Starting phenix.real_space_refine on Sat Mar 7 01:29:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tax_10429/03_2026/6tax_10429.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tax_10429/03_2026/6tax_10429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6tax_10429/03_2026/6tax_10429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tax_10429/03_2026/6tax_10429.map" model { file = "/net/cci-nas-00/data/ceres_data/6tax_10429/03_2026/6tax_10429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tax_10429/03_2026/6tax_10429.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 3 5.49 5 Mg 1 5.21 5 S 207 5.16 5 C 22436 2.51 5 N 6060 2.21 5 O 6526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35235 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 35201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4416, 35201 Classifications: {'peptide': 4416} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 181, 'TRANS': 4234} Chain breaks: 15 Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 67, 'ASP:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 90 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, ' ZN': 2, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 26222 SG CYS A3962 90.097 130.185 218.776 1.00165.01 S ATOM 26386 SG CYS A3982 86.969 128.250 221.967 1.00171.20 S ATOM 26411 SG CYS A3985 90.556 128.936 222.124 1.00173.12 S ATOM 26112 SG CYS A3947 80.309 123.526 217.441 0.50141.40 S ATOM 26137 SG CYS A3950 77.879 120.194 215.933 1.00139.88 S ATOM 26265 SG CYS A3967 77.339 123.186 214.009 1.00159.05 S ATOM 26290 SG CYS A3970 75.799 123.843 217.598 1.00161.62 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N CYS A3947 " occ=0.50 ... (4 atoms not shown) pdb=" SG CYS A3947 " occ=0.50 Time building chain proxies: 7.63, per 1000 atoms: 0.22 Number of scatterers: 35235 At special positions: 0 Unit cell: (128.96, 150.8, 242.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 207 16.00 P 3 15.00 Mg 1 11.99 O 6526 8.00 N 6060 7.00 C 22436 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 951 " - pdb=" SG CYS A 992 " distance=2.03 Simple disulfide: pdb=" SG CYS A2605 " - pdb=" SG CYS A2653 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5203 " pdb="ZN ZN A5203 " - pdb=" ND1 HIS A3964 " pdb="ZN ZN A5203 " - pdb=" SG CYS A3962 " pdb="ZN ZN A5203 " - pdb=" SG CYS A3982 " pdb="ZN ZN A5203 " - pdb=" SG CYS A3985 " pdb=" ZN A5204 " pdb="ZN ZN A5204 " - pdb=" SG CYS A3950 " pdb="ZN ZN A5204 " - pdb=" SG CYS A3967 " pdb="ZN ZN A5204 " - pdb=" SG CYS A3970 " pdb="ZN ZN A5204 " - pdb=" SG CYS A3947 " Number of angles added : 9 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8458 Finding SS restraints... Secondary structure from input PDB file: 219 helices and 15 sheets defined 62.2% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.78 Creating SS restraints... Processing helix chain 'A' and resid 477 through 489 Processing helix chain 'A' and resid 496 through 512 Processing helix chain 'A' and resid 521 through 540 Processing helix chain 'A' and resid 592 through 602 Processing helix chain 'A' and resid 603 through 605 No H-bonds generated for 'chain 'A' and resid 603 through 605' Processing helix chain 'A' and resid 608 through 612 removed outlier: 4.005A pdb=" N LYS A 612 " --> pdb=" O VAL A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 618 removed outlier: 3.672A pdb=" N CYS A 618 " --> pdb=" O LEU A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 636 Processing helix chain 'A' and resid 637 through 640 removed outlier: 4.070A pdb=" N ARG A 640 " --> pdb=" O PRO A 637 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 637 through 640' Processing helix chain 'A' and resid 643 through 656 removed outlier: 3.563A pdb=" N CYS A 656 " --> pdb=" O LEU A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 666 removed outlier: 3.981A pdb=" N LEU A 665 " --> pdb=" O ASP A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 672 Processing helix chain 'A' and resid 688 through 694 removed outlier: 3.791A pdb=" N TRP A 692 " --> pdb=" O PRO A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 703 removed outlier: 3.895A pdb=" N GLU A 702 " --> pdb=" O SER A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 720 removed outlier: 3.585A pdb=" N GLN A 715 " --> pdb=" O SER A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 726 Processing helix chain 'A' and resid 728 through 