Starting phenix.real_space_refine on Fri Aug 9 23:57:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fdt_29012/08_2024/8fdt_29012.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fdt_29012/08_2024/8fdt_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fdt_29012/08_2024/8fdt_29012.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fdt_29012/08_2024/8fdt_29012.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fdt_29012/08_2024/8fdt_29012.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fdt_29012/08_2024/8fdt_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 Residue "A PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 253": "OE1" <-> "OE2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A GLU 359": "OE1" <-> "OE2" Residue "A PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 422": "OD1" <-> "OD2" Residue "A PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 504": "OE1" <-> "OE2" Residue "A TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1089": "OE1" <-> "OE2" Residue "A TYR 1127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1312": "OE1" <-> "OE2" Residue "A GLU 1343": "OE1" <-> "OE2" Residue "A ASP 1380": "OD1" <-> "OD2" Residue "A GLU 1447": "OE1" <-> "OE2" Residue "A GLU 1448": "OE1" <-> "OE2" Residue "A PHE 1457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1459": "OE1" <-> "OE2" Residue "A ASP 1462": "OD1" <-> "OD2" Residue "A GLU 1551": "OE1" <-> "OE2" Residue "A PHE 1732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1738": "OE1" <-> "OE2" Residue "A GLU 1755": "OE1" <-> "OE2" Residue "A PHE 1998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1999": "OD1" <-> "OD2" Residue "A PHE 2156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2161": "OD1" <-> "OD2" Residue "A ARG 2183": "NH1" <-> "NH2" Residue "A GLU 2249": "OE1" <-> "OE2" Residue "A GLU 2254": "OE1" <-> "OE2" Residue "A GLU 2271": "OE1" <-> "OE2" Residue "A PHE 2291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2320": "OE1" <-> "OE2" Residue "A ASP 2340": "OD1" <-> "OD2" Residue "A TYR 2527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2559": "OD1" <-> "OD2" Residue "A GLU 2607": "OE1" <-> "OE2" Residue "A GLU 2670": "OE1" <-> "OE2" Residue "A ASP 2689": "OD1" <-> "OD2" Residue "A PHE 2751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 152": "OD1" <-> "OD2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 268": "OE1" <-> "OE2" Residue "B GLU 296": "OE1" <-> "OE2" Residue "B GLU 301": "OE1" <-> "OE2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 388": "OD1" <-> "OD2" Residue "B TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 160": "OD1" <-> "OD2" Residue "C ASP 193": "OD1" <-> "OD2" Residue "C ASP 325": "OD1" <-> "OD2" Residue "C ASP 359": "OD1" <-> "OD2" Residue "C TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 388": "OD1" <-> "OD2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 22.54, per 1000 atoms: 0.83 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.97 Conformation dependent library (CDL) restraints added in 5.2 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: 4.64 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: 17.87 Time building geometry restraints manager: 12.85 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: 96.51 - 104.12: 427 104.12 - 111.74: 13226 111.74 - 119.35: 10348 119.35 - 126.96: 13163 126.96 - 134.57: 404 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: 16.130 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 96.050 