Starting phenix.real_space_refine on Sun Jun 30 13:03:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w15_43715/06_2024/8w15_43715.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w15_43715/06_2024/8w15_43715.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w15_43715/06_2024/8w15_43715.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w15_43715/06_2024/8w15_43715.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w15_43715/06_2024/8w15_43715.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w15_43715/06_2024/8w15_43715.pdb" } resolution = 2.72 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: 4 Type Number sf(0) Gaussians S 133 5.16 5 C 13567 2.51 5 N 3660 2.21 5 O 3847 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 331": "OD1" <-> "OD2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A ASP 702": "OD1" <-> "OD2" Residue "A ASP 733": "OD1" <-> "OD2" Residue "A GLU 932": "OE1" <-> "OE2" Residue "A ASP 1493": "OD1" <-> "OD2" Residue "A ASP 1781": "OD1" <-> "OD2" Residue "A TYR 2435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3014": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 21207 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 19105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2431, 19105 Classifications: {'peptide': 2431} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 109, 'TRANS': 2321} Chain breaks: 17 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2102 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 16, 'TRANS': 262} Chain breaks: 2 Time building chain proxies: 11.26, per 1000 atoms: 0.53 Number of scatterers: 21207 At special positions: 0 Unit cell: (113.71, 135.29, 147.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 133 16.00 O 3847 8.00 N 3660 7.00 C 13567 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 177 " distance=2.03 Simple disulfide: pdb=" SG CYS A 799 " - pdb=" SG CYS A 834 " distance=2.03 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: 8.45 Conformation dependent library (CDL) restraints added in 4.5 seconds 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5186 Finding SS restraints... Secondary structure from input PDB file: 153 helices and 0 sheets defined 76.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.92 Creating SS restraints... Processing helix chain 'A' and resid 122 through 139 removed outlier: 3.694A pdb=" N VAL A 138 " --> pdb=" O CYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 163 Processing helix chain 'A' and resid 167 through 185 removed outlier: 3.519A pdb=" N ARG A 171 " --> pdb=" O GLU A 167 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A 176 " --> pdb=" O MET A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 203 Processing helix chain 'A' and resid 206 through 220 removed outlier: 3.734A pdb=" N ARG A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU A 219 " --> pdb=" O TRP A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 224 Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 228 through 245 removed outlier: 3.636A pdb=" N TYR A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) Proline residue: A 238 - end of helix removed outlier: 3.577A pdb=" N LYS A 245 " --> pdb=" O THR A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 267 removed outlier: 3.633A pdb=" N GLU A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) Proline residue: A 260 - end of helix removed outlier: 3.545A pdb=" N SER A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 270 No H-bonds generated for 'chain 'A' and resid 268 through 270' Processing helix chain 'A' and resid 271 through 284 Processing helix chain 'A' and resid 290 through 307 removed outlier: 3.702A pdb=" N ALA A 298 " --> pdb=" O ARG A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 327 removed outlier: 3.620A pdb=" N LEU A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 349 Processing helix chain 'A' and resid 350 through 353 Processing helix chain 'A' and resid 377 through 392 Processing helix chain 'A' and resid 396 through 413 Processing helix chain 'A' and resid 415 through 424 Processing helix chain 'A' and resid 706 through 720 removed outlier: 3.777A pdb=" N HIS A 710 " --> pdb=" O ALA A 706 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A 719 " --> pdb=" O LEU A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 753 removed outlier: 3.634A pdb=" N LEU A 752 " --> pdb=" O ALA A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 759 Processing helix chain 'A' and resid 776 through 786 removed outlier: 3.553A pdb=" N LEU A 781 " --> pdb=" O SER A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 811 removed outlier: 3.603A pdb=" N ARG A 792 " --> pdb=" O ASP A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 825 removed outlier: 3.502A pdb=" N GLY A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 832 No H-bonds generated for 'chain 'A' and resid 830 through 832' Processing helix chain 'A' and resid 833 through 843 removed outlier: 3.735A pdb=" N LEU A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A 843 " --> pdb=" O ARG A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 866 removed outlier: 5.074A pdb=" N MET A 862 " --> pdb=" O ARG A 858 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N SER A 863 " --> pdb=" O ASN A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 881 Processing helix chain 'A' and resid 882 through 885 Processing helix chain 'A' and resid 888 through 901 removed outlier: 3.543A pdb=" N GLU A 901 " --> pdb=" O GLU A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 913 removed outlier: 3.525A pdb=" N LYS A 913 " --> pdb=" O PHE A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 920 removed outlier: 3.997A pdb=" N ARG A 919 " --> pdb=" O GLU A 915 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY A 920 " --> pdb=" O ASN A 916 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 915 through 920' Processing helix chain 'A' and resid 929 through 938 Processing helix chain 'A' and resid 940 through 945 Processing helix chain 'A' and resid 947 through 965 Proline residue: A 963 - end of helix Processing helix chain 'A' and resid 975 through 989 removed outlier: 3.904A pdb=" N VAL A 987 " --> pdb=" O ASP A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1042 Processing helix chain 'A' and resid 1045 through 1063 Processing helix chain 'A' and resid 1093 through 1102 removed outlier: 3.868A pdb=" N ILE A1097 " --> pdb=" O MET A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1126 Processing helix chain 'A' and resid 1161 through 1184 Processing helix chain 'A' and resid 1260 through 1278 Processing helix chain 'A' and resid 1288 through 1305 Processing helix chain 'A' and resid 1306 through 1308 No H-bonds generated for 'chain 'A' and resid 1306 through 1308' Processing helix chain 'A' and resid 1316 through 1329 removed outlier: 3.686A pdb=" N SER A1326 " --> pdb=" O GLY A1322 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N SER A1329 " --> pdb=" O LYS A1325 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1347 Processing helix chain 'A' and resid 1380 through 1386 Processing helix chain 'A' and resid 1386 through 1401 removed outlier: 3.761A pdb=" N SER A1401 " --> pdb=" O LEU A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1448 