Starting phenix.real_space_refine on Thu Jun 19 17:38:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fd6_29003/06_2025/8fd6_29003.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fd6_29003/06_2025/8fd6_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/cci-nas-00/data/ceres_data/8fd6_29003/06_2025/8fd6_29003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fd6_29003/06_2025/8fd6_29003.map" model { file = "/net/cci-nas-00/data/ceres_data/8fd6_29003/06_2025/8fd6_29003.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fd6_29003/06_2025/8fd6_29003.cif" } 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. Time to flip 22 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22170 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 22052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2747, 22052 Classifications: {'peptide': 2747} Link IDs: {'PTRANS': 127, 'TRANS': 2619} Chain breaks: 6 Chain: "A" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 118 Unusual residues: {' MG': 1, 'ADP': 3, 'ATP': 1, 'VO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 11.98, per 1000 atoms: 0.54 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.34 Conformation dependent library (CDL) restraints added in 2.6 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... Secondary structure from input PDB file: 121 helices and 19 sheets defined 60.0% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.34 Creating SS restraints... Processing helix chain 'A' and resid 88 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 100 through 105 removed outlier: 4.004A pdb=" N HIS A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 114 removed outlier: 4.297A pdb=" N GLN A 111 " --> pdb=" O PRO A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 171 Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 178 through 188 removed outlier: 4.031A pdb=" N GLU A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 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 198 through 203 Processing helix chain 'A' and resid 242 through 274 removed outlier: 3.635A pdb=" N PHE A 272 " --> pdb=" O GLU A 268 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 290 Processing helix chain 'A' and resid 291 through 314 Processing helix chain 'A' and resid 322 through 343 removed outlier: 3.656A pdb=" N VAL A 326 " --> pdb=" O PRO A 322 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET A 343 " --> pdb=" O ASP A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 374 Processing helix chain 'A' and resid 380 through 385 Processing helix chain 'A' and resid 427 through 442 Processing helix chain 'A' and resid 443 through 445 No H-bonds generated for 'chain 'A' and resid 443 through 445' Processing helix chain 'A' and resid 456 through 468 Processing helix chain 'A' and resid 482 through 497 Processing helix chain 'A' and resid 505 through 508 removed outlier: 3.676A pdb=" N LEU A 508 " --> pdb=" O PHE A 505 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 505 through 508' Processing helix chain 'A' and resid 509 through 528 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) Processing helix chain 'A' and resid 574 through 579 removed outlier: 3.788A pdb=" N LYS A 579 " --> pdb=" O ASP A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 603 Processing helix chain 'A' and resid 606 through 625 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 634 through 659 Processing helix chain 'A' and resid 677 through 690 Processing helix chain 'A' and resid 695 through 697 No H-bonds generated for 'chain 'A' and resid 695 through 697' Processing helix chain 'A' and resid 698 through 710 Processing helix chain 'A' and resid 720 through 734 Processing helix chain 'A' and resid 745 through 762 Processing helix chain 'A' and resid 774 through 791 Processing helix chain 'A' and resid 805 through 810 Processing helix chain 'A' and resid 823 through 834 removed outlier: 3.553A pdb=" N HIS A 827 " --> pdb=" O GLY A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 842 Processing helix chain 'A' and resid 857 through 861 Processing helix chain 'A' and resid 897 through 904 removed outlier: 3.730A pdb=" N ARG A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS A 904 " --> pdb=" O THR A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 929 removed outlier: 3.515A pdb=" N SER A 929 " --> pdb=" O ALA A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 969 Processing helix chain 'A' and resid 970 through 972 No H-bonds generated for 'chain 'A' and resid 970 through 972' Processing helix chain 'A' and resid 976 through 986 Processing helix chain 'A' and resid 995 through 1021 removed outlier: 3.525A pdb=" N CYS A 999 " --> pdb=" O THR A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1049 removed outlier: 4.054A pdb=" N VAL A1040 " --> pdb=" O GLN A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1067 Processing helix chain 'A' and resid 1078 through 1080 No H-bonds generated for 'chain 'A' and resid 1078 through 1080' Processing helix chain 'A' and resid 1094 through 1097 Processing helix chain 'A' and resid 1116 through 1132 removed outlier: 3.502A pdb=" N HIS A1122 " --> pdb=" O ASP A1118 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU A1132 " --> pdb=" O THR A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1157 removed outlier: 3.649A pdb=" N ALA A1156 " --> pdb=" O SER A1152 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A1157 " --> pdb=" O ALA A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1172 through 1184 removed outlier: 4.295A pdb=" N LEU A1176 " --> pdb=" O THR A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1222 through 1234 Processing helix chain 'A' and resid 1269 through 1274 Processing helix chain 'A' and resid 1285 through 1301 removed outlier: 3.705A pdb=" N PHE A1296 " --> pdb=" O ILE A1292 " (cutoff:3.500A) Processing helix chain 'A' and resid 1307 through 1309 No H-bonds generated for 'chain 'A' and resid 1307 through 1309' Processing helix chain 'A' and resid 1310 through 1329 removed outlier: 3.640A pdb=" N THR A1315 " --> pdb=" O ALA A1311 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1356 removed outlier: 3.960A pdb=" N MET A1344 " --> pdb=" O SER A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1362 through 1379 Processing helix chain 'A' and resid 1384 through 1403 removed outlier: 3.686A pdb=" N ASP A1396 " --> pdb=" O ASP A1392 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1412 removed outlier: 3.642A pdb=" N ALA A1411 " --> pdb=" O ASP A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1449 removed outlier: 3.628A pdb=" N GLU A1447 " --> pdb=" O LYS A1443 " (cutoff:3.500A) Processing helix chain 'A' and resid 1457 through 1473 removed outlier: 3.948A pdb=" N GLN A1473 " --> pdb=" O ARG A1469 " (cutoff:3.500A) Processing helix chain 'A' and resid 1487 through 1500 Processing helix chain 'A' and resid 1513 through 1530 Processing helix chain 'A' and resid 1546 through 1560 removed outlier: 3.845A pdb=" N LEU A1550 " --> pdb=" O ASP A1546 " (cutoff:3.500A) Processing helix chain 'A' and resid 1568 through 1586 Processing helix chain 'A' and resid 1591 through 1606 removed outlier: 3.626A pdb=" N TYR A1596 " --> pdb=" O HIS A1592 " (cutoff:3.500A) Processing helix chain 'A' and resid 1619 through 1627 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 1643 through 1656 Processing helix chain 'A' and resid 1683 through 1709 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 1717 through 1765 removed outlier: 3.841A pdb=" N TYR A1721 " --> pdb=" O THR A1717 " (cutoff:3.500A) Processing helix chain 'A' and resid 1950 through 1980 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 1980 through 1995 Processing helix chain 'A' and resid 1999 through 2017 Processing helix chain 'A' and resid 2026 through 2031 removed outlier: 3.528A pdb=" N TYR A2030 " --> pdb=" O ALA A2026 " (cutoff:3.500A) Processing helix chain 'A' and resid 2033 through 2043 Processing helix chain 'A' and resid 2048 through 2060 