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.110 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.620 ------------------------------------------------------------------------------- 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= 0.354 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 *********************** 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 fitting. rotamer outliers: 8 poor density : 625 time to evaluate : 3.000 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: 0.4359 time to fit residues: 419.1858 Evaluate side-chains 352 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 350 time to evaluate : 2.937 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 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= 0.188 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 *********************** 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 fitting. rotamer outliers: 40 poor density : 402 time to evaluate : 2.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.6694 (tt) cc_final: 0.6439 (tp) REVERT: A 165 GLU cc_start: 0.6180 (mm-30) cc_final: 0.5787 (tm-30) REVERT: A 251 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6630 (pm20) REVERT: A 361 VAL cc_start: 0.7307 (p) cc_final: 0.6577 (m) REVERT: A 368 ARG cc_start: 0.8098 (mtm-85) cc_final: 0.7838 (mtm-85) REVERT: A 557 MET cc_start: 0.6883 (tpp) cc_final: 0.6585 (ttt) REVERT: A 586 MET cc_start: 0.8521 (mtp) cc_final: 0.8119 (mtp) REVERT: A 678 GLU cc_start: 0.7128 (pm20) cc_final: 0.6572 (mm-30) REVERT: A 1026 MET cc_start: 0.7762 (tmm) cc_final: 0.7177 (ttt) REVERT: A 1373 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7543 (mm-30) REVERT: A 1507 LYS cc_start: 0.7180 (mmtt) cc_final: 0.6743 (mtmm) REVERT: A 1541 GLU cc_start: 0.6735 (pt0) cc_final: 0.6534 (pt0) REVERT: A 1658 MET cc_start: 0.8264 (mtp) cc_final: 0.8007 (mtt) REVERT: A 1677 LYS cc_start: 0.7964 (mmtp) cc_final: 0.7669 (tmtt) REVERT: A 1762 GLU cc_start: 0.6034 (pp20) cc_final: 0.5718 (tt0) REVERT: A 1991 PHE cc_start: 0.8373 (t80) cc_final: 0.8085 (t80) REVERT: A 2204 GLU cc_start: 0.7580 (tp30) cc_final: 0.7289 (tp30) REVERT: A 2219 ARG cc_start: 0.7634 (tpt170) cc_final: 0.7395 (ttm170) REVERT: A 2252 LYS cc_start: 0.7580 (mtmm) cc_final: 0.7349 (mtmm) REVERT: A 2279 TYR cc_start: 0.5456 (m-10) cc_final: 0.4925 (m-10) REVERT: A 2702 ASP cc_start: 0.6708 (m-30) cc_final: 0.6501 (m-30) REVERT: A 2706 LYS cc_start: 0.6326 (tptp) cc_final: 0.5904 (mptt) REVERT: A 2725 MET cc_start: 0.6739 (mmt) cc_final: 0.6488 (mmt) REVERT: A 2821 MET cc_start: 0.8148 (mtp) cc_final: 0.7907 (mtm) REVERT: A 2863 SER cc_start: 0.7501 (t) cc_final: 0.6892 (p) REVERT: A 2911 ASP cc_start: 0.6375 (t0) cc_final: 0.5954 (m-30) REVERT: A 3083 VAL cc_start: 0.7420 (m) cc_final: 0.7184 (m) REVERT: B 114 ARG cc_start: 0.6022 (mtt90) cc_final: 0.5014 (ttt180) REVERT: B 183 PHE cc_start: 0.8333 (m-10) cc_final: 0.7888 (m-10) REVERT: B 206 ASP cc_start: 0.7798 (m-30) cc_final: 0.6961 (p0) REVERT: B 219 MET cc_start: 0.5571 (tmm) cc_final: 0.5001 (tmm) REVERT: B 240 MET cc_start: 0.2651 (mmm) cc_final: 0.2446 (tpt) REVERT: B 390 HIS cc_start: 0.3693 (t-90) cc_final: 0.3120 (t-170) REVERT: B 409 GLU cc_start: 0.7596 (pt0) cc_final: 0.7320 (pm20) REVERT: C 109 ARG cc_start: 0.7585 (tpt90) cc_final: 0.7348 (mtp-110) REVERT: C 189 MET cc_start: 0.6632 (mtt) cc_final: 0.5735 (mmt) REVERT: C 204 ASN cc_start: 0.6716 (t0) cc_final: 0.6405 (p0) REVERT: C 272 GLU cc_start: 0.7611 (tt0) cc_final: 0.7139 (tm-30) REVERT: C 353 PHE cc_start: 0.6968 (m-80) cc_final: 0.6721 (m-80) REVERT: C 374 MET cc_start: 0.7474 (tmm) cc_final: 0.6864 (tmm) outliers start: 40 outliers final: 24 residues processed: 423 average time/residue: 0.3988 time to fit residues: 265.9506 Evaluate side-chains 359 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 334 time to evaluate : 3.