through 1451 Processing helix chain 'A' and resid 1452 through 1464 removed outlier: 3.816A pdb=" N LYS A1458 " --> pdb=" O PRO A1454 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA A1459 " --> pdb=" O LEU A1455 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A1464 " --> pdb=" O LEU A1460 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1485 Processing helix chain 'A' and resid 1488 through 1493 removed outlier: 3.795A pdb=" N LEU A1492 " --> pdb=" O ASN A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1496 through 1511 removed outlier: 3.878A pdb=" N PHE A1506 " --> pdb=" O VAL A1502 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLU A1507 " --> pdb=" O LEU A1503 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR A1508 " --> pdb=" O LYS A1504 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A1511 " --> pdb=" O GLU A1507 " (cutoff:3.500A) Processing helix chain 'A' and resid 1520 through 1532 Processing helix chain 'A' and resid 1543 through 1557 Processing helix chain 'A' and resid 1565 through 1577 Proline residue: A1571 - end of helix removed outlier: 3.685A pdb=" N ASP A1575 " --> pdb=" O PRO A1571 " (cutoff:3.500A) Processing helix chain 'A' and resid 1590 through 1605 removed outlier: 3.604A pdb=" N GLN A1594 " --> pdb=" O GLU A1590 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A1605 " --> pdb=" O MET A1601 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1626 removed outlier: 3.843A pdb=" N LYS A1624 " --> pdb=" O GLN A1620 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN A1626 " --> pdb=" O CYS A1622 " (cutoff:3.500A) Processing helix chain 'A' and resid 1626 through 1647 Proline residue: A1643 - end of helix Processing helix chain 'A' and resid 1654 through 1668 removed outlier: 3.692A pdb=" N GLU A1666 " --> pdb=" O ASN A1662 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1674 removed outlier: 3.788A pdb=" N LEU A1673 " --> pdb=" O ALA A1669 " (cutoff:3.500A) Processing helix chain 'A' and resid 1676 through 1684 Processing helix chain 'A' and resid 1692 through 1711 removed outlier: 3.574A pdb=" N VAL A1709 " --> pdb=" O ALA A1705 " (cutoff:3.500A) Processing helix chain 'A' and resid 1715 through 1726 removed outlier: 3.735A pdb=" N GLN A1724 " --> pdb=" O LEU A1720 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU A1725 " --> pdb=" O SER A1721 " (cutoff:3.500A) Processing helix chain 'A' and resid 1729 through 1733 removed outlier: 4.446A pdb=" N ILE A1733 " --> pdb=" O PRO A1730 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1743 removed outlier: 3.533A pdb=" N ASP A1743 " --> pdb=" O ASN A1739 " (cutoff:3.500A) Processing helix chain 'A' and resid 1762 through 1784 Processing helix chain 'A' and resid 1792 through 1816 Processing helix chain 'A' and resid 1819 through 1832 Processing helix chain 'A' and resid 1834 through 1838 removed outlier: 3.576A pdb=" N GLY A1837 " --> pdb=" O GLY A1834 " (cutoff:3.500A) Processing helix chain 'A' and resid 1841 through 1851 Processing helix chain 'A' and resid 1856 through 1870 Processing helix chain 'A' and resid 1874 through 1882 removed outlier: 3.565A pdb=" N TRP A1878 " --> pdb=" O ASP A1874 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU A1880 " --> pdb=" O ARG A1876 " (cutoff:3.500A) Processing helix chain 'A' and resid 1915 through 1935 Processing helix chain 'A' and resid 1940 through 1957 removed outlier: 3.768A pdb=" N THR A1944 " --> pdb=" O SER A1940 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A1946 " --> pdb=" O HIS A1942 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N GLN A1952 " --> pdb=" O VAL A1948 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASP A1953 " --> pdb=" O ASN A1949 " (cutoff:3.500A) Processing helix chain 'A' and resid 1960 through 1973 Processing helix chain 'A' and resid 1973 through 1987 Processing helix chain 'A' and resid 1993 through 2006 removed outlier: 4.598A pdb=" N GLY A2006 " --> pdb=" O GLN A2002 " (cutoff:3.500A) Processing helix chain 'A' and resid 2008 through 2010 No H-bonds generated for 'chain 'A' and resid 2008 through 2010' Processing helix chain 'A' and resid 2011 through 2023 removed outlier: 3.592A pdb=" N THR A2017 " --> pdb=" O GLY A2013 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A2023 " --> pdb=" O TYR A2019 " (cutoff:3.500A) Processing helix chain 'A' and resid 2028 through 2045 Processing helix chain 'A' and resid 2050 through 2058 Processing helix chain 'A' and resid 2059 through 2073 Processing helix chain 'A' and resid 2074 through 2079 Processing helix chain 'A' and resid 2079 through 2094 removed outlier: 3.619A pdb=" N TYR A2083 " --> pdb=" O HIS A2079 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET A2094 " --> pdb=" O ARG A2090 " (cutoff:3.500A) Processing helix chain 'A' and resid 2123 through 2136 Processing helix chain 'A' and resid 2143 through 2152 removed outlier: 3.543A pdb=" N GLU A2148 " --> pdb=" O LEU A2144 " (cutoff:3.500A) Processing helix chain 'A' and resid 2154 through 2164 removed outlier: 4.237A pdb=" N ASN A2159 " --> pdb=" O ALA A2155 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ALA A2160 " --> pdb=" O GLU A2156 " (cutoff:3.500A) Processing helix chain 'A' and resid 2168 through 2170 No H-bonds generated for 'chain 'A' and resid 2168 through 2170' Processing helix chain 'A' and resid 2171 through 2184 removed outlier: 3.548A pdb=" N GLU A2182 " --> pdb=" O LEU A2178 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2208 removed outlier: 3.564A pdb=" N VAL A2198 " --> pdb=" O ALA A2194 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A2201 " --> pdb=" O GLU A2197 " (cutoff:3.500A) Processing helix chain 'A' and resid 2226 through 2237 removed outlier: 3.564A pdb=" N ASP A2234 " --> pdb=" O SER A2230 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A2235 " --> pdb=" O LYS A2231 " (cutoff:3.500A) Processing helix chain 'A' and resid 2238 through 2243 Processing helix chain 'A' and resid 2243 through 2257 removed outlier: 3.613A pdb=" N THR A2247 " --> pdb=" O GLN A2243 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA A2251 " --> pdb=" O THR A2247 " (cutoff:3.500A) Processing helix chain 'A' and resid 2258 through 2262 removed outlier: 3.747A pdb=" N LEU A2262 " --> pdb=" O VAL A2259 " (cutoff:3.500A) Processing helix chain 'A' and resid 2263 through 2267 Processing helix chain 'A' and resid 2269 through 2271 No H-bonds generated for 'chain 'A' and resid 2269 through 2271' Processing helix chain 'A' and resid 2272 through 2294 Processing helix chain 'A' and resid 2298 through 2313 Processing helix chain 'A' and resid 2315 through 2323 removed outlier: 3.776A pdb=" N VAL A2321 " --> pdb=" O GLY A2317 " (cutoff:3.500A) Processing helix chain 'A' and resid 2324 through 2326 No H-bonds generated for 'chain 'A' and resid 2324 through 2326' Processing helix chain 'A' and resid 2327 through 2347 Processing helix chain 'A' and resid 2380 through 2400 removed outlier: 3.890A pdb=" N THR A2384 " --> pdb=" O PRO A2380 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A2395 " --> pdb=" O ALA A2391 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLN A2398 " --> pdb=" O VAL A2394 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER A2399 " --> pdb=" O GLU A2395 " (cutoff:3.500A) Processing