Starting phenix.real_space_refine on Mon Mar 18 21:24:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd6_29003/03_2024/8fd6_29003_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd6_29003/03_2024/8fd6_29003.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd6_29003/03_2024/8fd6_29003.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd6_29003/03_2024/8fd6_29003.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd6_29003/03_2024/8fd6_29003_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd6_29003/03_2024/8fd6_29003_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.055 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: 7 Type Number sf(0) Gaussians V 1 8.30 5 P 9 5.49 5 Mg 1 5.21 5 S 111 5.16 5 C 14093 2.51 5 N 3832 2.21 5 O 4123 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 397": "OD1" <-> "OD2" Residue "A GLU 459": "OE1" <-> "OE2" Residue "A PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 632": "OD1" <-> "OD2" Residue "A PHE 703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 866": "OD1" <-> "OD2" Residue "A GLU 876": "OE1" <-> "OE2" Residue "A PHE 986": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1041": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1209": "OD1" <-> "OD2" Residue "A ASP 1215": "OD1" <-> "OD2" Residue "A GLU 1353": "OE1" <-> "OE2" Residue "A PHE 1654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1734": "OE1" <-> "OE2" Residue "A GLU 1963": "OE1" <-> "OE2" Residue "A ASP 2208": "OD1" <-> "OD2" Residue "A ASP 2340": "OD1" <-> "OD2" Residue "A TYR 2527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2607": "OE1" <-> "OE2" Residue "A ASP 3101": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22170 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 22170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2753, 22170 Unusual residues: {' MG': 1, 'ADP': 3, 'ATP': 1, 'VO4': 1} Classifications: {'peptide': 2747, 'undetermined': 6} Link IDs: {'PTRANS': 127, 'TRANS': 2619, None: 6} Not linked: pdbres="THR A3123 " pdbres="ATP A3201 " Not linked: pdbres="ATP A3201 " pdbres="ADP A3202 " Not linked: pdbres="ADP A3202 " pdbres="ADP A3203 " Not linked: pdbres="ADP A3203 " pdbres="ADP A3204 " Not linked: pdbres="ADP A3204 " pdbres="VO4 A3205 " Not linked: pdbres="VO4 A3205 " pdbres=" MG A3206 " Chain breaks: 6 Time building chain proxies: 11.48, per 1000 atoms: 0.52 Number of scatterers: 22170 At special positions: 0 Unit cell: (122.943, 170.052, 147.072, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) V 1 22.97 S 111 16.00 P 9 15.00 Mg 1 11.99 O 4123 8.00 N 3832 7.00 C 14093 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: 9.37 Conformation dependent library (CDL) restraints added in 4.6 seconds 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5216 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 113 helices and 18 sheets defined 53.3% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.24 Creating SS restraints... Processing helix chain 'A' and resid 89 through 97 removed outlier: 3.625A pdb=" N THR A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 104 No H-bonds generated for 'chain 'A' and resid 101 through 104' Processing helix chain 'A' and resid 108 through 113 Processing helix chain 'A' and resid 153 through 170 Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 179 through 187 removed outlier: 4.031A pdb=" N GLU A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 removed outlier: 3.643A pdb=" N GLN A 196 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A 197 " --> pdb=" O LYS A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 202 No H-bonds generated for 'chain 'A' and resid 199 through 202' Processing helix chain 'A' and resid 243 through 273 removed outlier: 3.635A 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 323 through 342 Processing helix chain 'A' and resid 347 through 373 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 428 through 444 removed outlier: 4.511A pdb=" N ALA A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 467 Processing helix chain 'A' and resid 483 through 496 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 529 removed outlier: 3.527A pdb=" N SER A 517 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN A 518 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLN A 519 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU A 529 " --> pdb=" O GLU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 580 removed outlier: 3.788A pdb=" N LYS A 579 " --> pdb=" O ASP A 575 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU A 580 " --> pdb=" O ASN A 576 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 575 through 580' Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 607 through 624 Proline residue: A 616 - end of helix removed outlier: 3.649A pdb=" N GLU A 623 " --> pdb=" O LYS A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 658 Processing helix chain 'A' and resid 678 through 689 Processing helix chain 'A' and resid 696 through 709 Proline residue: A 700 - end of helix Processing helix chain 'A' and resid 721 through 733 Processing helix chain 'A' and resid 746 through 761 Processing helix chain 'A' and resid 775 through 790 Processing helix chain 'A' and resid 806 through 810 Processing helix chain 'A' and resid 824 through 833 Processing helix chain 'A' and resid 839 through 841 No H-bonds generated for 'chain 'A' and resid 839 through 841' Processing helix chain 'A' and resid 858 through 860 No H-bonds generated for 'chain 'A' and resid 858 through 860' Processing helix chain 'A' and resid 898 through 902 Processing helix chain 'A' and resid 916 through 928 Processing helix chain 'A' and resid 956 through 971 Proline residue: A 970 - end of helix Processing helix chain 'A' and resid 977 through 987 removed outlier: 4.191A pdb=" N GLN A 987 " --> pdb=" O GLU A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1020 Processing helix chain 'A' and resid 1028 through 1048 removed outlier: 4.054A 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: 3.502A pdb=" N HIS A1122 " --> pdb=" O ASP A1118 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1156 removed outlier: 3.649A pdb=" N ALA A1156 " --> pdb=" O SER A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1173 through 1183 Processing helix chain 'A' and resid 1223 through 1233 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 1300 removed outlier: 3.705A pdb=" N PHE A1296 " --> pdb=" O ILE A1292 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1328 removed outlier: 4.208A pdb=" N GLU A1312 " --> pdb=" O THR A1309 " (cutoff:3.500A) Proline residue: A1313 - end of helix Processing helix chain 'A' and resid 1341 through 1357 Proline residue: A1357 - end of helix Processing helix chain 'A' and resid 1363 through 1378 Processing helix chain 'A' and resid 1385 through 1402 removed outlier: 3.686A pdb=" N ASP A1396 " --> pdb=" O ASP A1392 " (cutoff:3.500A) Processing helix chain 'A' and resid 1408 through 1411 No H-bonds generated for 'chain 'A' and resid 1408 through 1411' Processing helix chain 'A' and resid 1431 through 1448 removed outlier: 3.628A 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 1499 Processing helix chain 'A' and resid 1514 through 1529 Processing helix chain 'A' and resid 1547 through 1559 Processing helix chain 'A' and resid 1568 through 1585 Processing helix chain 'A' and resid 1592 through 1605 removed outlier: 3.626A pdb=" N TYR A1596 " --> pdb=" O HIS A1592 " (cutoff:3.500A) Processing helix chain 'A' and resid 1620 through 1626 removed outlier: 3.570A pdb=" N ALA A1625 " --> pdb=" O LYS A1621 " (cutoff:3.500A) Processing helix chain 'A' and resid 1628 through 1631 Processing helix chain 'A' and resid 1644 through 1656 Processing helix chain 'A' and resid 1684 through 1708 removed outlier: 3.823A pdb=" N LEU A1699 " --> pdb=" O VAL A1695 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N HIS A1700 " --> pdb=" O HIS A1696 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN A1701 " --> pdb=" O GLN A1697 " (cutoff:3.500A) Processing helix chain 'A' and resid 1718 through 1764 Processing helix chain 'A' and resid 1951 through 1979 removed outlier: 4.084A pdb=" N SER A1959 " --> pdb=" O ALA A1955 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ALA A1962 " --> pdb=" O LYS A1958 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN A1976 " --> pdb=" O GLU A1972 " (cutoff:3.500A) Processing helix chain 'A' and resid 1981 through 1994 Processing helix chain 'A' and resid 2000 through 2016 Processing helix chain 