Starting phenix.real_space_refine on Mon Jun 23 21:18:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fdt_29012/06_2025/8fdt_29012.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fdt_29012/06_2025/8fdt_29012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fdt_29012/06_2025/8fdt_29012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fdt_29012/06_2025/8fdt_29012.map" model { file = "/net/cci-nas-00/data/ceres_data/8fdt_29012/06_2025/8fdt_29012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fdt_29012/06_2025/8fdt_29012.cif" } resolution = 3.2 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= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians V 1 8.30 5 P 9 5.49 5 S 150 5.16 5 C 17195 2.51 5 N 4702 2.21 5 O 5039 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 1.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27096 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 21981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2736, 21981 Classifications: {'peptide': 2736} Link IDs: {'PTRANS': 127, 'TRANS': 2608} Chain breaks: 7 Chain: "B" Number of atoms: 2499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2499 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 11, 'TRANS': 304} Chain: "C" Number of atoms: 2499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2499 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 11, 'TRANS': 304} Chain: "A" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 117 Unusual residues: {'ADP': 3, 'ATP': 1, 'VO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 15.58, per 1000 atoms: 0.57 Number of scatterers: 27096 At special positions: 0 Unit cell: (125.241, 167.754, 172.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) V 1 22.97 S 150 16.00 P 9 15.00 O 5039 8.00 N 4702 7.00 C 17195 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: 6.92 Conformation dependent library (CDL) restraints added in 3.5 seconds 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6380 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 31 sheets defined 49.9% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.70 Creating SS restraints... Processing helix chain 'A' and resid 88 through 96 Processing helix chain 'A' and resid 100 through 105 removed outlier: 3.751A pdb=" N LEU A 105 " --> pdb=" O ILE A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 114 Processing helix chain 'A' and resid 153 through 171 Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 178 through 188 Processing helix chain 'A' and resid 192 through 197 removed outlier: 4.308A 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: 3.999A pdb=" N ILE A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE A 272 " --> pdb=" O GLU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 290 removed outlier: 3.647A pdb=" N TYR A 290 " --> pdb=" O TRP A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 315 Processing helix chain 'A' and resid 322 through 343 removed outlier: 3.756A pdb=" N VAL A 326 " --> pdb=" O PRO A 322 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N MET A 343 " --> pdb=" O ASP A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 374 removed outlier: 3.706A pdb=" N HIS A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 385 Processing helix chain 'A' and resid 427 through 443 Processing helix chain 'A' and resid 457 through 468 Processing helix chain 'A' and resid 482 through 497 Processing helix chain 'A' and resid 504 through 508 Processing helix chain 'A' and resid 509 through 532 removed outlier: 3.830A pdb=" N GLN A 518 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN A 519 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN A 532 " --> pdb=" O ARG A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 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: 3.645A pdb=" N GLU A 623 " --> pdb=" O LYS A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 659 removed outlier: 3.740A pdb=" N GLU A 659 " --> pdb=" O LYS A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 690 removed outlier: 3.570A pdb=" N ILE A 681 " --> pdb=" O PRO A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 694 Processing helix chain 'A' and resid 698 through 710 Processing helix chain 'A' and resid 720 through 734 removed outlier: 4.099A pdb=" N GLU A 726 " --> pdb=" O ALA A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 762 removed outlier: 3.585A pdb=" N VAL A 749 " --> pdb=" O GLY A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 790 removed outlier: 3.781A pdb=" N ARG A 788 " --> pdb=" O LYS A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 810 Processing helix chain 'A' and resid 823 through 834 removed outlier: 3.529A pdb=" N HIS A 827 " --> pdb=" O GLY A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 842 removed outlier: 3.593A pdb=" N LYS A 842 " --> pdb=" O GLU A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 861 Processing helix chain 'A' and resid 897 through 903 removed outlier: 3.589A pdb=" N ARG A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 928 Processing helix chain 'A' and resid 956 through 969 Processing helix chain 'A' and resid 970 through 973 removed outlier: 3.811A pdb=" N THR A 973 " --> pdb=" O PRO A 970 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 970 through 973' Processing helix chain 'A' and resid 976 through 988 Processing helix chain 'A' and resid 995 through 1021 Processing helix chain 'A' and resid 1027 through 1048 removed outlier: 3.997A pdb=" N VAL A1040 " --> pdb=" O GLN A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1066 Processing helix chain 'A' and resid 1078 through 1082 Processing helix chain 'A' and resid 1116 through 1132 removed outlier: 3.526A pdb=" N GLU A1132 " --> pdb=" O THR A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1157 removed outlier: 3.669A pdb=" N ALA A1156 " --> pdb=" O SER A1152 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A1157 " --> pdb=" O ALA A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1172 through 1184 removed outlier: 4.262A 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 removed outlier: 3.571A pdb=" N ARG A1274 " --> pdb=" O HIS A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1301 removed outlier: 3.621A pdb=" N PHE A1296 " --> pdb=" O ILE A1292 " (cutoff:3.500A) Processing helix chain 'A' and resid 1302 through 1304 No H-bonds generated for 'chain 'A' and resid 1302 through 1304' 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: 3.577A pdb=" N ALA A1316 " --> pdb=" O GLU A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1355 removed outlier: 3.809A 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: 3.511A pdb=" N ARG A1388 " --> pdb=" O GLU A1384 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1412 Processing helix chain 'A' and resid 1430 through 1449 removed outlier: 3.613A pdb=" N GLU A1447 " --> pdb=" O LYS A1443 " (cutoff:3.500A) Processing helix chain 'A' and resid 1457 through 1473 removed outlier: 3.585A pdb=" N GLN A1473 " --> pdb=" O ARG A1469 " (cutoff:3.500A) Processing helix chain 'A' and resid 1487 through 1499 Processing helix chain 'A' and resid 1513 through 1529 Processing helix chain 'A' and resid 1546 through 1560 removed outlier: 3.668A 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 Processing helix chain 'A' and resid 1618 through 1627 removed outlier: 3.857A pdb=" N ASP A1622 " --> pdb=" O GLU A1618 " (cutoff:3.500A) Processing helix chain 'A' and resid 1628 through 1633 Processing helix chain 'A' and resid 1643 through 1655 Processing helix chain 'A' and resid 1683 through 1709 removed outlier: 3.685A pdb=" N ASN A1690 " --> pdb=" O GLU A1686 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS A1700 " --> pdb=" O HIS A1696 " (cutoff:3.500A) Processing helix chain 'A' and resid 1717 through 1765 removed outlier: 3.632A pdb=" N TYR A1721 " --> pdb=" O THR A1717 " (cutoff:3.500A) Processing helix chain 'A' and resid 1950 through 1980 removed outlier: 3.840A pdb=" N GLU A1963 " --> pdb=" O SER A1959 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ARG A1966 " --> pdb=" O ALA A1962 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS A1975 " --> pdb=" O SER A1971 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASN A1976 " --> pdb=" O GLU A1972 " (cutoff:3.500A) Processing helix chain 'A' and resid 1980 through 1994 removed outlier: 3.552A pdb=" N ASP A1984 " --> pdb=" O THR A1980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1999 through 2017 Processing helix chain 'A' and resid 2026 through 2032 Processing helix chain 'A' and resid 2033 through 2043 removed outlier: 3.563A pdb=" N ARG A2039 " --> pdb=" O ASP A2035 " (cutoff:3.500A) Processing helix chain 'A' and resid 2048 through 2060 Processing helix chain 'A' and resid 2072 through 2082 removed outlier: 3.562A pdb=" N GLU A2076 " --> pdb=" O GLY A2072 " (cutoff:3.500A) Processing helix chain 'A' and resid 2083 through 2086 Processing helix chain 'A' and resid 2096 through 2108 Processing helix chain 'A' and resid 2115 through 2119 removed outlier: 3.531A pdb=" N SER A2118 " --> pdb=" O ASP A2115 " (cutoff:3.500A) 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 removed outlier: 4.132A pdb=" N SER A2172 " --> pdb=" O PRO A2168 " (cutoff:3.500A) Processing helix chain 'A' and resid 2182 through 2199 Processing helix chain 'A' and resid 2199 through 2234 Processing helix chain 'A' and resid 2240 through 2268 removed outlier: 3.920A pdb=" N ILE A2244 " --> pdb=" O ASP A2240 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE A2245 " --> pdb=" O ASP A2241 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A2268 " --> pdb=" O GLU A2264 " (cutoff:3.500A) Processing helix chain 'A' and resid 2268 through 2296 removed outlier: 3.819A pdb=" N TYR A2279 " --> pdb=" O VAL A2275 " (cutoff:3.500A) Proline residue: A2281 - end of helix Processing helix chain 'A' and resid 2297 through 2299 No H-bonds generated for 'chain 'A' and resid 2297 through 2299' Processing helix chain 'A' and resid 2306 through 2319 removed outlier: 3.513A pdb=" N PHE A2310 " --> pdb=" O SER A2306 " (cutoff:3.500A) Processing helix chain 'A' and resid 2329 through 2351 Processing helix chain 'A' and resid 2357 through 2372 Processing helix chain 'A' and resid 2379 through 2388 Processing helix chain 'A' and resid 2406 through 2417 Processing helix chain 'A' and resid 2418 through 2423 removed outlier: 6.047A pdb=" N ALA A2421 " --> pdb=" O CYS A2418 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A2423 " --> pdb=" O PRO A2420 " (cutoff:3.500A) Processing helix chain 'A' and resid 2424 through 2431 removed outlier: 3.580A pdb=" N GLN A2430 " --> pdb=" O ILE A2426 " (cutoff:3.500A) Processing helix chain 'A' and resid 2433 through 2440 removed outlier: 4.287A pdb=" N ILE A2437 " --> pdb=" O GLU A2433 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP A2440 " --> pdb=" O GLY A2436 " (cutoff:3.500A) Processing helix chain 'A' and resid 2459 through 2475 Processing helix chain 'A' and resid 2478 through 2492 Processing helix chain 'A' and resid 2497 through 2501 Processing helix chain 'A' and resid 2504 through 2512 removed outlier: 3.675A 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 2566 Processing helix chain 'A' and resid 2580 through 2592 Processing helix chain 'A' and resid 2613 through 2620 removed outlier: 3.626A pdb=" N LEU A2617 " --> pdb=" O PRO A2613 " (cutoff:3.500A) Processing helix chain 'A' and resid 2629 through 2642 removed outlier: 4.306A pdb=" N ALA A2633 " --> pdb=" O PRO A2629 " (cutoff:3.500A) Processing helix chain 'A' and resid 2652 through 2672 removed outlier: 4.236A pdb=" N ARG A2656 " --> pdb=" O ASN A2652 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A2672 " --> pdb=" O ILE A2668 " (cutoff:3.500A) Processing helix chain 'A' and resid 2673 through 2675 No H-bonds generated for 'chain 'A' and resid 2673 through 2675' Processing helix chain 'A' and resid 2686 through 2705 removed outlier: 3.602A pdb=" N LEU A2690 " --> pdb=" O GLY A2686 " (cutoff:3.500A) Processing helix chain 'A' and resid 2712 through 2716 removed outlier: 3.558A pdb=" N ILE A2716 " --> pdb=" O PRO A2713 " (cutoff:3.500A) Processing helix chain 'A' and resid 2717 through 2728 Processing helix chain 'A' and resid 2730 through 2734 removed outlier: 3.676A pdb=" N ARG A2733 " --> pdb=" O TYR A2730 " (cutoff:3.500A) Processing helix chain 'A' and resid 2736 through 2751 Processing helix chain 'A' and resid 2752 through 2757 Processing helix chain 'A' and resid 2779 through 2789 removed outlier: 3.756A pdb=" N PHE A2783 " --> pdb=" O ARG A2779 " (cutoff:3.500A) Processing helix chain 'A' and resid 2795 through 2799 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: 3.792A 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 helix chain 'B' and resid 287 through 299 removed outlier: 3.514A pdb=" N TYR B 291 " --> pdb=" O PRO B 287 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER B 292 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N SER B 293 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU B 296 " --> pdb=" O SER B 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 290 through 299 Processing sheet with id=AA1, first strand: chain 'A' and resid 206 through 211 removed outlier: 10.843A pdb=" N VAL A 217 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 11.578A pdb=" N THR A 233 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N LEU A 219 " --> pdb=" O PHE A 231 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 405 through 406 Processing sheet with id=AA3, first strand: chain 'A' and resid 446 through 450 removed outlier: 6.156A pdb=" N GLY A 446 " --> pdb=" O ARG A 582 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N LEU A 584 " --> pdb=" O GLY A 446 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER A 448 " --> pdb=" O LEU A 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 472 through 476 removed outlier: 6.533A pdb=" N LEU A 473 " --> pdb=" O CYS A 501 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ASP A 503 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N PHE A 475 " --> pdb=" O ASP A 503 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 542 through 545 removed outlier: 4.332A pdb=" N ILE A 542 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N CYS A 544 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL A 551 " --> pdb=" O CYS A 544 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 796 through 799 removed outlier: 7.245A pdb=" N GLN A 844 " --> pdb=" O ARG A 885 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N MET A 887 " --> pdb=" O GLN A 844 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE A 846 " --> pdb=" O MET A 887 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N GLU A 889 " --> pdb=" O ILE A 846 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N PHE A 848 " --> pdb=" O GLU A 889 " (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 1160 through 1166 removed outlier: 3.769A pdb=" N GLU A1161 " --> pdb=" O TRP A1203 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL A1254 " --> pdb=" O LEU A1206 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU A1136 " --> pdb=" O GLY A1255 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N CYS A1257 " --> pdb=" O LEU A1136 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU A1138 " --> pdb=" O CYS A1257 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1193 through 1195 removed outlier: 6.886A pdb=" N VAL A1193 " --> pdb=" O LYS A1247 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AB3, first strand: chain 'A' and resid 1504 through 1505 removed outlier: 6.729A pdb=" N TYR A1504 " --> pdb=" O ILE A1538 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N ASP A1540 " --> pdb=" O TYR A1504 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE A1537 " --> pdb=" O VAL A1610 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N THR A1612 " --> pdb=" O PHE A1537 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET A1539 " --> pdb=" O THR A1612 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU A1478 " --> pdb=" O PHE A1611 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N MET A1613 " --> pdb=" O LEU A1478 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LEU A1480 " --> pdb=" O MET A1613 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2088 through 2091 removed outlier: 6.525A pdb=" N LEU A2111 " --> pdb=" O PHE A2156 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N SER A2158 " --> pdb=" O LEU A2111 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL A2113 " --> pdb=" O SER A2158 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU A2066 " --> pdb=" O VAL A2177 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2132 through 2133 removed outlier: 4.466A pdb=" N VAL A2138 " --> pdb=" O LEU A2149 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2544 through 2548 removed outlier: 6.161A pdb=" N THR A2545 " --> pdb=" O MET A2573 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LYS A2575 " --> pdb=" O THR A2545 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE A2547 " --> pdb=" O LYS A2575 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL A2572 " --> pdb=" O PHE A2603 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N THR A2605 " --> pdb=" O VAL A2572 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU A2574 " --> pdb=" O THR A2605 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N GLU A2607 " --> pdb=" O LEU A2574 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET A2606 " --> pdb=" O MET A2521 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 2986 through 2988 Processing sheet with id=AB8, first strand: chain 'A' and resid 3047 through 3048 removed outlier: 3.887A pdb=" N PHE A3098 " --> pdb=" O VAL A3087 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU A3041 " --> pdb=" O LEU A3063 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 97 through 105 removed outlier: 7.646A pdb=" N GLU B 101 " --> pdb=" O GLU B 409 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N GLU B 409 " --> pdb=" O GLU B 101 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR B 103 " --> pdb=" O VAL B 407 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 386 " --> pdb=" O GLY B 399 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 112 through 117 removed outlier: 6.681A pdb=" N ALA B 127 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL B 115 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL B 125 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ASP B 137 " --> pdb=" O PHE B 143 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N PHE B 143 " --> pdb=" O ASP B 137 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 154 through 159 removed outlier: 3.747A pdb=" N ASP B 156 " --> pdb=" O CYS B 169 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER B 170 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N THR B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG B 187 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ASP B 179 " --> pdb=" O CYS B 185 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N CYS B 185 " --> pdb=" O ASP B 179 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 196 through 201 removed outlier: 6.591A pdb=" N ALA B 211 " --> pdb=" O SER B 197 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL B 199 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL B 209 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ILE B 201 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N HIS B 207 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER B 212 " --> pdb=" O THR B 216 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N THR B 216 " --> pdb=" O SER B 212 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS B 229 " --> pdb=" O MET B 219 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 238 through 243 removed outlier: 3.687A pdb=" N MET B 240 " --> pdb=" O CYS B 253 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL B 263 " --> pdb=" O CYS B 269 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N CYS B 269 " --> pdb=" O VAL B 263 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 280 through 285 removed outlier: 3.532A pdb=" N SER B 316 " --> pdb=" O THR B 320 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N THR B 320 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASP B 325 " --> pdb=" O CYS B 331 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N CYS B 331 " --> pdb=" O ASP B 325 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 342 through 347 Processing sheet with id=AC7, first strand: chain 'C' and resid 97 through 105 removed outlier: 4.324A pdb=" N GLU C 409 " --> pdb=" O PRO C 100 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL C 407 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ALA C 104 " --> pdb=" O VAL C 405 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL C 405 " --> pdb=" O ALA C 104 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 112 through 117 removed outlier: 6.820A pdb=" N VAL C 135 " --> pdb=" O GLU C 144 