helix chain 'A' and resid 2405 through 2411 removed outlier: 3.636A pdb=" N SER A2409 " --> pdb=" O LYS A2406 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY A2410 " --> pdb=" O ARG A2407 " (cutoff:3.500A) Processing helix chain 'A' and resid 2415 through 2428 Processing helix chain 'A' and resid 2432 through 2438 removed outlier: 3.851A pdb=" N VAL A2438 " --> pdb=" O SER A2434 " (cutoff:3.500A) Processing helix chain 'A' and resid 2439 through 2444 removed outlier: 3.642A pdb=" N TRP A2443 " --> pdb=" O PRO A2439 " (cutoff:3.500A) Processing helix chain 'A' and resid 2463 through 2468 removed outlier: 4.014A pdb=" N LEU A2467 " --> pdb=" O PRO A2463 " (cutoff:3.500A) Processing helix chain 'A' and resid 2469 through 2484 removed outlier: 3.864A pdb=" N GLU A2475 " --> pdb=" O GLU A2471 " (cutoff:3.500A) Processing helix chain 'A' and resid 2487 through 2502 Processing helix chain 'A' and resid 2523 through 2539 Processing helix chain 'A' and resid 2540 through 2542 No H-bonds generated for 'chain 'A' and resid 2540 through 2542' Processing helix chain 'A' and resid 2570 through 2590 removed outlier: 3.583A pdb=" N ILE A2580 " --> pdb=" O ILE A2576 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA A2587 " --> pdb=" O GLN A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2620 through 2624 Processing helix chain 'A' and resid 2645 through 2651 Processing helix chain 'A' and resid 2689 through 2693 Processing helix chain 'A' and resid 2694 through 2711 removed outlier: 3.736A pdb=" N CYS A2698 " --> pdb=" O ASP A2694 " (cutoff:3.500A) Processing helix chain 'A' and resid 2720 through 2735 Processing helix chain 'A' and resid 2736 through 2738 No H-bonds generated for 'chain 'A' and resid 2736 through 2738' Processing helix chain 'A' and resid 2740 through 2758 removed outlier: 3.634A pdb=" N PHE A2744 " --> pdb=" O GLU A2740 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2781 Proline residue: A2771 - end of helix Processing helix chain 'A' and resid 2783 through 2799 removed outlier: 3.688A pdb=" N GLU A2788 " --> pdb=" O LYS A2784 " (cutoff:3.500A) Proline residue: A2789 - end of helix removed outlier: 3.625A pdb=" N GLU A2795 " --> pdb=" O SER A2791 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG A2799 " --> pdb=" O GLU A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2802 through 2818 Processing helix chain 'A' and resid 2823 through 2828 removed outlier: 3.583A pdb=" N GLN A2828 " --> pdb=" O THR A2825 " (cutoff:3.500A) Processing helix chain 'A' and resid 2829 through 2842 Processing helix chain 'A' and resid 2852 through 2870 Processing helix chain 'A' and resid 2875 through 2891 removed outlier: 3.900A pdb=" N MET A2889 " --> pdb=" O MET A2885 " (cutoff:3.500A) Processing helix chain 'A' and resid 2898 through 2915 Processing helix chain 'A' and resid 2919 through 2933 removed outlier: 4.075A pdb=" N LYS A2928 " --> pdb=" O GLU A2924 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU A2929 " --> pdb=" O SER A2925 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL A2931 " --> pdb=" O VAL A2927 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP A2932 " --> pdb=" O LYS A2928 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG A2933 " --> pdb=" O LEU A2929 " (cutoff:3.500A) Processing helix chain 'A' and resid 2938 through 2957 removed outlier: 3.812A pdb=" N GLY A2956 " --> pdb=" O CYS A2952 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A2957 " --> pdb=" O MET A2953 " (cutoff:3.500A) Processing helix chain 'A' and resid 2980 through 2994 removed outlier: 3.674A pdb=" N ARG A2991 " --> pdb=" O VAL A2987 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A2992 " --> pdb=" O LEU A2988 " (cutoff:3.500A) Processing helix chain 'A' and resid 2996 through 3015 removed outlier: 3.517A pdb=" N VAL A3003 " --> pdb=" O GLU A2999 " (cutoff:3.500A) Proline residue: A3008 - end of helix Processing helix chain 'A' and resid 3021 through 3029 removed outlier: 3.625A pdb=" N ILE A3025 " --> pdb=" O MET A3021 " (cutoff:3.500A) Processing helix chain 'A' and resid 3035 through 3052 removed outlier: 4.023A pdb=" N THR A3041 " --> pdb=" O GLN A3037 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL A3042 " --> pdb=" O PHE A3038 " (cutoff:3.500A) Processing helix chain 'A' and resid 3057 through 3072 removed outlier: 4.732A pdb=" N SER A3068 " --> pdb=" O MET A3064 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASN A3069 " --> pdb=" O LEU A3065 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN A3072 " --> pdb=" O SER A3068 " (cutoff:3.500A) Processing helix chain 'A' and resid 3075 through 3090 Processing helix chain 'A' and resid 3099 through 3106 Processing helix chain 'A' and resid 3111 through 3127 Processing helix chain 'A' and resid 3135 through 3145 removed outlier: 3.650A pdb=" N PHE A3139 " --> pdb=" O ASP A3135 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU A3144 " --> pdb=" O GLN A3140 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A3145 " --> pdb=" O SER A3141 " (cutoff:3.500A) Processing helix chain 'A' and resid 3151 through 3162 removed outlier: 4.128A pdb=" N ASN A3162 " --> pdb=" O THR A3158 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 60 Processing helix chain 'B' and resid 62 through 81 Processing helix chain 'B' and resid 82 through 106 Processing helix chain 'B' and resid 115 through 135 removed outlier: 3.602A pdb=" N GLN B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA B 120 " --> pdb=" O GLU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 155 Processing helix chain 'B' and resid 157 through 173 Processing helix chain 'B' and resid 176 through 194 Processing helix chain 'B' and resid 196 through 215 Processing helix chain 'B' and resid 262 through 281 Processing helix chain 'B' and resid 288 through 298 removed outlier: 3.516A pdb=" N TYR B 298 " --> pdb=" O THR B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 332 Processing helix chain 'B' and resid 333 through 344 Processing helix chain 'B' and resid 349 through 365 1358 hydrogen bonds defined for protein. 3984 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.18 Time building geometry restraints manager: 9.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3447 1.32 - 1.44: 5449 1.44 - 1.57: 12528 1.57 - 1.70: 0 1.70 - 1.82: 193 Bond restraints: 21617 Sorted by residual: bond pdb=" C GLY A1071 " pdb=" O GLY A1071 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.35e-02 5.49e+03 9.58e+00 bond pdb=" N TRP A1072 " pdb=" CA TRP A1072 " ideal model delta sigma weight residual 1.462 1.426 0.036 1.31e-02 5.83e+03 7.59e+00 bond pdb=" C ALA A3079 " pdb=" O ALA A3079 " ideal model delta sigma weight residual 1.237 1.207 0.030 1.17e-02 7.31e+03 6.60e+00 bond pdb=" CA ARG A3073 " pdb=" C ARG A3073 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.10e-02 8.26e+03 5.60e+00 bond pdb=" CA HIS A1073 " pdb=" C HIS A1073 " ideal model delta sigma weight residual 1.531 1.506 0.025 1.08e-02 8.57e+03 5.50e+00 ... (remaining 21612 not shown) Histogram of bond angle deviations from ideal: 99.21 - 106.17: 570 106.17 - 113.12: 12183 113.12 - 120.08: 7269 120.08 - 127.04: 9075 127.04 - 133.99: 262 Bond angle restraints: 29359 Sorted by residual: angle pdb=" N VAL A1091 " pdb=" CA VAL A1091 " pdb=" C