET cc_start: 0.7317 (ptt) cc_final: 0.7112 (ptm) REVERT: D 170 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8704 (mp0) REVERT: D 255 MET cc_start: 0.9201 (pmm) cc_final: 0.8959 (pmm) REVERT: D 274 TRP cc_start: 0.6687 (OUTLIER) cc_final: 0.6060 (p90) REVERT: D 292 ASN cc_start: 0.8330 (OUTLIER) cc_final: 0.7907 (m-40) REVERT: E 186 MET cc_start: 0.8420 (mmm) cc_final: 0.7990 (mmm) REVERT: E 211 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8296 (pp) REVERT: E 499 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9003 (mm) REVERT: E 534 MET cc_start: 0.8587 (mtm) cc_final: 0.8197 (ttm) REVERT: E 588 PHE cc_start: 0.7403 (OUTLIER) cc_final: 0.6977 (t80) REVERT: E 646 MET cc_start: 0.8495 (mmm) cc_final: 0.7903 (mmp) REVERT: E 1073 MET cc_start: 0.8174 (mtm) cc_final: 0.7614 (mtm) REVERT: E 1127 MET cc_start: 0.5192 (tpp) cc_final: 0.4764 (tmm) REVERT: E 1197 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7936 (pmm) REVERT: F 211 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8303 (pp) REVERT: F 499 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9002 (mm) REVERT: F 534 MET cc_start: 0.8589 (mtm) cc_final: 0.8198 (ttm) REVERT: F 588 PHE cc_start: 0.7412 (OUTLIER) cc_final: 0.7013 (t80) REVERT: F 646 MET cc_start: 0.8460 (mmm) cc_final: 0.7851 (mmp) REVERT: F 1073 MET cc_start: 0.8175 (mtm) cc_final: 0.7619 (mtm) REVERT: F 1127 MET cc_start: 0.5186 (tpp) cc_final: 0.4750 (tmm) REVERT: F 1197 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7928 (pmm) REVERT: F 1323 TYR cc_start: 0.8861 (OUTLIER) cc_final: 0.8480 (m-80) outliers start: 141 outliers final: 72 residues processed: 483 average time/residue: 0.5443 time to fit residues: 459.8491 Evaluate side-chains 460 residues out of total 6270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 354 time to evaluate : 5.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 609 HIS Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 1004 CYS Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1109 ASP Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1196 ASN Chi-restraints excluded: chain A residue 1220 TYR Chi-restraints excluded: chain A residue 1311 ASN Chi-restraints excluded: chain A residue 1372 LEU Chi-restraints excluded: chain A residue 1465 LYS Chi-restraints excluded: chain A residue 1477 MET Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1581 GLU Chi-restraints excluded: chain A residue 1624 GLN Chi-restraints excluded: chain A residue 1629 ILE Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1712 ASP Chi-restraints excluded: chain A residue 1946 ILE Chi-restraints excluded: chain A residue 2000 GLU Chi-restraints excluded: chain A residue 2003 ASN Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2280 LEU Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2329 MET Chi-restraints excluded: chain A residue 2333 ILE Chi-restraints excluded: chain A residue 2533 THR Chi-restraints excluded: chain A residue 2540 GLN Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 609 HIS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 826 ASP Chi-restraints excluded: chain B residue 1004 CYS Chi-restraints excluded: chain B residue 1075 ILE Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1196 ASN Chi-restraints excluded: chain B residue 1220 TYR Chi-restraints excluded: chain B residue 1311 ASN Chi-restraints excluded: chain B residue 1372 LEU Chi-restraints excluded: chain B residue 1465 LYS Chi-restraints excluded: chain B residue 1477 MET Chi-restraints excluded: chain B residue 1484 LEU Chi-restraints excluded: chain B residue 1581 GLU Chi-restraints excluded: chain B residue 1624 GLN Chi-restraints excluded: chain B residue 1629 ILE Chi-restraints excluded: chain B residue 1637 LEU Chi-restraints excluded: chain B residue 1639 VAL Chi-restraints excluded: chain B residue 1666 LEU Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1712 ASP Chi-restraints excluded: chain B residue 1946 ILE Chi-restraints excluded: chain B residue 2000 GLU Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2280 LEU Chi-restraints excluded: chain B residue 2303 LEU Chi-restraints excluded: chain B residue 2329 MET Chi-restraints excluded: chain B residue 2333 ILE Chi-restraints excluded: chain B residue 2533 THR Chi-restraints excluded: chain B residue 2540 GLN Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 274 TRP Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 274 TRP Chi-restraints excluded: chain D residue 292 ASN Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain E residue 526 TYR Chi-restraints excluded: chain E residue 551 GLU Chi-restraints excluded: chain E residue 588 PHE Chi-restraints excluded: chain E residue 1182 VAL Chi-restraints excluded: chain E residue 1197 MET Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 266 CYS Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain F residue 526 TYR Chi-restraints excluded: chain F residue 551 GLU Chi-restraints excluded: chain F residue 588 PHE Chi-restraints excluded: chain F residue 1182 VAL Chi-restraints excluded: chain F residue 1197 MET Chi-restraints excluded: chain F residue 1323 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 423 optimal weight: 0.6980 chunk 273 optimal weight: 0.4980 chunk 408 optimal weight: 0.5980 chunk 206 optimal weight: 0.7980 chunk 134 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 chunk 435 optimal weight: 0.5980 chunk 466 optimal weight: 6.9990 chunk 338 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 537 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2124 GLN A2515 HIS ** B1725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2124 GLN B2515 HIS ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 58060 Z= 0.176 Angle : 0.583 10.836 78778 Z= 0.282 Chirality : 0.040 0.256 8944 Planarity : 0.004 0.057 10028 Dihedral : 4.651 63.173 7820 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.93 % Favored : 97.01 % Rotamer: Outliers : 1.82 % Allowed : 14.73 % Favored : 83.45 % 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: 1.75 (0.10), residues: 7024 helix: 2.16 (0.08), residues: 4286 sheet: -0.60 (0.21), residues: 672 loop : -0.31 (0.14), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP D 197 HIS 0.013 0.001 HIS A1730 PHE 0.026 0.001 PHE H 401 TYR 0.025 0.001 TYR D 184 ARG 0.004 0.000 ARG B1203 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 6270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 370 time to evaluate : 4.994 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: A 727 MET cc_start: 0.8577 (tpp) cc_final: 0.7785 (mmt) REVERT: A 756 MET cc_start: 0.9254 (mmt) cc_final: 0.9010 (mmm) REVERT: A 767 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.8572 (tm) REVERT: A 956 MET cc_start: 0.8990 (mmt) cc_final: 0.8536 (mmm) REVERT: A 994 MET cc_start: 0.9364 (mmm) cc_final: 0.8924 (mmm) REVERT: A 1004 CYS cc_start: 0.7921 (OUTLIER) cc_final: 0.6475 (p) REVERT: A 1031 MET cc_start: 0.9388 (tpt) cc_final: 0.9082 (tpp) REVERT: A 1097 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8392 (mp) REVERT: A 1109 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.8410 (t0) REVERT: A 1174 MET cc_start: 0.7136 (tpp) cc_final: 0.6777 (tpp) REVERT: A 1364 MET cc_start: 0.9271 (mmm) cc_final: 0.9055 (mmm) REVERT: A 1467 MET cc_start: 0.8345 (mmm) cc_final: 0.7581 (mpp) REVERT: A 1477 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7801 (tpt) REVERT: A 1481 MET cc_start: 0.7960 (mtt) cc_final: 0.7595 (mtt) REVERT: A 1515 MET cc_start: 0.9006 (mtm) cc_final: 0.8518 (mtt) REVERT: A 1581 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.7874 (pm20) REVERT: A 1595 MET cc_start: 0.8588 (mmm) cc_final: 0.8274 (mmt) REVERT: A 1624 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7912 (mp10) REVERT: A 1638 MET cc_start: 0.8668 (tpp) cc_final: 0.8166 (tpp) REVERT: A 1666 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8268 (mt) REVERT: A 1704 MET cc_start: 0.8647 (ttt) cc_final: 0.8322 (tmm) REVERT: A 1747 MET cc_start: 0.8318 (tpp) cc_final: 0.7694 (tpp) REVERT: A 2010 MET cc_start: 0.9211 (mmm) cc_final: 0.8774 (mmm) REVERT: A 2047 MET cc_start: 0.7390 (mmm) cc_final: 0.7071 (mmt) REVERT: A 2432 MET cc_start: 0.6961 (mmp) cc_final: 0.6195 (ptt) REVERT: A 2540 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.7748 (mp10) REVERT: B 123 MET cc_start: 0.2073 (tpp) cc_final: 0.1817 (tmm) REVERT: B 727 MET cc_start: 0.8575 (tpp) cc_final: 0.7785 (mmt) REVERT: B 756 MET cc_start: 0.9258 (mmt) cc_final: 0.9011 (mmm) REVERT: B 767 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.8568 (tm) REVERT: B 956 MET cc_start: 0.8990 (mmt) cc_final: 0.8537 (mmm) REVERT: B 994 MET cc_start: 0.9369 (mmm) cc_final: 0.8929 (mmm) REVERT: B 1004 CYS cc_start: 0.7928 (OUTLIER) cc_final: 0.6483 (p) REVERT: B 1031 MET cc_start: 0.9391 (tpt) cc_final: 0.8821 (tpt) REVERT: B 1097 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8403 (mp) REVERT: B 1109 ASP cc_start: 0.8700 (OUTLIER) cc_final: 0.8410 (t0) REVERT: B 1364 MET cc_start: 0.9275 (mmm) cc_final: 0.8977 (mmm) REVERT: B 1467 MET cc_start: 0.8316 (mmm) cc_final: 0.7564 (mpp) REVERT: B 1477 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.7993 (tpp) REVERT: B 1515 MET cc_start: 0.9001 (mtm) cc_final: 0.8722 (mtm) REVERT: B 1581 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.7867 (pm20) REVERT: B 1624 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7984 (mp10) REVERT: B 1638 MET cc_start: 0.8667 (tpp) cc_final: 0.8155 (tpp) REVERT: B 1666 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8263 (mt) REVERT: B 1704 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8273 (tmm) REVERT: B 1747 MET cc_start: 0.8312 (tpp) cc_final: 0.7626 (tpp) REVERT: B 1996 LYS cc_start: 0.9014 (mmtt) cc_final: 0.8785 (mmtt) REVERT: B 2000 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8185 (pt0) REVERT: B 2010 MET cc_start: 0.9246 (mmm) cc_final: 0.8791 (mmm) REVERT: B 2047 MET cc_start: 0.7385 (mmm) cc_final: 0.7064 (mmt) REVERT: B 2432 MET cc_start: 0.6917 (mmp) cc_final: 0.6134 (ptt) REVERT: B 2540 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.7745 (mp10) REVERT: C 100 MET cc_start: 0.9215 (ptt) cc_final: 0.9002 (ptt) REVERT: C 170 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8704 (mp0) REVERT: C 255 MET cc_start: 0.9282 (pmm) cc_final: 0.8962 (pmm) REVERT: C 274 TRP cc_start: 0.6568 (OUTLIER) cc_final: 0.5906 (p90) REVERT: C 292 ASN cc_start: 0.8336 (OUTLIER) cc_final: 0.7926 (m-40) REVERT: D 170 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8715 (mp0) REVERT: D 274 TRP cc_start: 0.6566 (OUTLIER) cc_final: 0.5915 (p90) REVERT: D 292 ASN cc_start: 0.8314 (OUTLIER) cc_final: 0.7900 (m-40) REVERT: E 186 MET cc_start: 0.8491 (mmm) cc_final: 0.8112 (mmm) REVERT: E 211 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8264 (pp) REVERT: E 499 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8999 (mm) REVERT: E 534 MET cc_start: 0.8622 (mtm) cc_final: 0.8229 (ttm) REVERT: E 588 PHE cc_start: 0.7262 (OUTLIER) cc_final: 0.6880 (t80) REVERT: E 646 MET cc_start: 0.8479 (mmm) cc_final: 0.7861 (mmp) REVERT: E 1073 MET cc_start: 0.7865 (mtm) cc_final: 0.7344 (mtm) REVERT: E 1127 MET cc_start: 0.5493 (tpp) cc_final: 0.5048 (tmm) REVERT: E 1197 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7914 (pmm) REVERT: F 211 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8292 (pp) REVERT: F 499 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8983 (mm) REVERT: F 534 MET cc_start: 0.8624 (mtm) cc_final: 0.8233 (ttm) REVERT: F 588 PHE cc_start: 0.7266 (OUTLIER) cc_final: 0.6881 (t80) REVERT: F 646 MET cc_start: 0.8477 (mmm) cc_final: 0.7861 (mmp) REVERT: F 1073 MET cc_start: 0.7864 (mtm) cc_final: 0.7359 (mtm) REVERT: F 1127 MET cc_start: 0.5484 (tpp) cc_final: 0.5033 (tmm) REVERT: F 1197 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7987 (pmm) REVERT: F 1243 MET cc_start: 0.8017 (ptm) cc_final: 0.7706 (ptt) REVERT: F 1323 TYR cc_start: 0.8856 (OUTLIER) cc_final: 0.8478 (m-80) outliers start: 112 outliers final: 68 residues processed: 460 average time/residue: 0.5417 time to fit residues: 434.7233 Evaluate side-chains 452 residues out of total 6270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 351 time to evaluate : 4.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 609 HIS Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 1004 CYS Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1109 ASP Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1196 ASN Chi-restraints excluded: chain A residue 1220 TYR Chi-restraints excluded: chain A residue 1311 ASN Chi-restraints excluded: chain A residue 1372 LEU Chi-restraints excluded: chain A residue 1465 LYS Chi-restraints excluded: chain A residue 1477 MET Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1581 GLU Chi-restraints excluded: chain A residue 1624 GLN Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1946 ILE Chi-restraints excluded: chain A residue 2000 GLU Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2280 LEU Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2329 MET Chi-restraints excluded: chain A residue 2333 ILE Chi-restraints excluded: chain A residue 2533 THR Chi-restraints excluded: chain A residue 2540 GLN Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 609 HIS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 826 ASP Chi-restraints excluded: chain B residue 1004 CYS Chi-restraints excluded: chain B residue 1075 ILE Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1196 ASN Chi-restraints excluded: chain B residue 1220 TYR Chi-restraints excluded: chain B residue 1311 ASN Chi-restraints excluded: chain B residue 1372 LEU Chi-restraints excluded: chain B residue 1465 LYS Chi-restraints excluded: chain B residue 1477 MET Chi-restraints excluded: chain B residue 1484 LEU Chi-restraints excluded: chain B residue 1581 GLU Chi-restraints excluded: chain B residue 1624 GLN Chi-restraints excluded: chain B residue 1637 LEU Chi-restraints excluded: chain B residue 1639 VAL Chi-restraints excluded: chain B residue 1666 LEU Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1704 MET Chi-restraints excluded: chain B residue 2000 GLU Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2280 LEU Chi-restraints excluded: chain B residue 2303 LEU Chi-restraints excluded: chain B residue 2329 MET Chi-restraints excluded: chain B residue 2333 ILE Chi-restraints excluded: chain B residue 2533 THR Chi-restraints excluded: chain B residue 2540 GLN Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 274 