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 154 through 159 removed outlier: 6.933A pdb=" N CYS C 169 " --> pdb=" O GLN C 155 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE C 157 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA C 167 " --> pdb=" O ILE C 157 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N PHE C 159 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LEU C 165 " --> pdb=" O PHE C 159 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE C 175 " --> pdb=" O THR C 188 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR C 188 " --> pdb=" O ILE C 175 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU C 177 " --> pdb=" O ILE C 186 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 196 through 201 removed outlier: 3.532A pdb=" N SER C 212 " --> pdb=" O THR C 216 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N THR C 216 " --> pdb=" O SER C 212 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE C 217 " --> pdb=" O THR C 230 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N THR C 230 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N MET C 219 " --> pdb=" O VAL C 228 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 238 through 243 removed outlier: 3.549A pdb=" N MET C 240 " --> pdb=" O CYS C 253 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL C 263 " --> pdb=" O CYS C 269 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N CYS C 269 " --> pdb=" O VAL C 263 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 280 through 285 removed outlier: 3.515A pdb=" N SER C 316 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR C 320 " --> pdb=" O SER C 316 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASP C 325 " --> pdb=" O CYS C 331 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N CYS C 331 " --> pdb=" O ASP C 325 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 342 through 347 1375 hydrogen bonds defined for protein. 3972 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: 16.34 Time building geometry restraints manager: 8.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 8895 1.35 - 1.49: 6941 1.49 - 1.63: 11619 1.63 - 1.77: 0 1.77 - 1.91: 248 Bond restraints: 27703 Sorted by residual: bond pdb=" C4 ADP A3204 " pdb=" C5 ADP A3204 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C4 ADP A3202 " pdb=" C5 ADP A3202 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C4 ADP A3203 " pdb=" C5 ADP A3203 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" N ARG B 98 " pdb=" CA ARG B 98 " ideal model delta sigma weight residual 1.455 1.490 -0.035 7.00e-03 2.04e+04 2.56e+01 bond pdb=" C5 ADP A3202 " pdb=" C6 ADP A3202 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.73e+01 ... (remaining 27698 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 36883 2.59 - 5.18: 621 5.18 - 7.77: 44 7.77 - 10.36: 14 10.36 - 12.95: 6 Bond angle restraints: 37568 Sorted by residual: angle pdb=" PB ATP A3201 " pdb=" O3B ATP A3201 " pdb=" PG ATP A3201 " ideal model delta sigma weight residual 139.87 129.63 10.24 1.00e+00 1.00e+00 1.05e+02 angle pdb=" PA ATP A3201 " pdb=" O3A ATP A3201 " pdb=" PB ATP A3201 " ideal model delta sigma weight residual 136.83 129.26 7.57 1.00e+00 1.00e+00 5.74e+01 angle pdb=" N PRO C 99 " pdb=" CA PRO C 99 " pdb=" C PRO C 99 " ideal model delta sigma weight residual 110.70 118.42 -7.72 1.22e+00 6.72e-01 4.00e+01 angle pdb=" N PRO B 99 " pdb=" CA PRO B 99 " pdb=" C PRO B 99 " ideal model delta sigma weight residual 110.70 117.56 -6.86 1.22e+00 6.72e-01 3.16e+01 angle pdb=" N VAL A1674 " pdb=" CA VAL A1674 " pdb=" C VAL A1674 " ideal model delta sigma weight residual 111.56 106.75 4.81 8.60e-01 1.35e+00 3.13e+01 ... (remaining 37563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.36: 16185 30.36 - 60.72: 468 60.72 - 91.08: 44 91.08 - 121.43: 1 121.43 - 151.79: 2 Dihedral angle restraints: 16700 sinusoidal: 6874 harmonic: 9826 Sorted by residual: dihedral pdb=" O1B ADP A3204 " pdb=" O3A ADP A3204 " pdb=" PB ADP A3204 " pdb=" PA ADP A3204 " ideal model delta sinusoidal sigma weight residual 300.00 148.20 151.79 1 2.00e+01 2.50e-03 4.51e+01 dihedral pdb=" C5' ADP A3202 " pdb=" O5' ADP A3202 " pdb=" PA ADP A3202 " pdb=" O2A ADP A3202 " ideal model delta sinusoidal sigma weight residual 300.00 169.69 130.31 1 2.00e+01 2.50e-03 3.95e+01 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 51.45 -111.45 1 2.00e+01 2.50e-03 3.28e+01 ... (remaining 16697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2924 0.043 - 0.085: 861 0.085 - 0.128: 322 0.128 - 0.171: 84 0.171 - 0.214: 18 Chirality restraints: 4209 Sorted by residual: chirality pdb=" C3' ADP A3203 " pdb=" C2' ADP A3203 " pdb=" C4' ADP A3203 " pdb=" O3' ADP A3203 " both_signs ideal model delta sigma weight residual False -2.51 -2.72 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C3' ADP A3204 " pdb=" C2' ADP A3204 " pdb=" C4' ADP A3204 " pdb=" O3' ADP A3204 " both_signs ideal model delta sigma weight residual False -2.51 -2.72 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CB VAL A 857 " pdb=" CA VAL A 857 " pdb=" CG1 VAL A 857 " pdb=" CG2 VAL A 857 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 4206 not shown) Planarity restraints: 4790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A2650 " -0.058 5.00e-02 4.00e+02 8.57e-02 1.17e+01 pdb=" N PRO A2651 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO A2651 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A2651 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1089 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.52e+00 pdb=" C GLU A1089 " -0.047 2.00e-02 2.50e+03 pdb=" O GLU A1089 " 0.018 2.00e-02 2.50e+03 pdb=" N TRP A1090 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A2456 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO A2457 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A2457 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A2457 " -0.027 5.00e-02 4.00e+02 ... (remaining 4787 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 15 2.25 - 2.92: 11105 2.92 - 3.58: 40983 3.58 - 4.24: 64646 4.24 - 4.90: 109814 Nonbonded interactions: 226563 Sorted by model distance: nonbonded pdb=" N GLN A 426 " pdb=" OE1 GLN A 426 " model vdw 1.592 3.120 nonbonded pdb=" OE2 GLU A 787 " pdb=" NH1 ARG A 788 " model vdw 2.146 3.120 nonbonded pdb=" OE1 GLU A 354 " pdb=" OG SER A 601 " model vdw 2.200 3.040 nonbonded pdb=" OG SER A 380 " pdb=" OE1 GLU A 382 " model vdw 2.200 3.040 nonbonded pdb=" O LEU A 599 " pdb=" N GLN A 602 " model vdw 2.207 3.120 ... (remaining 226558 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } 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: 3.350 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: 0.030 Extract box with map and model: 1.040 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 68.380 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 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 : 0.005 0.110 27703 Z= 0.349 Angle : 0.797 12.955 37568 Z= 0.497 Chirality : 0.050 0.214 4209 Planarity : 0.004 0.086 4790 Dihedral : 13.940 151.793 10320 Min Nonbonded Distance : 1.592 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.97 % Favored : 95.88 % Rotamer: Outliers : 0.27 % Allowed : 0.94 % Favored : 98.80 % 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: 0.21 (0.15), residues: 3348 helix: 1.30 (0.13), residues: 1537 sheet: -0.85 (0.23), residues: 511 loop : -0.77 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1093 HIS 0.008 0.001 HIS B 382 PHE 0.018 0.001 PHE B 347 TYR 0.019 0.002 TYR A 283 ARG 0.010 0.000 ARG A2260 Details of bonding type rmsd hydrogen bonds : bond 0.13967 ( 1375) hydrogen bonds : angle 6.14824 ( 3972) covalent geometry : bond 0.00541 (27703) covalent geometry : angle 0.79675 (37568) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 625 time to evaluate : 3.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.6716 (tt) cc_final: 0.6497 (tp) REVERT: A 165 GLU cc_start: 0.6249 (mm-30) cc_final: 0.5777 (tm-30) REVERT: A 361 VAL cc_start: 0.7386 (p) cc_final: 0.6706 (m) REVERT: A 557 MET cc_start: 0.6886 (tpp) cc_final: 0.6614 (mmm) REVERT: A 678 GLU cc_start: 0.6867 (pm20) cc_final: 0.6640 (mm-30) REVERT: A 1026 MET cc_start: 0.7677 (tmm) cc_final: 0.7047 (ttt) REVERT: A 1169 SER cc_start: 0.8427 (p) cc_final: 0.7602 (t) REVERT: A 1507 LYS cc_start: 0.7123 (mmtt) cc_final: 0.6898 (mtmm) REVERT: A 1658 MET cc_start: 0.7923 (mtp) cc_final: 0.7552 (mtp) REVERT: A 1677 LYS cc_start: 0.8239 (mmtp) cc_final: 0.7749 (tmtt) REVERT: A 1762 GLU cc_start: 0.6183 (pp20) cc_final: 0.5726 (tt0) REVERT: A 1981 ILE cc_start: 0.8266 (tt) cc_final: 0.7972 (tt) REVERT: A 2189 GLN cc_start: 0.7417 (mm-40) cc_final: 0.7117 (mt0) REVERT: A 2204 GLU cc_start: 0.7715 (tp30) cc_final: 0.7241 (tp30) REVERT: A 2219 ARG cc_start: 0.7264 (tpt170) cc_final: 0.6434 (tpt90) REVERT: A 2252 LYS cc_start: 0.7710 (mtmm) cc_final: 0.7184 (pttp) REVERT: A 2601 ARG cc_start: 0.8722 (mmt-90) cc_final: 0.8465 (mpt180) REVERT: A 2606 MET cc_start: 0.8069 (ptm) cc_final: 0.7602 (ptt) REVERT: A 2679 TRP cc_start: 0.7511 (m100) cc_final: 0.6978 (m100) REVERT: A 2706 LYS cc_start: 0.6506 (tptp) cc_final: 0.6113 (mptt) REVERT: A 2725 MET cc_start: 0.6825 (mmt) cc_final: 0.6525 (mmt) REVERT: A 2863 SER cc_start: 0.7538 (t) cc_final: 0.6918 (p) REVERT: A 2911 ASP cc_start: 0.6332 (t0) cc_final: 0.5914 (m-30) REVERT: B 114 ARG cc_start: 0.6062 (mtt90) cc_final: 0.5235 (ttt180) REVERT: B 156 ASP cc_start: 0.5948 (t0) cc_final: 0.5523 (m-30) REVERT: B 204 ASN cc_start: 0.7028 (p0) cc_final: 0.6713 (p0) REVERT: B 206 ASP cc_start: 0.7765 (m-30) cc_final: 0.6992 (p0) REVERT: B 219 MET cc_start: 0.5919 (tmm) cc_final: 0.5533 (tmm) REVERT: B 229 LYS cc_start: 0.5708 (ptpt) cc_final: 0.5434 (pptt) REVERT: B 390 HIS cc_start: 0.3893 (t-90) cc_final: 0.3368 (t-170) REVERT: C 189 MET cc_start: 0.6354 (mtt) cc_final: 0.5769 (mmt) REVERT: C 201 ILE cc_start: 0.7445 (mp) cc_final: 0.7186 (mt) REVERT: C 204 ASN cc_start: 0.6584 (t0) cc_final: 0.6260 (p0) REVERT: C 334 THR cc_start: 0.8205 (t) cc_final: 0.7770 (m) outliers start: 8 outliers final: 2 residues processed: 631 average time/residue: 0.4857 time to fit residues: 473.2455 Evaluate side-chains 352 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 350 time to evaluate : 3.