'A' and resid 2027 through 2030 No H-bonds generated for 'chain 'A' and resid 2027 through 2030' Processing helix chain 'A' and resid 2034 through 2043 Processing helix chain 'A' and resid 2049 through 2059 Processing helix chain 'A' and resid 2073 through 2083 Processing helix chain 'A' and resid 2097 through 2107 Processing helix chain 'A' and resid 2116 through 2118 No H-bonds generated for 'chain 'A' and resid 2116 through 2118' Processing helix chain 'A' and resid 2121 through 2128 Proline residue: A2125 - end of helix Processing helix chain 'A' and resid 2168 through 2171 No H-bonds generated for 'chain 'A' and resid 2168 through 2171' Processing helix chain 'A' and resid 2183 through 2198 Processing helix chain 'A' and resid 2200 through 2233 removed outlier: 3.614A pdb=" N GLU A2215 " --> pdb=" O LYS A2211 " (cutoff:3.500A) Processing helix chain 'A' and resid 2241 through 2278 removed outlier: 4.351A pdb=" N THR A2246 " --> pdb=" O ASP A2242 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR A2247 " --> pdb=" O THR A2243 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A2248 " --> pdb=" O ILE A2244 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLU A2249 " --> pdb=" O ILE A2245 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASN A2250 " --> pdb=" O THR A2246 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP A2266 " --> pdb=" O VAL A2262 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N MET A2269 " --> pdb=" O THR A2265 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A2271 " --> pdb=" O ILE A2267 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLN A2278 " --> pdb=" O THR A2274 " (cutoff:3.500A) Processing helix chain 'A' and resid 2280 through 2297 removed outlier: 3.728A pdb=" N ILE A2289 " --> pdb=" O ALA A2285 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR A2290 " --> pdb=" O CYS A2286 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS A2297 " --> pdb=" O MET A2293 " (cutoff:3.500A) Processing helix chain 'A' and resid 2307 through 2319 Processing helix chain 'A' and resid 2322 through 2324 No H-bonds generated for 'chain 'A' and resid 2322 through 2324' Processing helix chain 'A' and resid 2330 through 2352 removed outlier: 4.009A pdb=" N GLY A2352 " --> pdb=" O ARG A2348 " (cutoff:3.500A) Processing helix chain 'A' and resid 2355 through 2371 removed outlier: 4.060A pdb=" N ILE A2359 " --> pdb=" O GLN A2356 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A2360 " --> pdb=" O ASP A2357 " (cutoff:3.500A) Processing helix chain 'A' and resid 2380 through 2388 removed outlier: 3.880A pdb=" N HIS A2385 " --> pdb=" O ALA A2381 " (cutoff:3.500A) Processing helix chain 'A' and resid 2407 through 2418 removed outlier: 4.096A pdb=" N CYS A2418 " --> pdb=" O VAL A2414 " (cutoff:3.500A) Processing helix chain 'A' and resid 2425 through 2430 removed outlier: 3.603A pdb=" N GLN A2430 " --> pdb=" O ILE A2426 " (cutoff:3.500A) Processing helix chain 'A' and resid 2434 through 2439 Processing helix chain 'A' and resid 2444 through 2446 No H-bonds generated for 'chain 'A' and resid 2444 through 2446' Processing helix chain 'A' and resid 2460 through 2474 Processing helix chain 'A' and resid 2476 through 2490 removed outlier: 4.587A pdb=" N LEU A2480 " --> pdb=" O ASP A2477 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N HIS A2484 " --> pdb=" O ALA A2481 " (cutoff:3.500A) Processing helix chain 'A' and resid 2505 through 2511 Processing helix chain 'A' and resid 2530 through 2539 Processing helix chain 'A' and resid 2554 through 2566 Processing helix chain 'A' and resid 2581 through 2593 removed outlier: 3.743A pdb=" N HIS A2592 " --> pdb=" O GLU A2588 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N SER A2593 " --> pdb=" O LYS A2589 " (cutoff:3.500A) Processing helix chain 'A' and resid 2614 through 2618 Processing helix chain 'A' and resid 2630 through 2641 Processing helix chain 'A' and resid 2652 through 2670 removed outlier: 3.630A pdb=" N TYR A2658 " --> pdb=" O ALA A2655 " (cutoff:3.500A) Processing helix chain 'A' and resid 2672 through 2674 No H-bonds generated for 'chain 'A' and resid 2672 through 2674' Processing helix chain 'A' and resid 2687 through 2704 Processing helix chain 'A' and resid 2718 through 2722 Processing helix chain 'A' and resid 2724 through 2727 No H-bonds generated for 'chain 'A' and resid 2724 through 2727' Processing helix chain 'A' and resid 2737 through 2750 Processing helix chain 'A' and resid 2753 through 2755 No H-bonds generated for 'chain 'A' and resid 2753 through 2755' Processing helix chain 'A' and resid 2780 through 2788 Processing helix chain 'A' and resid 2796 through 2799 Processing helix chain 'A' and resid 2803 through 2805 No H-bonds generated for 'chain 'A' and resid 2803 through 2805' Processing helix chain 'A' and resid 2807 through 2824 Processing helix chain 'A' and resid 2854 through 2868 Processing helix chain 'A' and resid 2886 through 2916 Processing helix chain 'A' and resid 2924 through 2934 Processing helix chain 'A' and resid 2953 through 2976 Processing helix chain 'A' and resid 2995 through 3009 Processing helix chain 'A' and resid 3110 through 3115 Processing sheet with id= A, first strand: chain 'A' and resid 228 through 230 Processing sheet with id= B, first strand: chain 'A' and resid 388 through 391 Processing sheet with id= C, first strand: chain 'A' and resid 446 through 450 Processing sheet with id= D, first strand: chain 'A' and resid 472 through 476 removed outlier: 6.584A pdb=" N TRP A 499 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N PHE A 475 " --> pdb=" O TRP A 499 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N CYS A 501 " --> pdb=" O PHE A 475 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA A 558 " --> pdb=" O GLY A 500 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N PHE A 502 " --> pdb=" O ALA A 558 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N PHE A 560 " --> pdb=" O PHE A 502 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 543 through 546 removed outlier: 3.647A pdb=" N VAL A 551 " --> pdb=" O CYS A 544 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 905 through 908 removed outlier: 8.513A pdb=" N LEU A 765 " --> pdb=" O VAL A 884 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE A 886 " --> pdb=" O LEU A 765 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N MET A 767 " --> pdb=" O ILE A 886 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N PHE A 888 " --> pdb=" O MET A 767 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLN A 844 " --> pdb=" O ARG A 885 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N MET A 887 " --> pdb=" O GLN A 844 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE A 846 " --> pdb=" O MET A 887 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N GLU A 889 " --> pdb=" O ILE A 846 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N PHE A 848 " --> pdb=" O GLU A 889 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 811 through 813 Processing sheet with id= H, first strand: chain 'A' and resid 869 through 871 Processing sheet with id= I, first strand: chain 'A' and resid 1082 through 1084 Processing sheet with id= J, first strand: chain 'A' and resid 1277 through 1280 removed outlier: 3.646A pdb=" N LEU A1136 " --> pdb=" O PHE A1253 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU A1204 " --> pdb=" O GLN A1252 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N VAL A1254 " --> pdb=" O LEU A1204 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LEU A1206 " --> pdb=" O VAL A1254 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ALA A1256 " --> pdb=" O LEU A1206 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N CYS A1208 " --> pdb=" O ALA A1256 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1193 through 1196 removed outlier: 4.165A pdb=" N VAL A1193 " --> pdb=" O TRP A1245 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 1502 through 1505 removed outlier: 6.643A pdb=" N HIS A1608 " --> pdb=" O PHE A1537 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N MET A1539 " --> pdb=" O HIS A1608 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL A1610 " --> pdb=" O MET A1539 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU A1478 " --> pdb=" O PHE A1611 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N MET A1613 " --> pdb=" O LEU A1478 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU A1480 " --> pdb=" O MET A1613 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 2175 through 2179 removed outlier: 7.353A pdb=" N