TRP Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 274 TRP Chi-restraints excluded: chain D residue 292 ASN Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain E residue 526 TYR Chi-restraints excluded: chain E residue 551 GLU Chi-restraints excluded: chain E residue 588 PHE Chi-restraints excluded: chain E residue 1182 VAL Chi-restraints excluded: chain E residue 1197 MET Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 386 VAL Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain F residue 526 TYR Chi-restraints excluded: chain F residue 551 GLU Chi-restraints excluded: chain F residue 588 PHE Chi-restraints excluded: chain F residue 1182 VAL Chi-restraints excluded: chain F residue 1197 MET Chi-restraints excluded: chain F residue 1323 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 622 optimal weight: 0.4980 chunk 655 optimal weight: 0.6980 chunk 598 optimal weight: 0.9990 chunk 637 optimal weight: 0.9980 chunk 383 optimal weight: 0.8980 chunk 277 optimal weight: 0.7980 chunk 500 optimal weight: 10.0000 chunk 195 optimal weight: 0.8980 chunk 576 optimal weight: 9.9990 chunk 603 optimal weight: 0.0970 chunk 635 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1049 GLN ** A1725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2124 GLN A2515 HIS B1049 GLN ** B1725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2124 GLN B2515 HIS ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 58060 Z= 0.176 Angle : 0.592 13.455 78778 Z= 0.287 Chirality : 0.040 0.270 8944 Planarity : 0.004 0.057 10028 Dihedral : 4.654 63.577 7820 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.80 % Favored : 97.14 % Rotamer: Outliers : 1.88 % Allowed : 14.88 % Favored : 83.24 % 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: 1.74 (0.10), residues: 7024 helix: 2.15 (0.08), residues: 4276 sheet: -0.61 (0.21), residues: 684 loop : -0.29 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 197 HIS 0.016 0.001 HIS E 978 PHE 0.023 0.001 PHE A1122 TYR 0.027 0.001 TYR C 184 ARG 0.003 0.000 ARG D 115 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 6270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 362 time to evaluate : 5.011 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 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: A 727 MET cc_start: 0.8598 (tpp) cc_final: 0.7772 (mmt) REVERT: A 756 MET cc_start: 0.9262 (mmt) cc_final: 0.9014 (mmm) REVERT: A 767 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.8566 (tm) REVERT: A 956 MET cc_start: 0.8951 (mmt) cc_final: 0.8519 (mmm) REVERT: A 994 MET cc_start: 0.9365 (mmm) cc_final: 0.8919 (mmm) REVERT: A 1004 CYS cc_start: 0.8088 (OUTLIER) cc_final: 0.6752 (p) REVERT: A 1031 MET cc_start: 0.9396 (tpt) cc_final: 0.9126 (tpp) REVERT: A 1097 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8505 (mp) REVERT: A 1109 ASP cc_start: 0.8693 (OUTLIER) cc_final: 0.8405 (t0) REVERT: A 1174 MET cc_start: 0.7115 (tpp) cc_final: 0.6805 (tpp) REVERT: A 1364 MET cc_start: 0.9321 (mmm) cc_final: 0.9093 (mmm) REVERT: A 1467 MET cc_start: 0.8256 (mmm) cc_final: 0.7541 (mpp) REVERT: A 1477 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7822 (tpt) REVERT: A 1481 MET cc_start: 0.7964 (mtt) cc_final: 0.7610 (mtt) REVERT: A 1515 MET cc_start: 0.9029 (mtm) cc_final: 0.8534 (mtt) REVERT: A 1581 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.7884 (pm20) REVERT: A 1595 MET cc_start: 0.8585 (mmm) cc_final: 0.8265 (mmt) REVERT: A 1624 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8027 (mp10) REVERT: A 1638 MET cc_start: 0.8674 (tpp) cc_final: 0.8173 (tpp) REVERT: A 1666 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8261 (mt) REVERT: A 1704 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8301 (tmm) REVERT: A 1712 ASP cc_start: 0.8642 (OUTLIER) cc_final: 0.8298 (p0) REVERT: A 1747 MET cc_start: 0.8444 (tpp) cc_final: 0.7813 (tpp) REVERT: A 2010 MET cc_start: 0.9245 (mmm) cc_final: 0.8800 (mmm) REVERT: A 2026 MET cc_start: 0.9437 (ptp) cc_final: 0.9236 (mpp) REVERT: A 2047 MET cc_start: 0.7379 (mmm) cc_final: 0.7068 (mmt) REVERT: A 2089 MET cc_start: 0.9266 (ptp) cc_final: 0.9037 (ppp) REVERT: A 2432 MET cc_start: 0.6960 (mmp) cc_final: 0.6196 (ptt) REVERT: A 2498 ILE cc_start: 0.7809 (mm) cc_final: 0.7221 (pt) REVERT: A 2540 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.7722 (mp10) REVERT: B 123 MET cc_start: 0.2299 (tpp) cc_final: 0.2061 (tmm) REVERT: B 727 MET cc_start: 0.8597 (tpp) cc_final: 0.7769 (mmt) REVERT: B 756 MET cc_start: 0.9264 (mmt) cc_final: 0.9014 (mmm) REVERT: B 767 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.8566 (tm) REVERT: B 827 MET cc_start: 0.8952 (ptp) cc_final: 0.8691 (ppp) REVERT: B 956 MET cc_start: 0.8947 (mmt) cc_final: 0.8517 (mmm) REVERT: B 994 MET cc_start: 0.9368 (mmm) cc_final: 0.8921 (mmm) REVERT: B 1004 CYS cc_start: 0.8094 (OUTLIER) cc_final: 0.6753 (p) REVERT: B 1031 MET cc_start: 0.9391 (tpt) cc_final: 0.8818 (tpt) REVERT: B 1097 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8417 (mp) REVERT: B 1109 ASP cc_start: 0.8693 (OUTLIER) cc_final: 0.8404 (t0) REVERT: B 1364 MET cc_start: 0.9263 (mmm) cc_final: 0.8965 (mmm) REVERT: B 1467 MET cc_start: 0.8330 (mmm) cc_final: 0.7647 (mpp) REVERT: B 1477 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.7984 (tpp) REVERT: B 1515 MET cc_start: 0.9014 (mtm) cc_final: 0.8729 (mtm) REVERT: B 1578 MET cc_start: 0.9054 (tpp) cc_final: 0.8582 (tpp) REVERT: B 1581 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.7877 (pm20) REVERT: B 1595 MET cc_start: 0.8597 (mmm) cc_final: 0.8276 (mmt) REVERT: B 1624 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7979 (mp10) REVERT: B 1638 MET cc_start: 0.8677 (tpp) cc_final: 0.8169 (tpp) REVERT: B 1666 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8259 (mt) REVERT: B 1704 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8249 (tmm) REVERT: B 1712 ASP cc_start: 0.8635 (OUTLIER) cc_final: 0.8294 (p0) REVERT: B 1747 MET cc_start: 0.8468 (tpp) cc_final: 0.7817 (tpp) REVERT: B 2000 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8170 (pt0) REVERT: B 2010 MET cc_start: 0.9258 (mmm) cc_final: 0.8802 (mmm) REVERT: B 2047 MET cc_start: 0.7494 (mmm) cc_final: 0.7154 (mmt) REVERT: B 2089 MET cc_start: 0.9265 (ptp) cc_final: 0.9033 (ppp) REVERT: B 2432 MET cc_start: 0.6914 (mmp) cc_final: 0.6139 (ptt) REVERT: B 2498 ILE cc_start: 0.7806 (mm) cc_final: 0.7217 (pt) REVERT: B 2540 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.7717 (mp10) REVERT: C 100 MET cc_start: 0.9208 (ptt) cc_final: 0.8994 (ptt) REVERT: C 170 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8728 (mp0) REVERT: C 274 TRP cc_start: 0.6571 (OUTLIER) cc_final: 0.5902 (p90) REVERT: C 292 ASN cc_start: 0.8327 (OUTLIER) cc_final: 0.7920 (m-40) REVERT: D 170 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8727 (mp0) REVERT: D 274 TRP cc_start: 0.6769 (OUTLIER) cc_final: 0.6144 (p90) REVERT: D 292 ASN cc_start: 0.8304 (OUTLIER) cc_final: 0.7898 (m-40) REVERT: E 211 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8272 (pp) REVERT: E 499 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8976 (mm) REVERT: E 534 MET cc_start: 0.8621 (mtm) cc_final: 0.8227 (ttm) REVERT: E 588 PHE cc_start: 0.7318 (OUTLIER) cc_final: 0.6960 (t80) REVERT: E 646 MET cc_start: 0.8491 (mmm) cc_final: 0.7873 (mmp) REVERT: E 1073 MET cc_start: 0.7934 (mtm) cc_final: 0.7464 (mtm) REVERT: E 1127 MET cc_start: 0.5497 (tpp) cc_final: 0.5056 (tmm) REVERT: E 1197 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7906 (pmm) REVERT: F 211 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8280 (pp) REVERT: F 499 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8975 (mm) REVERT: F 534 MET cc_start: 0.8625 (mtm) cc_final: 0.8232 (ttm) REVERT: F 588 PHE cc_start: 0.7322 (OUTLIER) cc_final: 0.6960 (t80) REVERT: F 646 MET cc_start: 0.8491 (mmm) cc_final: 0.7874 (mmp) REVERT: F 1073 MET cc_start: 0.7999 (mtm) cc_final: 0.7500 (mtm) REVERT: F 1127 MET cc_start: 0.5483 (tpp) cc_final: 0.5042 (tmm) REVERT: F 1197 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7987 (pmm) REVERT: F 1323 TYR cc_start: 0.8857 (OUTLIER) cc_final: 0.8479 (m-80) outliers start: 116 outliers final: 66 residues processed: 456 average time/residue: 0.5467 time to fit residues: 433.8895 Evaluate side-chains 451 residues out of total 6270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 349 time to evaluate : 4.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 609 HIS Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 1004 CYS Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1109 ASP Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1196 ASN Chi-restraints excluded: chain A residue 1220 TYR Chi-restraints excluded: chain A residue 1311 ASN Chi-restraints excluded: chain A residue 1372 LEU Chi-restraints excluded: chain A residue 1465 LYS Chi-restraints excluded: chain A residue 1477 MET Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1581 GLU Chi-restraints excluded: chain A residue 1624 GLN Chi-restraints excluded: chain A residue 1629 ILE Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1704 MET Chi-restraints excluded: chain A residue 1712 ASP Chi-restraints excluded: chain A residue 2000 GLU Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2280 LEU Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2329 MET Chi-restraints excluded: chain A residue 2333 ILE Chi-restraints excluded: chain A residue 2533 THR Chi-restraints excluded: chain A residue 2540 GLN Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 609 HIS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 826 ASP Chi-restraints excluded: chain B residue 1004 CYS Chi-restraints excluded: chain B residue 1075 