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1091 SER Chi-restraints excluded: chain A residue 1503 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 282 optimal weight: 4.9990 chunk 253 optimal weight: 3.9990 chunk 140 optimal weight: 8.9990 chunk 86 optimal weight: 0.0770 chunk 171 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 262 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 159 optimal weight: 7.9990 chunk 195 optimal weight: 0.3980 chunk 304 optimal weight: 4.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 716 HIS A 922 ASN A1008 HIS A1166 ASN A1297 ASN A1577 GLN ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2000 GLN A2004 GLN A2114 GLN A2217 GLN A2270 GLN A2315 HIS ** A2434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2501 GLN A2532 HIS A2586 GLN A2875 HIS A3022 ASN A3051 ASN ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.149663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.117851 restraints weight = 49296.861| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.81 r_work: 0.3499 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27703 Z= 0.130 Angle : 0.606 11.290 37568 Z= 0.307 Chirality : 0.042 0.171 4209 Planarity : 0.005 0.082 4790 Dihedral : 6.462 140.733 3717 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.20 % Favored : 96.74 % Rotamer: Outliers : 1.34 % Allowed : 8.53 % Favored : 90.14 % 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: 0.63 (0.15), residues: 3348 helix: 1.72 (0.13), residues: 1545 sheet: -0.73 (0.22), residues: 499 loop : -0.64 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 136 HIS 0.005 0.001 HIS C 390 PHE 0.024 0.001 PHE B 183 TYR 0.026 0.002 TYR A1293 ARG 0.015 0.001 ARG A2260 Details of bonding type rmsd hydrogen bonds : bond 0.04246 ( 1375) hydrogen bonds : angle 4.62796 ( 3972) covalent geometry : bond 0.00287 (27703) covalent geometry : angle 0.60597 (37568) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 402 time to evaluate : 4.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.6655 (tt) cc_final: 0.6403 (tp) REVERT: A 165 GLU cc_start: 0.6271 (mm-30) cc_final: 0.5852 (tm-30) REVERT: A 251 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6818 (pm20) REVERT: A 361 VAL cc_start: 0.7438 (p) cc_final: 0.6588 (m) REVERT: A 368 ARG cc_start: 0.8589 (mtm-85) cc_final: 0.8272 (mtm-85) REVERT: A 399 LEU cc_start: 0.6901 (mt) cc_final: 0.6676 (pp) REVERT: A 557 MET cc_start: 0.7032 (tpp) cc_final: 0.6745 (ttt) REVERT: A 563 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8483 (mtm) REVERT: A 586 MET cc_start: 0.8622 (mtp) cc_final: 0.8218 (mtp) REVERT: A 678 GLU cc_start: 0.7428 (pm20) cc_final: 0.6625 (mm-30) REVERT: A 1026 MET cc_start: 0.7683 (tmm) cc_final: 0.7276 (ttt) REVERT: A 1111 ASP cc_start: 0.7296 (m-30) cc_final: 0.6803 (p0) REVERT: A 1183 TYR cc_start: 0.6459 (m-10) cc_final: 0.6254 (m-10) REVERT: A 1373 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7798 (mm-30) REVERT: A 1427 ILE cc_start: 0.8125 (tt) cc_final: 0.7883 (mt) REVERT: A 1507 LYS cc_start: 0.7395 (mmtt) cc_final: 0.6886 (mtmm) REVERT: A 1541 GLU cc_start: 0.6964 (pt0) cc_final: 0.6728 (pt0) REVERT: A 1658 MET cc_start: 0.8224 (mtp) cc_final: 0.7974 (mtt) REVERT: A 1677 LYS cc_start: 0.8075 (mmtp) cc_final: 0.7727 (tmtt) REVERT: A 1762 GLU cc_start: 0.6045 (pp20) cc_final: 0.5745 (tt0) REVERT: A 1991 PHE cc_start: 0.8444 (t80) cc_final: 0.8167 (t80) REVERT: A 2107 PHE cc_start: 0.7503 (m-80) cc_final: 0.7300 (m-10) REVERT: A 2189 GLN cc_start: 0.7568 (mm-40) cc_final: 0.7343 (mt0) REVERT: A 2204 GLU cc_start: 0.7911 (tp30) cc_final: 0.7629 (tp30) REVERT: A 2219 ARG cc_start: 0.7702 (tpt170) cc_final: 0.7377 (ttm170) REVERT: A 2252 LYS cc_start: 0.7517 (mtmm) cc_final: 0.7297 (mtmm) REVERT: A 2279 TYR cc_start: 0.5780 (m-10) cc_final: 0.5271 (m-10) REVERT: A 2702 ASP cc_start: 0.6877 (m-30) cc_final: 0.6666 (m-30) REVERT: A 2706 LYS cc_start: 0.6285 (tptp) cc_final: 0.5864 (mptt) REVERT: A 2725 MET cc_start: 0.6893 (mmt) cc_final: 0.6662 (mmt) REVERT: A 2821 MET cc_start: 0.8142 (mtp) cc_final: 0.7902 (mtm) REVERT: A 2863 SER cc_start: 0.7649 (t) cc_final: 0.7086 (p) REVERT: A 2911 ASP cc_start: 0.6641 (t0) cc_final: 0.6176 (m-30) REVERT: A 3083 VAL cc_start: 0.7548 (m) cc_final: 0.7302 (m) REVERT: B 114 ARG cc_start: 0.5912 (mtt90) cc_final: 0.4858 (ttt180) REVERT: B 156 ASP cc_start: 0.6048 (t0) cc_final: 0.5787 (m-30) REVERT: B 183 PHE cc_start: 0.8316 (m-10) cc_final: 0.7835 (m-10) REVERT: B 206 ASP cc_start: 0.7884 (m-30) cc_final: 0.6976 (p0) REVERT: B 219 MET cc_start: 0.5613 (tmm) cc_final: 0.4989 (tmm) REVERT: B 240 MET cc_start: 0.2465 (mmm) cc_final: 0.2261 (tpt) REVERT: B 285 TRP cc_start: 0.3579 (m100) cc_final: 0.3376 (m100) REVERT: B 390 HIS cc_start: 0.3758 (t-90) cc_final: 0.3255 (t-170) REVERT: B 409 GLU cc_start: 0.7688 (pt0) cc_final: 0.7328 (pm20) REVERT: C 109 ARG cc_start: 0.7713 (tpt90) cc_final: 0.7248 (mtp-110) REVERT: C 189 MET cc_start: 0.6743 (mtt) cc_final: 0.5811 (mmt) REVERT: C 204 ASN cc_start: 0.6716 (t0) cc_final: 0.6400 (p0) REVERT: C 272 GLU cc_start: 0.7740 (tt0) cc_final: 0.7174 (tm-30) REVERT: C 334 THR cc_start: 0.8294 (t) cc_final: 0.8009 (m) REVERT: C 353 PHE cc_start: 0.7102 (m-80) cc_final: 0.6821 (m-80) REVERT: C 374 MET cc_start: 0.7366 (tmm) cc_final: 0.6757 (tmm) outliers start: 40 outliers final: 24 residues processed: 423 average time/residue: 0.4612 time to fit residues: 312.3746 Evaluate side-chains 365 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 339 time to evaluate : 3.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 1091 SER Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1166 ASN Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1530 CYS Chi-restraints excluded: chain A residue 1551 GLU Chi-restraints excluded: chain A residue 1604 ILE Chi-restraints excluded: chain A residue 1699 LEU Chi-restraints excluded: chain A residue 2259 THR Chi-restraints excluded: chain A residue 2287 SER Chi-restraints excluded: chain A residue 2532 HIS Chi-restraints excluded: chain A residue 2612 VAL Chi-restraints excluded: chain A residue 2785 GLN Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 195 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 285 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 181 optimal weight: 0.0270 chunk 268 optimal weight: 0.0570 chunk 154 optimal weight: 8.9990 chunk 191 optimal weight: 0.8980 chunk 163 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 251 optimal weight: 5.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1021 HIS ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2315 HIS ** A2434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2532 HIS A2557 GLN A2773 GLN B 161 HIS ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.149991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.118241 restraints weight = 49325.729| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 3.15 r_work: 0.3492 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 27703 Z= 0.113 Angle : 0.561 8.122 37568 Z= 0.281 Chirality : 0.041 0.156 4209 Planarity : 0.004 0.080 4790 Dihedral : 6.038 127.574 3717 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.05 % Favored : 96.89 % Rotamer: Outliers : 1.57 % Allowed : 11.10 % Favored : 87.33 % 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: 0.89 (0.15), residues: 3348 helix: 1.97 (0.13), residues: 1539 sheet: -0.69 (0.22), residues: 500 loop : -0.52 (0.17), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 262 HIS 0.013 0.001 HIS A2532 PHE 0.032 0.001 PHE B 183 TYR 0.016 0.001 TYR A1293 ARG 0.006 0.000 ARG A2260 Details of bonding type rmsd hydrogen bonds : bond 0.03744 ( 1375) hydrogen bonds : angle 4.29829 ( 3972) covalent geometry : bond 0.00246 (27703) covalent geometry : angle 0.56101 (37568) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 364 time to evaluate : 3.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.6693 (tt) cc_final: 0.6465 (tp) REVERT: A 165 GLU cc_start: 0.6385 (mm-30) cc_final: 0.5883 (tm-30) REVERT: A 175 TYR cc_start: 0.6841 (m-80) cc_final: 0.6603 (m-80) REVERT: A 248 THR cc_start: 0.8351 (p) cc_final: 0.7848 (p) REVERT: A 361 VAL cc_start: 0.7393 (p) cc_final: 0.6584 (m) REVERT: A 399 LEU cc_start: 0.6873 (mt) cc_final: 0.6647 (pp) REVERT: A 563 MET cc_start: 0.8818 (ptm) cc_final: 0.8453 (mtm) REVERT: A 586 MET cc_start: 0.8634 (mtp) cc_final: 0.8269 (mtp) REVERT: A 678 GLU cc_start: 0.7428 (pm20) cc_final: 0.6910 (mm-30) REVERT: A 767 MET cc_start: 0.8030 (mtm) cc_final: 0.7566 (mtt) REVERT: A 1026 MET cc_start: 0.7839 (tmm) cc_final: 0.7537 (ttt) REVERT: A 1111 ASP cc_start: 0.7285 (m-30) cc_final: 0.6809 (p0) REVERT: A 1373 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7804 (mm-30) REVERT: A 1424 LYS cc_start: 0.8748 (ptmm) cc_final: 0.8114 (ptpp) REVERT: A 1507 LYS cc_start: 0.7418 (mmtt) cc_final: 0.6871 (mtmm) REVERT: A 1677 LYS cc_start: 0.8104 (mmtp) cc_final: 0.7581 (tmtt) REVERT: A 1686 GLU cc_start: 0.7538 (mp0) cc_final: 0.7071 (mp0) REVERT: A 1991 PHE cc_start: 0.8393 (t80) cc_final: 0.8067 (t80) REVERT: A 2107 PHE cc_start: 0.7583 (m-80) cc_final: 0.7375 (m-10) REVERT: A 2204 GLU cc_start: 0.7725 (tp30) cc_final: 0.7431 (tp30) REVERT: A 2219 ARG cc_start: 0.7739 (tpt170) cc_final: 0.7084 (ttm170) REVERT: A 2279 TYR cc_start: 0.5887 (m-10) cc_final: 0.5463 (m-10) REVERT: A 2702 ASP cc_start: 0.6944 (m-30) cc_final: 0.6674 (m-30) REVERT: A 2706 LYS cc_start: 0.6213 (tptp) cc_final: 0.5846 (mptt) REVERT: A 2725 MET cc_start: 0.6911 (mmt) cc_final: 0.6702 (mmt) REVERT: A 2863 SER cc_start: 0.7596 (t) cc_final: 0.7043 (p) REVERT: A 2911 ASP cc_start: 0.6636 (t0) cc_final: 0.6146 (m-30) REVERT: B 114 ARG cc_start: 0.5864 (mtt90) cc_final: 0.4812 (ttt-90) REVERT: B 156 ASP cc_start: 0.6013 (t0) cc_final: 0.5685 (m-30) REVERT: B 192 HIS cc_start: 0.5360 (t-90) cc_final: 0.4901 (t-90) REVERT: B 206 ASP cc_start: 0.7911 (m-30) cc_final: 0.6981 (p0) REVERT: B 240 MET cc_start: 0.2548 (mmm) cc_final: 0.2281 (tpt) REVERT: B 285 TRP cc_start: 0.3521 (m100) cc_final: 0.3279 (m100) REVERT: B 390 HIS cc_start: 0.4215 (t-90) cc_final: 0.3885 (t70) REVERT: C 109 ARG cc_start: 0.7605 (tpt90) cc_final: 0.7272 (mtp180) REVERT: C 189 MET cc_start: 0.6703 (mtt) cc_final: 0.5807 (mmt) REVERT: C 202 MET cc_start: 0.7935 (mmp) cc_final: 0.7707 (mmp) REVERT: C 204 ASN cc_start: 0.6731 (t0) cc_final: 0.6411 (p0) REVERT: C 272 GLU cc_start: 0.7703 (tt0) cc_final: 0.7073 (tm-30) REVERT: C 333 MET cc_start: 0.7150 (ppp) cc_final: 0.6622 (ppp) REVERT: C 334 THR cc_start: 0.8262 (t) cc_final: 0.7836 (m) REVERT: C 374 MET cc_start: 0.7086 (tmm) cc_final: 0.6401 (tmm) REVERT: C 388 ASP cc_start: 0.7478 (t0) cc_final: 0.7277 (t0) outliers start: 47 outliers final: 29 residues processed: 389 average time/residue: 0.4021 time to fit residues: 254.1813 Evaluate side-chains 360 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 331 time to evaluate : 3.