Processing helix chain 'A' and resid 2072 through 2082 Processing helix chain 'A' and resid 2096 through 2108 Processing helix chain 'A' and resid 2115 through 2119 Processing helix chain 'A' and resid 2120 through 2122 No H-bonds generated for 'chain 'A' and resid 2120 through 2122' Processing helix chain 'A' and resid 2123 through 2129 Processing helix chain 'A' and resid 2167 through 2172 Processing helix chain 'A' and resid 2182 through 2199 Processing helix chain 'A' and resid 2199 through 2234 removed outlier: 3.614A pdb=" N GLU A2215 " --> pdb=" O LYS A2211 " (cutoff:3.500A) Processing helix chain 'A' and resid 2240 through 2265 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) Processing helix chain 'A' and resid 2266 through 2277 removed outlier: 3.683A pdb=" N GLU A2271 " --> pdb=" O ILE A2267 " (cutoff:3.500A) Processing helix chain 'A' and resid 2279 through 2296 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) Processing helix chain 'A' and resid 2306 through 2320 removed outlier: 3.562A pdb=" N PHE A2310 " --> pdb=" O SER A2306 " (cutoff:3.500A) Processing helix chain 'A' and resid 2321 through 2325 Processing helix chain 'A' and resid 2329 through 2351 Processing helix chain 'A' and resid 2352 through 2353 No H-bonds generated for 'chain 'A' and resid 2352 through 2353' Processing helix chain 'A' and resid 2354 through 2356 No H-bonds generated for 'chain 'A' and resid 2354 through 2356' Processing helix chain 'A' and resid 2357 through 2372 Processing helix chain 'A' and resid 2379 through 2389 removed outlier: 3.880A pdb=" N HIS A2385 " --> pdb=" O ALA A2381 " (cutoff:3.500A) Processing helix chain 'A' and resid 2406 through 2417 Processing helix chain 'A' and resid 2424 through 2431 removed outlier: 3.603A pdb=" N GLN A2430 " --> pdb=" O ILE A2426 " (cutoff:3.500A) Processing helix chain 'A' and resid 2433 through 2440 removed outlier: 4.158A pdb=" N ILE A2437 " --> pdb=" O GLU A2433 " (cutoff:3.500A) Processing helix chain 'A' and resid 2443 through 2447 Processing helix chain 'A' and resid 2459 through 2475 Processing helix chain 'A' and resid 2478 through 2491 removed outlier: 3.817A pdb=" N MET A2485 " --> pdb=" O ALA A2481 " (cutoff:3.500A) Processing helix chain 'A' and resid 2504 through 2512 removed outlier: 3.636A pdb=" N ILE A2508 " --> pdb=" O ASP A2504 " (cutoff:3.500A) Processing helix chain 'A' and resid 2529 through 2540 Processing helix chain 'A' and resid 2553 through 2567 removed outlier: 3.942A pdb=" N LYS A2567 " --> pdb=" O ASN A2563 " (cutoff:3.500A) Processing helix chain 'A' and resid 2580 through 2592 removed outlier: 3.743A pdb=" N HIS A2592 " --> pdb=" O GLU A2588 " (cutoff:3.500A) Processing helix chain 'A' and resid 2613 through 2620 Processing helix chain 'A' and resid 2629 through 2642 removed outlier: 4.103A pdb=" N ALA A2633 " --> pdb=" O PRO A2629 " (cutoff:3.500A) Processing helix chain 'A' and resid 2652 through 2671 removed outlier: 4.022A pdb=" N ARG A2656 " --> pdb=" O ASN A2652 " (cutoff:3.500A) Processing helix chain 'A' and resid 2672 through 2675 Processing helix chain 'A' and resid 2686 through 2705 removed outlier: 3.564A pdb=" N LEU A2690 " --> pdb=" O GLY A2686 " (cutoff:3.500A) Processing helix chain 'A' and resid 2717 through 2723 removed outlier: 3.617A pdb=" N LEU A2721 " --> pdb=" O PRO A2717 " (cutoff:3.500A) Processing helix chain 'A' and resid 2723 through 2728 Processing helix chain 'A' and resid 2736 through 2751 removed outlier: 3.570A pdb=" N GLN A2740 " --> pdb=" O ASN A2736 " (cutoff:3.500A) Processing helix chain 'A' and resid 2752 through 2756 Processing helix chain 'A' and resid 2779 through 2789 removed outlier: 3.618A pdb=" N PHE A2783 " --> pdb=" O ARG A2779 " (cutoff:3.500A) Processing helix chain 'A' and resid 2795 through 2800 Processing helix chain 'A' and resid 2802 through 2805 Processing helix chain 'A' and resid 2806 through 2825 Processing helix chain 'A' and resid 2854 through 2869 Processing helix chain 'A' and resid 2885 through 2917 Processing helix chain 'A' and resid 2923 through 2935 removed outlier: 3.830A pdb=" N LYS A2935 " --> pdb=" O ASN A2931 " (cutoff:3.500A) Processing helix chain 'A' and resid 2952 through 2977 Processing helix chain 'A' and resid 2994 through 3010 Processing helix chain 'A' and resid 3109 through 3116 Processing sheet with id=AA1, first strand: chain 'A' and resid 206 through 211 removed outlier: 7.199A pdb=" N VAL A 206 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N SER A 223 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N SER A 208 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ILE A 221 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE A 210 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 10.520A pdb=" N VAL A 217 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 11.060A pdb=" N THR A 233 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N LEU A 219 " --> pdb=" O PHE A 231 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 388 through 391 Processing sheet with id=AA3, first strand: chain 'A' and resid 446 through 450 Processing sheet with id=AA4, first strand: chain 'A' and resid 472 through 476 Processing sheet with id=AA5, first strand: chain 'A' and resid 543 through 545 removed outlier: 3.647A pdb=" N VAL A 551 " --> pdb=" O CYS A 544 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 794 through 799 removed outlier: 7.027A pdb=" N GLY A 764 " --> pdb=" O GLY A 905 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N VAL A 907 " --> pdb=" O GLY A 764 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N MET A 766 " --> pdb=" O VAL A 907 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 811 through 813 Processing sheet with id=AA8, first strand: chain 'A' and resid 869 through 871 Processing sheet with id=AA9, first strand: chain 'A' and resid 1082 through 1084 Processing sheet with id=AB1, first strand: chain 'A' and resid 1160 through 1166 removed outlier: 6.416A pdb=" N GLU A1161 " --> pdb=" O VAL A1205 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N PHE A1207 " --> pdb=" O GLU A1161 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL A1163 " --> pdb=" O PHE A1207 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ASP A1209 " --> pdb=" O VAL A1163 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU A1165 " --> pdb=" O ASP A1209 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A1136 " --> pdb=" O PHE A1253 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL A1137 " --> pdb=" O VAL A1279 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1186 through 1188 removed outlier: 4.286A pdb=" N TYR A1186 " --> pdb=" O ALA A1196 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A1196 " --> pdb=" O TYR A1186 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL A1193 " --> pdb=" O LYS A1247 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AB4, first strand: chain 'A' and resid 1502 through 1505 removed outlier: 7.110A pdb=" N HIS A1477 " --> pdb=" O VAL A1635 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ASN A1637 " --> pdb=" O HIS A1477 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU A1479 " --> pdb=" O ASN A1637 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N PHE A1639 " --> pdb=" O LEU A1479 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ILE A1481 " --> pdb=" O PHE A1639 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2088 through 2091 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=AB6, first strand: chain 'A' and resid 2132 through 2134 Processing sheet with id=AB7, first strand: chain 'A' and resid 2544 through 2548 removed outlier: 6.386A pdb=" N THR A2545 " --> pdb=" O MET A2573 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LYS A2575 " --> pdb=" O THR A2545 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE A2547 " --> pdb=" O LYS A2575 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL A2572 " --> pdb=" O PHE A2603 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N THR A2605 " --> pdb=" O VAL A2572 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU A2574 " --> pdb=" O THR A2605 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N GLU A2607 " --> pdb=" O LEU A2574 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU A2520 " --> pdb=" O PHE A2623 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N PHE A2625 " --> pdb=" O LEU A2520 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N CYS A2522 " --> pdb=" O PHE A2625 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 2761 through 2763 removed outlier: 6.680A pdb=" N ILE A2772 " --> pdb=" O LEU A2762 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 2987 through 2988 Processing sheet with id=AC1, first strand: chain 'A' and resid 3052 through 3053 removed outlier: 3.838A pdb=" N PHE A3098 " --> pdb=" O VAL A3087 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU A3041 " --> pdb=" O LEU A3063 " (cutoff:3.500A) 1234 hydrogen bonds defined for protein. 