Starting phenix.real_space_refine on Tue Mar 19 04:03:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcy_28999/03_2024/8fcy_28999_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcy_28999/03_2024/8fcy_28999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcy_28999/03_2024/8fcy_28999.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcy_28999/03_2024/8fcy_28999.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcy_28999/03_2024/8fcy_28999_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcy_28999/03_2024/8fcy_28999_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.044 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 9 5.49 5 S 116 5.16 5 C 14723 2.51 5 N 3996 2.21 5 O 4298 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A ASP 279": "OD1" <-> "OD2" Residue "A GLU 331": "OE1" <-> "OE2" Residue "A PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 866": "OD1" <-> "OD2" Residue "A TYR 1183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1332": "OD1" <-> "OD2" Residue "A GLU 1353": "OE1" <-> "OE2" Residue "A ASP 1407": "OD1" <-> "OD2" Residue "A TYR 1512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1762": "OE1" <-> "OE2" Residue "A ASP 2148": "OD1" <-> "OD2" Residue "A GLU 2219": "OE1" <-> "OE2" Residue "A GLU 2497": "OE1" <-> "OE2" Residue "A ASP 2508": "OD1" <-> "OD2" Residue "A PHE 2607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3095": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23142 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 23142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2868, 23142 Unusual residues: {'ADP': 3, 'ATP': 1} Classifications: {'peptide': 2864, 'undetermined': 4} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 129, 'TRANS': 2734, None: 4} Not linked: pdbres="THR A3127 " pdbres="ADP A3201 " Not linked: pdbres="ADP A3201 " pdbres="ATP A3202 " Not linked: pdbres="ATP A3202 " pdbres="ADP A3203 " Not linked: pdbres="ADP A3203 " pdbres="ADP A3204 " Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 12.14, per 1000 atoms: 0.52 Number of scatterers: 23142 At special positions: 0 Unit cell: (128.688, 170.052, 151.668, 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 116 16.00 P 9 15.00 O 4298 8.00 N 3996 7.00 C 14723 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.92 Conformation dependent library (CDL) restraints added in 4.4 seconds 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5450 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 117 helices and 19 sheets defined 53.0% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.45 Creating SS restraints... Processing helix chain 'A' and resid 9 through 15 Processing helix chain 'A' and resid 36 through 54 removed outlier: 3.763A pdb=" N LYS A 41 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N VAL A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 96 removed outlier: 4.028A pdb=" N ASP A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 129 Processing helix chain 'A' and resid 142 through 169 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 179 through 187 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 199 through 201 No H-bonds generated for 'chain 'A' and resid 199 through 201' Processing helix chain 'A' and resid 243 through 273 removed outlier: 4.214A pdb=" N ILE A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE A 272 " --> pdb=" O GLU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 292 through 315 Processing helix chain 'A' and resid 322 through 340 Processing helix chain 'A' and resid 347 through 369 removed outlier: 3.579A pdb=" N HIS A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 384 No H-bonds generated for 'chain 'A' and resid 381 through 384' Processing helix chain 'A' and resid 398 through 400 No H-bonds generated for 'chain 'A' and resid 398 through 400' Processing helix chain 'A' and resid 428 through 442 Processing helix chain 'A' and resid 457 through 467 Processing helix chain 'A' and resid 485 through 496 removed outlier: 4.271A pdb=" N PHE A 490 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL A 496 " --> pdb=" O LEU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 507 No H-bonds generated for 'chain 'A' and resid 505 through 507' Processing helix chain 'A' and resid 510 through 531 removed outlier: 3.915A pdb=" N GLU A 529 " --> pdb=" O GLU A 525 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N HIS A 530 " --> pdb=" O ALA A 526 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N SER A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 601 Processing helix chain 'A' and resid 607 through 621 Proline residue: A 616 - end of helix Processing helix chain 'A' and resid 635 through 658 Processing helix chain 'A' and resid 678 through 690 Processing helix chain 'A' and resid 699 through 709 Processing helix chain 'A' and resid 721 through 733 removed outlier: 3.583A pdb=" N GLU A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 759 Processing helix chain 'A' and resid 776 through 790 Processing helix chain 'A' and resid 806 through 810 removed outlier: 4.235A pdb=" N TYR A 810 " --> pdb=" O ASP A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 833 Processing helix chain 'A' and resid 857 through 864 removed outlier: 5.005A pdb=" N SER A 862 " --> pdb=" O GLU A 858 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N VAL A 863 " --> pdb=" O ASN A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 902 Processing helix chain 'A' and resid 911 through 913 No H-bonds generated for 'chain 'A' and resid 911 through 913' Processing helix chain 'A' and resid 916 through 928 Processing helix chain 'A' and resid 956 through 971 removed outlier: 3.593A pdb=" N ILE A 967 " --> pdb=" O ASP A 963 " (cutoff:3.500A) Proline residue: A 970 - end of helix Processing helix chain 'A' and resid 978 through 987 removed outlier: 3.686A pdb=" N PHE A 986 " --> pdb=" O LEU A 982 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLN A 987 " --> pdb=" O GLU A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1020 removed outlier: 3.524A pdb=" N GLY A1001 " --> pdb=" O LEU A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1047 removed outlier: 3.673A pdb=" N ARG A1033 " --> pdb=" O GLU A1029 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG A1037 " --> pdb=" O ARG A1033 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL A1040 " --> pdb=" O GLN A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1066 Processing helix chain 'A' and resid 1079 through 1081 No H-bonds generated for 'chain 'A' and resid 1079 through 1081' Processing helix chain 'A' and resid 1093 through 1096 Processing helix chain 'A' and resid 1117 through 1131 removed outlier: 3.775A pdb=" N ALA A1124 " --> pdb=" O VAL A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1156 removed outlier: 3.879A pdb=" N ALA A1156 " --> pdb=" O SER A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1183 Processing helix chain 'A' and resid 1223 through 1233 removed outlier: 3.549A pdb=" N VAL A1232 " --> pdb=" O ILE A1228 " (cutoff:3.500A) Processing helix chain 'A' and resid 1270 through 1273 No H-bonds generated for 'chain 'A' and resid 1270 through 1273' Processing helix chain 'A' and resid 1286 through 1303 removed outlier: 3.936A pdb=" N THR A1295 " --> pdb=" O GLN A1291 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE A1296 " --> pdb=" O ILE A1292 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A1302 " --> pdb=" O ARG A1298 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N LEU A1303 " --> pdb=" O ALA A1299 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1327 removed outlier: 4.538A pdb=" N GLU A1312 " --> pdb=" O THR A1309 " (cutoff:3.500A) Proline residue: A1313 - end of helix removed outlier: 3.746A pdb=" N PHE A1321 " --> pdb=" O MET A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1341 through 1356 Processing helix chain 'A' and resid 1363 through 1378 Processing helix chain 'A' and resid 1385 through 1402 Processing helix chain 'A' and resid 1409 through 1412 No H-bonds generated for 'chain 'A' and resid 1409 through 1412' Processing helix chain 'A' and resid 1431 through 1448 removed outlier: 3.972A pdb=" N GLU A1447 " --> pdb=" O LYS A1443 " (cutoff:3.500A) Processing helix chain 'A' and resid 1458 through 1472 Processing helix chain 'A' and resid 1488 through 1498 Processing helix chain 'A' and resid 1514 through 1528 Processing helix chain 'A' and resid 1530 through 1532 No H-bonds generated for 'chain 'A' and resid 1530 through 1532' Processing helix chain 'A' and resid 1547 through 1557 Processing helix chain 'A' and resid 1568 through 1585 Processing helix chain 'A' and resid 1592 through 1605 Processing helix chain 'A' and resid 1618 through 1626 Processing helix chain 'A' and resid 1628 through 1632 Processing helix chain 'A' and resid 1644 through 1654 Processing helix chain 'A' and resid 1684 through 1708 Processing helix chain 'A' and resid 1718 through 1764 Processing helix chain 'A' and resid 1954 through 1983 removed outlier: 3.920A pdb=" N ASN A1980 " --> pdb=" O GLU A1976 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET A1982 " --> pdb=" O PHE A1978 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A1983 " --> pdb=" O LYS A1979 " (cutoff:3.500A) Processing helix chain 'A' and resid 1986 through 1997 Processing helix chain 'A' and resid 2004 through 2020 Processing helix chain 'A' and resid 2031 through 2034 No H-bonds generated for 'chain 'A' and resid 2031 through 2034' Processing helix chain 'A' and resid 2038 through 2046 Processing helix chain 'A' and resid 2053 through 2063 Processing helix chain 'A' and resid 2077 through 2085 Processing helix chain 'A' and resid 2101 through 2111 removed outlier: 3.778A pdb=" N PHE A2111 " --> pdb=" O SER A2107 " (cutoff:3.500A) Processing helix chain 'A' and resid 2125 through 2131 Proline residue: A2129 - end of helix Processing helix chain 'A' and resid 2172 through 2177 removed outlier: 3.686A pdb=" N ARG A2177 " --> pdb=" O ASP A2173 " (cutoff:3.500A) Processing helix chain 'A' and resid 2187 through 2201 Processing helix chain 'A' and resid 2204 through 2215 Processing helix chain 'A' and resid 2219 through 2238 removed outlier: 3.543A pdb=" N ARG A2225 " --> pdb=" O GLN A2221 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A2226 " --> pdb=" O LEU A2222 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU A2227 " --> pdb=" O ARG A2223 " (cutoff:3.500A) Processing helix chain 'A' and resid 2245 through 2301 removed outlier: 3.554A pdb=" N THR A2251 " --> pdb=" O THR A2247 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA A2259 " --> pdb=" O LEU A2255 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A2268 " --> pdb=" O ARG A2264 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ASP A2270 " --> pdb=" O VAL A2266 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ILE A2271 " --> pdb=" O GLU A2267 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET A2273 " --> pdb=" O THR A2269 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A2274 " --> pdb=" O ASP A2270 " (cutoff:3.500A) Proline residue: A2285 - end of helix removed outlier: 4.527A pdb=" N LYS A2301 " --> pdb=" O MET A2297 " (cutoff:3.500A) Processing helix chain 'A' and resid 2311 through 2323 Processing helix chain 'A' and resid 2326 through 2328 No H-bonds generated for 'chain 'A' and resid 2326 through 2328' Processing helix chain 'A' and resid 2336 through 2356 removed outlier: 3.640A pdb=" N ARG A2355 " --> pdb=" O ASN A2351 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY A2356 " --> pdb=" O ARG A2352 " (cutoff:3.500A) Processing helix chain 'A' and resid 2362 through 2376 Processing helix chain 'A' and resid 2384 through 2391 Processing helix chain 'A' and resid 2393 through 2395 No H-bonds generated for 'chain 'A' and resid 2393 through 2395' Processing helix chain 'A' and resid 2411 through 2422 removed outlier: 3.887A pdb=" N CYS A2422 " --> pdb=" O VAL A2418 " (cutoff:3.500A) Processing helix chain 'A' and resid 2430 through 2434 Processing helix chain 'A' and resid 2437 through 2444 Processing helix chain 'A' and resid 2464 through 2477 Processing helix chain 'A' and resid 2480 through 2495 removed outlier: 4.054A pdb=" N LEU A2484 " --> pdb=" O ASP A2481 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR A2493 " --> pdb=" O PHE A2490 " (cutoff:3.500A) Processing helix chain 'A' and resid 2501 through 2504 No H-bonds generated for 'chain 'A' and resid 2501 through 2504' Processing helix chain 'A' and resid 2509 through 2512 No H-bonds generated for 'chain 'A' and resid 2509 through 2512' Processing helix chain 'A' and resid 2534 through 2544 Processing helix chain 'A' and resid 2556 through 2569 removed outlier: 4.449A pdb=" N ASN A2560 " --> pdb=" O ALA A2556 " (cutoff:3.500A) Processing helix chain 'A' and resid 2585 through 2595 Processing helix chain 'A' and resid 2618 through 2623 Processing helix chain 'A' and resid 2635 through 2645 Processing helix chain 'A' and resid 2648 through 2652 Processing helix chain 'A' and resid 2658 through 2677 removed outlier: 3.875A pdb=" N LEU A2676 " --> pdb=" O ILE A2672 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ARG A2677 " --> pdb=" O GLN A2673 " (cutoff:3.500A) Processing helix chain 'A' and resid 2691 through 2708 Processing helix chain 'A' and resid 2722 through 2731 Processing helix chain 'A' and resid 2741 through 2754 Processing helix chain 'A' and resid 2757 through 2760 Processing helix chain 'A' and resid 2784 through 2792 Processing helix chain 'A' and resid 2800 through 2803 Processing helix chain 'A' and resid 2809 through 2827 Processing helix chain 'A' and resid 2858 through 2872 removed outlier: 3.806A pdb=" N THR A2865 " --> pdb=" O THR A2861 " (cutoff:3.500A) Processing helix chain 'A' and resid 2890 through 2920 Processing helix chain 'A' and resid 2928 through 2938 Processing helix chain 'A' and resid 2944 through 2946 No H-bonds generated for 'chain 'A' and resid 2944 through 2946' Processing helix chain 'A' and resid 2957 through 2980 Processing helix chain 'A' and resid 2985 through 2988 No H-bonds generated for 'chain 'A' and resid 2985 through 2988' Processing helix chain 'A' and resid 2993 through 2995 No H-bonds generated for 'chain 'A' and resid 2993 through 2995' Processing helix chain 'A' and resid 2999 through 3013 Processing helix chain 'A' and resid 3018 through 3020 No H-bonds generated for 'chain 'A' and resid 3018 through 3020' Processing helix chain 'A' and resid 3114 through 3120 Processing sheet with id= A, first strand: chain 'A' and resid 22 through 24 Processing sheet with id= B, first strand: chain 'A' and resid 228 through 230 removed outlier: 6.618A