736 removed outlier: 4.398A pdb=" N ARG A 732 " --> pdb=" O GLU A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 749 Processing helix chain 'A' and resid 750 through 757 removed outlier: 3.745A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 772 removed outlier: 4.005A pdb=" N ASP A 763 " --> pdb=" O VAL A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 801 removed outlier: 3.810A pdb=" N LYS A 784 " --> pdb=" O ASN A 780 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N TYR A 801 " --> pdb=" O LEU A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 827 Processing helix chain 'A' and resid 835 through 850 removed outlier: 3.905A pdb=" N ILE A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 889 removed outlier: 3.545A pdb=" N SER A 887 " --> pdb=" O ASN A 883 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 888 " --> pdb=" O TRP A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 918 removed outlier: 3.768A pdb=" N ILE A 918 " --> pdb=" O ARG A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 939 Processing helix chain 'A' and resid 942 through 951 removed outlier: 3.505A pdb=" N CYS A 951 " --> pdb=" O ILE A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 982 Processing helix chain 'A' and resid 994 through 1010 Processing helix chain 'A' and resid 1021 through 1031 Processing helix chain 'A' and resid 1032 through 1044 removed outlier: 3.796A pdb=" N GLN A1036 " --> pdb=" O PRO A1032 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASN A1044 " --> pdb=" O LEU A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1049 removed outlier: 3.735A pdb=" N ILE A1048 " --> pdb=" O ASN A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1072 Processing helix chain 'A' and resid 1079 through 1089 Processing helix chain 'A' and resid 1089 through 1102 removed outlier: 3.702A pdb=" N ARG A1102 " --> pdb=" O ASN A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1143 Processing helix chain 'A' and resid 1154 through 1159 Processing helix chain 'A' and resid 1166 through 1171 removed outlier: 3.554A pdb=" N ALA A1171 " --> pdb=" O LEU A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1190 through 1203 removed outlier: 3.760A pdb=" N ARG A1194 " --> pdb=" O SER A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1206 through 1218 Processing helix chain 'A' and resid 1234 through 1241 removed outlier: 3.753A pdb=" N LEU A1238 " --> pdb=" O LEU A1234 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU A1239 " --> pdb=" O PRO A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1257 removed outlier: 3.910A pdb=" N CYS A1245 " --> pdb=" O LEU A1241 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1270 Processing helix chain 'A' and resid 1271 through 1274 removed outlier: 3.960A pdb=" N VAL A1274 " --> pdb=" O LYS A1271 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1271 through 1274' Processing helix chain 'A' and resid 1276 through 1289 removed outlier: 3.676A pdb=" N LEU A1280 " --> pdb=" O LYS A1276 " (cutoff:3.500A) Processing helix chain 'A' and resid 1298 through 1329 removed outlier: 3.600A pdb=" N ARG A1302 " --> pdb=" O TRP A1298 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1346 removed outlier: 3.559A pdb=" N LEU A1342 " --> pdb=" O LEU A1338 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP A1346 " --> pdb=" O LEU A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1368 removed outlier: 4.276A pdb=" N LYS A1365 " --> pdb=" O PRO A1361 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA A1366 " --> pdb=" O GLN A1362 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1387 Processing helix chain 'A' and resid 1388 through 1398 Processing helix chain 'A' and resid 1400 through 1402 No H-bonds generated for 'chain 'A' and resid 1400 through 1402' Processing helix chain 'A' and resid 1403 through 1415 removed outlier: 3.919A pdb=" N ASP A1409 " --> pdb=" O LYS A1405 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE A1413 " --> pdb=" O ASP A1409 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER A1414 " --> pdb=" O LEU A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1440 removed outlier: 4.644A pdb=" N VAL A1425 " --> pdb=" O ASP A1421 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA A1426 " --> pdb=" O VAL A1422 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N SER A1437 " --> pdb=" O GLN A1433 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU A1438 " --> pdb=" O GLY A1434 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR A1440 " --> pdb=" O ALA A1436 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1464 removed outlier: 3.848A pdb=" N GLU A1457 " --> pdb=" O ASN A1453 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN A1464 " --> pdb=" O ARG A1460 " (cutoff:3.500A) Processing helix chain 'A' and resid 1467 through 1477 Processing helix chain 'A' and resid 1478 through 1487 removed outlier: 4.310A pdb=" N LYS A1486 " --> pdb=" O LEU A1482 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU A1487 " --> pdb=" O LYS A1483 " (cutoff:3.500A) Processing helix chain 'A' and resid 1497 through 1507 Processing helix chain 'A' and resid 1521 through 1525 Processing helix chain 'A' and resid 1545 through 1557 Processing helix chain 'A' and resid 1563 through 1594 removed outlier: 3.570A pdb=" N ASN A1567 " --> pdb=" O ASP A1563 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY A1594 " --> pdb=" O LEU A1590 " (cutoff:3.500A) Processing helix chain 'A' and resid 1630 through 1660 removed outlier: 3.637A pdb=" N GLU A1659 " --> pdb=" O GLN A1655 " (cutoff:3.500A) Processing helix chain 'A' and resid 1661 through 1666 removed outlier: 3.553A pdb=" N TYR A1666 " --> pdb=" O LEU A1663 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1679 removed outlier: 4.322A pdb=" N ARG A1679 " --> pdb=" O SER A1675 " (cutoff:3.500A) Processing helix chain 'A' and resid 1686 through 1691 Processing helix chain 'A' and resid 1699 through 1709 Processing helix chain 'A' and resid 1713 through 1726 Processing helix chain 'A' and resid 1726 through 1731 Processing helix chain 'A' and resid 1735 through 1750 removed outlier: 3.572A pdb=" N LYS A1739 " --> pdb=" O SER A1735 " (cutoff:3.500A) Processing helix chain 'A' and resid 1751 through 1754 Processing helix chain 'A' and resid 1760 through 1775 removed outlier: 3.594A pdb=" N THR A1773 " --> pdb=" O ALA A1769 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY A1775 " --> pdb=" O LEU A1771 " (cutoff:3.500A) Processing helix chain 'A' and resid 1798 through 1801 Processing helix chain 'A' and resid 1802 through 1810 removed outlier: 3.726A pdb=" N LEU A1807 " --> pdb=" O LEU A1803 " (cutoff:3.500A) Processing helix chain 'A' and resid 1832 through 1844 removed outlier: 3.899A pdb=" N VAL A1836 " --> pdb=" O THR A1832 " (cutoff:3.500A) Processing helix chain 'A' and resid 1859 through 1862 removed outlier: 3.803A pdb=" N LEU A1862 " --> pdb=" O ALA A1859 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1859 through 1862' Processing helix chain 'A' and resid 1863 through 1881 removed outlier: 3.832A pdb=" N ALA A1881 " --> pdb=" O LEU A1877 " (cutoff:3.500A) Processing helix chain 'A' and resid 1900 through 1905 Processing helix chain 'A' and resid 1906 through 1909 Processing helix chain 'A' and resid 1917 through 1930 Processing helix chain 'A' and resid 1937 through 1942 removed outlier: 3.949A pdb=" N THR A1940 " --> pdb=" O SER A1937 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A1941 " --> pdb=" O ALA A1938 " (cutoff:3.500A) Processing helix chain 'A' and resid 1959 through 1974 Processing helix chain 'A' and resid 1993 through 2002 removed outlier: 3.918A pdb=" N VAL A1997 " --> pdb=" O ASP A1993 " (cutoff:3.500A) Processing helix chain 'A' and resid 2027 through 2037 removed outlier: 3.655A pdb=" N PHE A2031 " --> pdb=" O GLY A2027 " (cutoff:3.500A) Processing helix chain 'A' and resid 2081 through 2085 Processing helix chain 'A' and resid 2086 through 2088 No H-bonds generated for 'chain 'A' and resid 2086 through 2088' Processing helix chain 'A' and resid 2116 through 2121 Processing helix chain 'A' and resid 2122 through 2137 Proline residue: A2128 - end of helix removed outlier: 4.080A pdb=" N ARG A2134 " --> pdb=" O GLN A2130 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLN A2137 " --> pdb=" O LYS A2133 " (cutoff:3.500A) Processing helix chain 'A' and resid 2154 through 2166 Processing helix chain 'A' and resid 2172 through 2193 removed outlier: 3.514A pdb=" N LEU A2176 " --> pdb=" O SER A2172 " (cutoff:3.500A) Processing helix chain 'A' and resid 2194 through 2203 Processing helix chain 'A' and resid 2207 through 2224 removed outlier: 3.791A pdb=" N PHE A2211 " --> pdb=" O GLY A2207 " (cutoff:3.500A) Processing helix chain 'A' and resid 2250 through 2255 removed outlier: 