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 1091 SER Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1398 VAL Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1551 GLU Chi-restraints excluded: chain A residue 1604 ILE Chi-restraints excluded: chain A residue 1699 LEU Chi-restraints excluded: chain A residue 2259 THR Chi-restraints excluded: chain A residue 2287 SER Chi-restraints excluded: chain A residue 2390 ASN Chi-restraints excluded: chain A residue 2505 LEU Chi-restraints excluded: chain A residue 2532 HIS Chi-restraints excluded: chain A residue 2612 VAL Chi-restraints excluded: chain A residue 2785 GLN Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 354 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 38 optimal weight: 2.9990 chunk 319 optimal weight: 9.9990 chunk 177 optimal weight: 4.9990 chunk 252 optimal weight: 0.9990 chunk 240 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 284 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 306 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2634 ASN ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.145910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.114040 restraints weight = 49955.045| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.95 r_work: 0.3432 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 27703 Z= 0.168 Angle : 0.591 9.667 37568 Z= 0.298 Chirality : 0.042 0.198 4209 Planarity : 0.004 0.078 4790 Dihedral : 6.010 123.126 3717 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.49 % Favored : 96.45 % Rotamer: Outliers : 2.17 % Allowed : 12.27 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.15), residues: 3348 helix: 1.92 (0.13), residues: 1539 sheet: -0.69 (0.23), residues: 488 loop : -0.50 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 246 HIS 0.012 0.001 HIS A2532 PHE 0.022 0.002 PHE B 183 TYR 0.025 0.002 TYR A1293 ARG 0.005 0.000 ARG A1302 Details of bonding type rmsd hydrogen bonds : bond 0.03883 ( 1375) hydrogen bonds : angle 4.30788 ( 3972) covalent geometry : bond 0.00395 (27703) covalent geometry : angle 0.59130 (37568) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 338 time to evaluate : 4.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.6315 (mm-30) cc_final: 0.5901 (tm-30) REVERT: A 175 TYR cc_start: 0.6661 (m-80) cc_final: 0.6432 (m-80) REVERT: A 201 LYS cc_start: 0.8136 (pptt) cc_final: 0.7916 (pptt) REVERT: A 361 VAL cc_start: 0.7468 (p) cc_final: 0.6584 (m) REVERT: A 479 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.6905 (pm20) REVERT: A 525 GLU cc_start: 0.6530 (tm-30) cc_final: 0.5942 (mm-30) REVERT: A 586 MET cc_start: 0.8696 (mtp) cc_final: 0.8310 (mtp) REVERT: A 678 GLU cc_start: 0.7598 (pm20) cc_final: 0.7044 (mm-30) REVERT: A 767 MET cc_start: 0.8253 (mtm) cc_final: 0.8021 (mtt) REVERT: A 1026 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7596 (ttt) REVERT: A 1111 ASP cc_start: 0.7509 (m-30) cc_final: 0.7087 (p0) REVERT: A 1373 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7991 (mm-30) REVERT: A 1424 LYS cc_start: 0.8685 (ptmm) cc_final: 0.8164 (ptpp) REVERT: A 1507 LYS cc_start: 0.7486 (mmtt) cc_final: 0.7259 (mtmm) REVERT: A 1541 GLU cc_start: 0.7125 (pt0) cc_final: 0.6908 (pt0) REVERT: A 1677 LYS cc_start: 0.8200 (mmtp) cc_final: 0.7667 (tmtt) REVERT: A 1977 GLN cc_start: 0.7207 (OUTLIER) cc_final: 0.6398 (mp10) REVERT: A 2076 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7401 (pm20) REVERT: A 2204 GLU cc_start: 0.7600 (tp30) cc_final: 0.7237 (tp30) REVERT: A 2219 ARG cc_start: 0.7575 (tpt170) cc_final: 0.7166 (tpt170) REVERT: A 2252 LYS cc_start: 0.7547 (mtmm) cc_final: 0.7076 (pttp) REVERT: A 2257 GLU cc_start: 0.7638 (tp30) cc_final: 0.7252 (tp30) REVERT: A 2279 TYR cc_start: 0.6180 (m-10) cc_final: 0.5817 (m-10) REVERT: A 2607 GLU cc_start: 0.8103 (tt0) cc_final: 0.7596 (mt-10) REVERT: A 2702 ASP cc_start: 0.7013 (m-30) cc_final: 0.6745 (m-30) REVERT: A 2706 LYS cc_start: 0.6277 (tptp) cc_final: 0.5929 (mptt) REVERT: A 2863 SER cc_start: 0.7632 (t) cc_final: 0.7036 (p) REVERT: A 2911 ASP cc_start: 0.6688 (t0) cc_final: 0.6168 (m-30) REVERT: B 192 HIS cc_start: 0.5061 (t-90) cc_final: 0.4600 (t-170) REVERT: B 204 ASN cc_start: 0.6978 (p0) cc_final: 0.6527 (p0) REVERT: B 285 TRP cc_start: 0.3566 (m100) cc_final: 0.3343 (m100) REVERT: B 324 TRP cc_start: 0.6137 (m-10) cc_final: 0.5420 (m-10) REVERT: C 189 MET cc_start: 0.6897 (mtt) cc_final: 0.5799 (mmt) REVERT: C 204 ASN cc_start: 0.6805 (t0) cc_final: 0.6445 (p0) REVERT: C 272 GLU cc_start: 0.7737 (tt0) cc_final: 0.7134 (tm-30) REVERT: C 324 TRP cc_start: 0.7299 (OUTLIER) cc_final: 0.6804 (m100) REVERT: C 333 MET cc_start: 0.7013 (OUTLIER) cc_final: 0.6531 (ppp) REVERT: C 353 PHE cc_start: 0.7459 (m-80) cc_final: 0.7116 (m-80) REVERT: C 374 MET cc_start: 0.6954 (tmm) cc_final: 0.6493 (tmm) REVERT: C 388 ASP cc_start: 0.7451 (t0) cc_final: 0.7226 (t0) outliers start: 65 outliers final: 38 residues processed: 380 average time/residue: 0.6625 time to fit residues: 425.4860 Evaluate side-chains 356 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 312 time to evaluate : 5.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1026 MET Chi-restraints excluded: chain A residue 1091 SER Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1391 THR Chi-restraints excluded: chain A residue 1398 VAL Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1551 GLU Chi-restraints excluded: chain A residue 1635 VAL Chi-restraints excluded: chain A residue 1699 LEU Chi-restraints excluded: chain A residue 1977 GLN Chi-restraints excluded: chain A residue 2076 GLU Chi-restraints excluded: chain A residue 2084 ASP Chi-restraints excluded: chain A residue 2259 THR Chi-restraints excluded: chain A residue 2287 SER Chi-restraints excluded: chain A residue 2390 ASN Chi-restraints excluded: chain A residue 2505 LEU Chi-restraints excluded: chain A residue 2612 VAL Chi-restraints excluded: chain A residue 2766 VAL Chi-restraints excluded: chain A residue 2785 GLN Chi-restraints excluded: chain A residue 2858 LEU Chi-restraints excluded: chain A residue 3048 CYS Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 366 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 194 optimal weight: 0.7980 chunk 206 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 229 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 241 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 220 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2013 HIS A2315 HIS A2532 HIS B 370 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.146191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.114119 restraints weight = 49552.152| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.74 r_work: 0.3448 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 27703 Z= 0.139 Angle : 0.561 9.331 37568 Z= 0.284 Chirality : 0.041 0.192 4209 Planarity : 0.004 0.077 4790 Dihedral : 5.862 117.916 3717 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.29 % Favored : 96.65 % Rotamer: Outliers : 2.41 % Allowed : 12.87 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.15), residues: 3348 helix: 1.95 (0.13), residues: 1531 sheet: -0.66 (0.23), residues: 476 loop : -0.49 (0.17), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 246 HIS 0.008 0.001 HIS A 104 PHE 0.022 0.001 PHE B 183 TYR 0.021 0.001 TYR A1293 ARG 0.008 0.000 ARG A2260 Details of bonding type rmsd hydrogen bonds : bond 0.03679 ( 1375) hydrogen bonds : angle 4.20109 ( 3972) covalent geometry : bond 0.00322 (27703) covalent geometry : angle 0.56105 (37568) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 335 time to evaluate : 3.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.6290 (mm-30) cc_final: 0.5808 (tm-30) REVERT: A 175 TYR cc_start: 0.6714 (m-80) cc_final: 0.6500 (m-80) REVERT: A 201 LYS cc_start: 0.8185 (pttt) cc_final: 0.7946 (pptt) REVERT: A 343 MET cc_start: 0.8079 (ptp) cc_final: 0.7726 (ptt) REVERT: A 361 VAL cc_start: 0.7413 (p) cc_final: 0.6508 (m) REVERT: A 479 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.6870 (pm20) REVERT: A 525 GLU cc_start: 0.6731 (tm-30) cc_final: 0.6127 (mm-30) REVERT: A 563 MET cc_start: 0.9125 (ptp) cc_final: 0.8749 (ptp) REVERT: A 586 MET cc_start: 0.8691 (mtp) cc_final: 0.8360 (mtp) REVERT: A 606 THR cc_start: 0.7888 (OUTLIER) cc_final: 0.7148 (t) REVERT: A 678 GLU cc_start: 0.7721 (pm20) cc_final: 0.7137 (mm-30) REVERT: A 1026 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7607 (ttt) REVERT: A 1111 ASP cc_start: 0.7424 (m-30) cc_final: 0.7083 (p0) REVERT: A 1373 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7867 (mm-30) REVERT: A 1424 LYS cc_start: 0.8631 (ptmm) cc_final: 0.8211 (ptpp) REVERT: A 1541 GLU cc_start: 0.7114 (pt0) cc_final: 0.6864 (pt0) REVERT: A 1575 MET cc_start: 0.7506 (tpp) cc_final: 0.7232 (mmt) REVERT: A 1677 LYS cc_start: 0.8213 (mmtp) cc_final: 0.7630 (tmtt) REVERT: A 1977 GLN cc_start: 0.7216 (OUTLIER) cc_final: 0.6412 (mp10) REVERT: A 2076 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7358 (pm20) REVERT: A 2204 GLU cc_start: 0.7587 (tp30) cc_final: 0.7242 (tp30) REVERT: A 2219 ARG cc_start: 0.7505 (tpt170) cc_final: 0.7099 (tpt170) REVERT: A 2252 LYS cc_start: 0.7675 (mtmm) cc_final: 0.7212 (pttp) REVERT: A 2257 GLU cc_start: 0.7581 (tp30) cc_final: 0.7333 (tp30) REVERT: A 2279 TYR cc_start: 0.6117 (m-10) cc_final: 0.5787 (m-10) REVERT: A 2553 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6382 (mp0) REVERT: A 2702 ASP cc_start: 0.6847 (m-30) cc_final: 0.6566 (m-30) REVERT: A 2706 LYS cc_start: 0.6236 (tptp) cc_final: 0.5891 (mptt) REVERT: A 2863 SER cc_start: 0.7634 (t) cc_final: 0.7034 (p) REVERT: A 2911 ASP cc_start: 0.6729 (t0) cc_final: 0.6279 (m-30) REVERT: B 192 HIS cc_start: 0.5009 (t-90) cc_final: 0.4439 (t-170) REVERT: B 206 ASP cc_start: 0.7901 (m-30) cc_final: 0.6812 (p0) REVERT: B 285 TRP cc_start: 0.3580 (m100) cc_final: 0.3371 (m100) REVERT: B 324 TRP cc_start: 0.6116 (m-10) cc_final: 0.5463 (m-10) REVERT: C 109 ARG cc_start: 0.7493 (mtt90) cc_final: 0.7068 (tpt90) REVERT: C 189 MET cc_start: 0.6925 (mtt) cc_final: 0.5845 (mmt) REVERT: C 204 ASN cc_start: 0.6874 (t0) cc_final: 0.6644 (t0) REVERT: C 272 GLU cc_start: 0.7751 (tt0) cc_final: 0.7165 (tm-30) REVERT: C 324 TRP cc_start: 0.7266 (OUTLIER) cc_final: 0.6414 (m100) REVERT: C 333 MET cc_start: 0.7148 (ppp) cc_final: 0.6642 (ppp) REVERT: C 374 MET cc_start: 0.6935 (tmm) cc_final: 0.6505 (tmm) REVERT: C 388 ASP cc_start: 0.7372 (t0) cc_final: 0.7153 (t0) outliers start: 72 outliers final: 46 residues processed: 383 average time/residue: 0.3889 time to fit residues: 241.8168 Evaluate side-chains 359 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 307 time to evaluate : 2.