pdb=" N ILE A 210 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ILE A 221 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N SER A 208 " --> pdb=" O ILE A 221 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 388 through 391 Processing sheet with id= D, first strand: chain 'A' and resid 446 through 450 Processing sheet with id= E, first strand: chain 'A' and resid 543 through 545 Processing sheet with id= F, first strand: chain 'A' and resid 766 through 768 removed outlier: 7.445A pdb=" N MET A 767 " --> pdb=" O ILE A 886 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N PHE A 888 " --> pdb=" O MET A 767 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N GLU A 793 " --> pdb=" O ARG A 843 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N TRP A 845 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL A 795 " --> pdb=" O TRP A 845 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL A 847 " --> pdb=" O VAL A 795 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N HIS A 797 " --> pdb=" O VAL A 847 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 811 through 814 removed outlier: 3.744A pdb=" N ASP A 814 " --> pdb=" O GLU A 819 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU A 819 " --> pdb=" O ASP A 814 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 869 through 872 removed outlier: 3.744A pdb=" N GLU A 876 " --> pdb=" O LEU A 872 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1082 through 1085 removed outlier: 3.503A pdb=" N GLU A1089 " --> pdb=" O SER A1085 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1277 through 1280 removed outlier: 3.538A pdb=" N VAL A1137 " --> pdb=" O PRO A1277 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU A1204 " --> pdb=" O GLN A1252 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL A1254 " --> pdb=" O LEU A1204 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LEU A1206 " --> pdb=" O VAL A1254 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ALA A1256 " --> pdb=" O LEU A1206 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N CYS A1208 " --> pdb=" O ALA A1256 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1236 through 1238 Processing sheet with id= L, first strand: chain 'A' and resid 1635 through 1638 removed outlier: 3.654A pdb=" N ILE A1481 " --> pdb=" O ASN A1637 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N SER A1502 " --> pdb=" O ALA A1536 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ILE A1538 " --> pdb=" O SER A1502 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N TYR A1504 " --> pdb=" O ILE A1538 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ASP A1540 " --> pdb=" O TYR A1504 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 2179 through 2182 removed outlier: 3.514A pdb=" N VAL A2181 " --> pdb=" O LEU A2070 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ILE A2159 " --> pdb=" O PRO A2069 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N ILE A2071 " --> pdb=" O ILE A2159 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LEU A2161 " --> pdb=" O ILE A2071 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A2115 " --> pdb=" O PHE A2160 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N SER A2162 " --> pdb=" O LEU A2115 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL A2117 " --> pdb=" O SER A2162 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N THR A2092 " --> pdb=" O LEU A2116 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N GLN A2118 " --> pdb=" O THR A2092 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N THR A2094 " --> pdb=" O GLN A2118 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 2136 through 2138 Processing sheet with id= O, first strand: chain 'A' and resid 2626 through 2629 removed outlier: 6.344A pdb=" N LEU A2524 " --> pdb=" O PHE A2627 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N PHE A2629 " --> pdb=" O LEU A2524 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N CYS A2526 " --> pdb=" O PHE A2629 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL A2576 " --> pdb=" O PHE A2607 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N THR A2609 " --> pdb=" O VAL A2576 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU A2578 " --> pdb=" O THR A2609 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N GLU A2611 " --> pdb=" O LEU A2578 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 2990 through 2992 removed outlier: 10.101A pdb=" N VAL A2991 " --> pdb=" O SER A3039 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLY A3041 " --> pdb=" O VAL A2991 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 3046 through 3048 removed outlier: 3.600A pdb=" N ALA A3123 " --> pdb=" O GLN A3048 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 3050 through 3052 Processing sheet with id= S, first strand: chain 'A' and resid 3086 through 3092 removed outlier: 3.855A pdb=" N PHE A3102 " --> pdb=" O VAL A3091 " (cutoff:3.500A) 1090 hydrogen bonds defined for protein. 3063 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.55 Time building geometry restraints manager: 10.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7339 1.34 - 1.46: 3206 1.46 - 1.57: 12890 1.57 - 1.69: 14 1.69 - 1.81: 194 Bond restraints: 23643 Sorted by residual: bond pdb=" N GLU A1312 " pdb=" CA GLU A1312 " ideal model delta sigma weight residual 1.462 1.491 -0.029 8.50e-03 1.38e+04 1.18e+01 bond pdb=" N ILE A 930 " pdb=" CA ILE A 930 " ideal model delta sigma weight residual 1.461 1.500 -0.039 1.23e-02 6.61e+03 1.02e+01 bond pdb=" N GLY A 811 " pdb=" CA GLY A 811 " ideal model delta sigma weight residual 1.448 1.476 -0.028 8.80e-03 1.29e+04 1.01e+01 bond pdb=" N VAL A1319 " pdb=" CA VAL A1319 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.57e+00 bond pdb=" N GLY A 823 " pdb=" CA GLY A 823 " ideal model delta sigma weight residual 1.446 1.477 -0.031 1.06e-02 8.90e+03 8.45e+00 ... (remaining 23638 not shown) Histogram of bond angle deviations from ideal: 99.42 - 107.49: 934 107.49 - 115.55: 14437 115.55 - 123.62: 15996 123.62 - 131.68: 645 131.68 - 139.74: 58 Bond angle restraints: 32070 Sorted by residual: angle pdb=" CA GLY A 811 " pdb=" C GLY A 811 " pdb=" O GLY A 811 " ideal model delta sigma weight residual 122.37 118.12 4.25 7.30e-01 1.88e+00 3.39e+01 angle pdb=" C ASP A 478 " pdb=" CA ASP A 478 " pdb=" CB ASP A 478 " ideal model delta sigma weight residual 117.23 110.42 6.81 1.36e+00 5.41e-01 2.51e+01 angle pdb=" CA GLY A 823 " pdb=" C GLY A 823 " pdb=" O GLY A 823 " ideal model delta sigma weight residual 122.28 117.78 4.50 1.00e+00 1.00e+00 2.03e+01 angle pdb=" N GLU A 855 " pdb=" CA GLU A 855 " pdb=" C GLU A 855 " ideal model delta sigma weight residual 113.43 108.42 5.01 1.26e+00 6.30e-01 1.58e+01 angle pdb=" N ILE A2553 " pdb=" CA ILE A2553 " pdb=" C ILE A2553 " ideal model delta sigma weight residual 113.53 109.87 3.66 9.80e-01 1.04e+00 1.40e+01 ... (remaining 32065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.33: 14040 35.33 - 70.66: 249 70.66 - 105.99: 36 105.99 - 141.33: 2 141.33 - 176.66: 2 Dihedral angle restraints: 14329 sinusoidal: 5941 harmonic: 8388 Sorted by residual: dihedral pdb=" C5' ADP A3201 " pdb=" O5' ADP A3201 " pdb=" PA ADP A3201 " pdb=" O2A ADP A3201 " ideal model delta sinusoidal sigma weight residual -60.00 116.66 -176.66 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP A3201 " pdb=" O3A ADP A3201 " pdb=" PA ADP A3201 " pdb=" PB ADP A3201 " ideal model delta sinusoidal sigma weight residual -60.00 94.28 -154.28 1 2.00e+01 2.50e-03 4.56e+01 dihedral pdb=" O1B ADP A3201 " pdb=" O3A ADP A3201 " pdb=" PB ADP A3201 " pdb=" PA ADP A3201 " ideal model delta sinusoidal sigma weight residual -60.00 75.11 -135.11 1 2.00e+01 2.50e-03 4.10e+01 ... (remaining 14326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2614 0.040 - 0.080: 724 0.080 - 0.119: 233 0.119 - 0.159: 36 0.159 - 0.199: 3 Chirality restraints: 3610 Sorted by residual: chirality pdb=" CB ILE A2715 " pdb=" CA ILE A2715 " pdb=" CG1 ILE A2715 " pdb=" CG2 ILE A2715 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" CB ILE A1481 " pdb=" CA ILE A1481 " pdb=" CG1 ILE A1481 " pdb=" CG2 ILE A1481 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.31e-01 chirality pdb=" CA MET A1318 " pdb=" N MET A1318 " pdb=" C MET A1318 " pdb=" CB MET A1318 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.16e-01 ... (remaining 3607 not shown) Planarity restraints: 4099 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A1680 " 0.051 5.00e-02 4.00e+02 7.64e-02 9.34e+00 pdb=" N PRO A1681 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO A1681 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A1681 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A2716 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO A2717 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A2717 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A2717 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A2654 " 0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO A2655 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A2655 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A2655 " 0.026 5.00e-02 4.00e+02 ... (remaining 4096 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3504 2.76 - 3.29: 23707 3.29 - 3.83: 38843 3.83 - 4.36: 44647 4.36 - 4.90: 76494 Nonbonded interactions: 187195 Sorted by model distance: nonbonded pdb=" O LYS A1579 " pdb=" NE2 GLN A1583 " model vdw 2.224 2.520 nonbonded pdb=" O THR A1573 " pdb=" OG1 THR A1576 " model vdw 2.236 2.440 nonbonded pdb=" O MET A 52 " pdb=" OG SER A 55 " model vdw 2.250 2.440 nonbonded pdb=" OG SER A2492 " pdb=" OE1 GLU A2497 " model vdw 2.258 2.440 nonbonded pdb=" OD1 ASP A1540 " pdb=" OG1 THR A1612 " model vdw 2.268 2.440 ... (remaining 187190 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 11.350 Check model and map are aligned: 0.380 Set scattering table: 0.210 Process input model: 68.030 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.090 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 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 0.039 23643 Z= 0.196 Angle : 0.586 9.117 32070 Z= 0.341 Chirality : 0.041 0.199 3610 Planarity : 0.004 0.076 4099 Dihedral : 14.750 176.657 8879 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.45 % Favored : 95.51 % Rotamer: Outliers : 0.12 % Allowed : 0.35 % Favored : 99.53 % 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: 0.50 (0.17), residues: 2852 helix: 1.51 (0.14), residues: 1566 sheet: -1.45 (0.35), residues: 224 loop : -1.01 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 246 HIS 0.004 0.001 HIS A2601 PHE 0.013 0.001 PHE A 61 TYR 0.019 0.001 TYR A1675 ARG 0.006 0.000 ARG A 33 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 387 time to evaluate : 2.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7668 (mm) cc_final: 0.7036 (tp) REVERT: A 134 MET cc_start: 0.6079 (mpp) cc_final: 0.5850 (tpt) REVERT: A 1052 ARG cc_start: 0.7205 (mtm180) cc_final: 0.6645 (ptt90) REVERT: A 1200 LEU cc_start: 0.8803 (mm) cc_final: 0.8335 (tp) REVERT: A 1310 TYR cc_start: 0.7027 (m-80) cc_final: 0.6702 (m-80) REVERT: A 1386 GLU cc_start: 0.7905 (pm20) cc_final: 0.7654 (pm20) REVERT: A 1575 MET cc_start: 0.8018 (mmm) cc_final: 0.7728 (mmt) REVERT: A 1653 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7229 (tm-30) REVERT: A 1658 MET cc_start: 0.8209 (tpp) cc_final: 0.7386 (ttm) REVERT: A 1726 ASN cc_start: 0.8448 (m-40) cc_final: 0.8091 (m-40) REVERT: A 1968 ARG cc_start: 0.6617 (mmt180) cc_final: 0.5163 (ttm110) REVERT: A 2200 LYS cc_start: 0.8211 (tppt) cc_final: 0.7931 (ttpp) REVERT: A 2505 GLN cc_start: 0.8325 (tm-30) cc_final: 0.7639 (mt0) REVERT: A 2545 ASN cc_start: 0.8753 (m-40) cc_final: 0.8549 (m-40) REVERT: A 2639 MET cc_start: 0.8548 (mtp) cc_final: 0.7929 (mtp) REVERT: A 3112 GLU cc_start: 0.7312 (mp0) cc_final: 0.6721 (mp0) outliers start: 3 outliers final: 0 residues processed: 388 average time/residue: 0.3809 time to fit residues: 224.2054 Evaluate side-chains 217 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 2.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 241 optimal weight: 6.9990 chunk 216 optimal weight: 20.0000 chunk 120 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 224 optimal weight: 4.9990 chunk 86 optimal weight: 0.0870 chunk 136 optimal weight: 0.7980 chunk 166 optimal weight: 6.9990 chunk 259 optimal weight: 5.9990 overall best weight: 2.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 HIS A 484 GLN ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1016 GLN A1297 ASN A1577 GLN ** A1583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1592 HIS ** A1602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1742 GLN A1743 GLN A1745 HIS A2019 GLN A2022 ASN ** A2236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2362 HIS A2450 GLN A2511 HIS ** A3012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3094 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 23643 Z= 0.394 Angle : 0.619 9.995 32070 Z= 0.310 Chirality : 0.043 0.246 3610 Planarity : 0.004 0.054 4099 Dihedral : 7.350 165.721 3181 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.22 % Favored : 94.74 % Rotamer: Outliers : 1.45 % Allowed : 8.20 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.16), residues: 2852 helix: 1.18 (0.13), residues: 1577 sheet: -1.71 (0.33), residues: 236 loop : -0.98 (0.20), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 68 HIS 0.017 0.001 HIS A 104 PHE 0.034 0.002 PHE A2295 TYR 0.017 0.002 TYR A2929 ARG 0.006 0.001 ARG A 843 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 221 time to evaluate : 2.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.6456 (mpp) cc_final: 0.6065 (tpt) REVERT: A 135 ASP cc_start: 0.7257 (OUTLIER) cc_final: 0.6903 (t0) REVERT: A 1052 ARG cc_start: 0.7152 (mtm180) cc_final: 0.6601 (ptt90) REVERT: A 1200 LEU cc_start: 0.8758 (mm) cc_final: 0.8266 (tp) REVERT: A 1310 TYR cc_start: 0.7343 (m-80) cc_final: 0.6678 (m-80) REVERT: A 1541 GLU cc_start: 0.7812 (tp30) cc_final: 0.7590 (tp30) REVERT: A 1574 LEU cc_start: 0.8713 (pp) cc_final: 0.8383 (pp) REVERT: A 1575 MET cc_start: 0.8062 (mmm) cc_final: 0.7741 (mmm) REVERT: A 1605 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8830 (tmm-80) REVERT: A 1726 ASN cc_start: 0.8607 (m-40) cc_final: 0.8235 (m-40) REVERT: A 1968 ARG cc_start: 0.6288 (mmt180) cc_final: 0.5060 (ttm110) REVERT: A 1979 LYS cc_start: 0.6689 (mmtm) cc_final: 0.5707 (tttt) REVERT: A 1998 TYR cc_start: 0.8401 (m-80) cc_final: 0.7645 (m-80) REVERT: A 2106 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8456 (pm20) REVERT: A 2200 LYS cc_start: 0.8243 (tppt) cc_final: 0.7936 (ttpp) REVERT: A 2274 GLN cc_start: 0.6598 (mp10) cc_final: 0.6256 (mp10) REVERT: A 2545 ASN cc_start: 0.8816 (m-40) cc_final: 0.8516 (m-40) REVERT: A 2559 PHE cc_start: 0.7252 (m-10) cc_final: 0.6952 (m-10) REVERT: A 2610 MET cc_start: 0.7196 (tpt) cc_final: 0.6960 (tpp) REVERT: A 3112 GLU cc_start: 0.7353 (mp0) cc_final: 0.7054 (mp0) outliers start: 37 outliers final: 24 residues processed: 246 average time/residue: 0.3927 time to fit residues: 150.1725 Evaluate side-chains 222 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 195 time to evaluate : 2.