3.820A pdb=" N LEU A2255 " --> pdb=" O ALA A2251 " (cutoff:3.500A) Processing helix chain 'A' and resid 2309 through 2318 Processing helix chain 'A' and resid 2330 through 2342 Processing helix chain 'A' and resid 2357 through 2374 Processing helix chain 'A' and resid 2387 through 2400 Processing helix chain 'A' and resid 2417 through 2440 removed outlier: 3.629A pdb=" N ILE A2421 " --> pdb=" O THR A2417 " (cutoff:3.500A) Processing helix chain 'A' and resid 2455 through 2464 Processing helix chain 'A' and resid 2492 through 2501 removed outlier: 3.554A pdb=" N ILE A2496 " --> pdb=" O SER A2492 " (cutoff:3.500A) Processing helix chain 'A' and resid 2521 through 2525 Processing helix chain 'A' and resid 2550 through 2564 removed outlier: 4.411A pdb=" N ASP A2564 " --> pdb=" O GLN A2560 " (cutoff:3.500A) Processing helix chain 'A' and resid 2571 through 2589 Processing helix chain 'A' and resid 2600 through 2615 Processing helix chain 'A' and resid 2617 through 2631 removed outlier: 3.729A pdb=" N LYS A2621 " --> pdb=" O ASP A2617 " (cutoff:3.500A) Processing helix chain 'A' and resid 2642 through 2654 Processing helix chain 'A' and resid 2660 through 2669 Processing helix chain 'A' and resid 2673 through 2677 removed outlier: 3.734A pdb=" N ASN A2677 " --> pdb=" O LYS A2674 " (cutoff:3.500A) Processing helix chain 'A' and resid 2678 through 2697 removed outlier: 3.782A pdb=" N ILE A2682 " --> pdb=" O SER A2678 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A2697 " --> pdb=" O PHE A2693 " (cutoff:3.500A) Processing helix chain 'A' and resid 2706 through 2722 Processing helix chain 'A' and resid 2737 through 2747 Processing helix chain 'A' and resid 2775 through 2791 removed outlier: 3.959A pdb=" N ILE A2779 " --> pdb=" O THR A2775 " (cutoff:3.500A) Processing helix chain 'A' and resid 2817 through 2819 No H-bonds generated for 'chain 'A' and resid 2817 through 2819' Processing helix chain 'A' and resid 2820 through 2825 removed outlier: 3.573A pdb=" N LEU A2824 " --> pdb=" O THR A2820 " (cutoff:3.500A) Processing helix chain 'A' and resid 2851 through 2856 removed outlier: 3.792A pdb=" N MET A2855 " --> pdb=" O ASP A2851 " (cutoff:3.500A) Processing helix chain 'A' and resid 2867 through 2880 Processing helix chain 'A' and resid 2885 through 2890 Processing helix chain 'A' and resid 2892 through 2907 Processing helix chain 'A' and resid 2913 through 2932 removed outlier: 3.632A pdb=" N TYR A2917 " --> pdb=" O GLY A2913 " (cutoff:3.500A) Processing helix chain 'A' and resid 2936 through 2948 Processing helix chain 'A' and resid 2955 through 2961 Processing helix chain 'A' and resid 2974 through 2984 removed outlier: 3.570A pdb=" N LEU A2978 " --> pdb=" O SER A2974 " (cutoff:3.500A) Processing helix chain 'A' and resid 3010 through 3018 removed outlier: 3.765A pdb=" N ILE A3014 " --> pdb=" O VAL A3010 " (cutoff:3.500A) Processing helix chain 'A' and resid 3037 through 3056 Processing helix chain 'A' and resid 3071 through 3077 removed outlier: 3.856A pdb=" N GLN A3077 " --> pdb=" O ASP A3073 " (cutoff:3.500A) Processing helix chain 'A' and resid 3113 through 3120 removed outlier: 3.857A pdb=" N PHE A3120 " --> pdb=" O VAL A3116 " (cutoff:3.500A) Processing helix chain 'A' and resid 3124 through 3128 removed outlier: 3.549A pdb=" N LEU A3128 " --> pdb=" O ILE A3125 " (cutoff:3.500A) Processing helix chain 'A' and resid 3140 through 3159 Processing helix chain 'A' and resid 3172 through 3177 Processing helix chain 'A' and resid 3183 through 3197 removed outlier: 3.952A pdb=" N SER A3187 " --> pdb=" O ASP A3183 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY A3197 " --> pdb=" O VAL A3193 " (cutoff:3.500A) Processing helix chain 'A' and resid 3204 through 3219 removed outlier: 3.967A pdb=" N LYS A3208 " --> pdb=" O GLU A3204 " (cutoff:3.500A) Processing helix chain 'A' and resid 3222 through 3229 Processing helix chain 'A' and resid 3230 through 3232 No H-bonds generated for 'chain 'A' and resid 3230 through 3232' Processing helix chain 'A' and resid 3236 through 3249 Processing helix chain 'A' and resid 3254 through 3263 removed outlier: 3.522A pdb=" N PHE A3258 " --> pdb=" O SER A3254 " (cutoff:3.500A) Processing helix chain 'A' and resid 3287 through 3295 Processing helix chain 'A' and resid 3309 through 3311 No H-bonds generated for 'chain 'A' and resid 3309 through 3311' Processing helix chain 'A' and resid 3313 through 