ILE A2155 " --> pdb=" O PRO A2065 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N ILE A2067 " --> pdb=" O ILE A2155 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU A2157 " --> pdb=" O ILE A2067 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ASP A2069 " --> pdb=" O LEU A2157 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N THR A2159 " --> pdb=" O ASP A2069 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU A2111 " --> pdb=" O PHE A2156 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N SER A2158 " --> pdb=" O LEU A2111 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL A2113 " --> pdb=" O SER A2158 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N THR A2088 " --> pdb=" O LEU A2112 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N GLN A2114 " --> pdb=" O THR A2088 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N THR A2090 " --> pdb=" O GLN A2114 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 2132 through 2134 Processing sheet with id= O, first strand: chain 'A' and resid 2621 through 2625 Processing sheet with id= P, first strand: chain 'A' and resid 3018 through 3023 Processing sheet with id= Q, first strand: chain 'A' and resid 3041 through 3043 removed outlier: 4.233A pdb=" N LEU A3041 " --> pdb=" O LEU A3063 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 3082 through 3088 removed outlier: 3.838A pdb=" N PHE A3098 " --> pdb=" O VAL A3087 " (cutoff:3.500A) 1068 hydrogen bonds defined for protein. 2949 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: 9.75 Time building geometry restraints manager: 9.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 7301 1.35 - 1.49: 5427 1.49 - 1.63: 9732 1.63 - 1.77: 5 1.77 - 1.91: 184 Bond restraints: 22649 Sorted by residual: bond pdb=" N ILE A1506 " pdb=" CA ILE A1506 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.19e-02 7.06e+03 1.08e+01 bond pdb=" N VAL A2113 " pdb=" CA VAL A2113 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 9.97e+00 bond pdb=" N LYS A2765 " pdb=" CA LYS A2765 " ideal model delta sigma weight residual 1.457 1.498 -0.040 1.29e-02 6.01e+03 9.83e+00 bond pdb=" N ILE A2299 " pdb=" CA ILE A2299 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.21e-02 6.83e+03 9.48e+00 bond pdb=" N LYS A1511 " pdb=" CA LYS A1511 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.10e-02 8.26e+03 9.29e+00 ... (remaining 22644 not shown) Histogram of bond angle deviations from ideal: 95.77 - 104.53: 398 104.53 - 113.29: 12838 113.29 - 122.06: 13585 122.06 - 130.82: 3784 130.82 - 139.58: 119 Bond angle restraints: 30724 Sorted by residual: angle pdb=" CA PRO A2628 " pdb=" N PRO A2628 " pdb=" CD PRO A2628 " ideal model delta sigma weight residual 112.00 106.06 5.94 1.40e+00 5.10e-01 1.80e+01 angle pdb=" N PRO A 956 " pdb=" CA PRO A 956 " pdb=" C PRO A 956 " ideal model delta sigma weight residual 113.65 108.33 5.32 1.35e+00 5.49e-01 1.55e+01 angle pdb=" CA SER A 955 " pdb=" C SER A 955 " pdb=" N PRO A 956 " ideal model delta sigma weight residual 116.90 122.16 -5.26 1.50e+00 4.44e-01 1.23e+01 angle pdb=" N GLU A2117 " pdb=" CA GLU A2117 " pdb=" C GLU A2117 " ideal model delta sigma weight residual 112.38 108.17 4.21 1.22e+00 6.72e-01 1.19e+01 angle pdb=" CA VAL A 695 " pdb=" C VAL A 695 " pdb=" O VAL A 695 " ideal model delta sigma weight residual 121.98 117.96 4.02 1.21e+00 6.83e-01 1.10e+01 ... (remaining 30719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.65: 13425 34.65 - 69.31: 257 69.31 - 103.96: 32 103.96 - 138.62: 1 138.62 - 173.27: 1 Dihedral angle restraints: 13716 sinusoidal: 5684 harmonic: 8032 Sorted by residual: dihedral pdb=" O2A ADP A3204 " pdb=" O3A ADP A3204 " pdb=" PA ADP A3204 " pdb=" PB ADP A3204 " ideal model delta sinusoidal sigma weight residual -60.00 113.27 -173.27 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O1B ADP A3204 " pdb=" O3A ADP A3204 " pdb=" PB ADP A3204 " pdb=" PA ADP A3204 " ideal model delta sinusoidal sigma weight residual -60.00 73.60 -133.60 1 2.00e+01 2.50e-03 4.06e+01 dihedral pdb=" CA MET A 406 " pdb=" C MET A 406 " pdb=" N ALA A 407 " pdb=" CA ALA A 407 " ideal model delta harmonic sigma weight residual -180.00 -156.26 -23.74 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 13713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2301 0.042 - 0.084: 812 0.084 - 0.125: 284 0.125 - 0.167: 53 0.167 - 0.209: 8 Chirality restraints: 3458 Sorted by residual: chirality pdb=" CB VAL A 749 " pdb=" CA VAL A 749 " pdb=" CG1 VAL A 749 " pdb=" CG2 VAL A 749 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA LEU A2157 " pdb=" N LEU A2157 " pdb=" C LEU A2157 " pdb=" CB LEU A2157 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.38e-01 chirality pdb=" CA PHE A1549 " pdb=" N PHE A1549 " pdb=" C PHE A1549 " pdb=" CB PHE A1549 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.81e-01 ... (remaining 3455 not shown) Planarity restraints: 3930 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A2627 " -0.081 5.00e-02 4.00e+02 1.20e-01 2.30e+01 pdb=" N PRO A2628 " 0.207 5.00e-02 4.00e+02 pdb=" CA PRO A2628 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO A2628 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 392 " 0.033 5.00e-02 4.00e+02 4.95e-02 3.93e+00 pdb=" N PRO A 393 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 393 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 393 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1320 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.22e+00 pdb=" C GLU A1320 " -0.031 2.00e-02 2.50e+03 pdb=" O GLU A1320 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE A1321 " 0.010 2.00e-02 2.50e+03 ... (remaining 3927 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 82 2.45 - 3.06: 15000 3.06 - 3.67: 33689 3.67 - 4.29: 50949 4.29 - 4.90: 84714 Nonbonded interactions: 184434 Sorted by model distance: nonbonded pdb=" O1 VO4 A3205 " pdb="MG MG A3206 " model vdw 1.835 2.170 nonbonded pdb=" OG1 THR A 458 " pdb="MG MG A3206 " model vdw 2.004 2.170 nonbonded pdb=" O2B ADP A3204 " pdb="MG MG A3206 " model vdw 2.086 2.170 nonbonded pdb=" O VAL A 474 " pdb=" NH2 ARG A 877 " model vdw 2.208 2.520 nonbonded pdb=" OD1 ASP A 279 " pdb=" OG1 THR A 282 " model vdw 2.213 2.440 ... (remaining 184429 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: 2.420 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: 11.020 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 62.100 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 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 : 0.007 0.078 22649 Z= 0.436 Angle : 0.740 8.013 30724 Z= 0.432 Chirality : 0.049 0.209 3458 Planarity : 0.005 0.120 3930 Dihedral : 14.426 173.273 8500 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.16 % Allowed : 0.86 % Favored : 98.97 % 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: 0.39 (0.16), residues: 2733 helix: 0.93 (0.14), residues: 1492 sheet: -0.48 (0.32), residues: 238 loop : -0.42 (0.20), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 779 HIS 0.017 0.001 HIS A1133 PHE 0.028 0.002 PHE A 389 TYR 0.029 0.002 TYR A1293 ARG 0.009 0.001 ARG A1408 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 349 time to evaluate : 2.573 Fit side-chains REVERT: A 183 LEU cc_start: 0.8259 (mm) cc_final: 0.7101 (pp) REVERT: A 605 ARG cc_start: 0.7422 (mtp-110) cc_final: 0.6768 (mtm110) REVERT: A 725 GLU cc_start: 0.6610 (pp20) cc_final: 0.5937 (mm-30) REVERT: A 734 MET cc_start: 0.8246 (mtt) cc_final: 0.7812 (mtm) REVERT: A 837 ARG cc_start: 0.6908 (mmt-90) cc_final: 0.6550 (mmt-90) REVERT: A 894 LYS cc_start: 0.7230 (ttpp) cc_final: 0.6883 (ptmm) REVERT: A 918 MET cc_start: 0.6984 (ttm) cc_final: 0.6518 (mtm) REVERT: A 989 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7269 (mm-30) REVERT: A 1240 THR cc_start: 0.7698 (p) cc_final: 0.7432 (p) REVERT: A 1300 MET cc_start: 0.7986 (ptt) cc_final: 0.7601 (ptt) REVERT: A 1343 GLU cc_start: 0.7337 (mt-10) cc_final: 0.6328 (mm-30) REVERT: A 1356 ARG cc_start: 0.6801 (ttp80) cc_final: 0.6030 (tpm170) REVERT: A 1408 ARG cc_start: 0.6977 (mtp-110) cc_final: 0.6623 (mtp85) REVERT: A 1511 LYS cc_start: 0.5492 (pttp) cc_final: 0.5222 (mtmm) REVERT: A 1540 ASP cc_start: 0.7442 (m-30) cc_final: 0.7119 (m-30) REVERT: A 1588 MET cc_start: 0.5903 (mmp) cc_final: 0.5499 (tmm) REVERT: A 1657 LYS cc_start: 0.6913 (pttt) cc_final: 0.6696 (pptt) REVERT: A 1664 ASN cc_start: 0.7749 (p0) cc_final: 0.7525 (p0) REVERT: A 1744 MET cc_start: 0.5504 (ttp) cc_final: 0.5293 (ttp) REVERT: A 1978 MET cc_start: 0.7738 (tpp) cc_final: 0.6506 (tpt) REVERT: A 2016 GLN cc_start: 0.6325 (mt0) cc_final: 0.6013 (mt0) REVERT: A 2139 LEU cc_start: 0.7622 (mt) cc_final: 0.7410 (mp) REVERT: A 2165 GLU cc_start: 0.6562 (mp0) cc_final: 0.5998 (mp0) REVERT: A 2222 GLN cc_start: 0.5970 (mt0) cc_final: 0.5143 (mm-40) REVERT: A 2380 ASP cc_start: 0.6557 (m-30) cc_final: 0.5922 (t0) REVERT: A 2504 ASP cc_start: 0.7517 (m-30) cc_final: 0.6272 (t0) REVERT: A 2573 MET cc_start: 0.8993 (ttm) cc_final: 0.8767 (ttp) REVERT: A 2618 ARG cc_start: 0.6962 (mtp-110) cc_final: 0.6275 (mtt90) REVERT: A 2691 ARG cc_start: 0.6774 (mtp85) cc_final: 0.6092 (mtp-110) REVERT: A 2702 ASP cc_start: 0.4972 (m-30) cc_final: 0.4685 (m-30) REVERT: A 2892 GLU cc_start: 0.6267 (tt0) cc_final: 0.6027 (pt0) REVERT: A 2914 GLN cc_start: 0.7093 (mm-40) cc_final: 0.6659 (mm-40) REVERT: A 2955 GLN cc_start: 0.6913 (mt0) cc_final: 0.6490 (pt0) outliers start: 4 outliers final: 2 residues processed: 350 average time/residue: 1.4507 time to fit residues: 577.2643 Evaluate side-chains 235 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 233 time to evaluate : 2.