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 GLU 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 169 optimal weight: 7.9990 chunk 94 optimal weight: 0.6980 chunk 253 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 304 optimal weight: 10.0000 chunk 329 optimal weight: 0.9980 chunk 271 optimal weight: 1.9990 chunk 302 optimal weight: 0.0050 chunk 103 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27703 Z= 0.176 Angle : 0.571 11.861 37568 Z= 0.285 Chirality : 0.041 0.151 4209 Planarity : 0.004 0.079 4790 Dihedral : 6.086 128.707 3717 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.26 % Favored : 96.68 % Rotamer: Outliers : 1.67 % Allowed : 11.17 % Favored : 87.16 % 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: 0.86 (0.15), residues: 3348 helix: 1.95 (0.13), residues: 1539 sheet: -0.69 (0.22), residues: 500 loop : -0.53 (0.17), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 262 HIS 0.010 0.001 HIS A2532 PHE 0.031 0.001 PHE B 183 TYR 0.016 0.001 TYR A1293 ARG 0.007 0.000 ARG A2260 *********************** 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 413 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 363 time to evaluate : 3.085 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: A 160 LEU cc_start: 0.6718 (tt) cc_final: 0.6487 (tp) REVERT: A 165 GLU cc_start: 0.6312 (mm-30) cc_final: 0.5862 (tm-30) REVERT: A 175 TYR cc_start: 0.6828 (m-80) cc_final: 0.6596 (m-80) REVERT: A 248 THR cc_start: 0.8336 (p) cc_final: 0.7794 (p) REVERT: A 361 VAL cc_start: 0.7301 (p) cc_final: 0.6598 (m) REVERT: A 586 MET cc_start: 0.8539 (mtp) cc_final: 0.8166 (mtp) REVERT: A 767 MET cc_start: 0.7884 (mtm) cc_final: 0.7544 (mtt) REVERT: A 1026 MET cc_start: 0.7853 (tmm) cc_final: 0.7368 (ttt) REVERT: A 1373 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7594 (mm-30) REVERT: A 1424 LYS cc_start: 0.8371 (ptmm) cc_final: 0.7968 (ptpp) REVERT: A 1507 LYS cc_start: 0.7205 (mmtt) cc_final: 0.6745 (mtmm) REVERT: A 1677 LYS cc_start: 0.8025 (mmtp) cc_final: 0.7563 (tmtt) REVERT: A 1686 GLU cc_start: 0.7204 (mp0) cc_final: 0.6833 (mp0) REVERT: A 1762 GLU cc_start: 0.5888 (pp20) cc_final: 0.5653 (tt0) REVERT: A 2204 GLU cc_start: 0.7420 (tp30) cc_final: 0.7117 (tp30) REVERT: A 2219 ARG cc_start: 0.7668 (tpt170) cc_final: 0.7085 (ttm170) REVERT: A 2252 LYS cc_start: 0.7568 (mtmm) cc_final: 0.7308 (mtmm) REVERT: A 2279 TYR cc_start: 0.5596 (m-10) cc_final: 0.5171 (m-10) REVERT: A 2702 ASP cc_start: 0.6694 (m-30) cc_final: 0.6439 (m-30) REVERT: A 2706 LYS cc_start: 0.6276 (tptp) cc_final: 0.5908 (mptt) REVERT: A 2725 MET cc_start: 0.6741 (mmt) cc_final: 0.6536 (mmt) REVERT: A 2821 MET cc_start: 0.8193 (mtp) cc_final: 0.7929 (mtm) REVERT: A 2863 SER cc_start: 0.7493 (t) cc_final: 0.6886 (p) REVERT: A 2911 ASP cc_start: 0.6386 (t0) cc_final: 0.5938 (m-30) REVERT: B 114 ARG cc_start: 0.5713 (mtt90) cc_final: 0.4416 (ttt180) REVERT: B 156 ASP cc_start: 0.4947 (OUTLIER) cc_final: 0.4218 (t0) REVERT: B 192 HIS cc_start: 0.5320 (t-90) cc_final: 0.4884 (t-90) REVERT: B 206 ASP cc_start: 0.7839 (m-30) cc_final: 0.6976 (p0) REVERT: B 390 HIS cc_start: 0.4133 (t-90) cc_final: 0.3703 (t-170) REVERT: C 189 MET cc_start: 0.6605 (mtt) cc_final: 0.5738 (mmt) REVERT: C 202 MET cc_start: 0.7796 (mmp) cc_final: 0.7560 (mmp) REVERT: C 204 ASN cc_start: 0.6727 (t0) cc_final: 0.6431 (p0) REVERT: C 272 GLU cc_start: 0.7582 (tt0) cc_final: 0.7062 (tm-30) REVERT: C 333 MET cc_start: 0.7235 (ppp) cc_final: 0.6747 (ppp) REVERT: C 374 MET cc_start: 0.7199 (tmm) cc_final: 0.6563 (tmm) outliers start: 50 outliers final: 32 residues processed: 389 average time/residue: 0.3916 time to fit residues: 245.0957 Evaluate side-chains 363 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 330 time to evaluate : 3.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL 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 1148 MET 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 2437 ILE 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 156 ASP 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 301 optimal weight: 8.9990 chunk 229 optimal weight: 0.0670 chunk 158 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 204 optimal weight: 0.0270 chunk 305 optimal weight: 7.9990 chunk 323 optimal weight: 10.0000 chunk 159 optimal weight: 8.9990 chunk 289 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 overall best weight: 1.6180 ------------------------------------------------------------------------------- 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** A2315 HIS A2634 ASN ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 27703 Z= 0.244 Angle : 0.583 10.554 37568 Z= 0.293 Chirality : 0.042 0.182 4209 Planarity : 0.004 0.078 4790 Dihedral : 5.998 123.138 3717 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.46 % Favored : 96.48 % Rotamer: Outliers : 2.31 % Allowed : 12.24 % Favored : 85.46 % 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: 1.94 (0.13), residues: 1539 sheet: -0.69 (0.23), residues: 488 loop : -0.49 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 246 HIS 0.014 0.001 HIS A2532 PHE 0.022 0.002 PHE C 183 TYR 0.024 0.002 TYR A1293 ARG 0.007 0.000 ARG C 98 *********************** 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 411 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 342 time to evaluate : 2.940 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: A 165 GLU cc_start: 0.6220 (mm-30) cc_final: 0.5862 (tm-30) REVERT: A 201 LYS cc_start: 0.7996 (pptt) cc_final: 0.7729 (pptt) REVERT: A 361 VAL cc_start: 0.7303 (p) cc_final: 0.6572 (m) REVERT: A 479 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.6699 (pm20) REVERT: A 525 GLU cc_start: 0.6159 (tm-30) cc_final: 0.5755 (mm-30) REVERT: A 586 MET cc_start: 0.8537 (mtp) cc_final: 0.8152 (mtp) REVERT: A 606 THR cc_start: 0.7796 (OUTLIER) cc_final: 0.7188 (t) REVERT: A 767 MET cc_start: 0.8042 (mtm) cc_final: 0.7817 (mtt) REVERT: A 1026 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7458 (ttt) REVERT: A 1373 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7727 (mm-30) REVERT: A 1424 LYS cc_start: 0.8410 (ptmm) cc_final: 0.8079 (ptpp) REVERT: A 1541 GLU cc_start: 0.6860 (pt0) cc_final: 0.6629 (pt0) REVERT: A 1677 LYS cc_start: 0.8065 (mmtp) cc_final: 0.7617 (tmtt) REVERT: A 1762 GLU cc_start: 0.5903 (pp20) cc_final: 0.5642 (tt0) REVERT: A 1977 GLN cc_start: 0.7189 (OUTLIER) cc_final: 0.6354 (mp10) REVERT: A 2076 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.7039 (pm20) REVERT: A 2204 GLU cc_start: 0.7215 (tp30) cc_final: 0.6847 (tp30) REVERT: A 2219 ARG cc_start: 0.7473 (tpt170) cc_final: 0.7056 (tpt170) REVERT: A 2252 LYS cc_start: 0.7589 (mtmm) cc_final: 0.7092 (pttp) REVERT: A 2257 GLU cc_start: 0.7551 (tp30) cc_final: 0.7201 (tp30) REVERT: A 2279 TYR cc_start: 0.5788 (m-10) cc_final: 0.5349 (m-10) REVERT: A 2553 GLU cc_start: 0.6896 (mm-30) cc_final: 0.6137 (mp0) REVERT: A 2607 GLU cc_start: 0.7437 (tt0) cc_final: 0.7056 (mt-10) REVERT: A 2702 ASP cc_start: 0.6711 (m-30) cc_final: 0.6448 (m-30) REVERT: A 2706 LYS cc_start: 0.6309 (tptp) cc_final: 0.5966 (mptt) REVERT: A 2863 SER cc_start: 0.7550 (t) cc_final: 0.6910 (p) REVERT: A 2911 ASP cc_start: 0.6420 (t0) cc_final: 0.5950 (m-30) REVERT: B 114 ARG cc_start: 0.6025 (mtt90) cc_final: 0.4595 (ttt180) REVERT: B 156 ASP cc_start: 0.5188 (OUTLIER) cc_final: 0.4310 (t70) REVERT: B 192 HIS cc_start: 0.5081 (t-90) cc_final: 0.4485 (t-170) REVERT: B 204 ASN cc_start: 0.6921 (p0) cc_final: 0.6439 (p0) REVERT: B 324 TRP cc_start: 0.6313 (m-10) cc_final: 0.5586 (m-10) REVERT: B 330 MET cc_start: 0.5269 (ppp) cc_final: 0.4750 (ppp) REVERT: C 189 MET cc_start: 0.6746 (mtt) cc_final: 0.5694 (mmt) REVERT: C 204 ASN cc_start: 0.6713 (t0) cc_final: 0.6401 (p0) REVERT: C 272 GLU cc_start: 0.7624 (tt0) cc_final: 0.7124 (tm-30) REVERT: C 324 TRP cc_start: 0.7295 (OUTLIER) cc_final: 0.6381 (m100) REVERT: C 333 MET cc_start: 0.7166 (OUTLIER) cc_final: 0.6198 (tmm) REVERT: C 353 PHE cc_start: 0.7300 (m-80) cc_final: 0.7010 (m-80) REVERT: C 374 MET cc_start: 0.7033 (tmm) cc_final: 0.6619 (tmm) outliers start: 69 outliers final: 40 residues processed: 388 average time/residue: 0.3809 time to fit residues: 237.3562 Evaluate side-chains 362 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 314 time to evaluate : 2.944 ------------------------------------------------------------------------------- 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 563 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 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 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 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 156 ASP Chi-restraints excluded: chain B residue 226 TYR 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 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 Chi-restraints excluded: chain C residue 377 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 269 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 241 optimal weight: 0.3980 chunk 133 optimal weight: 4.9990 chunk 276 optimal weight: 1.9990 chunk 223 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 165 optimal weight: 4.9990 chunk 290 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.8584 ------------------------------------------------------------------------------- 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 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 27703 Z= 0.260 Angle : 0.587 10.196 37568 Z= 0.297 Chirality : 0.042 0.217 4209 Planarity : 0.004 0.078 4790 Dihedral : 5.979 121.372 3717 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.46 % Favored : 96.48 % Rotamer: Outliers : 2.64 % Allowed : 13.11 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.15), residues: 3348 helix: 1.84 (0.13), residues: 1534 sheet: -0.69 (0.23), residues: 474 loop : -0.54 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 324 HIS 0.010 0.001 HIS A 104 PHE 0.024 0.002 PHE B 183 TYR 0.023 0.002 TYR A1293 ARG 0.007 0.001 ARG A2260 *********************** 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 423 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 344 time to evaluate : 2.943 