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 511 ARG Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1587 LEU Chi-restraints excluded: chain A residue 1603 VAL Chi-restraints excluded: chain A residue 1605 ARG Chi-restraints excluded: chain A residue 1745 HIS Chi-restraints excluded: chain A residue 2092 THR Chi-restraints excluded: chain A residue 2099 ASP Chi-restraints excluded: chain A residue 2106 GLU Chi-restraints excluded: chain A residue 2118 GLN Chi-restraints excluded: chain A residue 2175 CYS Chi-restraints excluded: chain A residue 2216 LEU Chi-restraints excluded: chain A residue 2714 ASN Chi-restraints excluded: chain A residue 2732 SER Chi-restraints excluded: chain A residue 2733 ILE Chi-restraints excluded: chain A residue 3036 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 144 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 216 optimal weight: 20.0000 chunk 176 optimal weight: 0.1980 chunk 71 optimal weight: 0.8980 chunk 260 optimal weight: 3.9990 chunk 281 optimal weight: 4.9990 chunk 231 optimal weight: 2.9990 chunk 258 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 208 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 157 GLN A1297 ASN ** A1583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2254 ASN ** A3012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23643 Z= 0.202 Angle : 0.528 9.703 32070 Z= 0.263 Chirality : 0.040 0.271 3610 Planarity : 0.004 0.045 4099 Dihedral : 7.087 152.286 3181 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.70 % Favored : 95.27 % Rotamer: Outliers : 1.45 % Allowed : 10.28 % Favored : 88.27 % 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: 0.33 (0.16), residues: 2852 helix: 1.30 (0.13), residues: 1578 sheet: -1.56 (0.33), residues: 241 loop : -0.97 (0.20), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 779 HIS 0.006 0.001 HIS A1745 PHE 0.020 0.001 PHE A2295 TYR 0.019 0.001 TYR A2294 ARG 0.005 0.000 ARG A1389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 219 time to evaluate : 2.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.6246 (mpp) cc_final: 0.5915 (tpt) REVERT: A 135 ASP cc_start: 0.7303 (OUTLIER) cc_final: 0.7037 (t0) REVERT: A 1052 ARG cc_start: 0.7133 (mtm180) cc_final: 0.6593 (ptt90) REVERT: A 1200 LEU cc_start: 0.8688 (mm) cc_final: 0.8223 (tp) REVERT: A 1310 TYR cc_start: 0.7331 (m-80) cc_final: 0.6666 (m-80) REVERT: A 1575 MET cc_start: 0.8161 (mmm) cc_final: 0.7757 (mmt) REVERT: A 1605 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8873 (tmm-80) REVERT: A 1657 LYS cc_start: 0.8955 (mmmm) cc_final: 0.8610 (mtmm) REVERT: A 1726 ASN cc_start: 0.8615 (m-40) cc_final: 0.8244 (m-40) REVERT: A 1744 MET cc_start: 0.7004 (tmm) cc_final: 0.6732 (ppp) REVERT: A 1968 ARG cc_start: 0.6302 (mmt180) cc_final: 0.4995 (ttm110) REVERT: A 1998 TYR cc_start: 0.8268 (m-80) cc_final: 0.7664 (m-80) REVERT: A 2083 MET cc_start: 0.8730 (mmm) cc_final: 0.8496 (mmm) REVERT: A 2106 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8452 (pm20) REVERT: A 2165 ASP cc_start: 0.8233 (p0) cc_final: 0.7970 (p0) REVERT: A 2200 LYS cc_start: 0.8322 (tppt) cc_final: 0.8002 (ttpp) REVERT: A 2274 GLN cc_start: 0.6631 (mp10) cc_final: 0.6301 (mp10) REVERT: A 2545 ASN cc_start: 0.8823 (m-40) cc_final: 0.8529 (m-40) REVERT: A 2610 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.7148 (tpp) REVERT: A 3112 GLU cc_start: 0.7207 (mp0) cc_final: 0.6996 (mp0) outliers start: 37 outliers final: 23 residues processed: 244 average time/residue: 0.3644 time to fit residues: 140.4802 Evaluate side-chains 230 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 203 time to evaluate : 2.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 511 ARG Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1513 THR Chi-restraints excluded: chain A residue 1587 LEU Chi-restraints excluded: chain A residue 1603 VAL Chi-restraints excluded: chain A residue 1605 ARG Chi-restraints excluded: chain A residue 1639 PHE Chi-restraints excluded: chain A residue 1981 GLN Chi-restraints excluded: chain A residue 2092 THR Chi-restraints excluded: chain A residue 2099 ASP Chi-restraints excluded: chain A residue 2106 GLU Chi-restraints excluded: chain A residue 2118 GLN Chi-restraints excluded: chain A residue 2216 LEU Chi-restraints excluded: chain A residue 2403 THR Chi-restraints excluded: chain A residue 2610 MET Chi-restraints excluded: chain A residue 2714 ASN Chi-restraints excluded: chain A residue 3036 ASP Chi-restraints excluded: chain A residue 3099 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 257 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 chunk 135 optimal weight: 0.0570 chunk 28 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 174 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 chunk 276 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 247 optimal weight: 0.0670 chunk 74 optimal weight: 1.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 HIS A 532 ASN A 844 GLN ** A1583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2084 ASN ** A3012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23643 Z= 0.148 Angle : 0.495 9.669 32070 Z= 0.246 Chirality : 0.039 0.265 3610 Planarity : 0.003 0.049 4099 Dihedral : 6.729 146.600 3181 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.52 % Favored : 95.44 % Rotamer: Outliers : 1.65 % Allowed : 11.58 % Favored : 86.77 % 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: 0.57 (0.16), residues: 2852 helix: 1.50 (0.13), residues: 1582 sheet: -1.28 (0.35), residues: 227 loop : -0.94 (0.20), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 246 HIS 0.016 0.001 HIS A 104 PHE 0.018 0.001 PHE A2295 TYR 0.017 0.001 TYR A2294 ARG 0.003 0.000 ARG A 843 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 223 time to evaluate : 2.892 Fit side-chains revert: symmetry clash REVERT: A 13 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6447 (pp20) REVERT: A 135 ASP cc_start: 0.7389 (OUTLIER) cc_final: 0.7139 (t0) REVERT: A 1052 ARG cc_start: 0.7092 (mtm180) cc_final: 0.6604 (ptt90) REVERT: A 1200 LEU cc_start: 0.8635 (mm) cc_final: 0.8173 (tp) REVERT: A 1310 TYR cc_start: 0.7286 (m-80) cc_final: 0.6796 (m-80) REVERT: A 1389 ARG cc_start: 0.7449 (mtm110) cc_final: 0.6597 (ptp-170) REVERT: A 1575 MET cc_start: 0.8211 (mmm) cc_final: 0.7904 (mmt) REVERT: A 1657 LYS cc_start: 0.8945 (mmmm) cc_final: 0.8600 (mtmm) REVERT: A 1726 ASN cc_start: 0.8598 (m-40) cc_final: 0.8235 (m-40) REVERT: A 1968 ARG cc_start: 0.6359 (mmt180) cc_final: 0.5034 (ttm110) REVERT: A 1998 TYR cc_start: 0.8203 (m-80) cc_final: 0.7722 (m-80) REVERT: A 2083 MET cc_start: 0.8751 (mmm) cc_final: 0.8530 (mmm) REVERT: A 2106 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8467 (pm20) REVERT: A 2118 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7962 (mt0) REVERT: A 2165 ASP cc_start: 0.8234 (p0) cc_final: 0.8011 (p0) REVERT: A 2200 LYS cc_start: 0.8336 (tppt) cc_final: 0.8012 (ttpp) REVERT: A 2228 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7364 (mt-10) REVERT: A 2545 ASN cc_start: 0.8828 (m-40) cc_final: 0.8527 (m-40) REVERT: A 2681 LEU cc_start: 0.9351 (tp) cc_final: 0.9103 (tp) outliers start: 42 outliers final: 24 residues processed: 252 average time/residue: 0.3884 time to fit residues: 155.5779 Evaluate side-chains 233 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 205 time to evaluate : 2.