3591 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: 11.88 Time building geometry restraints manager: 6.29 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: 0.00 - 1.60: 29298 1.60 - 3.21: 1200 3.21 - 4.81: 175 4.81 - 6.41: 43 6.41 - 8.01: 8 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: 81 2.45 - 3.06: 14933 3.06 - 3.67: 33570 3.67 - 4.29: 50570 4.29 - 4.90: 84616 Nonbonded interactions: 183770 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 3.120 nonbonded pdb=" OD1 ASP A 279 " pdb=" OG1 THR A 282 " model vdw 2.213 3.040 ... (remaining 183765 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: 3.550 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: 0.010 Extract box with map and model: 0.790 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 52.400 Find NCS groups from input model: 0.230 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: 0.000 Load rotamer database and sin/cos tables:11.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.270 ------------------------------------------------------------------------------- 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= 0.348 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 Details of bonding type rmsd hydrogen bonds : bond 0.14322 ( 1234) hydrogen bonds : angle 5.99930 ( 3591) covalent geometry : bond 0.00674 (22649) covalent geometry : angle 0.74021 (30724) *********************** 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 to be fit. rotamer outliers: 4 poor density : 349 time to evaluate : 2.431 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: 1.5236 time to fit residues: 607.9926 Evaluate side-chains 235 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 233 time to evaluate : 3.064 ------------------------------------------------------------------------------- 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: 274 random chunks: chunk 231 optimal weight: 0.5980 chunk 207 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 140 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 214 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 159 optimal weight: 9.9990 chunk 248 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN A 439 GLN A1027 GLN A1297 ASN ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1509 HIS A1745 HIS A2013 HIS A2100 ASN A2178 ASN A2358 HIS A2384 GLN A2541 ASN ** A2578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2634 ASN A2903 GLN A2966 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.176620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.150019 restraints weight = 27786.991| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 1.79 r_work: 0.3755 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3626 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22649 Z= 0.137 Angle : 0.570 9.511 30724 Z= 0.289 Chirality : 0.041 0.146 3458 Planarity : 0.004 0.066 3930 Dihedral : 7.107 174.777 3059 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.76 % Allowed : 8.17 % Favored : 90.07 % 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: 0.96 (0.16), residues: 2733 helix: 1.44 (0.14), residues: 1496 sheet: -0.26 (0.32), residues: 230 loop : -0.27 (0.20), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 779 HIS 0.005 0.001 HIS A1008 PHE 0.017 0.001 PHE A2435 TYR 0.025 0.001 TYR A1293 ARG 0.010 0.000 ARG A2637 Details of bonding type rmsd hydrogen bonds : bond 0.04650 ( 1234) hydrogen bonds : angle 4.45685 ( 3591) covalent geometry : bond 0.00305 (22649) covalent geometry : angle 0.56988 (30724) *********************** 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 309 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 266 time to evaluate : 2.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 LEU cc_start: 0.8144 (mm) cc_final: 0.7064 (pp) REVERT: A 605 ARG cc_start: 0.7780 (mtp-110) cc_final: 0.7188 (mtm110) REVERT: A 717 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7851 (ttt180) REVERT: A 725 GLU cc_start: 0.7324 (pp20) cc_final: 0.6691 (mm-30) REVERT: A 837 ARG cc_start: 0.7402 (mmt-90) cc_final: 0.7011 (mmt-90) REVERT: A 851 ASP cc_start: 0.6484 (m-30) cc_final: 0.6207 (m-30) REVERT: A 918 MET cc_start: 0.7471 (ttm) cc_final: 0.6963 (mtm) REVERT: A 989 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8024 (mm-30) REVERT: A 1099 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7877 (tt0) REVERT: A 1217 ASP cc_start: 0.7552 (p0) cc_final: 0.7340 (p0) REVERT: A 1240 THR cc_start: 0.7894 (p) cc_final: 0.7619 (p) REVERT: A 1308 ARG cc_start: 0.7422 (mmm-85) cc_final: 0.7150 (mmm-85) REVERT: A 1343 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7001 (mm-30) REVERT: A 1356 ARG cc_start: 0.7293 (ttp80) cc_final: 0.6420 (tpm170) REVERT: A 1393 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7339 (mt-10) REVERT: A 1408 ARG cc_start: 0.7439 (mtp-110) cc_final: 0.7145 (mtp85) REVERT: A 1511 LYS cc_start: 0.5652 (pttp) cc_final: 0.5410 (mtmm) REVERT: A 1540 ASP cc_start: 0.7931 (m-30) cc_final: 0.7608 (t70) REVERT: A 1588 MET cc_start: 0.6315 (mmp) cc_final: 0.5813 (tmm) REVERT: A 1593 GLU cc_start: 0.6806 (OUTLIER) cc_final: 0.6452 (mt-10) REVERT: A 1611 PHE cc_start: 0.7909 (m-80) cc_final: 0.7566 (t80) REVERT: A 1664 ASN cc_start: 0.7702 (p0) cc_final: 0.7467 (p0) REVERT: A 1741 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7313 (tp30) REVERT: A 1744 MET cc_start: 0.5897 (ttp) cc_final: 0.5622 (ttp) REVERT: A 2016 GLN cc_start: 0.6575 (mt0) cc_final: 0.6226 (mt0) REVERT: A 2020 GLN cc_start: 0.7231 (OUTLIER) cc_final: 0.6863 (mp10) REVERT: A 2209 LEU cc_start: 0.5548 (tp) cc_final: 0.5058 (tp) REVERT: A 2222 GLN cc_start: 0.6281 (mt0) cc_final: 0.5373 (mm-40) REVERT: A 2269 MET cc_start: 0.6511 (OUTLIER) cc_final: 0.6257 (tpt) REVERT: A 2279 TYR cc_start: 0.7237 (OUTLIER) cc_final: 0.6834 (m-80) REVERT: A 2380 ASP cc_start: 0.6788 (m-30) cc_final: 0.6204 (t0) REVERT: A 2504 ASP cc_start: 0.7683 (m-30) cc_final: 0.6549 (t0) REVERT: A 2607 GLU cc_start: 0.8102 (tp30) cc_final: 0.7833 (tt0) REVERT: A 2618 ARG cc_start: 0.7729 (mtp-110) cc_final: 0.7013 (mtt90) REVERT: A 2635 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7961 (mtt) REVERT: A 2691 ARG cc_start: 0.7616 (mtp85) cc_final: 0.7074 (mtp-110) REVERT: A 2892 GLU cc_start: 0.7212 (tt0) cc_final: 0.6974 (pt0) REVERT: A 2914 GLN cc_start: 0.7644 (mm-40) cc_final: 0.7285 (mm-40) REVERT: A 2955 GLN cc_start: 0.6977 (mt0) cc_final: 0.6736 (pt0) outliers start: 43 outliers final: 10 residues processed: 286 average time/residue: 1.4426 time to fit residues: 480.6202 Evaluate side-chains 247 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 230 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 VAL 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 997 LEU Chi-restraints excluded: chain A residue 1099 GLN Chi-restraints excluded: chain A residue 1309 THR 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 2188 SER Chi-restraints excluded: chain A residue 2269 MET Chi-restraints excluded: chain A residue 2279 TYR Chi-restraints excluded: chain A residue 2635 MET 