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 957 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 71 optimal weight: 0.4980 chunk 140 optimal weight: 0.0770 chunk 111 optimal weight: 0.7980 chunk 215 optimal weight: 0.0570 chunk 83 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 249 optimal weight: 0.8980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1509 HIS A1745 HIS A2013 HIS ** A2100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2178 ASN A2384 GLN A2541 ASN ** A2578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2966 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22649 Z= 0.160 Angle : 0.528 9.605 30724 Z= 0.263 Chirality : 0.039 0.145 3458 Planarity : 0.004 0.062 3930 Dihedral : 6.819 178.669 3059 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.60 % Allowed : 8.29 % Favored : 90.11 % 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: 0.79 (0.16), residues: 2733 helix: 1.28 (0.14), residues: 1505 sheet: -0.33 (0.32), residues: 239 loop : -0.31 (0.21), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 779 HIS 0.003 0.001 HIS A1008 PHE 0.014 0.001 PHE A3102 TYR 0.023 0.001 TYR A1293 ARG 0.011 0.000 ARG A2637 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 268 time to evaluate : 2.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 ASN cc_start: 0.7721 (t0) cc_final: 0.7495 (t0) REVERT: A 605 ARG cc_start: 0.7455 (mtp-110) cc_final: 0.6811 (mtm110) REVERT: A 717 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.8053 (ttt180) REVERT: A 725 GLU cc_start: 0.6844 (pp20) cc_final: 0.6205 (mm-30) REVERT: A 732 GLN cc_start: 0.7091 (OUTLIER) cc_final: 0.6855 (mm-40) REVERT: A 837 ARG cc_start: 0.6877 (mmt-90) cc_final: 0.6488 (mmt-90) REVERT: A 851 ASP cc_start: 0.6320 (m-30) cc_final: 0.6043 (m-30) REVERT: A 894 LYS cc_start: 0.7216 (ttpp) cc_final: 0.6894 (ptmt) REVERT: A 989 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7374 (mm-30) REVERT: A 1240 THR cc_start: 0.7614 (p) cc_final: 0.7343 (p) REVERT: A 1343 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6397 (mm-30) REVERT: A 1356 ARG cc_start: 0.6877 (ttp80) cc_final: 0.6101 (tpm170) REVERT: A 1408 ARG cc_start: 0.6903 (mtp-110) cc_final: 0.6538 (mtp85) REVERT: A 1412 MET cc_start: 0.6726 (OUTLIER) cc_final: 0.6018 (mmp) REVERT: A 1511 LYS cc_start: 0.5571 (pttp) cc_final: 0.5302 (mtmm) REVERT: A 1540 ASP cc_start: 0.7296 (m-30) cc_final: 0.6953 (m-30) REVERT: A 1593 GLU cc_start: 0.6216 (OUTLIER) cc_final: 0.5946 (mm-30) REVERT: A 1611 PHE cc_start: 0.7340 (m-80) cc_final: 0.6836 (t80) REVERT: A 1664 ASN cc_start: 0.7609 (p0) cc_final: 0.7379 (p0) REVERT: A 1741 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6597 (tp30) REVERT: A 1744 MET cc_start: 0.5387 (ttp) cc_final: 0.5039 (ttp) REVERT: A 2016 GLN cc_start: 0.6306 (mt0) cc_final: 0.5975 (mt0) REVERT: A 2020 GLN cc_start: 0.6791 (OUTLIER) cc_final: 0.6346 (mp10) REVERT: A 2222 GLN cc_start: 0.6071 (mt0) cc_final: 0.5218 (mm-40) REVERT: A 2279 TYR cc_start: 0.6732 (OUTLIER) cc_final: 0.6486 (m-80) REVERT: A 2380 ASP cc_start: 0.6510 (m-30) cc_final: 0.5940 (t0) REVERT: A 2504 ASP cc_start: 0.7620 (m-30) cc_final: 0.6328 (t0) REVERT: A 2691 ARG cc_start: 0.6608 (mtp85) cc_final: 0.5985 (mtp-110) REVERT: A 2702 ASP cc_start: 0.5595 (m-30) cc_final: 0.5155 (m-30) REVERT: A 2892 GLU cc_start: 0.6183 (tt0) cc_final: 0.5981 (pt0) REVERT: A 2914 GLN cc_start: 0.7056 (mm-40) cc_final: 0.6573 (mm-40) REVERT: A 2955 GLN cc_start: 0.6909 (mt0) cc_final: 0.6545 (pt0) outliers start: 39 outliers final: 6 residues processed: 286 average time/residue: 1.3921 time to fit residues: 456.6325 Evaluate side-chains 248 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 236 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 717 ARG Chi-restraints excluded: chain A residue 732 GLN Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain A residue 1593 GLU Chi-restraints excluded: chain A residue 2020 GLN Chi-restraints excluded: chain A residue 2169 ASP Chi-restraints excluded: chain A residue 2279 TYR Chi-restraints excluded: chain A residue 2771 ASP Chi-restraints excluded: chain A residue 2933 LEU Chi-restraints excluded: chain A residue 2947 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 138 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 170 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 250 optimal weight: 0.0770 chunk 270 optimal weight: 0.3980 chunk 222 optimal weight: 3.9990 chunk 248 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN ** A 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1614 ASN ** A2100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2178 ASN A2541 ASN ** A2578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2634 ASN ** A2740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22649 Z= 0.169 Angle : 0.511 9.880 30724 Z= 0.252 Chirality : 0.039 0.144 3458 Planarity : 0.004 0.035 3930 Dihedral : 6.446 172.539 3053 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.72 % Allowed : 11.04 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.16), residues: 2733 helix: 1.33 (0.14), residues: 1510 sheet: -0.31 (0.33), residues: 229 loop : -0.31 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 779 HIS 0.004 0.001 HIS A1008 PHE 0.013 0.001 PHE A2291 TYR 0.021 0.001 TYR A1665 ARG 0.004 0.000 ARG A2637 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 248 time to evaluate : 2.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 424 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8171 (mp) REVERT: A 605 ARG cc_start: 0.7431 (mtp-110) cc_final: 0.6797 (mtm110) REVERT: A 717 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.8130 (ttt180) REVERT: A 725 GLU cc_start: 0.6808 (pp20) cc_final: 0.6582 (pt0) REVERT: A 750 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6566 (mp0) REVERT: A 837 ARG cc_start: 0.6908 (mmt-90) cc_final: 0.6510 (mmt-90) REVERT: A 851 ASP cc_start: 0.6286 (m-30) cc_final: 0.6002 (m-30) REVERT: A 894 LYS cc_start: 0.7199 (ttpp) cc_final: 0.6877 (ptmm) REVERT: A 989 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7312 (mm-30) REVERT: A 1240 THR cc_start: 0.7622 (p) cc_final: 0.7361 (p) REVERT: A 1343 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6277 (mm-30) REVERT: A 1356 ARG cc_start: 0.6856 (ttp80) cc_final: 0.6121 (tpm170) REVERT: A 1408 ARG cc_start: 0.6868 (mtp-110) cc_final: 0.6615 (mtp85) REVERT: A 1412 MET cc_start: 0.6700 (OUTLIER) cc_final: 0.5954 (mmp) REVERT: A 1511 LYS cc_start: 0.5514 (pttp) cc_final: 0.5269 (mtmm) REVERT: A 1593 GLU cc_start: 0.6217 (OUTLIER) cc_final: 0.5922 (mm-30) REVERT: A 1611 PHE cc_start: 0.7335 (m-80) cc_final: 0.6864 (t80) REVERT: A 1649 GLN cc_start: 0.7044 (OUTLIER) cc_final: 0.6640 (mp10) REVERT: A 1664 ASN cc_start: 0.7692 (p0) cc_final: 0.7444 (p0) REVERT: A 2016 GLN cc_start: 0.6361 (mt0) cc_final: 0.5959 (mt0) REVERT: A 2020 GLN cc_start: 0.6797 (OUTLIER) cc_final: 0.6591 (mp10) REVERT: A 2093 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7201 (mt) REVERT: A 2222 GLN cc_start: 0.5943 (mt0) cc_final: 0.5130 (mm-40) REVERT: A 2380 ASP cc_start: 0.6512 (m-30) cc_final: 0.5912 (t0) REVERT: A 2504 ASP cc_start: 0.7610 (m-30) cc_final: 0.6310 (t0) REVERT: A 2607 GLU cc_start: 0.7555 (tp30) cc_final: 0.7293 (tt0) REVERT: A 2618 ARG cc_start: 0.6906 (mtp-110) cc_final: 0.6335 (mtm110) REVERT: A 2637 ARG cc_start: 0.6633 (ttm110) cc_final: 0.6417 (ttm110) REVERT: A 2691 ARG cc_start: 0.6588 (mtp85) cc_final: 0.5979 (mtp-110) REVERT: A 2702 ASP cc_start: 0.5345 (m-30) cc_final: 0.5031 (m-30) REVERT: A 2824 MET cc_start: 0.7826 (tpp) cc_final: 0.7423 (tpp) REVERT: A 2914 GLN cc_start: 0.6997 (mm-40) cc_final: 0.6546 (mm-40) REVERT: A 2955 GLN cc_start: 0.7053 (mt0) cc_final: 0.6571 (pt0) outliers start: 42 outliers final: 12 residues processed: 268 average time/residue: 1.3738 time to fit residues: 421.2393 Evaluate side-chains 251 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 231 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 717 ARG Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain A residue 1593 GLU Chi-restraints excluded: chain A residue 1649 GLN Chi-restraints excluded: chain A residue 2020 GLN Chi-restraints excluded: chain A residue 2093 LEU Chi-restraints excluded: chain A residue 2169 ASP Chi-restraints excluded: chain A residue 2374 VAL Chi-restraints excluded: chain A residue 2459 THR Chi-restraints excluded: chain A residue 2771 ASP Chi-restraints excluded: chain A residue 2817 MET Chi-restraints excluded: chain A residue 2933 LEU Chi-restraints excluded: chain A residue 2947 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 247 optimal weight: 4.9990 chunk 188 optimal weight: 0.0670 chunk 129 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 251 optimal weight: 0.9980 chunk 265 optimal weight: 0.9980 chunk 131 optimal weight: 6.9990 chunk 237 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN A 874 ASN ** A1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2178 ASN A2541 ASN ** A2740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22649 Z= 0.169 Angle : 0.507 6.592 30724 Z= 0.250 Chirality : 0.039 0.147 3458 Planarity : 0.004 0.043 3930 Dihedral : 6.331 168.074 3053 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.85 % Allowed : 11.90 % Favored : 86.25 % 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: 0.94 (0.17), residues: 2733 helix: 1.41 (0.14), residues: 1504 sheet: -0.25 (0.34), residues: 222 loop : -0.28 (0.20), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 779 HIS 0.004 0.001 HIS A1008 PHE 0.014 0.001 PHE A2291 TYR 0.020 0.001 TYR A1293 ARG 0.003 0.000 ARG A2637 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 243 time to evaluate : 2.511 Fit side-chains revert: symmetry clash REVERT: A 235 VAL cc_start: 0.7500 (OUTLIER) cc_final: 0.7263 (t) REVERT: A 424 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8160 (mp) REVERT: A 605 ARG cc_start: 0.7405 (mtp-110) cc_final: 0.6879 (mtm110) REVERT: A 717 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8161 (ttt180) REVERT: A 725 GLU cc_start: 0.6799 (pp20) cc_final: 0.6583 (pt0) REVERT: A 750 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6587 (mp0) REVERT: A 837 ARG cc_start: 0.7004 (mmt-90) cc_final: 0.6607 (mmt-90) REVERT: A 851 ASP cc_start: 0.6277 (m-30) cc_final: 0.6001 (m-30) REVERT: A 894 LYS cc_start: 0.7179 (ttpp) cc_final: 0.6955 (ptmt) REVERT: A 989 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7225 (mm-30) REVERT: A 1240 THR cc_start: 0.7626 (p) cc_final: 0.7356 (p) REVERT: A 1343 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6281 (mm-30) REVERT: A 1356 ARG cc_start: 0.6861 (ttp80) cc_final: 0.6127 (tpm170) REVERT: A 1408 ARG cc_start: 0.6955 (mtp-110) cc_final: 0.6678 (mtp85) REVERT: A 1412 MET cc_start: 0.6694 (OUTLIER) cc_final: 0.6087 (mmp) REVERT: A 1540 ASP cc_start: 0.7197 (m-30) cc_final: 0.6829 (m-30) REVERT: A 1611 PHE cc_start: 0.7334 (m-80) cc_final: 0.6875 (t80) REVERT: A 1664 ASN cc_start: 0.7732 (p0) cc_final: 0.7441 (p0) REVERT: A 2016 GLN cc_start: 0.6449 (mt0) cc_final: 0.6095 (mt0) REVERT: A 2093 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7283 (mt) REVERT: A 2222 GLN cc_start: 0.5771 (mt0) cc_final: 0.4952 (mm-40) REVERT: A 2380 ASP cc_start: 0.6530 (m-30) cc_final: 0.5895 (t0) REVERT: A 2504 ASP cc_start: 0.7613 (m-30) cc_final: 0.6362 (t0) REVERT: A 2607 GLU cc_start: 0.7531 (tp30) cc_final: 0.7326 (tt0) REVERT: A 2634 ASN cc_start: 0.6903 (OUTLIER) cc_final: 0.6632 (t0) REVERT: A 2691 ARG cc_start: 0.6611 (mtp85) cc_final: 0.5996 (mtp-110) REVERT: A 2702 ASP cc_start: 0.5794 (m-30) cc_final: 0.5245 (m-30) REVERT: A 2785 GLN cc_start: 0.6366 (OUTLIER) cc_final: 0.6023 (tm-30) REVERT: A 2788 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7117 (mt-10) REVERT: A 2914 GLN cc_start: 0.6990 (mm-40) cc_final: 0.6629 (mm-40) REVERT: A 2955 GLN cc_start: 0.7044 (mt0) cc_final: 0.6590 (pt0) outliers start: 45 outliers final: 16 residues processed: 269 average time/residue: 1.3161 time to fit residues: 407.9567 Evaluate side-chains 246 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 221 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 717 ARG Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1309 THR Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain A residue 2093 LEU Chi-restraints excluded: chain A residue 2169 ASP Chi-restraints excluded: chain A residue 2181 VAL Chi-restraints excluded: chain A residue 2188 SER Chi-restraints excluded: chain A residue 2374 VAL Chi-restraints excluded: chain A residue 2459 THR Chi-restraints excluded: chain A residue 2634 ASN Chi-restraints excluded: chain A residue 2771 ASP Chi-restraints excluded: chain A residue 2785 GLN Chi-restraints excluded: chain A residue 2788 GLU Chi-restraints excluded: chain A residue 2819 SER Chi-restraints excluded: chain A residue 2933 LEU Chi-restraints excluded: chain A residue 2947 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 221 optimal weight: 2.9990 chunk 150 optimal weight: 0.0040 chunk 3 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 226 optimal weight: 0.3980 chunk 183 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 135 optimal weight: 2.9990 chunk 238 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2178 ASN A2541 ASN ** A2578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22649 Z= 0.186 Angle : 0.517 9.262 30724 Z= 0.255 Chirality : 0.039 0.174 3458 Planarity : 0.004 0.048 3930 Dihedral : 6.316 164.664 3053 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.93 % Allowed : 12.80 % Favored : 85.27 % 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: 0.91 (0.16), residues: 2733 helix: 1.38 (0.14), residues: 1510 sheet: -0.19 (0.35), residues: 215 loop : -0.31 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 779 HIS 0.005 0.001 HIS A1008 PHE 0.020 0.001 PHE A2600 TYR 0.021 0.001 TYR A1665 ARG 0.007 0.000 ARG A2637 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 237 time to evaluate : 2.627 Fit side-chains revert: symmetry clash REVERT: A 235 VAL cc_start: 0.7503 (OUTLIER) cc_final: 0.7269 (t) REVERT: A 424 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8185 (mp) REVERT: A 605 ARG cc_start: 0.7507 (mtp-110) cc_final: 0.6987 (mtm110) REVERT: A 717 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.8181 (ttt180) REVERT: A 725 GLU cc_start: 0.6810 (pp20) cc_final: 0.6599 (pt0) REVERT: A 750 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6505 (mp0) REVERT: A 837 ARG cc_start: 0.7016 (mmt-90) cc_final: 0.6611 (mmt-90) REVERT: A 851 ASP cc_start: 0.6272 (m-30) cc_final: 0.5994 (m-30) REVERT: A 894 LYS cc_start: 0.7194 (ttpp) cc_final: 0.6834 (ptmt) REVERT: A 986 PHE cc_start: 0.8323 (m-80) cc_final: 0.8072 (m-80) REVERT: A 989 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7183 (mm-30) REVERT: A 1240 THR cc_start: 0.7604 (p) cc_final: 0.7330 (p) REVERT: A 1343 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6317 (mm-30) REVERT: A 1356 ARG cc_start: 0.6843 (ttp80) cc_final: 0.6140 (tpm170) REVERT: A 1540 ASP cc_start: 0.7287 (m-30) cc_final: 0.6941 (m-30) REVERT: A 1611 PHE cc_start: 0.7347 (m-80) cc_final: 0.6888 (t80) REVERT: A 1664 ASN cc_start: 0.7734 (p0) cc_final: 0.7434 (p0) REVERT: A 2016 GLN cc_start: 0.6439 (mt0) cc_final: 0.6157 (mt0) REVERT: A 2093 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7344 (mt) REVERT: A 2222 GLN cc_start: 0.5759 (mt0) cc_final: 0.4986 (mm-40) REVERT: A 2380 ASP cc_start: 0.6525 (m-30) cc_final: 0.5883 (t0) REVERT: A 2618 ARG cc_start: 0.6945 (mtp-110) cc_final: 0.6218 (mtt90) REVERT: A 2634 ASN cc_start: 0.6900 (OUTLIER) cc_final: 0.6655 (t0) REVERT: A 2691 ARG cc_start: 0.6751 (mtp85) cc_final: 0.6067 (mtp-110) REVERT: A 2702 ASP cc_start: 0.5835 (m-30) cc_final: 0.5247 (m-30) REVERT: A 2785 GLN cc_start: 0.6401 (OUTLIER) cc_final: 0.6122 (tt0) REVERT: A 2914 GLN cc_start: 0.7005 (mm-40) cc_final: 0.6651 (mm-40) REVERT: A 2955 GLN cc_start: 0.7050 (mt0) cc_final: 0.6589 (pt0) outliers start: 47 outliers final: 25 residues processed: 268 average time/residue: 1.2497 time to fit residues: 387.3762 Evaluate side-chains 252 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 220 time to evaluate : 2.