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: 0.6280 (mm-30) cc_final: 0.5782 (tm-30) REVERT: A 175 TYR cc_start: 0.6689 (m-80) cc_final: 0.6469 (m-80) REVERT: A 201 LYS cc_start: 0.8098 (pttt) cc_final: 0.7788 (pptt) REVERT: A 252 LYS cc_start: 0.7849 (tppt) cc_final: 0.7384 (ptmm) REVERT: A 343 MET cc_start: 0.7736 (ptp) cc_final: 0.7417 (ptt) REVERT: A 479 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.6723 (pm20) REVERT: A 525 GLU cc_start: 0.6364 (tm-30) cc_final: 0.5916 (mm-30) REVERT: A 586 MET cc_start: 0.8557 (mtp) cc_final: 0.8208 (mtp) REVERT: A 1026 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7515 (ttt) REVERT: A 1373 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7768 (mm-30) REVERT: A 1424 LYS cc_start: 0.8387 (ptmm) cc_final: 0.8086 (ptpp) REVERT: A 1541 GLU cc_start: 0.6941 (pt0) cc_final: 0.6693 (pt0) REVERT: A 1575 MET cc_start: 0.7478 (tpp) cc_final: 0.7269 (mmt) REVERT: A 1677 LYS cc_start: 0.8118 (mmtp) cc_final: 0.7605 (tmtt) REVERT: A 1762 GLU cc_start: 0.5954 (pp20) cc_final: 0.5703 (tt0) REVERT: A 1977 GLN cc_start: 0.7209 (OUTLIER) cc_final: 0.6382 (mp10) REVERT: A 2031 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8093 (mt) REVERT: A 2076 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7105 (pm20) REVERT: A 2204 GLU cc_start: 0.7244 (tp30) cc_final: 0.6878 (tp30) REVERT: A 2219 ARG cc_start: 0.7516 (tpt170) cc_final: 0.7098 (tpt170) REVERT: A 2252 LYS cc_start: 0.7666 (mtmm) cc_final: 0.7177 (pttp) REVERT: A 2260 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7666 (ptp90) REVERT: A 2279 TYR cc_start: 0.5912 (m-10) cc_final: 0.5564 (m-10) REVERT: A 2553 GLU cc_start: 0.6941 (mm-30) cc_final: 0.6205 (mp0) REVERT: A 2702 ASP cc_start: 0.6730 (m-30) cc_final: 0.6470 (m-30) REVERT: A 2706 LYS cc_start: 0.6331 (tptp) cc_final: 0.5988 (mptt) REVERT: A 2863 SER cc_start: 0.7531 (t) cc_final: 0.6893 (p) REVERT: A 2911 ASP cc_start: 0.6344 (t0) cc_final: 0.6040 (m-30) REVERT: B 114 ARG cc_start: 0.6103 (mtt90) cc_final: 0.4649 (ttt180) REVERT: B 156 ASP cc_start: 0.5154 (OUTLIER) cc_final: 0.4287 (t70) REVERT: B 192 HIS cc_start: 0.5158 (t-90) cc_final: 0.4786 (t-170) REVERT: B 204 ASN cc_start: 0.6888 (p0) cc_final: 0.6409 (p0) REVERT: B 285 TRP cc_start: 0.3728 (m100) cc_final: 0.3368 (m100) REVERT: B 324 TRP cc_start: 0.6271 (m-10) cc_final: 0.5633 (m-10) REVERT: B 330 MET cc_start: 0.5295 (ppp) cc_final: 0.4859 (ppp) REVERT: C 109 ARG cc_start: 0.7788 (tpt90) cc_final: 0.7263 (mtp-110) REVERT: C 204 ASN cc_start: 0.7081 (t0) cc_final: 0.6824 (t0) REVERT: C 272 GLU cc_start: 0.7630 (tt0) cc_final: 0.7202 (tm-30) REVERT: C 324 TRP cc_start: 0.7137 (OUTLIER) cc_final: 0.6916 (m100) REVERT: C 333 MET cc_start: 0.7310 (OUTLIER) cc_final: 0.6434 (tmm) REVERT: C 374 MET cc_start: 0.7013 (tmm) cc_final: 0.6612 (tmm) outliers start: 79 outliers final: 47 residues processed: 398 average time/residue: 0.3958 time to fit residues: 252.7261 Evaluate side-chains 363 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 307 time to evaluate : 2.