3326 removed outlier: 3.967A pdb=" N PHE A3317 " --> pdb=" O THR A3313 " (cutoff:3.500A) Processing helix chain 'A' and resid 3348 through 3365 removed outlier: 4.426A pdb=" N SER A3352 " --> pdb=" O GLN A3348 " (cutoff:3.500A) Processing helix chain 'A' and resid 3413 through 3420 removed outlier: 3.670A pdb=" N LEU A3417 " --> pdb=" O ASP A3413 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A3420 " --> pdb=" O LYS A3416 " (cutoff:3.500A) Processing helix chain 'A' and resid 3421 through 3426 removed outlier: 3.821A pdb=" N PHE A3426 " --> pdb=" O ILE A3422 " (cutoff:3.500A) Processing helix chain 'A' and resid 3476 through 3490 removed outlier: 4.979A pdb=" N GLN A3486 " --> pdb=" O GLN A3482 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N GLY A3487 " --> pdb=" O SER A3483 " (cutoff:3.500A) Processing helix chain 'A' and resid 3501 through 3512 Processing helix chain 'A' and resid 3517 through 3539 Processing helix chain 'A' and resid 3548 through 3555 Processing helix chain 'A' and resid 3556 through 3564 Processing helix chain 'A' and resid 3565 through 3590 removed outlier: 3.621A pdb=" N THR A3569 " --> pdb=" O THR A3565 " (cutoff:3.500A) Proline residue: A3580 - end of helix Processing helix chain 'A' and resid 3595 through 3600 Processing helix chain 'A' and resid 3604 through 3615 removed outlier: 3.694A pdb=" N GLN A3608 " --> pdb=" O PRO A3604 " (cutoff:3.500A) Processing helix chain 'A' and resid 3657 through 3676 removed outlier: 3.736A pdb=" N ILE A3661 " --> pdb=" O PHE A3657 " (cutoff:3.500A) Processing helix chain 'A' and resid 3680 through 3692 removed outlier: 3.785A pdb=" N THR A3692 " --> pdb=" O ILE A3688 " (cutoff:3.500A) Processing helix chain 'A' and resid 3692 through 3699 Processing helix chain 'A' and resid 3702 through 3722 Processing helix chain 'A' and resid 3727 through 3746 Processing helix chain 'A' and resid 3762 through 3784 removed outlier: 7.729A pdb=" N THR A3773 " --> pdb=" O GLN A3769 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ARG A3774 " --> pdb=" O HIS A3770 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE A3778 " --> pdb=" O ARG A3774 " (cutoff:3.500A) Processing helix chain 'A' and resid 3787 through 3800 removed outlier: 3.876A pdb=" N SER A3791 " --> pdb=" O GLN A3787 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN A3794 " --> pdb=" O SER A3790 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA A3796 " --> pdb=" O LEU A3792 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLU A3797 " --> pdb=" O SER A3793 " (cutoff:3.500A) Processing helix chain 'A' and resid 3807 through 3824 removed outlier: 3.671A pdb=" N ASP A3823 " --> pdb=" O MET A3819 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A3824 " --> pdb=" O LEU A3820 " (cutoff:3.500A) Processing helix chain 'A' and resid 3828 through 3839 Processing helix chain 'A' and resid 3839 through 3847 Processing helix chain 'A' and resid 3856 through 3890 removed outlier: 5.300A pdb=" N LEU A3885 " --> pdb=" O GLU A3881 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLY A3886 " --> pdb=" O HIS A3882 " (cutoff:3.500A) Processing helix chain 'A' and resid 3894 through 3910 removed outlier: 4.072A pdb=" N THR A3900 " --> pdb=" O PRO A3896 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER A3903 " --> pdb=" O THR A3899 " (cutoff:3.500A) Processing helix chain 'A' and resid 3917 through 3941 removed outlier: 3.894A pdb=" N PHE A3921 " --> pdb=" O THR A3917 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG A3941 " --> pdb=" O LYS A3937 " (cutoff:3.500A) Processing helix chain 'A' and resid 3967 through 3976 removed outlier: 4.341A pdb=" N ILE A3976 " --> pdb=" O GLN A3972 " (cutoff:3.500A) Processing helix chain 'A' and resid 3999 through 4026 removed outlier: 3.719A pdb=" N LYS A4003 " --> pdb=" O GLN A3999 " (cutoff:3.500A) Processing helix chain 'A' and resid 4035 through 4045 removed outlier: 3.562A pdb=" N ILE A4039 " --> pdb=" O GLU A4035 " (cutoff:3.500A) Processing helix chain 'A' and resid 4082 through 4089 Processing helix chain 'A' and resid 4092 through 4095 removed outlier: 3.596A pdb=" N GLU A4095 " --> pdb=" O SER A4092 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4092 through 4095' Processing helix chain 'A' and resid 4096 through 4111 removed outlier: 3.578A pdb=" N ILE A4100 " --> pdb=" O VAL A4096 " (cutoff:3.500A) Processing helix chain 'A' and resid 4116 through 