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 717 ARG Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1309 THR Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain A residue 1981 ILE Chi-restraints excluded: chain A residue 2093 LEU Chi-restraints excluded: chain A residue 2169 ASP Chi-restraints excluded: chain A residue 2181 VAL Chi-restraints excluded: chain A residue 2188 SER Chi-restraints excluded: chain A residue 2374 VAL Chi-restraints excluded: chain A residue 2406 THR Chi-restraints excluded: chain A residue 2459 THR Chi-restraints excluded: chain A residue 2634 ASN Chi-restraints excluded: chain A residue 2771 ASP Chi-restraints excluded: chain A residue 2785 GLN Chi-restraints excluded: chain A residue 2799 LEU Chi-restraints excluded: chain A residue 2819 SER Chi-restraints excluded: chain A residue 2901 LEU Chi-restraints excluded: chain A residue 2933 LEU Chi-restraints excluded: chain A residue 2947 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 89 optimal weight: 0.5980 chunk 239 optimal weight: 1.9990 chunk 52 optimal weight: 0.1980 chunk 156 optimal weight: 2.9990 chunk 65 optimal weight: 0.2980 chunk 266 optimal weight: 0.7980 chunk 220 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN A1008 HIS ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2178 ASN A2541 ASN ** A2740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3067 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22649 Z= 0.159 Angle : 0.502 9.560 30724 Z= 0.247 Chirality : 0.038 0.147 3458 Planarity : 0.004 0.043 3930 Dihedral : 6.190 161.047 3053 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.01 % Allowed : 13.50 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.17), residues: 2733 helix: 1.49 (0.14), residues: 1504 sheet: -0.21 (0.34), residues: 223 loop : -0.26 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A2956 HIS 0.003 0.001 HIS A2466 PHE 0.016 0.001 PHE A2600 TYR 0.019 0.001 TYR A1293 ARG 0.008 0.000 ARG A1408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 227 time to evaluate : 2.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 VAL cc_start: 0.7464 (OUTLIER) cc_final: 0.7226 (t) REVERT: A 424 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8148 (mp) REVERT: A 605 ARG cc_start: 0.7490 (mtp-110) cc_final: 0.6992 (mtm110) REVERT: A 717 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.8116 (ttt180) REVERT: A 725 GLU cc_start: 0.6793 (pp20) cc_final: 0.6579 (pt0) REVERT: A 750 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6503 (mp0) REVERT: A 851 ASP cc_start: 0.6258 (m-30) cc_final: 0.5989 (m-30) REVERT: A 894 LYS cc_start: 0.7185 (ttpp) cc_final: 0.6832 (ptmt) REVERT: A 986 PHE cc_start: 0.8344 (m-80) cc_final: 0.8065 (m-80) REVERT: A 989 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7185 (mm-30) REVERT: A 1186 TYR cc_start: 0.4843 (OUTLIER) cc_final: 0.4518 (m-80) REVERT: A 1240 THR cc_start: 0.7616 (p) cc_final: 0.7353 (p) REVERT: A 1343 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6306 (mm-30) REVERT: A 1356 ARG cc_start: 0.6828 (ttp80) cc_final: 0.6149 (tpm170) REVERT: A 1412 MET cc_start: 0.6669 (OUTLIER) cc_final: 0.6050 (mmp) REVERT: A 1540 ASP cc_start: 0.7288 (m-30) cc_final: 0.6954 (m-30) REVERT: A 1611 PHE cc_start: 0.7346 (m-80) cc_final: 0.6884 (t80) REVERT: A 1664 ASN cc_start: 0.7794 (p0) cc_final: 0.7464 (p0) REVERT: A 1665 TYR cc_start: 0.6707 (t80) cc_final: 0.6365 (t80) REVERT: A 2016 GLN cc_start: 0.6421 (mt0) cc_final: 0.6095 (mt0) REVERT: A 2093 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7359 (mt) REVERT: A 2222 GLN cc_start: 0.5760 (mt0) cc_final: 0.4870 (mm-40) REVERT: A 2634 ASN cc_start: 0.6969 (OUTLIER) cc_final: 0.6658 (t0) REVERT: A 2637 ARG cc_start: 0.6367 (ttm110) cc_final: 0.6118 (ttm110) REVERT: A 2691 ARG cc_start: 0.6739 (mtp85) cc_final: 0.6061 (mtp-110) REVERT: A 2702 ASP cc_start: 0.5576 (m-30) cc_final: 0.5071 (m-30) REVERT: A 2785 GLN cc_start: 0.6350 (OUTLIER) cc_final: 0.6079 (tt0) REVERT: A 2788 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7111 (mt-10) REVERT: A 2892 GLU cc_start: 0.6170 (OUTLIER) cc_final: 0.5846 (pt0) REVERT: A 2914 GLN cc_start: 0.7004 (mm-40) cc_final: 0.6572 (mm-40) REVERT: A 2955 GLN cc_start: 0.7069 (mt0) cc_final: 0.6588 (pt0) outliers start: 49 outliers final: 24 residues processed: 256 average time/residue: 1.2799 time to fit residues: 379.5336 Evaluate side-chains 248 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 213 time to evaluate : 2.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 717 ARG Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1186 TYR Chi-restraints excluded: chain A residue 1309 THR Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain A residue 1981 ILE Chi-restraints excluded: chain A residue 2020 GLN Chi-restraints excluded: chain A residue 2093 LEU Chi-restraints excluded: chain A residue 2169 ASP Chi-restraints excluded: chain A residue 2181 VAL Chi-restraints excluded: chain A residue 2188 SER Chi-restraints excluded: chain A residue 2373 THR Chi-restraints excluded: chain A residue 2406 THR Chi-restraints excluded: chain A residue 2459 THR Chi-restraints excluded: chain A residue 2521 MET Chi-restraints excluded: chain A residue 2634 ASN Chi-restraints excluded: chain A residue 2771 ASP Chi-restraints excluded: chain A residue 2785 GLN Chi-restraints excluded: chain A residue 2788 GLU Chi-restraints excluded: chain A residue 2799 LEU Chi-restraints excluded: chain A residue 2819 SER Chi-restraints excluded: chain A residue 2892 GLU Chi-restraints excluded: chain A residue 2933 LEU Chi-restraints excluded: chain A residue 2947 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 256 optimal weight: 0.0470 chunk 29 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 148 optimal weight: 0.0770 chunk 265 optimal weight: 0.9980 chunk 165 optimal weight: 0.6980 chunk 161 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2178 ASN A2541 ASN ** A2578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 22649 Z= 0.156 Angle : 0.497 10.436 30724 Z= 0.243 Chirality : 0.038 0.181 3458 Planarity : 0.004 0.042 3930 Dihedral : 6.080 156.267 3053 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.13 % Allowed : 13.91 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.17), residues: 2733 helix: 1.53 (0.14), residues: 1503 sheet: -0.25 (0.34), residues: 225 loop : -0.26 (0.20), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 779 HIS 0.005 0.001 HIS A1745 PHE 0.015 0.001 PHE A2600 TYR 0.019 0.001 TYR A1293 ARG 0.004 0.000 ARG A 658 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 231 time to evaluate : 2.575 Fit side-chains revert: symmetry clash REVERT: A 235 VAL cc_start: 0.7439 (OUTLIER) cc_final: 0.7197 (t) REVERT: A 424 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8127 (mp) REVERT: A 605 ARG cc_start: 0.7481 (mtp-110) cc_final: 0.6987 (mtm110) REVERT: A 717 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.8108 (ttt180) REVERT: A 725 GLU cc_start: 0.6773 (pp20) cc_final: 0.6557 (pt0) REVERT: A 750 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6504 (mp0) REVERT: A 851 ASP cc_start: 0.6287 (m-30) cc_final: 0.5980 (m-30) REVERT: A 894 LYS cc_start: 0.7164 (ttpp) cc_final: 0.6847 (ptmt) REVERT: A 986 PHE cc_start: 0.8318 (m-80) cc_final: 0.8085 (m-80) REVERT: A 989 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7172 (mm-30) REVERT: A 1186 TYR cc_start: 0.4874 (OUTLIER) cc_final: 0.4426 (m-80) REVERT: A 1240 THR cc_start: 0.7579 (p) cc_final: 0.7297 (p) REVERT: A 1343 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6314 (mm-30) REVERT: A 1356 ARG cc_start: 0.6829 (ttp80) cc_final: 0.6180 (tpm170) REVERT: A 1540 ASP cc_start: 0.7289 (m-30) cc_final: 0.6953 (m-30) REVERT: A 1611 PHE cc_start: 0.7326 (m-80) cc_final: 0.6865 (t80) REVERT: A 1664 ASN cc_start: 0.7801 (p0) cc_final: 0.7559 (p0) REVERT: A 2016 GLN cc_start: 0.6414 (mt0) cc_final: 0.6068 (mt0) REVERT: A 2093 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7453 (mt) REVERT: A 2222 GLN cc_start: 0.5770 (mt0) cc_final: 0.4979 (mm-40) REVERT: A 2634 ASN cc_start: 0.6896 (OUTLIER) cc_final: 0.6627 (t0) REVERT: A 2691 ARG cc_start: 0.6737 (mtp85) cc_final: 0.6057 (mtp-110) REVERT: A 2698 ASP cc_start: 0.5572 (t0) cc_final: 0.4753 (p0) REVERT: A 2702 ASP cc_start: 0.5541 (m-30) cc_final: 0.5035 (m-30) REVERT: A 2785 GLN