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 511 ARG Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1379 GLN Chi-restraints excluded: chain A residue 1513 THR Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1587 LEU Chi-restraints excluded: chain A residue 1639 PHE Chi-restraints excluded: chain A residue 1745 HIS Chi-restraints excluded: chain A residue 2099 ASP Chi-restraints excluded: chain A residue 2106 GLU Chi-restraints excluded: chain A residue 2118 GLN Chi-restraints excluded: chain A residue 2214 LEU Chi-restraints excluded: chain A residue 2269 THR Chi-restraints excluded: chain A residue 2403 THR Chi-restraints excluded: chain A residue 2998 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 230 optimal weight: 8.9990 chunk 156 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 205 optimal weight: 1.9990 chunk 114 optimal weight: 0.0670 chunk 235 optimal weight: 2.9990 chunk 191 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 141 optimal weight: 4.9990 chunk 248 optimal weight: 0.0030 chunk 69 optimal weight: 1.9990 overall best weight: 1.4134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 HIS ** A1583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1743 GLN A1745 HIS A2084 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23643 Z= 0.231 Angle : 0.524 10.500 32070 Z= 0.260 Chirality : 0.040 0.265 3610 Planarity : 0.004 0.057 4099 Dihedral : 6.619 152.704 3181 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.80 % Favored : 95.16 % Rotamer: Outliers : 1.81 % Allowed : 12.56 % Favored : 85.64 % 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: 0.54 (0.16), residues: 2852 helix: 1.47 (0.13), residues: 1581 sheet: -1.31 (0.34), residues: 242 loop : -0.94 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 246 HIS 0.013 0.001 HIS A1745 PHE 0.021 0.001 PHE A2220 TYR 0.016 0.001 TYR A2294 ARG 0.004 0.000 ARG A1389 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 211 time to evaluate : 2.758 Fit side-chains revert: symmetry clash REVERT: A 13 GLU cc_start: 0.6686 (OUTLIER) cc_final: 0.6407 (pp20) REVERT: A 135 ASP cc_start: 0.7489 (OUTLIER) cc_final: 0.7139 (t0) REVERT: A 1052 ARG cc_start: 0.7088 (mtm180) cc_final: 0.6615 (ptt90) REVERT: A 1200 LEU cc_start: 0.8628 (mm) cc_final: 0.8118 (tp) REVERT: A 1310 TYR cc_start: 0.7375 (m-80) cc_final: 0.6987 (m-80) REVERT: A 1389 ARG cc_start: 0.7442 (mtm110) cc_final: 0.6909 (ptp-170) REVERT: A 1575 MET cc_start: 0.8190 (mmm) cc_final: 0.7787 (mmm) REVERT: A 1657 LYS cc_start: 0.8972 (mmmm) cc_final: 0.8631 (mtmm) REVERT: A 1726 ASN cc_start: 0.8631 (m-40) cc_final: 0.8272 (m-40) REVERT: A 1968 ARG cc_start: 0.6336 (mmt180) cc_final: 0.4730 (ttm-80) REVERT: A 1998 TYR cc_start: 0.8304 (m-10) cc_final: 0.7769 (m-80) REVERT: A 2083 MET cc_start: 0.8750 (mmm) cc_final: 0.8527 (mmm) REVERT: A 2106 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8444 (pm20) REVERT: A 2118 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.8040 (mt0) REVERT: A 2165 ASP cc_start: 0.8340 (p0) cc_final: 0.8137 (p0) REVERT: A 2200 LYS cc_start: 0.8349 (tppt) cc_final: 0.8016 (ttpp) REVERT: A 2228 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7459 (mt-10) REVERT: A 2545 ASN cc_start: 0.8835 (m-40) cc_final: 0.8529 (m-40) outliers start: 46 outliers final: 33 residues processed: 244 average time/residue: 0.3617 time to fit residues: 140.9279 Evaluate side-chains 240 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 203 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 511 ARG Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1513 THR Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1587 LEU Chi-restraints excluded: chain A residue 1639 PHE Chi-restraints excluded: chain A residue 1745 HIS Chi-restraints excluded: chain A residue 2092 THR Chi-restraints excluded: chain A residue 2099 ASP Chi-restraints excluded: chain A residue 2106 GLU Chi-restraints excluded: chain A residue 2118 GLN Chi-restraints excluded: chain A residue 2216 LEU Chi-restraints excluded: chain A residue 2269 THR Chi-restraints excluded: chain A residue 2331 VAL Chi-restraints excluded: chain A residue 2403 THR Chi-restraints excluded: chain A residue 2733 ILE Chi-restraints excluded: chain A residue 2998 VAL Chi-restraints excluded: chain A residue 3036 ASP Chi-restraints excluded: chain A residue 3099 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 93 optimal weight: 5.9990 chunk 248 optimal weight: 0.0270 chunk 54 optimal weight: 0.0000 chunk 162 optimal weight: 0.0070 chunk 68 optimal weight: 4.9990 chunk 276 optimal weight: 2.9990 chunk 229 optimal weight: 6.9990 chunk 128 optimal weight: 0.0060 chunk 23 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 overall best weight: 0.1476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2005 GLN A2084 ASN A2351 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23643 Z= 0.122 Angle : 0.492 10.952 32070 Z= 0.242 Chirality : 0.038 0.294 3610 Planarity : 0.003 0.053 4099 Dihedral : 6.392 161.480 3181 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.21 % Favored : 95.76 % Rotamer: Outliers : 1.06 % Allowed : 13.50 % Favored : 85.44 % 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: 0.72 (0.16), residues: 2852 helix: 1.66 (0.13), residues: 1577 sheet: -1.08 (0.34), residues: 235 loop : -0.98 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2869 HIS 0.014 0.001 HIS A1745 PHE 0.015 0.001 PHE A1024 TYR 0.016 0.001 TYR A2294 ARG 0.004 0.000 ARG A1633 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 234 time to evaluate : 3.044 Fit side-chains revert: symmetry clash REVERT: A 13 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.6319 (pp20) REVERT: A 1052 ARG cc_start: 0.7029 (mtm180) cc_final: 0.6578 (ptt90) REVERT: A 1200 LEU cc_start: 0.8588 (mm) cc_final: 0.8091 (tp) REVERT: A 1310 TYR cc_start: 0.7229 (m-80) cc_final: 0.6846 (m-80) REVERT: A 1389 ARG cc_start: 0.7467 (mtm110) cc_final: 0.6891 (ptp-170) REVERT: A 1575 MET cc_start: 0.8149 (mmm) cc_final: 0.7676 (mmt) REVERT: A 1657 LYS cc_start: 0.8946 (mmmm) cc_final: 0.8644 (mtmm) REVERT: A 1658 MET cc_start: 0.8064 (tpp) cc_final: 0.7238 (ttm) REVERT: A 1726 ASN cc_start: 0.8578 (m-40) cc_final: 0.8237 (m-40) REVERT: A 1968 ARG cc_start: 0.6517 (mmt180) cc_final: 0.5137 (ttm110) REVERT: A 1998 TYR cc_start: 0.8137 (m-10) cc_final: 0.7802 (m-80) REVERT: A 2083 MET cc_start: 0.8679 (mmm) cc_final: 0.8430 (mmm) REVERT: A 2111 PHE cc_start: 0.8058 (m-80) cc_final: 0.7844 (m-80) REVERT: A 2200 LYS cc_start: 0.8315 (tppt) cc_final: 0.8034 (ttpp) REVERT: A 2545 ASN cc_start: 0.8886 (m-40) cc_final: 0.8589 (m-40) REVERT: A 2639 MET cc_start: 0.8387 (mtp) cc_final: 0.7781 (mtp) outliers start: 27 outliers final: 19 residues processed: 255 average time/residue: 0.3682 time to fit residues: 148.5684 Evaluate side-chains 228 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 208 time to evaluate : 2.