VAL A1091 " ideal model delta sigma weight residual 112.90 106.52 6.38 9.60e-01 1.09e+00 4.41e+01 angle pdb=" N ILE A1782 " pdb=" CA ILE A1782 " pdb=" C ILE A1782 " ideal model delta sigma weight residual 111.81 106.87 4.94 8.60e-01 1.35e+00 3.30e+01 angle pdb=" N VAL A2551 " pdb=" CA VAL A2551 " pdb=" C VAL A2551 " ideal model delta sigma weight residual 113.71 108.58 5.13 9.50e-01 1.11e+00 2.91e+01 angle pdb=" CA CYS A1074 " pdb=" CB CYS A1074 " pdb=" SG CYS A1074 " ideal model delta sigma weight residual 114.40 102.10 12.30 2.30e+00 1.89e-01 2.86e+01 angle pdb=" N HIS A1073 " pdb=" CA HIS A1073 " pdb=" C HIS A1073 " ideal model delta sigma weight residual 111.02 117.05 -6.03 1.25e+00 6.40e-01 2.33e+01 ... (remaining 29354 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 11557 17.73 - 35.46: 1192 35.46 - 53.19: 307 53.19 - 70.93: 61 70.93 - 88.66: 30 Dihedral angle restraints: 13147 sinusoidal: 5207 harmonic: 7940 Sorted by residual: dihedral pdb=" N HIS A1073 " pdb=" C HIS A1073 " pdb=" CA HIS A1073 " pdb=" CB HIS A1073 " ideal model delta harmonic sigma weight residual 122.80 137.29 -14.49 0 2.50e+00 1.60e-01 3.36e+01 dihedral pdb=" C HIS A1073 " pdb=" N HIS A1073 " pdb=" CA HIS A1073 " pdb=" CB HIS A1073 " ideal model delta harmonic sigma weight residual -122.60 -136.22 13.62 0 2.50e+00 1.60e-01 2.97e+01 dihedral pdb=" CA THR A2542 " pdb=" C THR A2542 " pdb=" N VAL A2543 " pdb=" CA VAL A2543 " ideal model delta harmonic sigma weight residual -180.00 -159.69 -20.31 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 13144 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 3476 0.117 - 0.234: 19 0.234 - 0.351: 0 0.351 - 0.467: 0 0.467 - 0.584: 1 Chirality restraints: 3496 Sorted by residual: chirality pdb=" CA HIS A1073 " pdb=" N HIS A1073 " pdb=" C HIS A1073 " pdb=" CB HIS A1073 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.54e+00 chirality pdb=" CA ALA A3074 " pdb=" N ALA A3074 " pdb=" C ALA A3074 " pdb=" CB ALA A3074 " both_signs ideal model delta sigma weight residual False 2.48 2.29 0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" CA THR A3080 " pdb=" N THR A3080 " pdb=" C THR A3080 " pdb=" CB THR A3080 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 3493 not shown) Planarity restraints: 3709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A1073 " -0.017 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C HIS A1073 " 0.061 2.00e-02 2.50e+03 pdb=" O HIS A1073 " -0.023 2.00e-02 2.50e+03 pdb=" N CYS A1074 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1070 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C LEU A1070 " 0.041 2.00e-02 2.50e+03 pdb=" O LEU A1070 " -0.015 2.00e-02 2.50e+03 pdb=" N GLY A1071 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A1073 " -0.022 2.00e-02 2.50e+03 1.81e-02 4.94e+00 pdb=" CG HIS A1073 " 0.036 2.00e-02 2.50e+03 pdb=" ND1 HIS A1073 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 HIS A1073 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS A1073 " -0.009 2.00e-02 2.50e+03 pdb=" NE2 HIS A1073 " -0.008 2.00e-02 2.50e+03 ... (remaining 3706 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 382 2.69 - 3.24: 21894 3.24 - 3.79: 34789 3.79 - 4.35: 46994 4.35 - 4.90: 76492 Nonbonded interactions: 180551 Sorted by model distance: nonbonded pdb=" O LEU A 837 " pdb=" OG1 THR A 841 " model vdw 2.133 2.440 nonbonded pdb=" O LEU A2731 " pdb=" OG SER A2735 " model vdw 2.169 2.440 nonbonded pdb=" OG SER A1043 " pdb=" OG1 THR A1049 " model vdw 2.207 2.440 nonbonded pdb=" CB ALA A3074 " pdb=" CD PRO A3075 " model vdw 2.248 3.860 nonbonded pdb=" OH TYR A1533 " pdb=" OD1 ASP A1575 " model vdw 2.252 2.440 ... (remaining 180546 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 7.720 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 59.330 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 21617 Z= 0.195 Angle : 0.574 12.297 29359 Z= 0.295 Chirality : 0.038 0.584 3496 Planarity : 0.004 0.045 3709 Dihedral : 16.090 88.656 7955 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.89 % Favored : 97.08 % Rotamer: Outliers : 1.36 % Allowed : 15.81 % Favored : 82.83 % Cbeta Deviations : 0.04 % 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: 0.92 (0.17), residues: 2668 helix: 1.03 (0.12), residues: 1877 sheet: None (None), residues: 0 loop : -0.20 (0.24), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1072 HIS 0.011 0.001 HIS A1073 PHE 0.018 0.001 PHE B 81 TYR 0.010 0.001 TYR A1277 ARG 0.002 0.000 ARG A2741 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 96 time to evaluate : 2.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1614 MET cc_start: 0.8896 (mtm) cc_final: 0.7995 (mtm) outliers start: 32 outliers final: 22 residues processed: 123 average time/residue: 1.1403 time to fit residues: 164.8371 Evaluate side-chains 113 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 91 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 733 ASP Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1329 SER Chi-restraints excluded: chain A residue 1495 ASP Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1689 THR Chi-restraints excluded: chain A residue 1780 GLU Chi-restraints excluded: chain A residue 1841 THR Chi-restraints excluded: chain A residue 1855 THR Chi-restraints excluded: chain A residue 2050 ASN Chi-restraints excluded: chain A residue 2421 ASN Chi-restraints excluded: chain A residue 2553 CYS Chi-restraints excluded: chain A residue 2656 THR Chi-restraints excluded: chain A residue 2704 GLU Chi-restraints excluded: chain A residue 3068 SER Chi-restraints excluded: chain A residue 3076 VAL Chi-restraints excluded: chain A residue 3078 MET Chi-restraints excluded: chain A residue 3080 THR Chi-restraints excluded: chain A residue 3085 CYS Chi-restraints excluded: chain A residue 3119 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 227 optimal weight: 5.9990 chunk 204 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 211 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 157 optimal weight: 9.9990 chunk 245 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1697 GLN A2267 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21617 Z= 0.284 Angle : 0.603 10.364 29359 Z= 0.301 Chirality : 0.040 0.184 3496 Planarity : 0.004 0.045 3709 Dihedral : 4.858 56.981 2934 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.19 % Favored : 96.78 % Rotamer: Outliers : 3.14 % Allowed : 14.03 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.17), residues: 2668 helix: 1.33 (0.12), residues: 1937 sheet: None (None), residues: 0 loop : -0.31 (0.26), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A3062 HIS 0.004 0.001 HIS A1856 PHE 0.014 0.001 PHE A1525 TYR 0.013 0.001 TYR A2382 ARG 0.003 0.000 ARG A3060 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 104 time to evaluate : 2.