ILE Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1196 ASN Chi-restraints excluded: chain B residue 1220 TYR Chi-restraints excluded: chain B residue 1311 ASN Chi-restraints excluded: chain B residue 1372 LEU Chi-restraints excluded: chain B residue 1465 LYS Chi-restraints excluded: chain B residue 1477 MET Chi-restraints excluded: chain B residue 1484 LEU Chi-restraints excluded: chain B residue 1581 GLU Chi-restraints excluded: chain B residue 1624 GLN Chi-restraints excluded: chain B residue 1637 LEU Chi-restraints excluded: chain B residue 1639 VAL Chi-restraints excluded: chain B residue 1666 LEU Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1704 MET Chi-restraints excluded: chain B residue 1712 ASP Chi-restraints excluded: chain B residue 2000 GLU Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2280 LEU Chi-restraints excluded: chain B residue 2303 LEU Chi-restraints excluded: chain B residue 2329 MET Chi-restraints excluded: chain B residue 2333 ILE Chi-restraints excluded: chain B residue 2533 THR Chi-restraints excluded: chain B residue 2540 GLN Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 274 TRP Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 274 TRP Chi-restraints excluded: chain D residue 292 ASN Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain E residue 526 TYR Chi-restraints excluded: chain E residue 551 GLU Chi-restraints excluded: chain E residue 588 PHE Chi-restraints excluded: chain E residue 1182 VAL Chi-restraints excluded: chain E residue 1197 MET Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 386 VAL Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain F residue 526 TYR Chi-restraints excluded: chain F residue 551 GLU Chi-restraints excluded: chain F residue 588 PHE Chi-restraints excluded: chain F residue 1182 VAL Chi-restraints excluded: chain F residue 1197 MET Chi-restraints excluded: chain F residue 1323 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 418 optimal weight: 1.9990 chunk 674 optimal weight: 1.9990 chunk 411 optimal weight: 0.9990 chunk 319 optimal weight: 0.0470 chunk 468 optimal weight: 0.9990 chunk 707 optimal weight: 9.9990 chunk 651 optimal weight: 0.6980 chunk 563 optimal weight: 8.9990 chunk 58 optimal weight: 0.5980 chunk 435 optimal weight: 0.0770 chunk 345 optimal weight: 1.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2124 GLN A2515 HIS ** B1725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2515 HIS ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 978 HIS ** F 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 978 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 58060 Z= 0.167 Angle : 0.605 11.835 78778 Z= 0.291 Chirality : 0.040 0.259 8944 Planarity : 0.004 0.057 10028 Dihedral : 4.643 64.340 7820 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.86 % Favored : 97.08 % Rotamer: Outliers : 1.70 % Allowed : 15.15 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.10), residues: 7024 helix: 2.14 (0.08), residues: 4272 sheet: -0.58 (0.21), residues: 674 loop : -0.33 (0.14), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 197 HIS 0.017 0.001 HIS E 978 PHE 0.022 0.001 PHE B1122 TYR 0.027 0.001 TYR C 184 ARG 0.012 0.000 ARG B 859 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 6270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 372 time to evaluate : 5.036 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 REVERT: A 277 MET cc_start: -0.0953 (mmt) cc_final: -0.1192 (mmt) REVERT: A 727 MET cc_start: 0.8577 (tpp) cc_final: 0.7755 (mmt) REVERT: A 756 MET cc_start: 0.9280 (mmt) cc_final: 0.9022 (mmm) REVERT: A 767 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.8586 (tm) REVERT: A 779 LEU cc_start: 0.9599 (mt) cc_final: 0.9384 (mt) REVERT: A 956 MET cc_start: 0.8914 (mmt) cc_final: 0.8499 (mmm) REVERT: A 994 MET cc_start: 0.9348 (mmm) cc_final: 0.8899 (mmm) REVERT: A 1004 CYS cc_start: 0.8079 (OUTLIER) cc_final: 0.6753 (p) REVERT: A 1097 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8421 (mp) REVERT: A 1109 ASP cc_start: 0.8677 (OUTLIER) cc_final: 0.8369 (t0) REVERT: A 1174 MET cc_start: 0.6783 (tpp) cc_final: 0.6440 (tpp) REVERT: A 1364 MET cc_start: 0.9302 (mmm) cc_final: 0.9074 (mmm) REVERT: A 1467 MET cc_start: 0.8362 (mmm) cc_final: 0.7605 (mpp) REVERT: A 1481 MET cc_start: 0.7931 (mtt) cc_final: 0.7593 (mtt) REVERT: A 1515 MET cc_start: 0.9028 (mtm) cc_final: 0.8534 (mtt) REVERT: A 1578 MET cc_start: 0.9055 (tpp) cc_final: 0.8619 (tpp) REVERT: A 1581 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.7898 (pm20) REVERT: A 1595 MET cc_start: 0.8521 (mmm) cc_final: 0.8242 (mmt) REVERT: A 1624 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8010 (mp10) REVERT: A 1638 MET cc_start: 0.8683 (tpp) cc_final: 0.8179 (tpp) REVERT: A 1666 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8273 (mt) REVERT: A 1704 