cc_start: 0.6330 (OUTLIER) cc_final: 0.5938 (tt0) REVERT: A 2788 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7110 (mt-10) REVERT: A 2789 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8711 (mp) REVERT: A 2892 GLU cc_start: 0.6167 (OUTLIER) cc_final: 0.5848 (pt0) REVERT: A 2914 GLN cc_start: 0.7066 (mm-40) cc_final: 0.6644 (mm-40) REVERT: A 2955 GLN cc_start: 0.7069 (mt0) cc_final: 0.6579 (pt0) outliers start: 52 outliers final: 29 residues processed: 266 average time/residue: 1.2904 time to fit residues: 397.1781 Evaluate side-chains 254 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 214 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 717 ARG Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 807 ASP Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1186 TYR Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1309 THR Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain A residue 1570 GLU Chi-restraints excluded: chain A residue 1744 MET Chi-restraints excluded: chain A residue 1981 ILE Chi-restraints excluded: chain A residue 2020 GLN Chi-restraints excluded: chain A residue 2093 LEU Chi-restraints excluded: chain A residue 2181 VAL Chi-restraints excluded: chain A residue 2188 SER Chi-restraints excluded: chain A residue 2269 MET Chi-restraints excluded: chain A residue 2374 VAL Chi-restraints excluded: chain A residue 2406 THR Chi-restraints excluded: chain A residue 2521 MET Chi-restraints excluded: chain A residue 2634 ASN Chi-restraints excluded: chain A residue 2771 ASP Chi-restraints excluded: chain A residue 2785 GLN Chi-restraints excluded: chain A residue 2788 GLU Chi-restraints excluded: chain A residue 2789 LEU Chi-restraints excluded: chain A residue 2819 SER Chi-restraints excluded: chain A residue 2892 GLU Chi-restraints excluded: chain A residue 2933 LEU Chi-restraints excluded: chain A residue 2947 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 163 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 158 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 168 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN A1027 GLN ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2013 HIS ** A2100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2178 ASN A2358 HIS A2541 ASN ** A2578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2968 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 22649 Z= 0.331 Angle : 0.623 11.890 30724 Z= 0.307 Chirality : 0.042 0.170 3458 Planarity : 0.005 0.041 3930 Dihedral : 6.518 159.490 3053 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.34 % Allowed : 14.44 % Favored : 83.22 % 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: 0.52 (0.16), residues: 2733 helix: 1.06 (0.13), residues: 1511 sheet: -0.31 (0.34), residues: 216 loop : -0.50 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1129 HIS 0.006 0.001 HIS A2665 PHE 0.023 0.002 PHE A 272 TYR 0.023 0.002 TYR A1293 ARG 0.007 0.000 ARG A2637 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 228 time to evaluate : 2.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 VAL cc_start: 0.7528 (OUTLIER) cc_final: 0.7289 (t) REVERT: A 394 LYS cc_start: 0.7156 (pttm) cc_final: 0.6814 (pptt) REVERT: A 424 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8309 (mp) REVERT: A 605 ARG cc_start: 0.7486 (mtp-110) cc_final: 0.6926 (mtm110) REVERT: A 725 GLU cc_start: 0.6627 (pp20) cc_final: 0.6006 (mm-30) REVERT: A 750 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6504 (mp0) REVERT: A 851 ASP cc_start: 0.6311 (m-30) cc_final: 0.6024 (m-30) REVERT: A 894 LYS cc_start: 0.7344 (ttpp) cc_final: 0.6894 (ptmm) REVERT: A 989 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7204 (mm-30) REVERT: A 1240 THR cc_start: 0.7632 (p) cc_final: 0.7349 (p) REVERT: A 1343 GLU cc_start: 0.7386 (mt-10) cc_final: 0.6403 (mm-30) REVERT: A 1356 ARG cc_start: 0.6757 (ttp80) cc_final: 0.5949 (tpm170) REVERT: A 1540 ASP cc_start: 0.7512 (m-30) cc_final: 0.7187 (m-30) REVERT: A 1611 PHE cc_start: 0.7499 (m-80) cc_final: 0.6964 (t80) REVERT: A 1613 MET cc_start: 0.7678 (mtp) cc_final: 0.7442 (mtp) REVERT: A 1664 ASN cc_start: 0.7885 (p0) cc_final: 0.7482 (p0) REVERT: A 1665 TYR cc_start: 0.6791 (t80) cc_final: 0.6434 (t80) REVERT: A 2016 GLN cc_start: 0.6608 (mt0) cc_final: 0.6337 (mt0) REVERT: A 2165 GLU cc_start: 0.6551 (mp0) cc_final: 0.6023 (mp0) REVERT: A 2209 LEU cc_start: 0.4789 (tp) cc_final: 0.4546 (tp) REVERT: A 2222 GLN cc_start: 0.5717 (mt0) cc_final: 0.4943 (mm-40) REVERT: A 2269 MET cc_start: 0.6181 (OUTLIER) cc_final: 0.5918 (tpt) REVERT: A 2634 ASN cc_start: 0.7422 (OUTLIER) cc_final: 0.7013 (t0) REVERT: A 2637 ARG cc_start: 0.6332 (ttm110) cc_final: 0.6119 (ttm110) REVERT: A 2691 ARG cc_start: 0.6735 (mtp85) cc_final: 0.6052 (mtp-110) REVERT: A 2702 ASP cc_start: 0.5626 (m-30) cc_final: 0.5204 (m-30) REVERT: A 2785 GLN cc_start: 0.6407 (OUTLIER) cc_final: 0.6008 (tt0) REVERT: A 2789 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8824 (mt) REVERT: A 2914 GLN cc_start: 0.6930 (mm-40) cc_final: 0.6562 (mm-40) REVERT: A 2955 GLN cc_start: 0.6928 (mt0) cc_final: 0.6546 (pt0) outliers start: 57 outliers final: 27 residues processed: 262 average time/residue: 1.3035 time to fit residues: 394.4258 Evaluate side-chains 252 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 218 time to evaluate : 2.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 807 ASP Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 957 MET Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1309 THR Chi-restraints excluded: chain A residue 1570 GLU Chi-restraints excluded: chain A residue 1981 ILE Chi-restraints excluded: chain A residue 2169 ASP Chi-restraints excluded: chain A residue 2181 VAL Chi-restraints excluded: chain A residue 2188 SER Chi-restraints excluded: chain A residue 2269 MET Chi-restraints excluded: chain A residue 2373 THR Chi-restraints excluded: chain A residue 2374 VAL Chi-restraints excluded: chain A residue 2406 THR Chi-restraints excluded: chain A residue 2634 ASN Chi-restraints excluded: chain A residue 2785 GLN Chi-restraints excluded: chain A residue 2789 LEU Chi-restraints excluded: chain A residue 2799 LEU Chi-restraints excluded: chain A residue 2819 SER Chi-restraints excluded: chain A residue 2933 LEU Chi-restraints excluded: chain A residue 2947 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 241 optimal weight: 1.9990 chunk 253 optimal weight: 0.6980 chunk 231 optimal weight: 0.9980 chunk 246 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 193 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 223 optimal weight: 0.7980 chunk 233 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN ** A 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2013 HIS ** A2100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2541 ASN ** A2578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 22649 Z= 0.196 Angle : 0.544 12.132 30724 Z= 0.268 Chirality : 0.039 0.198 3458 Planarity : 0.004 0.041 3930 Dihedral : 6.334 157.891 3053 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.68 % Allowed : 15.39 % Favored : 82.93 % 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: 0.73 (0.16), residues: 2733 helix: 1.26 (0.14), residues: 1506 sheet: -0.39 (0.34), residues: 221 loop : -0.39 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 779 HIS 0.004 0.001 HIS A 763 PHE 0.014 0.001 PHE A2291 TYR 0.020 0.001 TYR A1293 ARG 0.006 0.000 ARG A2618 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 228 time to evaluate : 2.