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 511 ARG Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1587 LEU Chi-restraints excluded: chain A residue 1639 PHE Chi-restraints excluded: chain A residue 1964 LEU Chi-restraints excluded: chain A residue 2099 ASP Chi-restraints excluded: chain A residue 2145 THR Chi-restraints excluded: chain A residue 2331 VAL Chi-restraints excluded: chain A residue 2998 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 266 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 157 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 232 optimal weight: 6.9990 chunk 154 optimal weight: 9.9990 chunk 275 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 chunk 168 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2005 GLN A2022 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 23643 Z= 0.230 Angle : 0.537 11.530 32070 Z= 0.264 Chirality : 0.040 0.290 3610 Planarity : 0.004 0.054 4099 Dihedral : 6.365 173.202 3181 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.70 % Favored : 95.27 % Rotamer: Outliers : 1.45 % Allowed : 14.29 % Favored : 84.26 % 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: 0.64 (0.16), residues: 2852 helix: 1.58 (0.13), residues: 1577 sheet: -1.17 (0.34), residues: 242 loop : -0.95 (0.20), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A2869 HIS 0.013 0.001 HIS A1745 PHE 0.020 0.001 PHE A2295 TYR 0.015 0.001 TYR A2294 ARG 0.004 0.000 ARG A 843 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 209 time to evaluate : 2.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.6432 (pp20) REVERT: A 135 ASP cc_start: 0.7503 (OUTLIER) cc_final: 0.7111 (t0) REVERT: A 188 ASN cc_start: 0.7736 (t0) cc_final: 0.7329 (t0) REVERT: A 1052 ARG cc_start: 0.7067 (mtm180) cc_final: 0.6608 (ptt90) REVERT: A 1200 LEU cc_start: 0.8550 (mm) cc_final: 0.8120 (tp) REVERT: A 1310 TYR cc_start: 0.7298 (m-80) cc_final: 0.6924 (m-80) REVERT: A 1389 ARG cc_start: 0.7428 (mtm110) cc_final: 0.7030 (ptm160) REVERT: A 1575 MET cc_start: 0.8083 (mmm) cc_final: 0.7758 (mmt) REVERT: A 1579 LYS cc_start: 0.7438 (pttm) cc_final: 0.7226 (pttm) REVERT: A 1657 LYS cc_start: 0.8974 (mmmm) cc_final: 0.8689 (mtmm) REVERT: A 1726 ASN cc_start: 0.8617 (m-40) cc_final: 0.8271 (m-40) REVERT: A 1968 ARG cc_start: 0.6474 (mmt180) cc_final: 0.4851 (ttm-80) REVERT: A 1998 TYR cc_start: 0.8300 (m-10) cc_final: 0.7876 (m-80) REVERT: A 2083 MET cc_start: 0.8682 (mmm) cc_final: 0.8421 (mmm) REVERT: A 2200 LYS cc_start: 0.8325 (tppt) cc_final: 0.8055 (ttpp) REVERT: A 2545 ASN cc_start: 0.8848 (m-40) cc_final: 0.8549 (m-40) outliers start: 37 outliers final: 29 residues processed: 236 average time/residue: 0.3547 time to fit residues: 133.9576 Evaluate side-chains 232 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 201 time to evaluate : 2.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 511 ARG Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 743 GLU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1587 LEU Chi-restraints excluded: chain A residue 1639 PHE Chi-restraints excluded: chain A residue 1960 LEU Chi-restraints excluded: chain A residue 1964 LEU Chi-restraints excluded: chain A residue 2092 THR Chi-restraints excluded: chain A residue 2099 ASP Chi-restraints excluded: chain A residue 2145 THR Chi-restraints excluded: chain A residue 2216 LEU Chi-restraints excluded: chain A residue 2269 THR Chi-restraints excluded: chain A residue 2331 VAL Chi-restraints excluded: chain A residue 2403 THR Chi-restraints excluded: chain A residue 2733 ILE Chi-restraints excluded: chain A residue 2998 VAL Chi-restraints excluded: chain A residue 3036 ASP Chi-restraints excluded: chain A residue 3099 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 170 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 53 optimal weight: 0.0470 chunk 175 optimal weight: 4.9990 chunk 187 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 216 optimal weight: 8.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 922 ASN A1745 HIS A2022 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23643 Z= 0.175 Angle : 0.513 11.713 32070 Z= 0.251 Chirality : 0.039 0.301 3610 Planarity : 0.004 0.054 4099 Dihedral : 6.210 172.619 3181 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.49 % Favored : 95.48 % Rotamer: Outliers : 1.26 % Allowed : 14.64 % Favored : 84.11 % 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: 0.66 (0.16), residues: 2852 helix: 1.59 (0.13), residues: 1577 sheet: -1.13 (0.35), residues: 231 loop : -0.96 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A2869 HIS 0.011 0.001 HIS A1745 PHE 0.017 0.001 PHE A2295 TYR 0.016 0.001 TYR A2294 ARG 0.004 0.000 ARG A1633 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 207 time to evaluate : 2.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6366 (pp20) REVERT: A 188 ASN cc_start: 0.7767 (t0) cc_final: 0.7372 (t0) REVERT: A 767 MET cc_start: 0.8650 (mtm) cc_final: 0.8432 (mtm) REVERT: A 1052 ARG cc_start: 0.7054 (mtm180) cc_final: 0.6609 (ptt90) REVERT: A 1200 LEU cc_start: 0.8544 (mm) cc_final: 0.8122 (tp) REVERT: A 1389 ARG cc_start: 0.7503 (mtm110) cc_final: 0.7053 (ptm160) REVERT: A 1575 MET cc_start: 0.8091 (mmm) cc_final: 0.7742 (mmt) REVERT: A 1657 LYS cc_start: 0.8968 (mmmm) cc_final: 0.8685 (mtmm) REVERT: A 1658 MET cc_start: 0.8074 (tpp) cc_final: 0.7270 (ttm) REVERT: A 1726 ASN cc_start: 0.8610 (m-40) cc_final: 0.8267 (m-40) REVERT: A 1968 ARG cc_start: 0.6541 (mmt180) cc_final: 0.5139 (ttm110) REVERT: A 1998 TYR cc_start: 0.8247 (m-10) cc_final: 0.7858 (m-80) REVERT: A 2200 LYS cc_start: 0.8347 (tppt) cc_final: 0.8075 (ttpp) REVERT: A 2545 ASN cc_start: 0.8850 (m-40) cc_final: 0.8548 (m-40) REVERT: A 2639 MET cc_start: 0.8423 (mtp) cc_final: 0.7824 (mtp) outliers start: 32 outliers final: 25 residues processed: 233 average time/residue: 0.3642 time to fit residues: 135.6003 Evaluate side-chains 228 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 202 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1587 LEU Chi-restraints excluded: chain A residue 1639 PHE Chi-restraints excluded: chain A residue 1745 HIS Chi-restraints excluded: chain A residue 1960 LEU Chi-restraints excluded: chain A residue 1964 LEU Chi-restraints excluded: chain A residue 2099 ASP Chi-restraints excluded: chain A residue 2145 THR Chi-restraints excluded: chain A residue 2178 VAL Chi-restraints excluded: chain A residue 2216 LEU Chi-restraints excluded: chain A residue 2331 VAL Chi-restraints excluded: chain A residue 2733 ILE Chi-restraints excluded: chain A residue 2998 VAL Chi-restraints excluded: chain A residue 3099 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 250 optimal weight: 0.7980 chunk 264 optimal weight: 7.9990 chunk 240 optimal weight: 0.7980 chunk 256 optimal weight: 0.0370 chunk 154 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 201 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 232 optimal weight: 2.9990 chunk 242 optimal weight: 0.9980 chunk 255 optimal weight: 0.9980 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 HIS A 922 ASN A2022 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23643 Z= 0.157 Angle : 0.508 12.019 32070 Z= 0.248 Chirality : 0.039 0.287 3610 Planarity : 0.003 0.055 4099 Dihedral : 5.997 159.296 3181 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.49 % Favored : 95.48 % Rotamer: Outliers : 1.33 % Allowed : 14.64 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.16), residues: 2852 helix: 1.63 (0.13), residues: 1571 sheet: -1.08 (0.35), residues: 231 loop : -0.92 (0.20), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A2869 HIS 0.016 0.001 HIS A 104 PHE 0.020 0.001 PHE A1227 TYR 0.016 0.001 TYR A2294 ARG 0.004 0.000 ARG A1633 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 214 time to evaluate : 2.