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1026 MET Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1398 VAL Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1551 GLU Chi-restraints excluded: chain A residue 1604 ILE Chi-restraints excluded: chain A residue 1635 VAL Chi-restraints excluded: chain A residue 1699 LEU Chi-restraints excluded: chain A residue 1977 GLN Chi-restraints excluded: chain A residue 2076 GLU Chi-restraints excluded: chain A residue 2084 ASP Chi-restraints excluded: chain A residue 2259 THR Chi-restraints excluded: chain A residue 2287 SER Chi-restraints excluded: chain A residue 2390 ASN Chi-restraints excluded: chain A residue 2505 LEU Chi-restraints excluded: chain A residue 2506 THR Chi-restraints excluded: chain A residue 2520 LEU Chi-restraints excluded: chain A residue 2542 THR Chi-restraints excluded: chain A residue 2612 VAL Chi-restraints excluded: chain A residue 2766 VAL Chi-restraints excluded: chain A residue 2785 GLN Chi-restraints excluded: chain A residue 2858 LEU Chi-restraints excluded: chain A residue 2930 ILE Chi-restraints excluded: chain A residue 3048 CYS Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 366 TRP Chi-restraints excluded: chain C residue 377 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 9 optimal weight: 5.9990 chunk 234 optimal weight: 8.9990 chunk 290 optimal weight: 6.9990 chunk 332 optimal weight: 9.9990 chunk 213 optimal weight: 0.9990 chunk 185 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 239 optimal weight: 3.9990 chunk 217 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 253 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2013 HIS ** A2114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2315 HIS A2343 GLN A2532 HIS ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 ASN ** 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 = 0.4001 r_free = 0.4001 target = 0.142677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.110397 restraints weight = 49830.608| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.91 r_work: 0.3371 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 27703 Z= 0.218 Angle : 0.645 11.126 37568 Z= 0.326 Chirality : 0.044 0.195 4209 Planarity : 0.005 0.078 4790 Dihedral : 6.114 121.040 3716 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.12 % Favored : 95.82 % Rotamer: Outliers : 2.57 % Allowed : 13.94 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.15), residues: 3348 helix: 1.60 (0.13), residues: 1538 sheet: -0.75 (0.23), residues: 478 loop : -0.63 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A2679 HIS 0.007 0.001 HIS A 466 PHE 0.025 0.002 PHE A 560 TYR 0.024 0.002 TYR A1293 ARG 0.008 0.001 ARG A 652 Details of bonding type rmsd hydrogen bonds : bond 0.04220 ( 1375) hydrogen bonds : angle 4.46460 ( 3972) covalent geometry : bond 0.00519 (27703) covalent geometry : angle 0.64518 (37568) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 326 time to evaluate : 3.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.6093 (mm-30) cc_final: 0.5629 (tm-30) REVERT: A 175 TYR cc_start: 0.6705 (m-80) cc_final: 0.6475 (m-80) REVERT: A 343 MET cc_start: 0.8031 (ptp) cc_final: 0.7660 (ptt) REVERT: A 479 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7118 (pm20) REVERT: A 525 GLU cc_start: 0.6667 (tm-30) cc_final: 0.5983 (mm-30) REVERT: A 563 MET cc_start: 0.9179 (ptp) cc_final: 0.8606 (mtm) REVERT: A 678 GLU cc_start: 0.7650 (pm20) cc_final: 0.6961 (mm-30) REVERT: A 787 GLU cc_start: 0.8459 (tm-30) cc_final: 0.7874 (tm-30) REVERT: A 971 TYR cc_start: 0.6860 (m-80) cc_final: 0.6559 (m-80) REVERT: A 1000 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8570 (mt) REVERT: A 1026 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7716 (ttt) REVERT: A 1111 ASP cc_start: 0.7668 (m-30) cc_final: 0.7420 (p0) REVERT: A 1373 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8275 (mm-30) REVERT: A 1424 LYS cc_start: 0.8837 (ptmm) cc_final: 0.8334 (ptpp) REVERT: A 1541 GLU cc_start: 0.7215 (pt0) cc_final: 0.6942 (pt0) REVERT: A 1677 LYS cc_start: 0.8254 (mmtp) cc_final: 0.7670 (tmtt) REVERT: A 1977 GLN cc_start: 0.7206 (OUTLIER) cc_final: 0.6385 (mp10) REVERT: A 2076 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7414 (pm20) REVERT: A 2204 GLU cc_start: 0.7561 (tp30) cc_final: 0.7196 (tp30) REVERT: A 2219 ARG cc_start: 0.7611 (tpt170) cc_final: 0.7180 (tpt170) REVERT: A 2257 GLU cc_start: 0.7679 (tp30) cc_final: 0.7450 (tp30) REVERT: A 2434 GLN cc_start: 0.5991 (pp30) cc_final: 0.5696 (pp30) REVERT: A 2553 GLU cc_start: 0.7354 (mm-30) cc_final: 0.6902 (tp30) REVERT: A 2570 ARG cc_start: 0.7693 (tpt-90) cc_final: 0.7414 (mmm-85) REVERT: A 2702 ASP cc_start: 0.6666 (m-30) cc_final: 0.6383 (m-30) REVERT: A 2706 LYS cc_start: 0.6286 (tptp) cc_final: 0.5912 (mptt) REVERT: A 2863 SER cc_start: 0.7562 (t) cc_final: 0.6936 (p) REVERT: A 2911 ASP cc_start: 0.6597 (t0) cc_final: 0.6218 (m-30) REVERT: B 192 HIS cc_start: 0.5350 (t-90) cc_final: 0.4883 (t-170) REVERT: B 202 MET cc_start: 0.3746 (mtm) cc_final: 0.3523 (mtm) REVERT: B 204 ASN cc_start: 0.6963 (p0) cc_final: 0.6760 (p0) REVERT: B 206 ASP cc_start: 0.7839 (m-30) cc_final: 0.6729 (p0) REVERT: B 285 TRP cc_start: 0.3515 (m100) cc_final: 0.3312 (m100) REVERT: B 324 TRP cc_start: 0.5952 (m-10) cc_final: 0.5390 (m-10) REVERT: C 109 ARG cc_start: 0.7504 (mtt90) cc_final: 0.7164 (tpt90) REVERT: C 187 ARG cc_start: 0.6514 (mtm-85) cc_final: 0.6218 (ttm170) REVERT: C 272 GLU cc_start: 0.7717 (tt0) cc_final: 0.7167 (tm-30) REVERT: C 333 MET cc_start: 0.7285 (ppp) cc_final: 0.6676 (ppp) REVERT: C 374 MET cc_start: 0.6905 (tmm) cc_final: 0.6520 (tmm) outliers start: 77 outliers final: 55 residues processed: 380 average time/residue: 0.4009 time to fit residues: 247.8485 Evaluate side-chains 363 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 303 time to evaluate : 3.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1026 MET Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1181 ASP Chi-restraints excluded: chain A residue 1345 THR Chi-restraints excluded: chain A residue 1391 THR Chi-restraints excluded: chain A residue 1398 VAL Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1551 GLU Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1604 ILE Chi-restraints excluded: chain A residue 1635 VAL Chi-restraints excluded: chain A residue 1637 ASN Chi-restraints excluded: chain A residue 1699 LEU Chi-restraints excluded: chain A residue 1977 GLN Chi-restraints excluded: chain A residue 2076 GLU Chi-restraints excluded: chain A residue 2084 ASP Chi-restraints excluded: chain A residue 2259 THR Chi-restraints excluded: chain A residue 2287 SER Chi-restraints excluded: chain A residue 2390 ASN Chi-restraints excluded: chain A residue 2505 LEU Chi-restraints excluded: chain A residue 2532 HIS Chi-restraints excluded: chain A residue 2542 THR Chi-restraints excluded: chain A residue 2612 VAL Chi-restraints excluded: chain A residue 2766 VAL Chi-restraints excluded: chain A residue 2785 GLN Chi-restraints excluded: chain A residue 2858 LEU Chi-restraints excluded: chain A residue 2930 ILE Chi-restraints excluded: chain A residue 2994 VAL Chi-restraints excluded: chain A residue 3048 CYS Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 366 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 249 optimal weight: 5.9990 chunk 306 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 178 optimal weight: 9.9990 chunk 136 optimal weight: 0.0770 chunk 120 optimal weight: 0.9990 chunk 298 optimal weight: 3.9990 chunk 331 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 229 optimal weight: 3.9990 overall best weight: 0.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2315 HIS ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.145612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.113729 restraints weight = 49388.579| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.79 r_work: 0.3423 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 27703 Z= 0.119 Angle : 0.571 10.362 37568 Z= 0.287 Chirality : 0.041 0.165 4209 Planarity : 0.004 0.075 4790 Dihedral : 5.833 108.990 3716 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.08 % Favored : 96.86 % Rotamer: Outliers : 1.94 % Allowed : 15.18 % Favored : 82.88 % 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: 0.81 (0.15), residues: 3348 helix: 1.88 (0.13), residues: 1527 sheet: -0.76 (0.23), residues: 476 loop : -0.48 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 246 HIS 0.027 0.001 HIS A2532 PHE 0.017 0.001 PHE A1457 TYR 0.025 0.001 TYR B 138 ARG 0.007 0.000 ARG A1414 Details of bonding type rmsd hydrogen bonds : bond 0.03623 ( 1375) hydrogen bonds : angle 4.17744 ( 3972) covalent geometry : bond 0.00269 (27703) covalent geometry : angle 0.57090 (37568) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 327 time to evaluate : 2.