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ARG 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 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 1128 THR Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain A residue 1172 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 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 2031 LEU Chi-restraints excluded: chain A residue 2038 LEU 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 2260 ARG 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 156 ASP 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 333 MET 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 108 optimal weight: 2.9990 chunk 291 optimal weight: 0.0170 chunk 64 optimal weight: 0.7980 chunk 190 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 324 optimal weight: 0.8980 chunk 269 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 overall best weight: 0.7422 ------------------------------------------------------------------------------- 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** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 27703 Z= 0.172 Angle : 0.557 10.565 37568 Z= 0.280 Chirality : 0.041 0.168 4209 Planarity : 0.004 0.076 4790 Dihedral : 5.749 112.059 3717 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.26 % Favored : 96.68 % Rotamer: Outliers : 1.91 % Allowed : 14.51 % Favored : 83.58 % 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: 0.93 (0.15), residues: 3348 helix: 1.98 (0.13), residues: 1531 sheet: -0.69 (0.23), residues: 491 loop : -0.43 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 246 HIS 0.006 0.001 HIS A2532 PHE 0.017 0.001 PHE B 183 TYR 0.019 0.001 TYR A1293 ARG 0.007 0.000 ARG A1414 *********************** 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 384 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 327 time to evaluate : 3.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.6229 (mm-30) cc_final: 0.5759 (tm-30) REVERT: A 175 TYR cc_start: 0.6665 (m-80) cc_final: 0.6406 (m-80) REVERT: A 252 LYS cc_start: 0.7795 (tppt) cc_final: 0.7366 (ptmm) REVERT: A 343 MET cc_start: 0.7665 (ptp) cc_final: 0.7356 (ptt) REVERT: A 479 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.6806 (pm20) REVERT: A 525 GLU cc_start: 0.6360 (tm-30) cc_final: 0.5860 (mm-30) REVERT: A 606 THR cc_start: 0.7722 (OUTLIER) cc_final: 0.7106 (t) REVERT: A 787 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7263 (tm-30) REVERT: A 1000 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8318 (mt) REVERT: A 1026 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7440 (ttt) REVERT: A 1424 LYS cc_start: 0.8365 (ptmm) cc_final: 0.8072 (ptpp) REVERT: A 1541 GLU cc_start: 0.6829 (pt0) cc_final: 0.6571 (pt0) REVERT: A 1575 MET cc_start: 0.7392 (tpp) cc_final: 0.7103 (mmt) REVERT: A 1677 LYS cc_start: 0.8037 (mmtp) cc_final: 0.7549 (tmtt) REVERT: A 1762 GLU cc_start: 0.5954 (pp20) cc_final: 0.5690 (tt0) REVERT: A 1977 GLN cc_start: 0.7213 (OUTLIER) cc_final: 0.6386 (mp10) REVERT: A 2076 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.7011 (pm20) REVERT: A 2204 GLU cc_start: 0.7196 (tp30) cc_final: 0.6855 (tp30) REVERT: A 2219 ARG cc_start: 0.7397 (tpt170) cc_final: 0.6982 (tpt170) REVERT: A 2252 LYS cc_start: 0.7802 (mtmm) cc_final: 0.7321 (pttp) REVERT: A 2257 GLU cc_start: 0.7302 (tp30) cc_final: 0.7076 (tp30) REVERT: A 2279 TYR cc_start: 0.5902 (m-10) cc_final: 0.5542 (m-10) REVERT: A 2553 GLU cc_start: 0.6913 (mm-30) cc_final: 0.6184 (mp0) REVERT: A 2706 LYS cc_start: 0.6309 (tptp) cc_final: 0.5937 (mptt) REVERT: A 2863 SER cc_start: 0.7483 (t) cc_final: 0.6865 (p) REVERT: A 2911 ASP cc_start: 0.6455 (t0) cc_final: 0.6065 (m-30) REVERT: A 3065 LEU cc_start: 0.6188 (OUTLIER) cc_final: 0.5938 (tt) REVERT: B 114 ARG cc_start: 0.6060 (mtt90) cc_final: 0.4606 (ttt90) REVERT: B 156 ASP cc_start: 0.4829 (OUTLIER) cc_final: 0.4142 (t70) REVERT: B 192 HIS cc_start: 0.5108 (t-90) cc_final: 0.4726 (t-170) REVERT: B 204 ASN cc_start: 0.6920 (p0) cc_final: 0.6426 (p0) REVERT: B 285 TRP cc_start: 0.3750 (m100) cc_final: 0.3405 (m100) REVERT: B 324 TRP cc_start: 0.6188 (m-10) cc_final: 0.5579 (m-10) REVERT: B 330 MET cc_start: 0.5260 (ppp) cc_final: 0.4898 (ppp) REVERT: C 202 MET cc_start: 0.7787 (mmp) cc_final: 0.7540 (mmp) REVERT: C 204 ASN cc_start: 0.7161 (t0) cc_final: 0.6668 (p0) REVERT: C 272 GLU cc_start: 0.7660 (tt0) cc_final: 0.7177 (tm-30) REVERT: C 333 MET cc_start: 0.7285 (OUTLIER) cc_final: 0.6344 (tmm) REVERT: C 374 MET cc_start: 0.6923 (tmm) cc_final: 0.6658 (tmm) outliers start: 57 outliers final: 36 residues processed: 366 average time/residue: 0.3844 time to fit residues: 227.1571 Evaluate side-chains 353 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 308 time to evaluate : 2.958 ------------------------------------------------------------------------------- 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 1128 THR Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1181 ASP 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 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 3048 CYS Chi-restraints excluded: chain A residue 3065 LEU Chi-restraints excluded: chain B residue 156 ASP 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 333 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.2304 > 50: distance: 51 - 57: 34.608 distance: 57 - 58: 40.779 distance: 58 - 59: 19.713 distance: 58 - 61: 45.551 distance: 59 - 60: 44.998 distance: 59 - 68: 17.667 distance: 61 - 62: 57.322 distance: 62 - 63: 34.578 distance: 62 - 64: 33.592 distance: 64 - 66: 35.477 distance: 65 - 67: 38.822 distance: 66 - 67: 26.603 distance: 68 - 69: 17.969 distance: 69 - 70: 56.720 distance: 69 - 72: 45.207 distance: 70 - 71: 28.247 distance: 70 - 75: 39.103 distance: 72 - 73: 46.274 distance: 72 - 74: 21.390 distance: 75 - 76: 42.995 distance: 76 - 77: 47.097 distance: 76 - 79: 44.044 distance: 77 - 82: 38.589 distance: 79 - 80: 28.803 distance: 79 - 81: 30.013 distance: 82 - 83: 3.188 distance: 83 - 84: 45.851 distance: 83 - 86: 39.393 distance: 84 - 85: 41.462 distance: 84 - 89: 27.233 distance: 85 - 112: 61.802 distance: 86 - 87: 40.140 distance: 86 - 88: 35.141 distance: 89 - 90: 52.510 distance: 90 - 91: 11.063 distance: 90 - 93: 29.797 distance: 91 - 92: 57.583 distance: 91 - 100: 32.252 distance: 92 - 120: 32.331 distance: 93 - 94: 25.133 distance: 94 - 95: 12.564 distance: 95 - 96: 52.899 distance: 96 - 97: 24.205 distance: 97 - 98: 16.866 distance: 97 - 99: 43.001 distance: 100 - 101: 32.681 distance: 101 - 102: 13.975 distance: 101 - 104: 22.241 distance: 102 - 103: 39.083 distance: 102 - 106: 40.060 distance: 103 - 129: 44.228 distance: 104 - 105: 30.084 distance: 106 - 107: 8.042 distance: 107 - 108: 29.502 distance: 107 - 110: 29.759 distance: 108 - 109: 13.871 distance: 108 - 112: 4.746 distance: 109 - 135: 28.501 distance: 110 - 111: 18.268 distance: 112 - 113: 24.100 distance: 113 - 114: 55.762 distance: 113 - 116: 38.037 distance: 114 - 120: 39.705 distance: 115 - 141: 34.547 distance: 116 - 117: 31.143 distance: 117 - 118: 16.060 distance: 117 - 119: 46.872 distance: 120 - 121: 44.259 distance: 121 - 122: 43.287 distance: 121 - 124: 25.828 distance: 122 - 129: 30.519 distance: 123 - 147: 36.379 distance: 124 - 125: 23.732 distance: 126 - 127: 29.981 distance: 126 - 128: 5.767 distance: 129 - 130: 27.328 distance: 130 - 131: 27.360 distance: 130 - 133: 24.691 distance: 131 - 132: 50.777 distance: 131 - 135: 23.236 distance: 132 - 155: 30.946 distance: 133 - 134: 35.215