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1025 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8501 (ttp) REVERT: A 2047 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8846 (pp) REVERT: A 2421 ASN cc_start: 0.9026 (OUTLIER) cc_final: 0.8564 (t0) REVERT: A 2938 SER cc_start: 0.8852 (OUTLIER) cc_final: 0.8621 (p) outliers start: 74 outliers final: 25 residues processed: 165 average time/residue: 1.0595 time to fit residues: 206.6763 Evaluate side-chains 122 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 93 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 731 ASP Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1025 MET Chi-restraints excluded: chain A residue 1313 ILE Chi-restraints excluded: chain A residue 1333 MET Chi-restraints excluded: chain A residue 1495 ASP Chi-restraints excluded: chain A residue 1552 ASP Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1579 LEU Chi-restraints excluded: chain A residue 1780 GLU Chi-restraints excluded: chain A residue 1782 ILE Chi-restraints excluded: chain A residue 2047 LEU Chi-restraints excluded: chain A residue 2050 ASN Chi-restraints excluded: chain A residue 2421 ASN Chi-restraints excluded: chain A residue 2486 THR Chi-restraints excluded: chain A residue 2656 THR Chi-restraints excluded: chain A residue 2704 GLU Chi-restraints excluded: chain A residue 2820 ASP Chi-restraints excluded: chain A residue 2873 ASP Chi-restraints excluded: chain A residue 2904 CYS Chi-restraints excluded: chain A residue 2938 SER Chi-restraints excluded: chain A residue 3076 VAL Chi-restraints excluded: chain A residue 3085 CYS Chi-restraints excluded: chain A residue 3119 CYS Chi-restraints excluded: chain A residue 3143 LEU Chi-restraints excluded: chain A residue 3157 LEU Chi-restraints excluded: chain B residue 53 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 136 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 245 optimal weight: 0.9990 chunk 265 optimal weight: 8.9990 chunk 218 optimal weight: 0.5980 chunk 243 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 197 optimal weight: 0.0970 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN A1697 GLN ** A2050 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21617 Z= 0.163 Angle : 0.543 9.603 29359 Z= 0.266 Chirality : 0.037 0.267 3496 Planarity : 0.004 0.050 3709 Dihedral : 4.650 58.853 2920 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.77 % Favored : 97.19 % Rotamer: Outliers : 2.71 % Allowed : 14.96 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.17), residues: 2668 helix: 1.58 (0.12), residues: 1926 sheet: None (None), residues: 0 loop : -0.26 (0.25), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1877 HIS 0.004 0.001 HIS A2647 PHE 0.013 0.001 PHE A1525 TYR 0.009 0.001 TYR A2382 ARG 0.003 0.000 ARG A3127 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 109 time to evaluate : 1.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8200 (tm-30) REVERT: A 1025 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8277 (ttp) REVERT: A 2060 MET cc_start: 0.9314 (tpt) cc_final: 0.8970 (tpt) REVERT: A 2709 TRP cc_start: 0.8789 (OUTLIER) cc_final: 0.8504 (t60) REVERT: B 213 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8699 (pp20) outliers start: 64 outliers final: 22 residues processed: 163 average time/residue: 1.0656 time to fit residues: 205.5303 Evaluate side-chains 118 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 92 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 731 ASP Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1025 MET Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1313 ILE Chi-restraints excluded: chain A residue 1495 ASP Chi-restraints excluded: chain A residue 1552 ASP Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1579 LEU Chi-restraints excluded: chain A residue 1593 THR Chi-restraints excluded: chain A residue 1689 THR Chi-restraints excluded: chain A residue 1780 GLU Chi-restraints excluded: chain A residue 2183 ILE Chi-restraints excluded: chain A residue 2259 VAL Chi-restraints excluded: chain A residue 2704 GLU Chi-restraints excluded: chain A residue 2709 TRP Chi-restraints excluded: chain A residue 2873 ASP Chi-restraints excluded: chain A residue 3025 ILE Chi-restraints excluded: chain A residue 3085 CYS Chi-restraints excluded: chain A residue 3143 LEU Chi-restraints excluded: chain A residue 3157 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 213 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 242 optimal weight: 10.0000 chunk 184 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 164 optimal weight: 3.9990 chunk 246 optimal weight: 9.9990 chunk 260 optimal weight: 9.9990 chunk 128 optimal weight: 7.9990 chunk 233 optimal weight: 2.9990 chunk 70 optimal weight: 0.0070 overall best weight: 1.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21617 Z= 0.215 Angle : 0.545 8.617 29359 Z= 0.266 Chirality : 0.038 0.277 3496 Planarity : 0.004 0.068 3709 Dihedral : 4.309 57.829 2912 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.04 % Favored : 96.93 % Rotamer: Outliers : 3.18 % Allowed : 15.30 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.17), residues: 2668 helix: 1.68 (0.12), residues: 1924 sheet: None (None), residues: 0 loop : -0.22 (0.25), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1699 HIS 0.003 0.001 HIS A2855 PHE 0.011 0.001 PHE A1525 TYR 0.017 0.001 TYR A1799 ARG 0.007 0.000 ARG A3060 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 99 time to evaluate : 2.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 CYS cc_start: 0.9424 (OUTLIER) cc_final: 0.9218 (t) REVERT: A 228 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8552 (mtpm) REVERT: A 1025 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8298 (ttp) REVERT: A 2055 MET cc_start: 0.9075 (tpt) cc_final: 0.8872 (mmm) REVERT: A 2060 MET cc_start: 0.9323 (tpt) cc_final: 0.8896 (tpt) REVERT: A 2421 ASN cc_start: 0.8962 (OUTLIER) cc_final: 0.8464 (t0) REVERT: A 2709 TRP cc_start: 0.8821 (OUTLIER) cc_final: 0.8548 (t60) REVERT: A 2938 SER cc_start: 0.8796 (OUTLIER) cc_final: 0.8513 (p) REVERT: B 49 GLN cc_start: 0.7021 (OUTLIER) cc_final: 0.6789 (tt0) REVERT: B 213 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8734 (pp20) outliers start: 75 outliers final: 30 residues processed: 160 average time/residue: 0.9767 time to fit residues: 187.7684 Evaluate side-chains 128 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 90 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 162 CYS Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 731 ASP Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1025 MET Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1313 ILE Chi-restraints excluded: chain A residue 1333 MET Chi-restraints excluded: chain A residue 1495 ASP Chi-restraints excluded: chain A residue 1552 ASP Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1579 LEU Chi-restraints excluded: chain A residue 1593 THR Chi-restraints excluded: chain A residue 1650 MET Chi-restraints excluded: chain A residue 1689 THR Chi-restraints excluded: chain A residue 1780 GLU Chi-restraints excluded: chain A residue 1782 ILE Chi-restraints excluded: chain A residue 1915 MET Chi-restraints excluded: chain A residue 2009 LEU Chi-restraints excluded: chain A residue 2259 VAL Chi-restraints excluded: chain A residue 2421 ASN Chi-restraints excluded: chain A residue 2486 THR Chi-restraints excluded: chain A residue 2704 GLU Chi-restraints excluded: chain A residue 2709 TRP Chi-restraints excluded: chain A residue 2889 MET Chi-restraints excluded: chain A residue 2904 CYS Chi-restraints excluded: chain A residue 2938 SER Chi-restraints excluded: chain A residue 3076 VAL Chi-restraints excluded: chain A residue 3085 CYS Chi-restraints excluded: chain A residue 3119 CYS Chi-restraints excluded: chain A residue 3143 LEU Chi-restraints excluded: chain A residue 3157 LEU Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 213 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 217 optimal weight: 0.8980 chunk 148 optimal weight: 0.4980 chunk 3 optimal weight: 6.