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 193 optimal weight: 2.9990 chunk 241 optimal weight: 0.3980 chunk 247 optimal weight: 0.4980 chunk 132 optimal weight: 2.9990 chunk 271 optimal weight: 0.0370 chunk 165 optimal weight: 0.9990 chunk 189 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 147 optimal weight: 0.5980 chunk 270 optimal weight: 0.0000 overall best weight: 0.3062 ------------------------------------------------------------------------------- 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 A1166 ASN ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2100 ASN A2541 ASN ** A2578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.180205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.153544 restraints weight = 27490.537| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 1.81 r_work: 0.3782 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3653 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.1585 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= 0.105 Angle : 0.517 10.322 30724 Z= 0.258 Chirality : 0.039 0.147 3458 Planarity : 0.004 0.044 3930 Dihedral : 6.702 175.724 3053 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.72 % Allowed : 10.75 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.16), residues: 2733 helix: 1.72 (0.14), residues: 1493 sheet: -0.12 (0.32), residues: 230 loop : -0.18 (0.21), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 779 HIS 0.003 0.001 HIS A2597 PHE 0.013 0.001 PHE A2435 TYR 0.022 0.001 TYR A1665 ARG 0.004 0.000 ARG A1308 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 1234) hydrogen bonds : angle 4.13873 ( 3591) covalent geometry : bond 0.00224 (22649) covalent geometry : angle 0.51654 (30724) *********************** 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 300 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 258 time to evaluate : 2.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 LEU cc_start: 0.8127 (mm) cc_final: 0.7085 (pp) REVERT: A 235 VAL cc_start: 0.7613 (OUTLIER) cc_final: 0.7377 (t) REVERT: A 605 ARG cc_start: 0.7692 (mtp-110) cc_final: 0.7111 (mtm110) REVERT: A 725 GLU cc_start: 0.7097 (pp20) cc_final: 0.6763 (pt0) REVERT: A 750 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7315 (mp0) REVERT: A 989 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8003 (mm-30) REVERT: A 1240 THR cc_start: 0.7885 (p) cc_final: 0.7582 (p) REVERT: A 1308 ARG cc_start: 0.7503 (mmm-85) cc_final: 0.7276 (mmm-85) REVERT: A 1343 GLU cc_start: 0.7498 (mt-10) cc_final: 0.6928 (mm-30) REVERT: A 1356 ARG cc_start: 0.7288 (ttp80) cc_final: 0.6444 (tpm170) REVERT: A 1412 MET cc_start: 0.7264 (mmp) cc_final: 0.6718 (mmp) REVERT: A 1540 ASP cc_start: 0.7850 (m-30) cc_final: 0.7555 (t70) REVERT: A 1588 MET cc_start: 0.6360 (mmp) cc_final: 0.5794 (tmm) REVERT: A 1611 PHE cc_start: 0.7907 (m-80) cc_final: 0.7661 (t80) REVERT: A 1664 ASN cc_start: 0.7758 (p0) cc_final: 0.7484 (p0) REVERT: A 2016 GLN cc_start: 0.6468 (mt0) cc_final: 0.6150 (mt0) REVERT: A 2209 LEU cc_start: 0.5467 (tp) cc_final: 0.4976 (tp) REVERT: A 2222 GLN cc_start: 0.6215 (mt0) cc_final: 0.5289 (mm-40) REVERT: A 2279 TYR cc_start: 0.7191 (OUTLIER) cc_final: 0.6387 (m-80) REVERT: A 2380 ASP cc_start: 0.6752 (m-30) cc_final: 0.6151 (t0) REVERT: A 2501 GLN cc_start: 0.7847 (mm110) cc_final: 0.7614 (mp10) REVERT: A 2504 ASP cc_start: 0.7600 (m-30) cc_final: 0.6501 (t0) REVERT: A 2607 GLU cc_start: 0.7927 (tp30) cc_final: 0.7661 (tt0) REVERT: A 2637 ARG cc_start: 0.7101 (ttm110) cc_final: 0.6883 (ttm110) REVERT: A 2691 ARG cc_start: 0.7571 (mtp85) cc_final: 0.7023 (mtp-110) REVERT: A 2698 ASP cc_start: 0.6492 (t0) cc_final: 0.5559 (t0) REVERT: A 2702 ASP cc_start: 0.5944 (m-30) cc_final: 0.5656 (m-30) REVERT: A 2824 MET cc_start: 0.7436 (tpp) cc_final: 0.7041 (tpp) REVERT: A 2892 GLU cc_start: 0.7091 (tt0) cc_final: 0.6866 (pt0) REVERT: A 2914 GLN cc_start: 0.7635 (mm-40) cc_final: 0.7267 (mm-40) REVERT: A 2955 GLN cc_start: 0.7095 (mt0) cc_final: 0.6727 (pt0) REVERT: A 2972 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7140 (mm) outliers start: 42 outliers final: 12 residues processed: 281 average time/residue: 1.3430 time to fit residues: 435.0816 Evaluate side-chains 244 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 228 time to evaluate : 2.412 ------------------------------------------------------------------------------- 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 398 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 598 MET 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 2188 SER Chi-restraints excluded: chain A residue 2279 TYR Chi-restraints excluded: chain A residue 2374 VAL Chi-restraints excluded: chain A residue 2459 THR Chi-restraints excluded: chain A residue 2704 THR Chi-restraints excluded: chain A residue 2933 LEU Chi-restraints excluded: chain A residue 2947 VAL Chi-restraints excluded: chain A residue 2972 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 7 optimal weight: 3.9990 chunk 209 optimal weight: 0.9980 chunk 172 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 142 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN A1076 ASN A1166 ASN A2013 HIS A2178 ASN A2541 ASN ** A2578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.171439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.145899 restraints weight = 27976.967| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 1.93 r_work: 0.3729 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22649 Z= 0.174 Angle : 0.581 7.109 30724 Z= 0.290 Chirality : 0.041 0.150 3458 Planarity : 0.004 0.049 3930 Dihedral : 6.956 178.117 3053 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.05 % Allowed : 11.98 % Favored : 85.97 % 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: 1.06 (0.16), residues: 2733 helix: 1.54 (0.13), residues: 1500 sheet: -0.29 (0.33), residues: 221 loop : -0.25 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 779 HIS 0.008 0.001 HIS A1008 PHE 0.019 0.002 PHE A 272 TYR 0.023 0.002 TYR A1293 ARG 0.003 0.000 ARG A2570 Details of bonding type rmsd hydrogen bonds : bond 0.04351 ( 1234) hydrogen bonds : angle 4.20551 ( 3591) covalent geometry : bond 0.00416 (22649) covalent geometry : angle 0.58077 (30724) *********************** 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 287 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 237 time to evaluate : 2.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 LEU cc_start: 0.8157 (mm) cc_final: 0.7114 (pp) REVERT: A 605 ARG cc_start: 0.7705 (mtp-110) cc_final: 0.7147 (mtm110) REVERT: A 658 ARG cc_start: 0.6032 (ttp-110) cc_final: 0.5805 (ttp-110) REVERT: A 717 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7831 (ttt180) REVERT: A 725 GLU cc_start: 0.7396 (pp20) cc_final: 0.6813 (mm-30) REVERT: A 750 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7367 (mp0) REVERT: A 986 PHE cc_start: 0.8576 (m-80) cc_final: 0.8327 (m-80) REVERT: A 989 GLU cc_start: 0.8424 (mt-10) cc_final: 0.7967 (mm-30) REVERT: A 1240 THR cc_start: 0.7934 (p) cc_final: 0.7674 (p) REVERT: A 1343 GLU cc_start: 0.7718 (mt-10) cc_final: 0.6964 (mm-30) REVERT: A 1356 ARG cc_start: 0.7205 (ttp80) cc_final: 0.6316 (tpm170) REVERT: A 1540 ASP cc_start: 0.7886 (m-30) cc_final: 0.7537 (t70) REVERT: A 1588 MET cc_start: 0.6357 (mmp) cc_final: 0.5772 (tmm) REVERT: A 1611 PHE cc_start: 0.7945 (m-80) cc_final: 0.7622 (t80) REVERT: A 1654 PHE cc_start: 0.7855 (t80) cc_final: 0.7629 (t80) REVERT: A 1664 ASN cc_start: 0.7791 (p0) cc_final: 0.7495 (p0) REVERT: A 2016 GLN cc_start: 0.6757 (mt0) cc_final: 0.6498 (mt0) REVERT: A 2209 LEU cc_start: 0.5456 (tp) cc_final: 0.5000 (tp) REVERT: A 2222 GLN cc_start: 0.6250 (mt0) cc_final: 0.5350 (mm-40) REVERT: A 2279 TYR cc_start: 0.7346 (OUTLIER) cc_final: 0.6575 (m-80) REVERT: A 2380 ASP cc_start: 0.6873 (m-30) cc_final: 0.6253 (t0) REVERT: A 2501 GLN cc_start: 0.7788 (mm110) cc_final: 0.7577 (mp10) REVERT: A 2618 ARG cc_start: 0.7684 (mtp-110) cc_final: 0.7066 (mtt90) REVERT: A 2634 ASN cc_start: 0.7399 (OUTLIER) cc_final: 0.7155 (t0) REVERT: A 2691 ARG cc_start: 0.7629 (mtp85) cc_final: 0.7098 (mtp-110) REVERT: A 2698 ASP cc_start: 0.6675 (t0) cc_final: 0.5830 (t0) REVERT: A 2702 ASP cc_start: 0.6172 (m-30) cc_final: 0.5771 (m-30) REVERT: A 2785 GLN cc_start: 0.7045 (OUTLIER) cc_final: 0.6816 (tt0) REVERT: A 2824 MET cc_start: 0.7610 (tpp) cc_final: 0.7372 (tpp) REVERT: A 2892 GLU cc_start: 0.7135 (tt0) cc_final: 0.6909 (pt0) REVERT: A 2914 GLN cc_start: 0.7698 (mm-40) cc_final: 0.7336 (mm-40) REVERT: A 2955 GLN cc_start: 0.7101 (mt0) cc_final: 0.6774 (pt0) outliers start: 50 outliers final: 23 residues processed: 263 average time/residue: 1.4133 time to fit residues: 427.4899 Evaluate side-chains 248 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 220 time to evaluate : 2.