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8287 (tmm) REVERT: A 1712 ASP cc_start: 0.8634 (OUTLIER) cc_final: 0.8268 (p0) REVERT: A 1747 MET cc_start: 0.8449 (tpp) cc_final: 0.7792 (tpp) REVERT: A 1796 MET cc_start: 0.8552 (mmm) cc_final: 0.8208 (tpp) REVERT: A 2010 MET cc_start: 0.9215 (mmm) cc_final: 0.8763 (mmm) REVERT: A 2047 MET cc_start: 0.7444 (mmm) cc_final: 0.7124 (mmt) REVERT: A 2089 MET cc_start: 0.9276 (ptp) cc_final: 0.9019 (ppp) REVERT: A 2498 ILE cc_start: 0.7806 (mm) cc_final: 0.7216 (pt) REVERT: A 2540 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.7698 (mp10) REVERT: B 123 MET cc_start: 0.2316 (tpp) cc_final: 0.2087 (tmm) REVERT: B 727 MET cc_start: 0.8577 (tpp) cc_final: 0.7751 (mmt) REVERT: B 756 MET cc_start: 0.9281 (mmt) cc_final: 0.9022 (mmm) REVERT: B 767 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.8583 (tm) REVERT: B 779 LEU cc_start: 0.9603 (mt) cc_final: 0.9383 (mt) REVERT: B 824 ILE cc_start: 0.9405 (tp) cc_final: 0.9195 (tp) REVERT: B 827 MET cc_start: 0.8857 (ptp) cc_final: 0.8617 (ppp) REVERT: B 956 MET cc_start: 0.8913 (mmt) cc_final: 0.8493 (mmm) REVERT: B 994 MET cc_start: 0.9340 (mmm) cc_final: 0.8912 (mmm) REVERT: B 1004 CYS cc_start: 0.8082 (OUTLIER) cc_final: 0.6754 (p) REVERT: B 1031 MET cc_start: 0.9393 (tpt) cc_final: 0.8820 (tpt) REVERT: B 1097 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8336 (mp) REVERT: B 1109 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8394 (t0) REVERT: B 1364 MET cc_start: 0.9254 (mmm) cc_final: 0.8958 (mmm) REVERT: B 1467 MET cc_start: 0.8413 (mmm) cc_final: 0.7675 (mpp) REVERT: B 1477 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.7986 (tpp) REVERT: B 1515 MET cc_start: 0.9012 (mtm) cc_final: 0.8704 (mtm) REVERT: B 1578 MET cc_start: 0.9051 (tpp) cc_final: 0.8615 (tpp) REVERT: B 1581 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.7882 (pm20) REVERT: B 1595 MET cc_start: 0.8447 (mmm) cc_final: 0.8156 (mmt) REVERT: B 1624 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8012 (mp10) REVERT: B 1638 MET cc_start: 0.8683 (tpp) cc_final: 0.8178 (tpp) REVERT: B 1666 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8199 (mt) REVERT: B 1704 MET cc_start: 0.8646 (ttt) cc_final: 0.8239 (tmm) REVERT: B 1712 ASP cc_start: 0.8625 (OUTLIER) cc_final: 0.8262 (p0) REVERT: B 1747 MET cc_start: 0.8458 (tpp) cc_final: 0.7780 (tpp) REVERT: B 1796 MET cc_start: 0.8563 (mmm) cc_final: 0.8220 (tpp) REVERT: B 2010 MET cc_start: 0.9236 (mmm) cc_final: 0.8781 (mmm) REVERT: B 2047 MET cc_start: 0.7440 (mmm) cc_final: 0.7118 (mmt) REVERT: B 2089 MET cc_start: 0.9273 (ptp) cc_final: 0.9015 (ppp) REVERT: B 2498 ILE cc_start: 0.7801 (mm) cc_final: 0.7211 (pt) REVERT: B 2540 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.7633 (mp10) REVERT: C 100 MET cc_start: 0.9201 (ptt) cc_final: 0.8981 (ptt) REVERT: C 170 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8724 (mp0) REVERT: C 274 TRP cc_start: 0.6805 (OUTLIER) cc_final: 0.6145 (p90) REVERT: C 292 ASN cc_start: 0.8310 (OUTLIER) cc_final: 0.7887 (m-40) REVERT: D 76 ASN cc_start: 0.8427 (m-40) cc_final: 0.7885 (t0) REVERT: D 170 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8720 (mp0) REVERT: D 274 TRP cc_start: 0.6773 (OUTLIER) cc_final: 0.6122 (p90) REVERT: D 292 ASN cc_start: 0.8286 (OUTLIER) cc_final: 0.7864 (m-40) REVERT: E 211 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8216 (pp) REVERT: E 499 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8979 (mm) REVERT: E 534 MET cc_start: 0.8612 (mtm) cc_final: 0.8210 (ttm) REVERT: E 588 PHE cc_start: 0.7308 (OUTLIER) cc_final: 0.6939 (t80) REVERT: E 646 MET cc_start: 0.8507 (mmm) cc_final: 0.7884 (mmp) REVERT: E 1073 MET cc_start: 0.7755 (mtm) cc_final: 0.7273 (mtm) REVERT: E 1127 MET cc_start: 0.5481 (tpp) cc_final: 0.5041 (tmm) REVERT: E 1197 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7911 (pmm) REVERT: F 211 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8227 (pp) REVERT: F 499 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8979 (mm) REVERT: F 534 MET cc_start: 0.8614 (mtm) cc_final: 0.8187 (ttm) REVERT: F 588 PHE cc_start: 0.7230 (OUTLIER) cc_final: 0.6899 (t80) REVERT: F 646 MET cc_start: 0.8504 (mmm) cc_final: 0.7885 (mmp) REVERT: F 1073 MET cc_start: 0.7864 (mtm) cc_final: 0.7352 (mtm) REVERT: F 1127 MET cc_start: 0.5489 (tpp) cc_final: 0.5040 (tmm) REVERT: F 1197 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.8154 (pmm) REVERT: F 1323 TYR cc_start: 0.8855 (OUTLIER) cc_final: 0.8478 (m-80) outliers start: 105 outliers final: 68 residues processed: 452 average time/residue: 0.5342 time to fit residues: 421.5248 Evaluate side-chains 452 residues out of total 6270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 351 time to evaluate : 5.