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 chunk 222 optimal weight: 6.9990 chunk 180 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 133 optimal weight: 0.9980 chunk 234 optimal weight: 0.0970 chunk 65 optimal weight: 2.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 21617 Z= 0.157 Angle : 0.535 9.378 29359 Z= 0.259 Chirality : 0.037 0.220 3496 Planarity : 0.004 0.081 3709 Dihedral : 4.217 57.508 2912 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.77 % Favored : 97.19 % Rotamer: Outliers : 2.84 % Allowed : 16.07 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.17), residues: 2668 helix: 1.82 (0.12), residues: 1917 sheet: None (None), residues: 0 loop : -0.17 (0.25), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1699 HIS 0.003 0.000 HIS A2647 PHE 0.012 0.001 PHE A3086 TYR 0.015 0.001 TYR A1799 ARG 0.009 0.000 ARG A3060 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 104 time to evaluate : 2.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8264 (tm-30) REVERT: A 228 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8564 (mtpm) REVERT: A 992 LEU cc_start: 0.6049 (OUTLIER) cc_final: 0.4968 (pp) REVERT: A 1025 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8248 (ttp) REVERT: A 2060 MET cc_start: 0.9326 (tpt) cc_final: 0.8894 (tpt) REVERT: A 2421 ASN cc_start: 0.8897 (OUTLIER) cc_final: 0.8417 (t0) REVERT: A 2709 TRP cc_start: 0.8770 (OUTLIER) cc_final: 0.8493 (t60) REVERT: A 2938 SER cc_start: 0.8712 (OUTLIER) cc_final: 0.8422 (p) REVERT: A 3072 GLN cc_start: 0.9195 (OUTLIER) cc_final: 0.8812 (pp30) REVERT: B 213 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8768 (pp20) outliers start: 67 outliers final: 26 residues processed: 159 average time/residue: 1.0910 time to fit residues: 205.8309 Evaluate side-chains 127 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 92 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 731 ASP Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1025 MET Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1495 ASP Chi-restraints excluded: chain A residue 1539 LYS Chi-restraints excluded: chain A residue 1552 ASP Chi-restraints excluded: chain A residue 1579 LEU Chi-restraints excluded: chain A residue 1593 THR Chi-restraints excluded: chain A residue 1780 GLU Chi-restraints excluded: chain A residue 1782 ILE Chi-restraints excluded: chain A residue 2183 ILE Chi-restraints excluded: chain A residue 2259 VAL Chi-restraints excluded: chain A residue 2421 ASN Chi-restraints excluded: chain A residue 2486 THR Chi-restraints excluded: chain A residue 2704 GLU Chi-restraints excluded: chain A residue 2709 TRP Chi-restraints excluded: chain A residue 2793 LEU Chi-restraints excluded: chain A residue 2872 LEU Chi-restraints excluded: chain A residue 2904 CYS Chi-restraints excluded: chain A residue 2938 SER Chi-restraints excluded: chain A residue 3067 LEU Chi-restraints excluded: chain A residue 3072 GLN Chi-restraints excluded: chain A residue 3085 CYS Chi-restraints excluded: chain A residue 3119 CYS Chi-restraints excluded: chain A residue 3143 LEU Chi-restraints excluded: chain A residue 3157 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 213 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 87 optimal weight: 9.9990 chunk 235 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 216 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21617 Z= 0.283 Angle : 0.582 11.579 29359 Z= 0.278 Chirality : 0.040 0.236 3496 Planarity : 0.004 0.080 3709 Dihedral : 4.243 57.787 2911 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.30 % Favored : 96.66 % Rotamer: Outliers : 2.97 % Allowed : 16.41 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.17), residues: 2668 helix: 1.80 (0.12), residues: 1939 sheet: None (None), residues: 0 loop : -0.22 (0.25), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1699 HIS 0.003 0.001 HIS A2940 PHE 0.011 0.001 PHE A1525 TYR 0.021 0.001 TYR A1799 ARG 0.004 0.000 ARG A2755 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 96 time to evaluate : 2.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8261 (tm-30) REVERT: A 228 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8583 (mtpm) REVERT: A 992 LEU cc_start: 0.6146 (OUTLIER) cc_final: 0.5014 (pp) REVERT: A 1025 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8272 (ttp) REVERT: A 2055 MET cc_start: 0.8765 (mmt) cc_final: 0.8490 (mmm) REVERT: A 2421 ASN cc_start: 0.8985 (OUTLIER) cc_final: 0.8484 (t0) REVERT: A 2709 TRP cc_start: 0.8821 (OUTLIER) cc_final: 0.8585 (t60) REVERT: A 2938 SER cc_start: 0.8771 (OUTLIER) cc_final: 0.8483 (p) REVERT: B 49 GLN cc_start: 0.6864 (OUTLIER) cc_final: 0.6615 (tt0) REVERT: B 213 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8706 (pp20) outliers start: 70 outliers final: 31 residues processed: 153 average time/residue: 1.0562 time to fit residues: 192.1045 Evaluate side-chains 133 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 93 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 731 ASP Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1025 MET Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1313 ILE Chi-restraints excluded: chain A residue 1539 LYS Chi-restraints excluded: chain A residue 1552 ASP Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1579 LEU Chi-restraints excluded: chain A residue 1593 THR Chi-restraints excluded: chain A residue 1689 THR Chi-restraints excluded: chain A residue 1780 GLU Chi-restraints excluded: chain A residue 1782 ILE Chi-restraints excluded: chain A residue 1783 VAL Chi-restraints excluded: chain A residue 1841 THR Chi-restraints excluded: chain A residue 2259 VAL Chi-restraints excluded: chain A residue 2421 ASN Chi-restraints excluded: chain A residue 2486 THR Chi-restraints excluded: chain A residue 2704 GLU Chi-restraints excluded: chain A residue 2709 TRP Chi-restraints excluded: chain A residue 2872 LEU Chi-restraints excluded: chain A residue 2889 MET Chi-restraints excluded: chain A residue 2904 CYS Chi-restraints excluded: chain A residue 2938 SER Chi-restraints excluded: chain A residue 3029 LEU Chi-restraints excluded: chain A residue 3085 CYS Chi-restraints excluded: chain A residue 3119 CYS Chi-restraints excluded: chain A residue 3143 LEU Chi-restraints excluded: chain A residue 3157 LEU Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 213 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 251 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 148 optimal weight: 0.0010 chunk 190 optimal weight: 5.9990 chunk 147 optimal weight: 8.9990 chunk 219 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 260 optimal weight: 0.0370 chunk 162 optimal weight: 8.9990 chunk 158 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 overall best weight: 0.9468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21617 Z= 0.167 Angle : 0.550 11.647 29359 Z= 0.261 Chirality : 0.037 0.213 3496 Planarity : 0.004 0.079 3709 Dihedral : 4.188 56.843 2909 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.85 % Favored : 97.11 % Rotamer: Outliers : 2.76 % Allowed : 16.74 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.17), residues: 2668 helix: 1.93 (0.12), residues: 1922 sheet: None (None), residues: 0 loop : -0.17 (0.25), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1877 HIS 0.003 0.001 HIS A2647 PHE 0.012 0.001 PHE A1525 TYR 0.015 0.001 TYR A1799 ARG 0.002 0.000 ARG A2907 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 100 time to evaluate : 2.