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.6289 (mm-30) cc_final: 0.5780 (tm-30) REVERT: A 194 LYS cc_start: 0.8558 (mmtt) cc_final: 0.8161 (mmmt) REVERT: A 201 LYS cc_start: 0.8060 (pptt) cc_final: 0.7781 (pptt) REVERT: A 479 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7019 (pm20) REVERT: A 525 GLU cc_start: 0.6706 (tm-30) cc_final: 0.6035 (mm-30) REVERT: A 606 THR cc_start: 0.7712 (OUTLIER) cc_final: 0.7033 (t) REVERT: A 678 GLU cc_start: 0.7696 (pm20) cc_final: 0.7054 (mm-30) REVERT: A 787 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7839 (tm-30) REVERT: A 971 TYR cc_start: 0.6763 (m-80) cc_final: 0.6481 (m-80) REVERT: A 1000 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8365 (mt) REVERT: A 1026 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7478 (ttt) REVERT: A 1111 ASP cc_start: 0.7557 (m-30) cc_final: 0.7332 (p0) REVERT: A 1424 LYS cc_start: 0.8697 (ptmm) cc_final: 0.8303 (ptpp) REVERT: A 1541 GLU cc_start: 0.7176 (pt0) cc_final: 0.6945 (pt0) REVERT: A 1677 LYS cc_start: 0.8166 (mmtp) cc_final: 0.7629 (tmtt) REVERT: A 1977 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.6474 (mp10) REVERT: A 2013 HIS cc_start: 0.7386 (t-90) cc_final: 0.7110 (t70) REVERT: A 2204 GLU cc_start: 0.7507 (tp30) cc_final: 0.7207 (tp30) REVERT: A 2219 ARG cc_start: 0.7565 (tpt170) cc_final: 0.7236 (tpm170) REVERT: A 2257 GLU cc_start: 0.7444 (tp30) cc_final: 0.7181 (tp30) REVERT: A 2434 GLN cc_start: 0.5974 (pp30) cc_final: 0.5561 (pp30) REVERT: A 2553 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6728 (tp30) REVERT: A 2706 LYS cc_start: 0.6295 (tptp) cc_final: 0.5921 (mptt) REVERT: A 2863 SER cc_start: 0.7543 (t) cc_final: 0.6924 (p) REVERT: A 2911 ASP cc_start: 0.6580 (t0) cc_final: 0.6262 (m-30) REVERT: B 192 HIS cc_start: 0.5236 (t-90) cc_final: 0.4823 (t-170) REVERT: B 204 ASN cc_start: 0.6824 (p0) cc_final: 0.6600 (p0) REVERT: B 206 ASP cc_start: 0.7944 (m-30) cc_final: 0.6794 (p0) REVERT: B 285 TRP cc_start: 0.3411 (m100) cc_final: 0.3079 (m100) REVERT: B 296 GLU cc_start: 0.3674 (OUTLIER) cc_final: 0.3016 (pm20) REVERT: B 324 TRP cc_start: 0.5840 (m-10) cc_final: 0.5182 (m-10) REVERT: C 109 ARG cc_start: 0.7539 (mtt90) cc_final: 0.7068 (tpt90) REVERT: C 124 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7633 (ptt) REVERT: C 187 ARG cc_start: 0.6507 (mtm-85) cc_final: 0.6204 (mmm-85) REVERT: C 272 GLU cc_start: 0.7705 (tt0) cc_final: 0.7477 (tm-30) REVERT: C 333 MET cc_start: 0.7229 (OUTLIER) cc_final: 0.6464 (tmm) REVERT: C 374 MET cc_start: 0.7044 (tmm) cc_final: 0.6548 (tmm) outliers start: 58 outliers final: 35 residues processed: 368 average time/residue: 0.3931 time to fit residues: 236.6901 Evaluate side-chains 350 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 307 time to evaluate : 3.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1026 MET Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1551 GLU Chi-restraints excluded: chain A residue 1604 ILE Chi-restraints excluded: chain A residue 1635 VAL Chi-restraints excluded: chain A residue 1699 LEU Chi-restraints excluded: chain A residue 1977 GLN Chi-restraints excluded: chain A residue 2390 ASN Chi-restraints excluded: chain A residue 2505 LEU Chi-restraints excluded: chain A residue 2506 THR Chi-restraints excluded: chain A residue 2542 THR Chi-restraints excluded: chain A residue 2612 VAL Chi-restraints excluded: chain A residue 2766 VAL Chi-restraints excluded: chain A residue 2785 GLN Chi-restraints excluded: chain A residue 2858 LEU Chi-restraints excluded: chain A residue 2930 ILE Chi-restraints excluded: chain A residue 2994 VAL Chi-restraints excluded: chain A residue 3048 CYS Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 366 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 117 optimal weight: 0.7980 chunk 191 optimal weight: 0.9990 chunk 124 optimal weight: 0.2980 chunk 224 optimal weight: 0.9980 chunk 223 optimal weight: 0.6980 chunk 227 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 170 optimal weight: 0.7980 chunk 305 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2315 HIS ** A2434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2532 HIS ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.146586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.114831 restraints weight = 49376.043| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.77 r_work: 0.3436 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 27703 Z= 0.114 Angle : 0.569 12.535 37568 Z= 0.283 Chirality : 0.041 0.165 4209 Planarity : 0.004 0.076 4790 Dihedral : 5.625 96.347 3716 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.17 % Favored : 96.77 % Rotamer: Outliers : 1.87 % Allowed : 15.58 % Favored : 82.55 % 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 (0.15), residues: 3348 helix: 1.98 (0.13), residues: 1536 sheet: -0.69 (0.23), residues: 482 loop : -0.41 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 246 HIS 0.004 0.001 HIS A 530 PHE 0.015 0.001 PHE A1457 TYR 0.025 0.001 TYR B 138 ARG 0.006 0.000 ARG A1414 Details of bonding type rmsd hydrogen bonds : bond 0.03463 ( 1375) hydrogen bonds : angle 4.09981 ( 3972) covalent geometry : bond 0.00256 (27703) covalent geometry : angle 0.56872 (37568) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 326 time to evaluate : 2.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.6238 (mm-30) cc_final: 0.5724 (tm-30) REVERT: A 175 TYR cc_start: 0.6569 (m-80) cc_final: 0.6350 (m-80) REVERT: A 194 LYS cc_start: 0.8561 (mmtt) cc_final: 0.8162 (mmmt) REVERT: A 201 LYS cc_start: 0.8131 (pptt) cc_final: 0.7862 (pptt) REVERT: A 252 LYS cc_start: 0.7921 (tppt) cc_final: 0.7439 (ptmm) REVERT: A 479 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7137 (pm20) REVERT: A 525 GLU cc_start: 0.6895 (tm-30) cc_final: 0.6163 (mm-30) REVERT: A 606 THR cc_start: 0.7734 (OUTLIER) cc_final: 0.7024 (t) REVERT: A 678 GLU cc_start: 0.7702 (pm20) cc_final: 0.6988 (mm-30) REVERT: A 787 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7825 (tm-30) REVERT: A 971 TYR cc_start: 0.6716 (m-80) cc_final: 0.6410 (m-80) REVERT: A 1000 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8341 (mt) REVERT: A 1026 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7531 (ttt) REVERT: A 1111 ASP cc_start: 0.7647 (m-30) cc_final: 0.7347 (p0) REVERT: A 1373 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7673 (mm-30) REVERT: A 1541 GLU cc_start: 0.7233 (pt0) cc_final: 0.6930 (pt0) REVERT: A 1677 LYS cc_start: 0.8088 (mmtp) cc_final: 0.7567 (tmtt) REVERT: A 1977 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.6468 (mp10) REVERT: A 2013 HIS cc_start: 0.7564 (t-90) cc_final: 0.7299 (t70) REVERT: A 2204 GLU cc_start: 0.7469 (tp30) cc_final: 0.7137 (tp30) REVERT: A 2219 ARG cc_start: 0.7535 (tpt170) cc_final: 0.7175 (tpm170) REVERT: A 2257 GLU cc_start: 0.7513 (tp30) cc_final: 0.7287 (tp30) REVERT: A 2553 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6740 (tp30) REVERT: A 2706 LYS cc_start: 0.6226 (tptp) cc_final: 0.5862 (mptt) REVERT: A 2806 GLU cc_start: 0.7256 (pt0) cc_final: 0.7024 (pt0) REVERT: A 2863 SER cc_start: 0.7579 (t) cc_final: 0.6977 (p) REVERT: A 2911 ASP cc_start: 0.6549 (t0) cc_final: 0.6252 (m-30) REVERT: B 192 HIS cc_start: 0.5192 (t-90) cc_final: 0.4795 (t-170) REVERT: B 204 ASN cc_start: 0.6920 (p0) cc_final: 0.6674 (p0) REVERT: B 206 ASP cc_start: 0.7916 (m-30) cc_final: 0.6773 (p0) REVERT: B 221 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.8002 (pm20) REVERT: B 296 GLU cc_start: 0.3299 (OUTLIER) cc_final: 0.2716 (pm20) REVERT: B 323 MET cc_start: 0.3947 (OUTLIER) cc_final: 0.3535 (mpp) REVERT: B 324 TRP cc_start: 0.5803 (m-10) cc_final: 0.5177 (m-10) REVERT: B 330 MET cc_start: 0.5553 (ppp) cc_final: 0.5042 (ppp) REVERT: B 363 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7146 (tp) REVERT: C 109 ARG cc_start: 0.7544 (mtt90) cc_final: 0.6993 (tpt90) REVERT: C 124 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.7562 (ptp) REVERT: C 272 GLU cc_start: 0.7746 (tt0) cc_final: 0.7451 (tm-30) REVERT: C 333 MET cc_start: 0.7193 (OUTLIER) cc_final: 0.6341 (tmm) REVERT: C 374 MET cc_start: 0.6903 (tmm) cc_final: 0.6403 (tmm) outliers start: 56 outliers final: 35 residues processed: 360 average time/residue: 0.3904 time to fit residues: 229.8988 Evaluate side-chains 351 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 305 time to evaluate : 3.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1026 MET Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1506 ILE Chi-restraints excluded: chain A residue 1551 GLU Chi-restraints excluded: chain A residue 1604 ILE Chi-restraints excluded: chain A residue 1635 VAL Chi-restraints excluded: chain A residue 1680 GLN Chi-restraints excluded: chain A residue 1699 LEU Chi-restraints excluded: chain A residue 1977 GLN Chi-restraints excluded: chain A residue 2028 THR Chi-restraints excluded: chain A residue 2220 LEU Chi-restraints excluded: chain A residue 2390 ASN Chi-restraints excluded: chain A residue 2505 LEU Chi-restraints excluded: chain A residue 2506 THR Chi-restraints excluded: chain A residue 2612 VAL Chi-restraints excluded: chain A residue 2766 VAL Chi-restraints excluded: chain A residue 2785 GLN Chi-restraints excluded: chain A residue 2858 LEU Chi-restraints excluded: chain A residue 2994 VAL Chi-restraints excluded: chain A residue 3048 CYS Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 377 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 287 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 256 optimal weight: 0.3980 chunk 89 optimal weight: 0.9980 chunk 72 optimal weight: 0.0470 chunk 12 optimal weight: 5.9990 chunk 304 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 282 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2315 HIS ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.147742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.116468 restraints weight = 49286.379| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.76 r_work: 0.3465 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 27703 Z= 0.106 Angle : 0.558 11.941 37568 Z= 0.277 Chirality : 0.041 0.221 4209 Planarity : 0.004 0.075 4790 Dihedral : 5.437 85.367 3716 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.14 % Favored : 96.80 % Rotamer: Outliers : 1.81 % Allowed : 15.65 % Favored : 82.55 % 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: 1.08 (0.15), residues: 3348 helix: 2.14 (0.13), residues: 1525 sheet: -0.62 (0.23), residues: 482 loop : -0.39 (0.17), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 246 HIS 0.005 0.001 HIS A2358 PHE 0.015 0.001 PHE A1457 TYR 0.024 0.001 TYR B 138 ARG 0.006 0.000 ARG C 242 Details of bonding type rmsd hydrogen bonds : bond 0.03328 ( 1375) hydrogen bonds : angle 3.99492 ( 3972) covalent geometry : bond 0.00236 (27703) covalent geometry : angle 0.55814 (37568) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 327 time to evaluate : 3.