4138 removed outlier: 4.209A pdb=" N LEU A4120 " --> pdb=" O ASP A4116 " (cutoff:3.500A) Processing helix chain 'A' and resid 4142 through 4156 removed outlier: 3.830A pdb=" N VAL A4146 " --> pdb=" O ASN A4142 " (cutoff:3.500A) Processing helix chain 'A' and resid 4171 through 4198 removed outlier: 3.646A pdb=" N GLU A4197 " --> pdb=" O SER A4193 " (cutoff:3.500A) Processing helix chain 'A' and resid 4204 through 4219 Processing helix chain 'A' and resid 4222 through 4236 Processing helix chain 'A' and resid 4237 through 4245 removed outlier: 3.939A pdb=" N VAL A4241 " --> pdb=" O GLY A4237 " (cutoff:3.500A) Processing helix chain 'A' and resid 4251 through 4255 Processing helix chain 'A' and resid 4256 through 4262 removed outlier: 3.903A pdb=" N ILE A4260 " --> pdb=" O PRO A4256 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA A4261 " --> pdb=" O ARG A4257 " (cutoff:3.500A) Processing helix chain 'A' and resid 4271 through 4276 removed outlier: 3.510A pdb=" N LEU A4274 " --> pdb=" O ASP A4271 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A4275 " --> pdb=" O ARG A4272 " (cutoff:3.500A) Processing helix chain 'A' and resid 4279 through 4293 removed outlier: 3.807A pdb=" N VAL A4283 " --> pdb=" O GLU A4279 " (cutoff:3.500A) Processing helix chain 'A' and resid 4296 through 4304 removed outlier: 4.037A pdb=" N GLY A4300 " --> pdb=" O THR A4296 " (cutoff:3.500A) Processing helix chain 'A' and resid 4309 through 4331 removed outlier: 4.144A pdb=" N SER A4331 " --> pdb=" O ALA A4327 " (cutoff:3.500A) Processing helix chain 'A' and resid 4342 through 4353 Processing helix chain 'A' and resid 4358 through 4370 removed outlier: 3.554A pdb=" N SER A4367 " --> pdb=" O CYS A4363 " (cutoff:3.500A) Processing helix chain 'A' and resid 4384 through 4403 removed outlier: 3.915A pdb=" N THR A4388 " --> pdb=" O ILE A4384 " (cutoff:3.500A) Processing helix chain 'A' and resid 4405 through 4407 No H-bonds generated for 'chain 'A' and resid 4405 through 4407' Processing helix chain 'A' and resid 4408 through 4417 Processing helix chain 'A' and resid 4418 through 4422 removed outlier: 3.713A pdb=" N ALA A4422 " --> pdb=" O VAL A4419 " (cutoff:3.500A) Processing helix chain 'A' and resid 4522 through 4544 removed outlier: 3.824A pdb=" N HIS A4543 " --> pdb=" O VAL A4539 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN A4544 " --> pdb=" O GLY A4540 " (cutoff:3.500A) Processing helix chain 'A' and resid 4544 through 4552 removed outlier: 3.683A pdb=" N LEU A4548 " --> pdb=" O ASN A4544 " (cutoff:3.500A) Processing helix chain 'A' and resid 4559 through 4578 Processing helix chain 'A' and resid 4581 through 4596 Processing helix chain 'A' and resid 4613 through 4633 Processing helix chain 'A' and resid 4638 through 4648 Processing helix chain 'A' and resid 4655 through 4660 removed outlier: 3.832A pdb=" N LYS A4659 " --> pdb=" O ASN A4655 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A4660 " --> pdb=" O PRO A4656 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4655 through 4660' Processing helix chain 'A' and resid 4665 through 4669 removed outlier: 4.126A pdb=" N PHE A4668 " --> pdb=" O PRO A4665 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A4669 " --> pdb=" O ALA A4666 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4665 through 4669' Processing helix chain 'A' and resid 4691 through 4702 Processing helix chain 'A' and resid 4708 through 4717 Processing helix chain 'A' and resid 4717 through 4722 Processing helix chain 'A' and resid 4723 through 4725 No H-bonds generated for 'chain 'A' and resid 4723 through 4725' Processing helix chain 'A' and resid 4726 through 4741 Processing helix chain 'A' and resid 4751 through 4757 Processing helix chain 'A' and resid 4761 through 4783 Processing helix chain 'A' and resid 4785 through 4790 Processing helix chain 'A' and resid 4820 through 4845 removed outlier: 3.660A pdb=" N THR A4824 " --> pdb=" O GLY A4820 " (cutoff:3.500A) Processing helix chain 'A' and resid 4859 through 4863 removed outlier: 3.748A pdb=" N HIS A4862 " --> pdb=" O ALA A4859 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A4863 " --> pdb=" O ASP A4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4859 through 4863' Processing helix chain 'A' and resid 4867 through 4872 Processing helix chain 'A' and resid 4872 through 4878 Processing helix chain 'A' and resid 4895 through 4905 Processing helix