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8304 (tm-30) REVERT: A 228 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8569 (mtpm) REVERT: A 992 LEU cc_start: 0.6148 (OUTLIER) cc_final: 0.5018 (pp) REVERT: A 1025 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8269 (ttp) REVERT: A 1536 TYR cc_start: 0.8801 (t80) cc_final: 0.8478 (t80) REVERT: A 2055 MET cc_start: 0.8792 (mmt) cc_final: 0.8512 (mmm) REVERT: A 2421 ASN cc_start: 0.8920 (OUTLIER) cc_final: 0.8432 (t0) REVERT: A 2709 TRP cc_start: 0.8765 (OUTLIER) cc_final: 0.8494 (t60) REVERT: A 2938 SER cc_start: 0.8738 (OUTLIER) cc_final: 0.8453 (p) REVERT: A 3072 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.8807 (pp30) REVERT: B 213 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8719 (pp20) outliers start: 65 outliers final: 31 residues processed: 152 average time/residue: 1.1661 time to fit residues: 208.4186 Evaluate side-chains 133 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 93 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 731 ASP Chi-restraints excluded: chain A residue 733 ASP Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1025 MET Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1313 ILE Chi-restraints excluded: chain A residue 1495 ASP Chi-restraints excluded: chain A residue 1552 ASP Chi-restraints excluded: chain A residue 1579 LEU Chi-restraints excluded: chain A residue 1593 THR Chi-restraints excluded: chain A residue 1689 THR Chi-restraints excluded: chain A residue 1780 GLU Chi-restraints excluded: chain A residue 1782 ILE Chi-restraints excluded: chain A residue 1841 THR Chi-restraints excluded: chain A residue 2183 ILE Chi-restraints excluded: chain A residue 2259 VAL Chi-restraints excluded: chain A residue 2421 ASN Chi-restraints excluded: chain A residue 2486 THR Chi-restraints excluded: chain A residue 2704 GLU Chi-restraints excluded: chain A residue 2709 TRP Chi-restraints excluded: chain A residue 2793 LEU Chi-restraints excluded: chain A residue 2872 LEU Chi-restraints excluded: chain A residue 2889 MET Chi-restraints excluded: chain A residue 2904 CYS Chi-restraints excluded: chain A residue 2938 SER Chi-restraints excluded: chain A residue 3029 LEU Chi-restraints excluded: chain A residue 3067 LEU Chi-restraints excluded: chain A residue 3072 GLN Chi-restraints excluded: chain A residue 3119 CYS Chi-restraints excluded: chain A residue 3143 LEU Chi-restraints excluded: chain A residue 3157 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 213 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 160 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 155 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 128 optimal weight: 0.0070 chunk 24 optimal weight: 1.9990 chunk 204 optimal weight: 0.9990 overall best weight: 1.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1697 GLN B 293 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21617 Z= 0.186 Angle : 0.552 12.095 29359 Z= 0.263 Chirality : 0.038 0.189 3496 Planarity : 0.004 0.076 3709 Dihedral : 4.133 56.872 2908 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.07 % Favored : 96.89 % Rotamer: Outliers : 2.42 % Allowed : 17.21 % Favored : 80.37 % 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: 2.09 (0.17), residues: 2668 helix: 1.97 (0.12), residues: 1935 sheet: None (None), residues: 0 loop : -0.14 (0.25), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1699 HIS 0.003 0.001 HIS A2647 PHE 0.034 0.001 PHE A3070 TYR 0.021 0.001 TYR A1799 ARG 0.011 0.000 ARG A3137 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 94 time to evaluate : 2.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8336 (tm-30) REVERT: A 228 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8577 (mtpm) REVERT: A 992 LEU cc_start: 0.6115 (OUTLIER) cc_final: 0.4964 (pp) REVERT: A 1025 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8265 (ttp) REVERT: A 1650 MET cc_start: 0.9497 (OUTLIER) cc_final: 0.9091 (mmm) REVERT: A 2055 MET cc_start: 0.8820 (mmt) cc_final: 0.8483 (mmm) REVERT: A 2421 ASN cc_start: 0.8930 (OUTLIER) cc_final: 0.8444 (t0) REVERT: A 2938 SER cc_start: 0.8736 (OUTLIER) cc_final: 0.8447 (p) REVERT: B 49 GLN cc_start: 0.6993 (OUTLIER) cc_final: 0.6779 (tt0) REVERT: B 213 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8725 (pp20) outliers start: 57 outliers final: 30 residues processed: 139 average time/residue: 1.1515 time to fit residues: 188.6108 Evaluate side-chains 128 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 89 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 731 ASP Chi-restraints excluded: chain A residue 733 ASP Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1025 MET Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1313 ILE Chi-restraints excluded: chain A residue 1495 ASP Chi-restraints excluded: chain A residue 1552 ASP Chi-restraints excluded: chain A residue 1579 LEU Chi-restraints excluded: chain A residue 1593 THR Chi-restraints excluded: chain A residue 1650 MET Chi-restraints excluded: chain A residue 1689 THR Chi-restraints excluded: chain A residue 1780 GLU Chi-restraints excluded: chain A residue 1782 ILE Chi-restraints excluded: chain A residue 1841 THR Chi-restraints excluded: chain A residue 2183 ILE Chi-restraints excluded: chain A residue 2259 VAL Chi-restraints excluded: chain A residue 2421 ASN Chi-restraints excluded: chain A residue 2486 THR Chi-restraints excluded: chain A residue 2704 GLU Chi-restraints excluded: chain A residue 2872 LEU Chi-restraints excluded: chain A residue 2904 CYS Chi-restraints excluded: chain A residue 2938 SER Chi-restraints excluded: chain A residue 3029 LEU Chi-restraints excluded: chain A residue 3067 LEU Chi-restraints excluded: chain A residue 3119 CYS Chi-restraints excluded: chain A residue 3143 LEU Chi-restraints excluded: chain A residue 3157 LEU Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 213 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 236 optimal weight: 2.9990 chunk 249 optimal weight: 0.9990 chunk 227 optimal weight: 1.9990 chunk 242 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 190 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 219 optimal weight: 5.9990 chunk 229 optimal weight: 1.9990 chunk 241 optimal weight: 8.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1697 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21617 Z= 0.226 Angle : 0.572 12.888 29359 Z= 0.272 Chirality : 0.038 0.196 3496 Planarity : 0.004 0.070 3709 Dihedral : 4.150 57.125 2908 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.89 % Favored : 97.08 % Rotamer: Outliers : 2.29 % Allowed : 17.42 % Favored : 80.29 % 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: 2.09 (0.17), residues: 2668 helix: 1.96 (0.12), residues: 1939 sheet: None (None), residues: 0 loop : -0.13 (0.25), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1699 HIS 0.003 0.001 HIS A2647 PHE 0.030 0.001 PHE A3070 TYR 0.026 0.001 TYR A1799 ARG 0.009 0.000 ARG A 792 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 93 time to evaluate : 2.