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.6430 (mm-30) cc_final: 0.5906 (tm-30) REVERT: A 175 TYR cc_start: 0.6585 (m-80) cc_final: 0.6352 (m-80) REVERT: A 194 LYS cc_start: 0.8615 (mmtt) cc_final: 0.8228 (mmmt) REVERT: A 201 LYS cc_start: 0.7846 (pptt) cc_final: 0.7602 (pptt) REVERT: A 252 LYS cc_start: 0.7866 (tppt) cc_final: 0.7412 (ptmm) REVERT: A 479 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8135 (mp0) REVERT: A 525 GLU cc_start: 0.6755 (tm-30) cc_final: 0.6052 (mm-30) REVERT: A 606 THR cc_start: 0.7838 (OUTLIER) cc_final: 0.7164 (t) REVERT: A 678 GLU cc_start: 0.7724 (pm20) cc_final: 0.7058 (mm-30) REVERT: A 787 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7784 (tm-30) REVERT: A 1000 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8301 (mt) REVERT: A 1006 MET cc_start: 0.7174 (mtm) cc_final: 0.6829 (mtm) REVERT: A 1026 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7475 (ttt) REVERT: A 1373 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7653 (mm-30) REVERT: A 1677 LYS cc_start: 0.8063 (mmtp) cc_final: 0.7540 (tmtt) REVERT: A 1977 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.6481 (mp10) REVERT: A 2013 HIS cc_start: 0.7421 (t-90) cc_final: 0.7142 (t70) REVERT: A 2130 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7492 (tm-30) REVERT: A 2204 GLU cc_start: 0.7397 (tp30) cc_final: 0.7015 (tp30) REVERT: A 2219 ARG cc_start: 0.7600 (tpt170) cc_final: 0.7255 (tpm170) REVERT: A 2257 GLU cc_start: 0.7530 (tp30) cc_final: 0.7297 (tp30) REVERT: A 2553 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6827 (tp30) REVERT: A 2706 LYS cc_start: 0.6195 (tptp) cc_final: 0.5792 (mptt) REVERT: A 2863 SER cc_start: 0.7623 (t) cc_final: 0.7046 (p) REVERT: A 2911 ASP cc_start: 0.6407 (t0) cc_final: 0.6159 (m-30) REVERT: B 142 ASP cc_start: 0.7442 (t0) cc_final: 0.7006 (t70) REVERT: B 192 HIS cc_start: 0.5117 (t-90) cc_final: 0.4685 (t-170) REVERT: B 204 ASN cc_start: 0.6905 (p0) cc_final: 0.6661 (p0) REVERT: B 206 ASP cc_start: 0.7994 (m-30) cc_final: 0.6858 (p0) REVERT: B 221 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.8007 (pm20) REVERT: B 296 GLU cc_start: 0.3354 (OUTLIER) cc_final: 0.2741 (pm20) REVERT: B 323 MET cc_start: 0.4008 (OUTLIER) cc_final: 0.3521 (mpp) REVERT: B 324 TRP cc_start: 0.5939 (m-10) cc_final: 0.5306 (m-10) REVERT: B 330 MET cc_start: 0.5353 (ppp) cc_final: 0.4935 (ppp) REVERT: B 363 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7100 (tp) REVERT: C 109 ARG cc_start: 0.7540 (mtt90) cc_final: 0.6997 (tpt90) REVERT: C 124 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7636 (ptt) REVERT: C 202 MET cc_start: 0.7862 (mmp) cc_final: 0.7622 (mmp) REVERT: C 204 ASN cc_start: 0.6945 (t0) cc_final: 0.6606 (p0) REVERT: C 272 GLU cc_start: 0.7749 (tt0) cc_final: 0.7475 (tm-30) REVERT: C 333 MET cc_start: 0.7236 (OUTLIER) cc_final: 0.6366 (tmm) REVERT: C 374 MET cc_start: 0.6824 (tmm) cc_final: 0.6340 (tmm) outliers start: 54 outliers final: 37 residues processed: 362 average time/residue: 0.3960 time to fit residues: 233.8286 Evaluate side-chains 361 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 313 time to evaluate : 2.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1026 MET Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1551 GLU Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1604 ILE Chi-restraints excluded: chain A residue 1635 VAL Chi-restraints excluded: chain A residue 1637 ASN Chi-restraints excluded: chain A residue 1680 GLN Chi-restraints excluded: chain A residue 1699 LEU Chi-restraints excluded: chain A residue 1977 GLN Chi-restraints excluded: chain A residue 2076 GLU Chi-restraints excluded: chain A residue 2220 LEU Chi-restraints excluded: chain A residue 2390 ASN Chi-restraints excluded: chain A residue 2505 LEU Chi-restraints excluded: chain A residue 2506 THR Chi-restraints excluded: chain A residue 2542 THR Chi-restraints excluded: chain A residue 2612 VAL Chi-restraints excluded: chain A residue 2766 VAL Chi-restraints excluded: chain A residue 2785 GLN Chi-restraints excluded: chain A residue 2858 LEU Chi-restraints excluded: chain A residue 2994 VAL Chi-restraints excluded: chain A residue 3048 CYS Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 354 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 313 optimal weight: 9.9990 chunk 197 optimal weight: 7.9990 chunk 264 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 161 optimal weight: 8.9990 chunk 302 optimal weight: 4.9990 chunk 281 optimal weight: 0.6980 chunk 203 optimal weight: 0.8980 chunk 298 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2315 HIS ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.145991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.114173 restraints weight = 49436.613| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.88 r_work: 0.3421 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 27703 Z= 0.136 Angle : 0.582 11.559 37568 Z= 0.288 Chirality : 0.041 0.195 4209 Planarity : 0.004 0.075 4790 Dihedral : 5.468 84.358 3716 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.49 % Favored : 96.45 % Rotamer: Outliers : 1.74 % Allowed : 16.15 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.15), residues: 3348 helix: 2.06 (0.13), residues: 1534 sheet: -0.56 (0.23), residues: 476 loop : -0.42 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 136 HIS 0.004 0.001 HIS A 530 PHE 0.043 0.001 PHE A2077 TYR 0.026 0.001 TYR B 138 ARG 0.006 0.000 ARG C 242 Details of bonding type rmsd hydrogen bonds : bond 0.03498 ( 1375) hydrogen bonds : angle 4.04602 ( 3972) covalent geometry : bond 0.00320 (27703) covalent geometry : angle 0.58152 (37568) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 317 time to evaluate : 2.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.6347 (mm-30) cc_final: 0.5836 (tm-30) REVERT: A 175 TYR cc_start: 0.6609 (m-80) cc_final: 0.6384 (m-80) REVERT: A 194 LYS cc_start: 0.8623 (mmtt) cc_final: 0.8224 (mmmt) REVERT: A 201 LYS cc_start: 0.7877 (pptt) cc_final: 0.7588 (pptt) REVERT: A 252 LYS cc_start: 0.7989 (tppt) cc_final: 0.7508 (ptmm) REVERT: A 479 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7028 (pm20) REVERT: A 525 GLU cc_start: 0.7083 (tm-30) cc_final: 0.6300 (mm-30) REVERT: A 606 THR cc_start: 0.7733 (OUTLIER) cc_final: 0.7123 (t) REVERT: A 678 GLU cc_start: 0.7646 (pm20) cc_final: 0.6926 (mm-30) REVERT: A 787 GLU cc_start: 0.8318 (tm-30) cc_final: 0.7877 (tm-30) REVERT: A 1000 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8393 (mt) REVERT: A 1006 MET cc_start: 0.7186 (mtm) cc_final: 0.6840 (mtm) REVERT: A 1026 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7524 (ttt) REVERT: A 1373 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7704 (mm-30) REVERT: A 1677 LYS cc_start: 0.8136 (mmtp) cc_final: 0.7592 (tmtt) REVERT: A 1977 GLN cc_start: 0.7237 (OUTLIER) cc_final: 0.6429 (mp10) REVERT: A 2130 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7497 (tm-30) REVERT: A 2204 GLU cc_start: 0.7459 (tp30) cc_final: 0.7102 (tp30) REVERT: A 2219 ARG cc_start: 0.7616 (tpt170) cc_final: 0.7052 (tpm170) REVERT: A 2257 GLU cc_start: 0.7581 (tp30) cc_final: 0.7365 (tp30) REVERT: A 2423 LYS cc_start: 0.7642 (mmtp) cc_final: 0.7387 (mmtt) REVERT: A 2553 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6897 (tp30) REVERT: A 2706 LYS cc_start: 0.6237 (tptp) cc_final: 0.5849 (mptt) REVERT: A 2806 GLU cc_start: 0.7395 (pt0) cc_final: 0.7178 (pt0) REVERT: A 2863 SER cc_start: 0.7662 (t) cc_final: 0.7074 (p) REVERT: A 2911 ASP cc_start: 0.6418 (t0) cc_final: 0.6158 (m-30) REVERT: B 142 ASP cc_start: 0.7485 (t0) cc_final: 0.7119 (t70) REVERT: B 192 HIS cc_start: 0.5167 (t-90) cc_final: 0.4774 (t-170) REVERT: B 204 ASN cc_start: 0.6912 (p0) cc_final: 0.6673 (p0) REVERT: B 206 ASP cc_start: 0.7919 (m-30) cc_final: 0.6775 (p0) REVERT: B 221 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8017 (pm20) REVERT: B 296 GLU cc_start: 0.3265 (OUTLIER) cc_final: 0.2767 (pm20) REVERT: B 323 MET cc_start: 0.4097 (OUTLIER) cc_final: 0.3568 (mpp) REVERT: B 324 TRP cc_start: 0.5953 (m-10) cc_final: 0.5182 (m-10) REVERT: B 330 MET cc_start: 0.5425 (ppp) cc_final: 0.5002 (ppp) REVERT: B 363 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7064 (tp) REVERT: C 272 GLU cc_start: 0.7781 (tt0) cc_final: 0.7481 (tm-30) REVERT: C 333 MET cc_start: 0.7229 (OUTLIER) cc_final: 0.6648 (ppp) REVERT: C 374 MET cc_start: 0.6804 (tmm) cc_final: 0.6415 (tmm) outliers start: 52 outliers final: 36 residues processed: 352 average time/residue: 0.3890 time to fit residues: 224.1454 Evaluate side-chains 352 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 306 time to evaluate : 2.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1026 MET Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1551 GLU Chi-restraints excluded: chain A residue 1635 VAL Chi-restraints excluded: chain A residue 1637 ASN Chi-restraints excluded: chain A residue 1680 GLN Chi-restraints excluded: chain A residue 1699 LEU Chi-restraints excluded: chain A residue 1977 GLN Chi-restraints excluded: chain A residue 2028 THR Chi-restraints excluded: chain A residue 2076 GLU Chi-restraints excluded: chain A residue 2220 LEU Chi-restraints excluded: chain A residue 2390 ASN Chi-restraints excluded: chain A residue 2505 LEU Chi-restraints excluded: chain A residue 2542 THR Chi-restraints excluded: chain A residue 2612 VAL Chi-restraints excluded: chain A residue 2766 VAL Chi-restraints excluded: chain A residue 2785 GLN Chi-restraints excluded: chain A residue 2858 LEU Chi-restraints excluded: chain A residue 2994 VAL Chi-restraints excluded: chain A residue 3048 CYS Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 377 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 326 optimal weight: 0.2980 chunk 55 optimal weight: 0.0010 chunk 178 optimal weight: 5.9990 chunk 263 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 293 optimal weight: 5.9990 chunk 309 optimal weight: 10.0000 chunk 236 optimal weight: 0.1980 chunk 69 optimal weight: 0.1980 chunk 196 optimal weight: 0.0060 chunk 27 optimal weight: 5.9990 overall best weight: 0.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS A 426 GLN ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2270 GLN ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.149322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.118298 restraints weight = 49219.268| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.79 r_work: 0.3492 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 27703 Z= 0.102 Angle : 0.563 11.254 37568 Z= 0.279 Chirality : 0.040 0.182 4209 Planarity : 0.004 0.074 4790 Dihedral : 5.260 78.606 3716 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.87 % Favored : 97.07 % Rotamer: Outliers : 1.40 % Allowed : 16.72 % Favored : 81.88 % 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: 1.16 (0.15), residues: 3348 helix: 2.22 (0.13), residues: 1530 sheet: -0.64 (0.23), residues: 487 loop : -0.36 (0.17), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 246 HIS 0.007 0.001 HIS C 207 PHE 0.038 0.001 PHE A2077 TYR 0.023 0.001 TYR B 138 ARG 0.006 0.000 ARG C 242 Details of bonding type rmsd hydrogen bonds : bond 0.03161 ( 1375) hydrogen bonds : angle 3.91971 ( 3972) covalent geometry : bond 0.00222 (27703) covalent geometry : angle 0.56343 (37568) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14926.63 seconds wall clock time: 261 minutes 6.41 seconds (15666.41 seconds total)