chain 'A' and resid 4930 through 4941 Processing helix chain 'A' and resid 4947 through 4957 removed outlier: 3.837A pdb=" N SER A4952 " --> pdb=" O ASN A4948 " (cutoff:3.500A) Processing helix chain 'A' and resid 4960 through 4980 removed outlier: 4.061A pdb=" N THR A4980 " --> pdb=" O GLY A4976 " (cutoff:3.500A) Processing helix chain 'A' and resid 4988 through 4994 Processing helix chain 'A' and resid 5003 through 5011 removed outlier: 3.834A pdb=" N LEU A5007 " --> pdb=" O THR A5003 " (cutoff:3.500A) Processing helix chain 'A' and resid 5012 through 5013 No H-bonds generated for 'chain 'A' and resid 5012 through 5013' Processing helix chain 'A' and resid 5014 through 5016 No H-bonds generated for 'chain 'A' and resid 5014 through 5016' Processing helix chain 'A' and resid 5017 through 5036 Processing helix chain 'A' and resid 5045 through 5049 Processing helix chain 'A' and resid 5053 through 5066 removed outlier: 4.157A pdb=" N GLU A5066 " --> pdb=" O THR A5062 " (cutoff:3.500A) Processing helix chain 'A' and resid 5068 through 5084 removed outlier: 4.283A pdb=" N LEU A5074 " --> pdb=" O ASP A5070 " (cutoff:3.500A) Processing helix chain 'A' and resid 5098 through 5107 Processing helix chain 'A' and resid 5114 through 5121 removed outlier: 3.955A pdb=" N VAL A5118 " --> pdb=" O ILE A5114 " (cutoff:3.500A) Processing helix chain 'A' and resid 5131 through 5149 removed outlier: 3.655A pdb=" N GLY A5149 " --> pdb=" O ARG A5145 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1149 through 1151 removed outlier: 6.497A pdb=" N GLN A1149 " --> pdb=" O VAL A1232 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 1541 through 1544 removed outlier: 3.673A pdb=" N GLY A1612 " --> pdb=" O TYR A1606 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1792 through 1796 removed outlier: 6.218A pdb=" N ASN A1793 " --> pdb=" O ILE A1890 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N CYS A1892 " --> pdb=" O ASN A1793 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE A1795 " --> pdb=" O CYS A1892 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N TYR A1854 " --> pdb=" O VAL A1889 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LEU A1891 " --> pdb=" O TYR A1854 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU A1856 " --> pdb=" O LEU A1891 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU A1825 " --> pdb=" O LEU A1857 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 1982 through 1987 removed outlier: 6.505A pdb=" N LYS A1983 " --> pdb=" O HIS A2017 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ASP A2019 " --> pdb=" O LYS A1983 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE A1985 " --> pdb=" O ASP A2019 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER A1953 " --> pdb=" O ILE A2061 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N VAL A2091 " --> pdb=" O VAL A1948 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE A1950 " --> pdb=" O VAL A2091 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 2040 through 2042 Processing sheet with id=AA6, first strand: chain 'A' and resid 2266 through 2269 Processing sheet with id=AA7, first strand: chain 'A' and resid 2282 through 2285 Processing sheet with id=AA8, first strand: chain 'A' and resid 2407 through 2411 removed outlier: 6.402A pdb=" N LYS A2408 " --> pdb=" O PHE A2446 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ASP A2448 " --> pdb=" O LYS A2408 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL A2410 " --> pdb=" O ASP A2448 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL A2377 " --> pdb=" O ALA A2483 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N CYS A2485 " --> pdb=" O VAL A2377 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE A2379 " --> pdb=" O CYS A2485 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2467 through 2468 Processing sheet with id=AB1, first strand: chain 'A' and resid 2762 through 2768 removed outlier: 6.216A pdb=" N GLN A2762 " --> pdb=" O VAL A2799 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N VAL A2801 " --> pdb=" O GLN A2762 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N HIS A2764 " --> pdb=" O VAL A2801 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL A2803 " --> pdb=" O HIS A2764 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL A2766 " --> pdb=" O VAL A2803 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N GLY A2841 " --> pdb=" O