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8319 (tm-30) REVERT: A 228 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8586 (mtpm) REVERT: A 992 LEU cc_start: 0.6136 (OUTLIER) cc_final: 0.4961 (pp) REVERT: A 1025 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8224 (ttp) REVERT: A 1650 MET cc_start: 0.9509 (OUTLIER) cc_final: 0.9093 (mmm) REVERT: A 2055 MET cc_start: 0.8848 (mmt) cc_final: 0.8526 (mmm) REVERT: A 2421 ASN cc_start: 0.8961 (OUTLIER) cc_final: 0.8469 (t0) REVERT: A 2938 SER cc_start: 0.8746 (OUTLIER) cc_final: 0.8468 (p) REVERT: B 213 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8713 (pp20) outliers start: 54 outliers final: 34 residues processed: 137 average time/residue: 1.1034 time to fit residues: 179.7081 Evaluate side-chains 134 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 92 time to evaluate : 2.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 731 ASP Chi-restraints excluded: chain A residue 733 ASP Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1025 MET Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1313 ILE Chi-restraints excluded: chain A residue 1495 ASP Chi-restraints excluded: chain A residue 1552 ASP Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1579 LEU Chi-restraints excluded: chain A residue 1593 THR Chi-restraints excluded: chain A residue 1650 MET Chi-restraints excluded: chain A residue 1689 THR Chi-restraints excluded: chain A residue 1780 GLU Chi-restraints excluded: chain A residue 1782 ILE Chi-restraints excluded: chain A residue 1783 VAL Chi-restraints excluded: chain A residue 1841 THR Chi-restraints excluded: chain A residue 2183 ILE Chi-restraints excluded: chain A residue 2259 VAL Chi-restraints excluded: chain A residue 2421 ASN Chi-restraints excluded: chain A residue 2486 THR Chi-restraints excluded: chain A residue 2704 GLU Chi-restraints excluded: chain A residue 2872 LEU Chi-restraints excluded: chain A residue 2889 MET Chi-restraints excluded: chain A residue 2904 CYS Chi-restraints excluded: chain A residue 2938 SER Chi-restraints excluded: chain A residue 3029 LEU Chi-restraints excluded: chain A residue 3119 CYS Chi-restraints excluded: chain A residue 3143 LEU Chi-restraints excluded: chain A residue 3157 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 213 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 159 optimal weight: 0.0870 chunk 256 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 268 optimal weight: 4.9990 chunk 247 optimal weight: 6.9990 chunk 214 optimal weight: 0.7980 chunk 22 optimal weight: 0.0070 chunk 165 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1872 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2303 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21617 Z= 0.163 Angle : 0.556 13.011 29359 Z= 0.264 Chirality : 0.037 0.207 3496 Planarity : 0.004 0.069 3709 Dihedral : 4.101 56.175 2908 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.96 % Favored : 97.00 % Rotamer: Outliers : 1.91 % Allowed : 17.59 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.17), residues: 2668 helix: 2.07 (0.12), residues: 1928 sheet: None (None), residues: 0 loop : -0.14 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1877 HIS 0.003 0.000 HIS A2647 PHE 0.024 0.001 PHE A3070 TYR 0.020 0.001 TYR A1536 ARG 0.007 0.000 ARG A 792 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 97 time to evaluate : 2.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8381 (tm-30) REVERT: A 228 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8578 (mtpm) REVERT: A 992 LEU cc_start: 0.6060 (OUTLIER) cc_final: 0.4902 (pp) REVERT: A 1025 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8241 (ttp) REVERT: A 2055 MET cc_start: 0.8854 (mmt) cc_final: 0.8536 (mmm) REVERT: A 2421 ASN cc_start: 0.8903 (OUTLIER) cc_final: 0.8429 (t0) REVERT: A 2938 SER cc_start: 0.8714 (OUTLIER) cc_final: 0.8429 (p) REVERT: B 213 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8744 (pp20) outliers start: 45 outliers final: 31 residues processed: 134 average time/residue: 1.0457 time to fit residues: 167.1092 Evaluate side-chains 128 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 90 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 731 ASP Chi-restraints excluded: chain A residue 733 ASP Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1025 MET Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1313 ILE Chi-restraints excluded: chain A residue 1495 ASP Chi-restraints excluded: chain A residue 1552 ASP Chi-restraints excluded: chain A residue 1579 LEU Chi-restraints excluded: chain A residue 1593 THR Chi-restraints excluded: chain A residue 1689 THR Chi-restraints excluded: chain A residue 1780 GLU Chi-restraints excluded: chain A residue 1782 ILE Chi-restraints excluded: chain A residue 1783 VAL Chi-restraints excluded: chain A residue 1841 THR Chi-restraints excluded: chain A residue 2183 ILE Chi-restraints excluded: chain A residue 2259 VAL Chi-restraints excluded: chain A residue 2421 ASN Chi-restraints excluded: chain A residue 2486 THR Chi-restraints excluded: chain A residue 2704 GLU Chi-restraints excluded: chain A residue 2872 LEU Chi-restraints excluded: chain A residue 2889 MET Chi-restraints excluded: chain A residue 2904 CYS Chi-restraints excluded: chain A residue 2938 SER Chi-restraints excluded: chain A residue 3029 LEU Chi-restraints excluded: chain A residue 3119 CYS Chi-restraints excluded: chain A residue 3143 LEU Chi-restraints excluded: chain A residue 3157 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 213 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 170 optimal weight: 0.0970 chunk 228 optimal weight: 0.9980 chunk 65 optimal weight: 0.0010 chunk 197 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 214 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 220 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1872 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.072375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.056238 restraints weight = 60158.290| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.13 r_work: 0.2961 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 21617 Z= 0.154 Angle : 0.555 13.027 29359 Z= 0.262 Chirality : 0.037 0.193 3496 Planarity : 0.004 0.068 3709 Dihedral : 4.041 53.745 2908 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.77 % Favored : 97.19 % Rotamer: Outliers : 1.82 % Allowed : 17.93 % Favored : 80.25 % 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: 2.28 (0.17), residues: 2668 helix: 2.14 (0.12), residues: 1929 sheet: None (None), residues: 0 loop : -0.14 (0.25), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1878 HIS 0.003 0.000 HIS A1856 PHE 0.022 0.001 PHE A3070 TYR 0.012 0.001 TYR A2954 ARG 0.007 0.000 ARG A 792 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5249.41 seconds wall clock time: 94 minutes 11.10 seconds (5651.10 seconds total)