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 398 VAL 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 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 2169 ASP Chi-restraints excluded: chain A residue 2181 VAL Chi-restraints excluded: chain A residue 2188 SER Chi-restraints excluded: chain A residue 2279 TYR Chi-restraints excluded: chain A residue 2374 VAL Chi-restraints excluded: chain A residue 2406 THR Chi-restraints excluded: chain A residue 2573 MET Chi-restraints excluded: chain A residue 2585 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 212 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 71 optimal weight: 0.0170 chunk 213 optimal weight: 0.9980 chunk 184 optimal weight: 1.9990 chunk 164 optimal weight: 0.6980 chunk 250 optimal weight: 0.0370 chunk 0 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 263 optimal weight: 0.8980 chunk 237 optimal weight: 3.9990 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN A1076 ASN A1166 ASN ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2013 HIS ** A2128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2541 ASN ** A2578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.179350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.152324 restraints weight = 27703.395| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 1.81 r_work: 0.3768 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3640 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.1804 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= 0.112 Angle : 0.523 7.280 30724 Z= 0.261 Chirality : 0.039 0.148 3458 Planarity : 0.004 0.048 3930 Dihedral : 6.785 176.909 3053 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.68 % Allowed : 13.54 % Favored : 84.78 % 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: 1.27 (0.16), residues: 2733 helix: 1.72 (0.14), residues: 1501 sheet: -0.24 (0.33), residues: 220 loop : -0.17 (0.21), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 779 HIS 0.006 0.001 HIS A1745 PHE 0.013 0.001 PHE A2291 TYR 0.020 0.001 TYR A1293 ARG 0.006 0.000 ARG A1308 Details of bonding type rmsd hydrogen bonds : bond 0.03781 ( 1234) hydrogen bonds : angle 4.04145 ( 3591) covalent geometry : bond 0.00249 (22649) covalent geometry : angle 0.52253 (30724) *********************** 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 289 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 248 time to evaluate : 2.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 LEU cc_start: 0.8120 (mm) cc_final: 0.7091 (pp) REVERT: A 235 VAL cc_start: 0.7644 (OUTLIER) cc_final: 0.7393 (t) REVERT: A 605 ARG cc_start: 0.7698 (mtp-110) cc_final: 0.7199 (mtm110) REVERT: A 717 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7841 (ttt180) REVERT: A 725 GLU cc_start: 0.7312 (pp20) cc_final: 0.6669 (mm-30) REVERT: A 750 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7228 (mp0) REVERT: A 807 ASP cc_start: 0.8773 (OUTLIER) cc_final: 0.8473 (t70) REVERT: A 989 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7942 (mm-30) REVERT: A 1240 THR cc_start: 0.7853 (p) cc_final: 0.7576 (p) REVERT: A 1343 GLU cc_start: 0.7468 (mt-10) cc_final: 0.6856 (mm-30) REVERT: A 1356 ARG cc_start: 0.7204 (ttp80) cc_final: 0.6351 (tpm170) REVERT: A 1412 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.7023 (mmp) REVERT: A 1540 ASP cc_start: 0.7848 (m-30) cc_final: 0.7496 (t70) REVERT: A 1588 MET cc_start: 0.6328 (mmp) cc_final: 0.5713 (tmm) REVERT: A 1611 PHE cc_start: 0.7863 (m-80) cc_final: 0.7532 (t80) REVERT: A 1664 ASN cc_start: 0.7764 (p0) cc_final: 0.7458 (p0) REVERT: A 1665 TYR cc_start: 0.6899 (t80) cc_final: 0.6684 (t80) REVERT: A 2016 GLN cc_start: 0.6651 (mt0) cc_final: 0.6335 (mt0) REVERT: A 2093 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7635 (mt) REVERT: A 2209 LEU cc_start: 0.5449 (tp) cc_final: 0.4921 (tp) REVERT: A 2222 GLN cc_start: 0.6084 (mt0) cc_final: 0.5233 (mm-40) REVERT: A 2279 TYR cc_start: 0.7165 (OUTLIER) cc_final: 0.6519 (m-80) REVERT: A 2371 LYS cc_start: 0.7848 (ptmm) cc_final: 0.7027 (mmtm) REVERT: A 2380 ASP cc_start: 0.6806 (m-30) cc_final: 0.6208 (t0) REVERT: A 2501 GLN cc_start: 0.7727 (mm110) cc_final: 0.7492 (mp10) REVERT: A 2634 ASN cc_start: 0.7273 (OUTLIER) cc_final: 0.7029 (t0) REVERT: A 2691 ARG cc_start: 0.7555 (mtp85) cc_final: 0.7000 (mtp-110) REVERT: A 2698 ASP cc_start: 0.6602 (t0) cc_final: 0.5799 (t0) REVERT: A 2702 ASP cc_start: 0.6062 (m-30) cc_final: 0.5663 (m-30) REVERT: A 2892 GLU cc_start: 0.7107 (tt0) cc_final: 0.6845 (pt0) REVERT: A 2914 GLN cc_start: 0.7611 (mm-40) cc_final: 0.7274 (mm-40) REVERT: A 2955 GLN cc_start: 0.7099 (mt0) cc_final: 0.6748 (pt0) outliers start: 41 outliers final: 18 residues processed: 275 average time/residue: 1.3970 time to fit residues: 441.7994 Evaluate side-chains 247 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 221 time to evaluate : 2.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 398 VAL 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 1154 LEU Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain A residue 2000 GLN 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 2279 TYR Chi-restraints excluded: chain A residue 2374 VAL Chi-restraints excluded: chain A residue 2585 MET Chi-restraints excluded: chain A residue 2634 ASN Chi-restraints excluded: chain A residue 2819 SER Chi-restraints excluded: chain A residue 2933 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 114 optimal weight: 0.2980 chunk 213 optimal weight: 0.7980 chunk 234 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 159 optimal weight: 10.0000 chunk 201 optimal weight: 0.7980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN A1166 ASN ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2013 HIS ** A2128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2178 ASN A2541 ASN ** A2578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2968 GLN A3004 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.170498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.144978 restraints weight = 27773.411| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 1.88 r_work: 0.3721 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 22649 Z= 0.192 Angle : 0.604 10.397 30724 Z= 0.301 Chirality : 0.042 0.167 3458 Planarity : 0.004 0.046 3930 Dihedral : 7.015 177.736 3053 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.26 % Allowed : 13.91 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.16), residues: 2733 helix: 1.47 (0.13), residues: 1500 sheet: -0.37 (0.32), residues: 221 loop : -0.33 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 779 HIS 0.008 0.001 HIS A1008 PHE 0.020 0.002 PHE A 272 TYR 0.023 0.002 TYR A1293 ARG 0.005 0.000 ARG A2637 Details of bonding type rmsd hydrogen bonds : bond 0.04414 ( 1234) hydrogen bonds : angle 4.21098 ( 3591) covalent geometry : bond 0.00463 (22649) covalent geometry : angle 0.60370 (30724) *********************** 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 285 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 230 time to evaluate : 2.306 Fit side-chains revert: symmetry clash REVERT: A 183 LEU cc_start: 0.8170 (mm) cc_final: 0.7136 (pp) REVERT: A 235 VAL cc_start: 0.7709 (OUTLIER) cc_final: 0.7461 (t) REVERT: A 605 ARG cc_start: 0.7714 (mtp-110) cc_final: 0.7155 (mtm110) REVERT: A 717 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7935 (ttt180) REVERT: A 725 GLU cc_start: 0.7415 (pp20) cc_final: 0.6812 (mm-30) REVERT: A 750 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7357 (mp0) REVERT: A 989 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7979 (mm-30) REVERT: A 1240 THR cc_start: 0.7844 (p) cc_final: 0.7555 (p) REVERT: A 1343 GLU cc_start: 0.7742 (mt-10) cc_final: 0.6992 (mm-30) REVERT: A 1356 ARG cc_start: 0.7236 (ttp80) cc_final: 0.6338 (tpm170) REVERT: A 1359 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7114 (mt-10) REVERT: A 1412 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.7107 (mmp) REVERT: A 1540 ASP cc_start: 0.7973 (m-30) cc_final: 0.7606 (t70) REVERT: A 1588 MET cc_start: 0.6381 (mmp) cc_final: 0.5787 (tmm) REVERT: A 1611 PHE cc_start: 0.7939 (m-80) cc_final: 0.7617 (t80) REVERT: A 1664 ASN cc_start: 0.7810 (p0) cc_final: 0.7467 (p0) REVERT: A 2016 GLN cc_start: 0.6905 (mt0) cc_final: 0.6616 (mt0) REVERT: A 2093 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7704 (mt) REVERT: A 2169 ASP cc_start: 0.7034 (OUTLIER) cc_final: 0.6687 (t0) REVERT: A 2209 LEU cc_start: 0.5499 (tp) cc_final: 0.5063 (tp) REVERT: A 2222 GLN cc_start: 0.5963 (mt0) cc_final: 0.5162 (mm-40) REVERT: A 2371 LYS cc_start: 0.7847 (ptmm) cc_final: 0.7028 (mmtm) REVERT: A 2585 MET cc_start: 0.6879 (OUTLIER) cc_final: 0.5531 (mpp) REVERT: A 2618 ARG cc_start: 0.7769 (mtp-110) cc_final: 0.7183 (mtt90) REVERT: A 2634 ASN cc_start: 0.7420 (OUTLIER) cc_final: 0.7079 (t0) REVERT: A 2691 ARG cc_start: 0.7665 (mtp85) cc_final: 0.7105 (mtp-110) REVERT: A 2698 ASP cc_start: 0.6710 (t0) cc_final: 0.5945 (t70) REVERT: A 2702 ASP cc_start: 0.6376 (m-30) cc_final: 0.5911 (m-30) REVERT: A 2785 GLN cc_start: 0.7053 (OUTLIER) cc_final: 0.6825 (tt0) REVERT: A 2788 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7381 (mt-10) REVERT: A 2892 GLU cc_start: 0.7176 (tt0) cc_final: 0.6942 (pt0) REVERT: A 2914 GLN cc_start: 0.7705 (mm-40) cc_final: 0.7361 (mm-40) REVERT: A 2955 GLN cc_start: 0.7144 (mt0) cc_final: 0.6800 (pt0) outliers start: 55 outliers final: 23 residues processed: 266 average time/residue: 1.3429 time to fit residues: 412.7213 Evaluate side-chains 250 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 216 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 658 ARG 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 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 1359 GLU 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 2269 MET Chi-restraints excluded: chain A residue 2585 MET Chi-restraints excluded: chain A residue 2634 ASN Chi-restraints excluded: chain A residue 2704 THR 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 2901 LEU 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: 274 random chunks: chunk 52 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 259 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 220 optimal weight: 0.8980 chunk 268 optimal weight: 6.9990 chunk 149 optimal weight: 0.5980 chunk 195 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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** A2013 HIS ** A2128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2217 GLN A2541 ASN ** A2578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.172506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.147127 restraints weight = 27763.033| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 1.95 r_work: 0.3744 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22649 Z= 0.134 Angle : 0.548 10.925 30724 Z= 0.274 Chirality : 0.040 0.149 3458 Planarity : 0.004 0.049 3930 Dihedral : 6.905 176.162 3053 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.09 % Allowed : 14.40 % Favored : 83.50 % 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: 1.09 (0.16), residues: 2733 helix: 1.60 (0.13), residues: 1504 sheet: -0.44 (0.32), residues: 226 loop : -0.26 (0.20), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 779 HIS 0.004 0.001 HIS A1745 PHE 0.014 0.001 PHE A2291 TYR 0.022 0.001 TYR A1293 ARG 0.007 0.000 ARG A2637 Details of bonding type rmsd hydrogen bonds : bond 0.03981 ( 1234) hydrogen bonds : angle 4.09798 ( 3591) covalent geometry : bond 0.00314 (22649) covalent geometry : angle 0.54753 (30724) *********************** 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 284 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 233 time to evaluate : 2.548 Fit side-chains revert: symmetry clash REVERT: A 183 LEU cc_start: 0.8142 (mm) cc_final: 0.7116 (pp) REVERT: A 235 VAL cc_start: 0.7671 (OUTLIER) cc_final: 0.7417 (t) REVERT: A 605 ARG cc_start: 0.7714 (mtp-110) cc_final: 0.7229 (mtm110) REVERT: A 717 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7950 (ttt180) REVERT: A 725 GLU cc_start: 0.7387 (pp20) cc_final: 0.6771 (mm-30) REVERT: A 732 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7659 (tm-30) REVERT: A 750 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7288 (mp0) REVERT: A 989 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7986 (mm-30) REVERT: A 1045 TRP cc_start: 0.7576 (m100) cc_final: 0.7232 (m100) REVERT: A 1240 THR cc_start: 0.7867 (p) cc_final: 0.7597 (p) REVERT: A 1343 GLU cc_start: 0.7538 (mt-10) cc_final: 0.6945 (mm-30) REVERT: A 1356 ARG cc_start: 0.7248 (ttp80) cc_final: 0.6358 (tpm170) REVERT: A 1359 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.7104 (mt-10) REVERT: A 1412 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.7130 (mmp) REVERT: A 1540 ASP cc_start: 0.8010 (m-30) cc_final: 0.7579 (t70) REVERT: A 1588 MET cc_start: 0.6336 (mmp) cc_final: 0.5809 (tmm) REVERT: A 1611 PHE cc_start: 0.7915 (m-80) cc_final: 0.7600 (t80) REVERT: A 1664 ASN cc_start: 0.7822 (p0) cc_final: 0.7438 (p0) REVERT: A 1665 TYR cc_start: 0.6870 (t80) cc_final: 0.6454 (t80) REVERT: A 2016 GLN cc_start: 0.6914 (mt0) cc_final: 0.6626 (mt0) REVERT: A 2093 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7690 (mt) REVERT: A 2169 ASP cc_start: 0.7002 (OUTLIER) cc_final: 0.6646 (t0) REVERT: A 2209 LEU cc_start: 0.5524 (tp) cc_final: 0.5229 (tp) REVERT: A 2222 GLN cc_start: 0.5911 (mt0) cc_final: 0.5117 (mm-40) REVERT: A 2371 LYS cc_start: 0.7810 (ptmm) cc_final: 0.6971 (mmtm) REVERT: A 2634 ASN cc_start: 0.7339 (OUTLIER) cc_final: 0.7113 (t0) REVERT: A 2691 ARG cc_start: 0.7724 (mtp85) cc_final: 0.7167 (mtp-110) REVERT: A 2698 ASP cc_start: 0.6672 (t0) cc_final: 0.5902 (t70) REVERT: A 2702 ASP cc_start: 0.6337 (m-30) cc_final: 0.5880 (m-30) REVERT: A 2788 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7379 (mt-10) REVERT: A 2892 GLU cc_start: 0.7152 (tt0) cc_final: 0.6898 (pt0) REVERT: A 2914 GLN cc_start: 0.7684 (mm-40) cc_final: 0.7343 (mm-40) REVERT: A 2955 GLN cc_start: 0.7111 (mt0) cc_final: 0.6748 (pt0) outliers start: 51 outliers final: 23 residues processed: 268 average time/residue: 1.3997 time to fit residues: 432.8185 Evaluate side-chains 246 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 214 time to evaluate : 2.