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.6369 (pp20) REVERT: A 188 ASN cc_start: 0.7735 (t0) cc_final: 0.7369 (t0) REVERT: A 1052 ARG cc_start: 0.6998 (mtm180) cc_final: 0.6618 (ptt90) REVERT: A 1200 LEU cc_start: 0.8540 (mm) cc_final: 0.8116 (tp) REVERT: A 1389 ARG cc_start: 0.7518 (mtm110) cc_final: 0.7069 (ptm160) REVERT: A 1441 ARG cc_start: 0.8294 (mmm160) cc_final: 0.8024 (mmm-85) REVERT: A 1575 MET cc_start: 0.8089 (mmm) cc_final: 0.7744 (mmm) REVERT: A 1657 LYS cc_start: 0.8968 (mmmm) cc_final: 0.8686 (mtmm) REVERT: A 1658 MET cc_start: 0.8073 (tpp) cc_final: 0.7268 (ttm) REVERT: A 1726 ASN cc_start: 0.8603 (m-40) cc_final: 0.8262 (m-40) REVERT: A 1968 ARG cc_start: 0.6542 (mmt180) cc_final: 0.4806 (ttm-80) REVERT: A 1998 TYR cc_start: 0.8254 (m-10) cc_final: 0.7898 (m-80) REVERT: A 2083 MET cc_start: 0.8694 (mmm) cc_final: 0.8481 (mmm) REVERT: A 2200 LYS cc_start: 0.8348 (tppt) cc_final: 0.8074 (ttpp) REVERT: A 2545 ASN cc_start: 0.8850 (m-40) cc_final: 0.8553 (m-40) REVERT: A 2639 MET cc_start: 0.8385 (mtp) cc_final: 0.7764 (mtp) outliers start: 34 outliers final: 32 residues processed: 240 average time/residue: 0.3605 time to fit residues: 138.3860 Evaluate side-chains 234 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 201 time to evaluate : 2.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1587 LEU Chi-restraints excluded: chain A residue 1639 PHE Chi-restraints excluded: chain A residue 1745 HIS Chi-restraints excluded: chain A residue 1960 LEU Chi-restraints excluded: chain A residue 1964 LEU Chi-restraints excluded: chain A residue 2092 THR Chi-restraints excluded: chain A residue 2099 ASP Chi-restraints excluded: chain A residue 2145 THR Chi-restraints excluded: chain A residue 2178 VAL Chi-restraints excluded: chain A residue 2216 LEU Chi-restraints excluded: chain A residue 2331 VAL Chi-restraints excluded: chain A residue 2733 ILE Chi-restraints excluded: chain A residue 2998 VAL Chi-restraints excluded: chain A residue 3099 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 168 optimal weight: 3.9990 chunk 271 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 128 optimal weight: 0.0570 chunk 188 optimal weight: 0.5980 chunk 284 optimal weight: 5.9990 chunk 262 optimal weight: 0.1980 chunk 226 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 175 optimal weight: 4.9990 chunk 139 optimal weight: 0.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 HIS A2022 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 23643 Z= 0.145 Angle : 0.511 12.076 32070 Z= 0.249 Chirality : 0.039 0.292 3610 Planarity : 0.004 0.056 4099 Dihedral : 5.778 145.075 3181 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.33 % Allowed : 14.76 % Favored : 83.91 % 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: 0.75 (0.16), residues: 2852 helix: 1.69 (0.13), residues: 1565 sheet: -1.05 (0.35), residues: 231 loop : -0.95 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A2869 HIS 0.023 0.001 HIS A 104 PHE 0.027 0.001 PHE A1227 TYR 0.016 0.001 TYR A2294 ARG 0.004 0.000 ARG A1633 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 213 time to evaluate : 2.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.6689 (OUTLIER) cc_final: 0.6370 (pp20) REVERT: A 134 MET cc_start: 0.7318 (tpt) cc_final: 0.5890 (mpp) REVERT: A 135 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.6945 (t0) REVERT: A 188 ASN cc_start: 0.7719 (t0) cc_final: 0.7363 (t0) REVERT: A 1052 ARG cc_start: 0.7027 (mtm180) cc_final: 0.6674 (ptt90) REVERT: A 1200 LEU cc_start: 0.8534 (mm) cc_final: 0.8113 (tp) REVERT: A 1389 ARG cc_start: 0.7520 (mtm110) cc_final: 0.7071 (ptm160) REVERT: A 1441 ARG cc_start: 0.8277 (mmm160) cc_final: 0.8071 (mmm-85) REVERT: A 1575 MET cc_start: 0.8087 (mmm) cc_final: 0.7745 (mmm) REVERT: A 1657 LYS cc_start: 0.8964 (mmmm) cc_final: 0.8685 (mtmm) REVERT: A 1658 MET cc_start: 0.8066 (tpp) cc_final: 0.7270 (ttm) REVERT: A 1726 ASN cc_start: 0.8582 (m-40) cc_final: 0.8248 (m-40) REVERT: A 1968 ARG cc_start: 0.6532 (mmt180) cc_final: 0.4806 (ttm-80) REVERT: A 1998 TYR cc_start: 0.8213 (m-10) cc_final: 0.7902 (m-80) REVERT: A 2083 MET cc_start: 0.8698 (mmm) cc_final: 0.8489 (mmm) REVERT: A 2106 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8261 (pm20) REVERT: A 2200 LYS cc_start: 0.8332 (tppt) cc_final: 0.8058 (ttpp) REVERT: A 2545 ASN cc_start: 0.8893 (m-40) cc_final: 0.8595 (m-40) REVERT: A 2639 MET cc_start: 0.8361 (mtp) cc_final: 0.7739 (mtp) outliers start: 34 outliers final: 30 residues processed: 240 average time/residue: 0.3598 time to fit residues: 137.3707 Evaluate side-chains 236 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 203 time to evaluate : 2.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1460 VAL Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1587 LEU Chi-restraints excluded: chain A residue 1639 PHE Chi-restraints excluded: chain A residue 1960 LEU Chi-restraints excluded: chain A residue 1964 LEU Chi-restraints excluded: chain A residue 2092 THR Chi-restraints excluded: chain A residue 2099 ASP Chi-restraints excluded: chain A residue 2106 GLU Chi-restraints excluded: chain A residue 2145 THR Chi-restraints excluded: chain A residue 2178 VAL Chi-restraints excluded: chain A residue 2331 VAL Chi-restraints excluded: chain A residue 2733 ILE Chi-restraints excluded: chain A residue 2998 VAL Chi-restraints excluded: chain A residue 3099 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 180 optimal weight: 0.7980 chunk 241 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 209 optimal weight: 0.8980 chunk 33 optimal weight: 0.0770 chunk 63 optimal weight: 2.9990 chunk 227 optimal weight: 0.0470 chunk 95 optimal weight: 2.9990 chunk 233 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 HIS A 922 ASN A2022 ASN A3094 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.116140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.092984 restraints weight = 42707.709| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.04 r_work: 0.3119 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23643 Z= 0.144 Angle : 0.516 11.909 32070 Z= 0.250 Chirality : 0.039 0.280 3610 Planarity : 0.004 0.055 4099 Dihedral : 5.534 126.016 3181 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.41 % Allowed : 14.76 % 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: 0.78 (0.16), residues: 2852 helix: 1.72 (0.13), residues: 1566 sheet: -1.00 (0.36), residues: 229 loop : -0.94 (0.20), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A2869 HIS 0.029 0.001 HIS A 104 PHE 0.024 0.001 PHE A1227 TYR 0.026 0.001 TYR A 18 ARG 0.004 0.000 ARG A1633 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4823.37 seconds wall clock time: 87 minutes 54.21 seconds (5274.21 seconds total)