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 LEU cc_start: 0.8199 (mm) cc_final: 0.7105 (pp) REVERT: A 235 VAL cc_start: 0.7471 (OUTLIER) cc_final: 0.7222 (t) REVERT: A 284 ILE cc_start: 0.7689 (OUTLIER) cc_final: 0.7233 (mp) REVERT: A 424 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8272 (mp) REVERT: A 605 ARG cc_start: 0.7498 (mtp-110) cc_final: 0.7000 (mtm110) REVERT: A 725 GLU cc_start: 0.6574 (pp20) cc_final: 0.5959 (mm-30) REVERT: A 750 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6459 (mp0) REVERT: A 837 ARG cc_start: 0.6977 (mmt-90) cc_final: 0.6647 (mmt-90) REVERT: A 851 ASP cc_start: 0.6283 (m-30) cc_final: 0.5995 (m-30) REVERT: A 894 LYS cc_start: 0.7307 (ttpp) cc_final: 0.6843 (ptmt) REVERT: A 989 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7206 (mm-30) REVERT: A 1240 THR cc_start: 0.7617 (p) cc_final: 0.7330 (p) REVERT: A 1343 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6355 (mm-30) REVERT: A 1356 ARG cc_start: 0.6748 (ttp80) cc_final: 0.5970 (tpm170) REVERT: A 1540 ASP cc_start: 0.7387 (m-30) cc_final: 0.7041 (m-30) REVERT: A 1611 PHE cc_start: 0.7397 (m-80) cc_final: 0.6929 (t80) REVERT: A 1664 ASN cc_start: 0.7794 (p0) cc_final: 0.7404 (p0) REVERT: A 2016 GLN cc_start: 0.6478 (mt0) cc_final: 0.6106 (mt0) REVERT: A 2209 LEU cc_start: 0.4737 (tp) cc_final: 0.4449 (tp) REVERT: A 2222 GLN cc_start: 0.5609 (mt0) cc_final: 0.4863 (mm-40) REVERT: A 2504 ASP cc_start: 0.7451 (m-30) cc_final: 0.6230 (t0) REVERT: A 2634 ASN cc_start: 0.6995 (OUTLIER) cc_final: 0.6649 (t0) REVERT: A 2691 ARG cc_start: 0.6705 (mtp85) cc_final: 0.6029 (mtp-110) REVERT: A 2698 ASP cc_start: 0.5735 (t0) cc_final: 0.4529 (p0) REVERT: A 2702 ASP cc_start: 0.5846 (m-30) cc_final: 0.5112 (m-30) REVERT: A 2785 GLN cc_start: 0.6299 (OUTLIER) cc_final: 0.6076 (tt0) REVERT: A 2914 GLN cc_start: 0.7074 (mm-40) cc_final: 0.6706 (mm-40) REVERT: A 2955 GLN cc_start: 0.7075 (mt0) cc_final: 0.6601 (pt0) outliers start: 41 outliers final: 27 residues processed: 256 average time/residue: 1.3164 time to fit residues: 389.3160 Evaluate side-chains 251 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 218 time to evaluate : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1309 THR Chi-restraints excluded: chain A residue 1332 ASP Chi-restraints excluded: chain A residue 1570 GLU Chi-restraints excluded: chain A residue 1981 ILE Chi-restraints excluded: chain A residue 2020 GLN Chi-restraints excluded: chain A residue 2181 VAL Chi-restraints excluded: chain A residue 2188 SER Chi-restraints excluded: chain A residue 2373 THR Chi-restraints excluded: chain A residue 2374 VAL Chi-restraints excluded: chain A residue 2406 THR Chi-restraints excluded: chain A residue 2521 MET Chi-restraints excluded: chain A residue 2634 ASN Chi-restraints excluded: chain A residue 2785 GLN Chi-restraints excluded: chain A residue 2799 LEU Chi-restraints excluded: chain A residue 2819 SER Chi-restraints excluded: chain A residue 2933 LEU Chi-restraints excluded: chain A residue 2947 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 261 optimal weight: 0.9980 chunk 159 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 273 optimal weight: 2.9990 chunk 252 optimal weight: 5.9990 chunk 218 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 168 optimal weight: 0.4980 chunk 133 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2114 GLN A2178 ASN A2541 ASN ** A2578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 22649 Z= 0.220 Angle : 0.558 12.682 30724 Z= 0.274 Chirality : 0.040 0.148 3458 Planarity : 0.004 0.045 3930 Dihedral : 6.310 155.810 3053 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.56 % Allowed : 15.72 % Favored : 82.72 % 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: 0.70 (0.16), residues: 2733 helix: 1.24 (0.14), residues: 1510 sheet: -0.41 (0.34), residues: 221 loop : -0.42 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 779 HIS 0.004 0.001 HIS A 763 PHE 0.014 0.001 PHE A 272 TYR 0.021 0.001 TYR A1293 ARG 0.007 0.000 ARG A2637 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 224 time to evaluate : 2.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 LEU cc_start: 0.8206 (mm) cc_final: 0.7116 (pp) REVERT: A 235 VAL cc_start: 0.7468 (OUTLIER) cc_final: 0.7224 (t) REVERT: A 284 ILE cc_start: 0.7688 (OUTLIER) cc_final: 0.7197 (mp) REVERT: A 424 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8267 (mp) REVERT: A 605 ARG cc_start: 0.7517 (mtp-110) cc_final: 0.6959 (mtm110) REVERT: A 725 GLU cc_start: 0.6593 (pp20) cc_final: 0.5977 (mm-30) REVERT: A 750 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6427 (mp0) REVERT: A 837 ARG cc_start: 0.6972 (mmt-90) cc_final: 0.6653 (mmt-90) REVERT: A 851 ASP cc_start: 0.6287 (m-30) cc_final: 0.6002 (m-30) REVERT: A 894 LYS cc_start: 0.7316 (ttpp) cc_final: 0.6841 (ptmt) REVERT: A 989 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7202 (mm-30) REVERT: A 1240 THR cc_start: 0.7643 (p) cc_final: 0.7360 (p) REVERT: A 1343 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6377 (mm-30) REVERT: A 1356 ARG cc_start: 0.6879 (ttp80) cc_final: 0.6153 (tpm170) REVERT: A 1540 ASP cc_start: 0.7423 (m-30) cc_final: 0.7083 (m-30) REVERT: A 1611 PHE cc_start: 0.7414 (m-80) cc_final: 0.6885 (t80) REVERT: A 1664 ASN cc_start: 0.7809 (p0) cc_final: 0.7404 (p0) REVERT: A 1665 TYR cc_start: 0.6811 (t80) cc_final: 0.6524 (t80) REVERT: A 2016 GLN cc_start: 0.6518 (mt0) cc_final: 0.6257 (mt0) REVERT: A 2114 GLN cc_start: 0.7466 (OUTLIER) cc_final: 0.7009 (mm-40) REVERT: A 2222 GLN cc_start: 0.5618 (mt0) cc_final: 0.4870 (mm-40) REVERT: A 2504 ASP cc_start: 0.7460 (m-30) cc_final: 0.6233 (t0) REVERT: A 2634 ASN cc_start: 0.6977 (OUTLIER) cc_final: 0.6749 (t0) REVERT: A 2637 ARG cc_start: 0.6439 (ttm110) cc_final: 0.6237 (ttm110) REVERT: A 2691 ARG cc_start: 0.6711 (mtp85) cc_final: 0.6032 (mtp-110) REVERT: A 2698 ASP cc_start: 0.5701 (t0) cc_final: 0.4574 (p0) REVERT: A 2702 ASP cc_start: 0.5861 (m-30) cc_final: 0.5145 (m-30) REVERT: A 2785 GLN cc_start: 0.6320 (OUTLIER) cc_final: 0.6085 (tt0) REVERT: A 2914 GLN cc_start: 0.7058 (mm-40) cc_final: 0.6685 (mm-40) REVERT: A 2955 GLN cc_start: 0.7074 (mt0) cc_final: 0.6602 (pt0) outliers start: 38 outliers final: 29 residues processed: 253 average time/residue: 1.3277 time to fit residues: 388.1668 Evaluate side-chains 254 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 218 time to evaluate : 2.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 807 ASP Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1309 THR Chi-restraints excluded: chain A residue 1332 ASP Chi-restraints excluded: chain A residue 1570 GLU Chi-restraints excluded: chain A residue 1981 ILE Chi-restraints excluded: chain A residue 2020 GLN Chi-restraints excluded: chain A residue 2114 GLN Chi-restraints excluded: chain A residue 2169 ASP Chi-restraints excluded: chain A residue 2181 VAL Chi-restraints excluded: chain A residue 2188 SER Chi-restraints excluded: chain A residue 2373 THR Chi-restraints excluded: chain A residue 2374 VAL Chi-restraints excluded: chain A residue 2406 THR Chi-restraints excluded: chain A residue 2521 MET Chi-restraints excluded: chain A residue 2634 ASN Chi-restraints excluded: chain A residue 2785 GLN Chi-restraints excluded: chain A residue 2799 LEU Chi-restraints excluded: chain A residue 2819 SER Chi-restraints excluded: chain A residue 2933 LEU Chi-restraints excluded: chain A residue 2947 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.4288 > 50: distance: 20 - 127: 21.051 distance: 23 - 124: 27.024 distance: 50 - 51: 3.489 distance: 51 - 52: 16.842 distance: 51 - 54: 20.338 distance: 52 - 53: 17.526 distance: 52 - 59: 5.311 distance: 54 - 55: 24.075 distance: 56 - 57: 9.773 distance: 59 - 60: 3.906 distance: 60 - 61: 23.837 distance: 60 - 63: 19.852 distance: 61 - 62: 16.435 distance: 61 - 68: 15.346 distance: 63 - 64: 10.133 distance: 64 - 65: 5.383 distance: 65 - 66: 20.645 distance: 65 - 67: 18.500 distance: 68 - 69: 11.711 distance: 69 - 70: 17.416 distance: 69 - 72: 28.294 distance: 70 - 71: 16.662 distance: 70 - 75: 9.257 distance: 72 - 73: 34.838 distance: 72 - 74: 24.737 distance: 75 - 76: 18.147 distance: 76 - 77: 9.972 distance: 76 - 79: 29.650 distance: 77 - 78: 4.757 distance: 77 - 83: 7.764 distance: 79 - 80: 23.316 distance: 80 - 82: 13.956 distance: 83 - 84: 24.972 distance: 84 - 85: 20.176 distance: 84 - 87: 28.095 distance: 85 - 86: 18.755 distance: 85 - 90: 37.085 distance: 87 - 88: 11.879 distance: 87 - 89: 12.817 distance: 90 - 91: 33.708 distance: 91 - 92: 17.300 distance: 91 - 94: 40.452 distance: 92 - 93: 28.007 distance: 92 - 98: 18.784 distance: 94 - 95: 34.780 distance: 95 - 96: 38.140 distance: 95 - 97: 25.703 distance: 98 - 99: 14.092 distance: 99 - 100: 23.530 distance: 99 - 102: 20.017 distance: 100 - 101: 12.810 distance: 100 - 107: 10.391 distance: 102 - 103: 7.280 distance: 103 - 104: 13.599 distance: 104 - 105: 14.134 distance: 104 - 106: 19.267 distance: 107 - 108: 26.099 distance: 108 - 109: 15.078 distance: 108 - 111: 14.603 distance: 109 - 110: 35.590 distance: 109 - 116: 10.037 distance: 111 - 112: 25.697 distance: 112 - 113: 11.895 distance: 113 - 114: 14.833 distance: 113 - 115: 8.784 distance: 116 - 117: 21.597 distance: 117 - 118: 27.009 distance: 117 - 120: 30.913 distance: 118 - 119: 13.380 distance: 118 - 124: 5.840 distance: 120 - 121: 15.856 distance: 121 - 122: 8.748 distance: 121 - 123: 10.029 distance: 124 - 125: 7.084 distance: 125 - 126: 23.661 distance: 125 - 128: 29.715 distance: 126 - 127: 14.951 distance: 126 - 130: 8.264