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 398 VAL 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 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 1359 GLU Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain A residue 1981 ILE Chi-restraints excluded: chain A residue 2000 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 2181 VAL Chi-restraints excluded: chain A residue 2188 SER Chi-restraints excluded: chain A residue 2374 VAL Chi-restraints excluded: chain A residue 2634 ASN Chi-restraints excluded: chain A residue 2704 THR 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 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: 274 random chunks: chunk 140 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 206 optimal weight: 0.7980 chunk 69 optimal weight: 0.2980 chunk 165 optimal weight: 0.8980 chunk 160 optimal weight: 0.7980 chunk 262 optimal weight: 2.9990 chunk 257 optimal weight: 0.9980 chunk 181 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** A2013 HIS A2100 ASN ** A2128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2217 GLN A2540 GLN A2541 ASN ** A2578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2785 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.173350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.147958 restraints weight = 27768.199| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 1.94 r_work: 0.3751 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22649 Z= 0.126 Angle : 0.547 11.592 30724 Z= 0.272 Chirality : 0.040 0.188 3458 Planarity : 0.004 0.048 3930 Dihedral : 6.846 176.875 3053 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.85 % Allowed : 14.94 % 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: 1.17 (0.16), residues: 2733 helix: 1.68 (0.13), residues: 1498 sheet: -0.38 (0.32), residues: 224 loop : -0.25 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 779 HIS 0.004 0.001 HIS A1008 PHE 0.014 0.001 PHE A2291 TYR 0.021 0.001 TYR A1293 ARG 0.010 0.000 ARG A2637 Details of bonding type rmsd hydrogen bonds : bond 0.03854 ( 1234) hydrogen bonds : angle 4.05914 ( 3591) covalent geometry : bond 0.00291 (22649) covalent geometry : angle 0.54681 (30724) *********************** 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 274 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 229 time to evaluate : 4.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 LEU cc_start: 0.8143 (mm) cc_final: 0.7117 (pp) REVERT: A 235 VAL cc_start: 0.7646 (OUTLIER) cc_final: 0.7386 (t) REVERT: A 605 ARG cc_start: 0.7685 (mtp-110) cc_final: 0.7189 (mtm110) REVERT: A 717 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7856 (ttt180) REVERT: A 725 GLU cc_start: 0.7399 (pp20) cc_final: 0.6769 (mm-30) REVERT: A 732 GLN cc_start: 0.8029 (mm-40) cc_final: 0.7626 (tm-30) REVERT: A 750 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: A 989 GLU cc_start: 0.8378 (mt-10) cc_final: 0.7941 (mm-30) REVERT: A 1240 THR cc_start: 0.7812 (p) cc_final: 0.7532 (p) REVERT: A 1343 GLU cc_start: 0.7477 (mt-10) cc_final: 0.6895 (mm-30) REVERT: A 1356 ARG cc_start: 0.7207 (ttp80) cc_final: 0.6279 (tpm170) REVERT: A 1359 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.7114 (mt-10) REVERT: A 1412 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.7169 (mmp) REVERT: A 1540 ASP cc_start: 0.8010 (m-30) cc_final: 0.7529 (t70) REVERT: A 1588 MET cc_start: 0.6345 (mmp) cc_final: 0.5791 (tmm) REVERT: A 1611 PHE cc_start: 0.7942 (m-80) cc_final: 0.7584 (t80) REVERT: A 1664 ASN cc_start: 0.7829 (p0) cc_final: 0.7449 (p0) REVERT: A 1665 TYR cc_start: 0.6918 (t80) cc_final: 0.6421 (t80) REVERT: A 2016 GLN cc_start: 0.6873 (mt0) cc_final: 0.6547 (mt0) REVERT: A 2169 ASP cc_start: 0.6948 (OUTLIER) cc_final: 0.6565 (t0) REVERT: A 2222 GLN cc_start: 0.5925 (mt0) cc_final: 0.5128 (mm-40) REVERT: A 2269 MET cc_start: 0.6745 (tpt) cc_final: 0.6297 (tpt) REVERT: A 2371 LYS cc_start: 0.7930 (ptmm) cc_final: 0.6997 (mmtm) REVERT: A 2618 ARG cc_start: 0.7682 (mtp-110) cc_final: 0.7086 (mtt90) REVERT: A 2634 ASN cc_start: 0.7319 (OUTLIER) cc_final: 0.7012 (t0) REVERT: A 2691 ARG cc_start: 0.7669 (mtp85) cc_final: 0.7088 (mtp-110) REVERT: A 2698 ASP cc_start: 0.6614 (t0) cc_final: 0.6335 (t0) REVERT: A 2702 ASP cc_start: 0.6306 (m-30) cc_final: 0.5955 (m-30) REVERT: A 2788 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7361 (mt-10) REVERT: A 2892 GLU cc_start: 0.7107 (tt0) cc_final: 0.6845 (pt0) REVERT: A 2914 GLN cc_start: 0.7638 (mm-40) cc_final: 0.7307 (mm-40) REVERT: A 2955 GLN cc_start: 0.7124 (mt0) cc_final: 0.6753 (pt0) outliers start: 45 outliers final: 25 residues processed: 260 average time/residue: 1.3914 time to fit residues: 417.7334 Evaluate side-chains 253 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 220 time to evaluate : 2.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 398 VAL 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 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 1359 GLU Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain A residue 1981 ILE Chi-restraints excluded: chain A residue 2000 GLN Chi-restraints excluded: chain A residue 2020 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 2406 THR Chi-restraints excluded: chain A residue 2585 MET Chi-restraints excluded: chain A residue 2634 ASN Chi-restraints excluded: chain A residue 2704 THR 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 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: 274 random chunks: chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 136 optimal weight: 0.0980 chunk 104 optimal weight: 1.9990 chunk 226 optimal weight: 1.9990 chunk 201 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 154 optimal weight: 0.0050 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 874 ASN A1008 HIS ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2013 HIS ** A2128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2217 GLN A2541 ASN ** A2578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2785 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.174203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.148902 restraints weight = 27561.876| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 1.90 r_work: 0.3768 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3640 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22649 Z= 0.114 Angle : 0.538 12.044 30724 Z= 0.267 Chirality : 0.039 0.148 3458 Planarity : 0.004 0.049 3930 Dihedral : 6.790 177.334 3053 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.68 % Allowed : 15.18 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.16), residues: 2733 helix: 1.75 (0.13), residues: 1498 sheet: -0.33 (0.32), residues: 223 loop : -0.23 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 779 HIS 0.007 0.001 HIS A1745 PHE 0.014 0.001 PHE A2291 TYR 0.020 0.001 TYR A1293 ARG 0.009 0.000 ARG A2637 Details of bonding type rmsd hydrogen bonds : bond 0.03706 ( 1234) hydrogen bonds : angle 4.01830 ( 3591) covalent geometry : bond 0.00260 (22649) covalent geometry : angle 0.53782 (30724) *********************** 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 to be fit. rotamer outliers: 41 poor density : 228 time to evaluate : 2.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 LEU cc_start: 0.8131 (mm) cc_final: 0.7120 (pp) REVERT: A 235 VAL cc_start: 0.7621 (OUTLIER) cc_final: 0.7363 (t) REVERT: A 605 ARG cc_start: 0.7658 (mtp-110) cc_final: 0.7191 (mtm110) REVERT: A 717 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7819 (ttt180) REVERT: A 725 GLU cc_start: 0.7361 (pp20) cc_final: 0.6789 (mm-30) REVERT: A 732 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7624 (tm-30) REVERT: A 750 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7254 (mp0) REVERT: A 989 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7944 (mm-30) REVERT: A 1240 THR cc_start: 0.7862 (p) cc_final: 0.7595 (p) REVERT: A 1343 GLU cc_start: 0.7440 (mt-10) cc_final: 0.6909 (mm-30) REVERT: A 1356 ARG cc_start: 0.7233 (ttp80) cc_final: 0.6356 (tpm170) REVERT: A 1412 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.7170 (mmp) REVERT: A 1540 ASP cc_start: 0.7975 (m-30) cc_final: 0.7569 (t70) REVERT: A 1588 MET cc_start: 0.6343 (mmp) cc_final: 0.5803 (tmm) REVERT: A 1611 PHE cc_start: 0.7933 (m-80) cc_final: 0.7576 (t80) REVERT: A 1664 ASN cc_start: 0.7810 (p0) cc_final: 0.7434 (p0) REVERT: A 1665 TYR cc_start: 0.6883 (t80) cc_final: 0.6384 (t80) REVERT: A 1978 MET cc_start: 0.7497 (tpp) cc_final: 0.7204 (tpt) REVERT: A 2016 GLN cc_start: 0.6899 (mt0) cc_final: 0.6567 (mt0) REVERT: A 2222 GLN cc_start: 0.5891 (mt0) cc_final: 0.5088 (mm-40) REVERT: A 2371 LYS cc_start: 0.7976 (ptmm) cc_final: 0.7033 (mmtm) REVERT: A 2634 ASN cc_start: 0.7269 (OUTLIER) cc_final: 0.7016 (t0) REVERT: A 2637 ARG cc_start: 0.7183 (ttm110) cc_final: 0.6915 (ttm110) REVERT: A 2691 ARG cc_start: 0.7603 (mtp85) cc_final: 0.7039 (mtp-110) REVERT: A 2698 ASP cc_start: 0.6616 (t0) cc_final: 