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 609 HIS Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 1004 CYS Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1109 ASP Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1196 ASN Chi-restraints excluded: chain A residue 1220 TYR Chi-restraints excluded: chain A residue 1311 ASN Chi-restraints excluded: chain A residue 1372 LEU Chi-restraints excluded: chain A residue 1465 LYS Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1581 GLU Chi-restraints excluded: chain A residue 1624 GLN Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1704 MET Chi-restraints excluded: chain A residue 1712 ASP Chi-restraints excluded: chain A residue 2000 GLU Chi-restraints excluded: chain A residue 2164 THR Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2280 LEU Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2329 MET Chi-restraints excluded: chain A residue 2333 ILE Chi-restraints excluded: chain A residue 2540 GLN Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 609 HIS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 826 ASP Chi-restraints excluded: chain B residue 1004 CYS Chi-restraints excluded: chain B residue 1075 ILE Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1196 ASN Chi-restraints excluded: chain B residue 1220 TYR Chi-restraints excluded: chain B residue 1311 ASN Chi-restraints excluded: chain B residue 1372 LEU Chi-restraints excluded: chain B residue 1465 LYS Chi-restraints excluded: chain B residue 1477 MET Chi-restraints excluded: chain B residue 1484 LEU Chi-restraints excluded: chain B residue 1581 GLU Chi-restraints excluded: chain B residue 1624 GLN Chi-restraints excluded: chain B residue 1637 LEU Chi-restraints excluded: chain B residue 1666 LEU Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1712 ASP Chi-restraints excluded: chain B residue 1946 ILE Chi-restraints excluded: chain B residue 2000 GLU Chi-restraints excluded: chain B residue 2164 THR Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2280 LEU Chi-restraints excluded: chain B residue 2303 LEU Chi-restraints excluded: chain B residue 2329 MET Chi-restraints excluded: chain B residue 2333 ILE Chi-restraints excluded: chain B residue 2540 GLN Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 274 TRP Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 274 TRP Chi-restraints excluded: chain D residue 292 ASN Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain E residue 526 TYR Chi-restraints excluded: chain E residue 551 GLU Chi-restraints excluded: chain E residue 588 PHE Chi-restraints excluded: chain E residue 978 HIS Chi-restraints excluded: chain E residue 1182 VAL Chi-restraints excluded: chain E residue 1197 MET Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 386 VAL Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain F residue 526 TYR Chi-restraints excluded: chain F residue 551 GLU Chi-restraints excluded: chain F residue 588 PHE Chi-restraints excluded: chain F residue 978 HIS Chi-restraints excluded: chain F residue 1182 VAL Chi-restraints excluded: chain F residue 1197 MET Chi-restraints excluded: chain F residue 1323 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 447 optimal weight: 8.9990 chunk 600 optimal weight: 8.9990 chunk 172 optimal weight: 2.9990 chunk 519 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 156 optimal weight: 20.0000 chunk 564 optimal weight: 0.0980 chunk 236 optimal weight: 10.0000 chunk 579 optimal weight: 6.9990 chunk 71 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2124 GLN A2515 HIS ** B1725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1992 ASN B2124 GLN B2515 HIS ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 978 HIS ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 978 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.085241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.055707 restraints weight = 291114.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 86)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.056782 restraints weight = 131459.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.057806 restraints weight = 82219.817| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 58060 Z= 0.207 Angle : 0.614 11.893 78778 Z= 0.298 Chirality : 0.041 0.297 8944 Planarity : 0.004 0.057 10028 Dihedral : 4.631 64.184 7820 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.71 % Favored : 97.24 % Rotamer: Outliers : 1.75 % Allowed : 15.25 % Favored : 83.00 % 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: 1.72 (0.10), residues: 7024 helix: 2.12 (0.08), residues: 4278 sheet: -0.64 (0.21), residues: 676 loop : -0.27 (0.14), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 197 HIS 0.045 0.001 HIS F 978 PHE 0.022 0.001 PHE A1122 TYR 0.026 0.001 TYR C 184 ARG 0.013 0.000 ARG B 859 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11210.85 seconds wall clock time: 200 minutes 17.94 seconds (12017.94 seconds total)