0.6360 (t0) REVERT: A 2702 ASP cc_start: 0.6272 (m-30) cc_final: 0.5937 (m-30) REVERT: A 2788 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7361 (mt-10) REVERT: A 2892 GLU cc_start: 0.7131 (tt0) cc_final: 0.6877 (pt0) REVERT: A 2914 GLN cc_start: 0.7640 (mm-40) cc_final: 0.7350 (mm-40) REVERT: A 2955 GLN cc_start: 0.7110 (mt0) cc_final: 0.6762 (pt0) outliers start: 41 outliers final: 26 residues processed: 257 average time/residue: 1.3997 time to fit residues: 414.5858 Evaluate side-chains 254 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 222 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 398 VAL 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 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 1412 MET Chi-restraints excluded: chain A residue 1744 MET Chi-restraints excluded: chain A residue 1746 LEU Chi-restraints excluded: chain A residue 1981 ILE Chi-restraints excluded: chain A residue 2000 GLN 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 2406 THR Chi-restraints excluded: chain A residue 2585 MET Chi-restraints excluded: chain A residue 2634 ASN Chi-restraints excluded: chain A residue 2704 THR 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 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: 274 random chunks: chunk 218 optimal weight: 0.0970 chunk 162 optimal weight: 7.9990 chunk 238 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 chunk 250 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 203 optimal weight: 0.9990 chunk 201 optimal weight: 0.5980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN ** A2128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2217 GLN A2541 ASN ** A2578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2785 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.173992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.148598 restraints weight = 27779.131| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 1.94 r_work: 0.3763 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22649 Z= 0.121 Angle : 0.553 12.681 30724 Z= 0.273 Chirality : 0.039 0.148 3458 Planarity : 0.004 0.049 3930 Dihedral : 6.788 178.697 3053 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.44 % Allowed : 15.63 % 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: 1.21 (0.16), residues: 2733 helix: 1.72 (0.13), residues: 1504 sheet: -0.33 (0.32), residues: 223 loop : -0.27 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 286 HIS 0.004 0.001 HIS A1745 PHE 0.014 0.001 PHE A2291 TYR 0.020 0.001 TYR A1293 ARG 0.007 0.000 ARG A2637 Details of bonding type rmsd hydrogen bonds : bond 0.03735 ( 1234) hydrogen bonds : angle 4.02466 ( 3591) covalent geometry : bond 0.00281 (22649) covalent geometry : angle 0.55278 (30724) ********************** 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 257 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 222 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 LEU cc_start: 0.8136 (mm) cc_final: 0.7122 (pp) REVERT: A 235 VAL cc_start: 0.7613 (OUTLIER) cc_final: 0.7358 (t) REVERT: A 605 ARG cc_start: 0.7668 (mtp-110) cc_final: 0.7190 (mtm110) REVERT: A 717 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7800 (ttt180) REVERT: A 725 GLU cc_start: 0.7376 (pp20) cc_final: 0.6780 (mm-30) REVERT: A 732 GLN cc_start: 0.8030 (mm-40) cc_final: 0.7626 (tm-30) REVERT: A 750 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: A 887 MET cc_start: 0.8624 (mtt) cc_final: 0.8420 (ptp) REVERT: A 957 MET cc_start: 0.7879 (tpt) cc_final: 0.7478 (tpp) REVERT: A 989 GLU cc_start: 0.8368 (mt-10) cc_final: 0.7949 (mm-30) REVERT: A 1240 THR cc_start: 0.7860 (p) cc_final: 0.7599 (p) REVERT: A 1343 GLU cc_start: 0.7448 (mt-10) cc_final: 0.6907 (mm-30) REVERT: A 1356 ARG cc_start: 0.7281 (ttp80) cc_final: 0.6391 (tpm170) REVERT: A 1412 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.7206 (mmp) REVERT: A 1540 ASP cc_start: 0.8000 (m-30) cc_final: 0.7592 (t70) REVERT: A 1588 MET cc_start: 0.6348 (mmp) cc_final: 0.5745 (tmm) REVERT: A 1611 PHE cc_start: 0.7939 (m-80) cc_final: 0.7581 (t80) REVERT: A 1664 ASN cc_start: 0.7876 (p0) cc_final: 0.7474 (p0) REVERT: A 1677 LYS cc_start: 0.7486 (mttp) cc_final: 0.7278 (mppt) REVERT: A 2016 GLN cc_start: 0.6903 (mt0) cc_final: 0.6567 (mt0) REVERT: A 2222 GLN cc_start: 0.5898 (mt0) cc_final: 0.5093 (mm-40) REVERT: A 2371 LYS cc_start: 0.8000 (ptmm) cc_final: 0.7062 (mmtm) REVERT: A 2634 ASN cc_start: 0.7278 (OUTLIER) cc_final: 0.7050 (t0) REVERT: A 2691 ARG cc_start: 0.7611 (mtp85) cc_final: 0.7049 (mtp-110) REVERT: A 2698 ASP cc_start: 0.6617 (t0) cc_final: 0.5896 (t70) REVERT: A 2702 ASP cc_start: 0.6281 (m-30) cc_final: 0.5855 (m-30) REVERT: A 2788 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7307 (mt-10) REVERT: A 2892 GLU cc_start: 0.7134 (tt0) cc_final: 0.6879 (pt0) REVERT: A 2914 GLN cc_start: 0.7647 (mm-40) cc_final: 0.7352 (mm-40) REVERT: A 2955 GLN cc_start: 0.7101 (mt0) cc_final: 0.6763 (pt0) outliers start: 35 outliers final: 24 residues processed: 248 average time/residue: 1.3866 time to fit residues: 394.8732 Evaluate side-chains 250 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 220 time to evaluate : 2.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 398 VAL 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 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 1412 MET Chi-restraints excluded: chain A residue 1981 ILE Chi-restraints excluded: chain A residue 2000 GLN 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 2406 THR Chi-restraints excluded: chain A residue 2585 MET Chi-restraints excluded: chain A residue 2634 ASN Chi-restraints excluded: chain A residue 2704 THR 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 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-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.8204 > 50: distance: 89 - 206: 12.552 distance: 92 - 216: 9.659 distance: 99 - 219: 13.753 distance: 158 - 159: 5.971 distance: 159 - 160: 3.489 distance: 159 - 162: 12.849 distance: 160 - 161: 8.807 distance: 160 - 167: 15.295 distance: 162 - 163: 15.619 distance: 163 - 164: 18.814 distance: 164 - 165: 22.140 distance: 165 - 166: 17.127 distance: 167 - 168: 14.322 distance: 168 - 169: 12.385 distance: 168 - 171: 31.550 distance: 169 - 170: 27.384 distance: 169 - 174: 44.331 distance: 171 - 172: 25.549 distance: 171 - 173: 14.584 distance: 174 - 175: 11.976 distance: 175 - 176: 15.720 distance: 175 - 178: 28.179 distance: 176 - 177: 25.345 distance: 176 - 180: 17.302 distance: 178 - 179: 13.599 distance: 180 - 186: 14.156 distance: 181 - 182: 5.514 distance: 181 - 184: 12.609 distance: 182 - 183: 3.228 distance: 182 - 187: 4.233 distance: 184 - 185: 19.027 distance: 185 - 186: 25.196 distance: 187 - 188: 8.177 distance: 188 - 189: 15.277 distance: 188 - 191: 12.570 distance: 189 - 190: 9.297 distance: 189 - 195: 20.604 distance: 192 - 193: 10.581 distance: 192 - 194: 19.173 distance: 195 - 196: 14.879 distance: 196 - 199: 7.172 distance: 197 - 198: 8.768 distance: 197 - 203: 9.299 distance: 199 - 200: 7.994 distance: 200 - 201: 14.845 distance: 201 - 202: 14.484 distance: 203 - 204: 5.382 distance: 204 - 205: 11.792 distance: 204 - 207: 19.710 distance: 205 - 206: 4.569 distance: 205 - 208: 8.146 distance: 208 - 209: 10.204 distance: 209 - 210: 6.904 distance: 209 - 212: 14.094 distance: 210 - 211: 21.005 distance: 210 - 216: 15.339 distance: 212 - 213: 12.064 distance: 212 - 214: 22.810 distance: 213 - 215: 20.693 distance: 216 - 217: 10.039 distance: 217 - 218: 8.839 distance: 217 - 220: 14.256 distance: 218 - 219: 19.633 distance: 218 - 227: 4.253 distance: 220 - 221: 17.898 distance: 221 - 222: 11.270 distance: 221 - 223: 13.790 distance: 222 - 224: 8.187 distance: 223 - 225: 4.188 distance: 224 - 226: 15.055 distance: 225 - 226: 9.899 distance: 227 - 228: 9.220 distance: 228 - 229: 19.049 distance: 228 - 231: 12.263 distance: 229 - 230: 31.578 distance: 229 - 235: 14.181 distance: 231 - 232: 29.301 distance: 231 - 233: 9.330 distance: 232 - 234: 13.014