TYR A2798 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N SER A2800 " --> pdb=" O GLY A2841 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N VAL A2843 " --> pdb=" O SER A2800 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL A2802 " --> pdb=" O VAL A2843 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE A2845 " --> pdb=" O VAL A2802 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU A2804 " --> pdb=" O ILE A2845 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU A2726 " --> pdb=" O GLY A2844 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N SER A2846 " --> pdb=" O LEU A2726 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N LEU A2728 " --> pdb=" O SER A2846 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE A2727 " --> pdb=" O VAL A2861 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 3026 through 3028 removed outlier: 3.540A pdb=" N VAL A3060 " --> pdb=" O GLU A3026 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL A3059 " --> pdb=" O ILE A3108 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ILE A3110 " --> pdb=" O VAL A3059 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU A3061 " --> pdb=" O ILE A3110 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N GLU A3112 " --> pdb=" O LEU A3061 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 3080 through 3082 Processing sheet with id=AB4, first strand: chain 'A' and resid 3304 through 3307 removed outlier: 9.257A pdb=" N ARG A3397 " --> pdb=" O ALA A3272 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N PHE A3274 " --> pdb=" O ARG A3397 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N VAL A3399 " --> pdb=" O PHE A3274 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLU A3276 " --> pdb=" O VAL A3399 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3958 through 3959 Processing sheet with id=AB6, first strand: chain 'A' and resid 4880 through 4883 1800 hydrogen bonds defined for protein. 5283 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.55 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10236 1.33 - 1.46: 7316 1.46 - 1.58: 18095 1.58 - 1.70: 5 1.70 - 1.82: 303 Bond restraints: 35955 Sorted by residual: bond pdb=" C4 ATP A5201 " pdb=" C5 ATP A5201 " ideal model delta sigma weight residual 1.388 1.454 -0.066 1.00e-02 1.00e+04 4.31e+01 bond pdb=" C5 ATP A5201 " pdb=" C6 ATP A5201 " ideal model delta sigma weight residual 1.409 1.466 -0.057 1.00e-02 1.00e+04 3.28e+01 bond pdb=" C5 ATP A5201 " pdb=" N7 ATP A5201 " ideal model delta sigma weight residual 1.387 1.334 0.053 1.00e-02 1.00e+04 2.78e+01 bond pdb=" C4 ATP A5201 " pdb=" N9 ATP A5201 " ideal model delta sigma weight residual 1.374 1.322 0.052 1.00e-02 1.00e+04 2.68e+01 bond pdb=" C8 ATP A5201 " pdb=" N7 ATP A5201 " ideal model delta sigma weight residual 1.310 1.350 -0.040 1.00e-02 1.00e+04 1.61e+01 ... (remaining 35950 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.83: 47949 3.83 - 7.65: 649 7.65 - 11.48: 56 11.48 - 15.31: 7 15.31 - 19.14: 2 Bond angle restraints: 48663 Sorted by residual: angle pdb=" PB ATP A5201 " pdb=" O3B ATP A5201 " pdb=" PG ATP A5201 " ideal model delta sigma weight residual 139.87 121.13 18.74 1.00e+00 1.00e+00 3.51e+02 angle pdb=" PA ATP A5201 " pdb=" O3A ATP A5201 " pdb=" PB ATP A5201 " ideal model delta sigma weight residual 136.83 121.91 14.92 1.00e+00 1.00e+00 2.23e+02 angle pdb=" C5 ATP A5201 " pdb=" C4 ATP A5201 " pdb=" N3 ATP A5201 " ideal model delta sigma weight residual 126.80 118.94 7.86 1.00e+00 1.00e+00 6.18e+01 angle pdb=" N3 ATP A5201 " pdb=" C4 ATP A5201 " pdb=" N9 ATP A5201 " ideal model delta sigma weight residual 127.04 134.61 -7.57 1.15e+00 7.59e-01 4.35e+01 angle pdb=" N GLU A4279 " pdb=" CA GLU A4279 " pdb=" C GLU A4279 " ideal model delta sigma weight residual 114.56 107.03 7.53 1.27e+00 6.20e-01 3.52e+01 ... (remaining 48658 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 20577 16.70 - 33.40: 1088 33.40 - 50.10: 197 50.10 - 66.79: 16 66.79 - 83.49: 34 Dihedral angle restraints: 21912 sinusoidal: 8926 harmonic: 12986 Sorted by residual: dihedral pdb=" CA VAL A3122 " pdb=" C VAL A3122 " pdb=" N PRO A3123 " pdb=" CA PRO A3123 " ideal model delta harmonic sigma weight residual 180.00 119.33 60.67 0 5.00e+00 4.00e-02 1.47e+02 dihedral pdb=" CA GLU A1170 " pdb=" C GLU A1170 " pdb=" N ALA A1171 " pdb=" CA ALA A1171 " ideal model delta harmonic sigma weight residual 180.00 132.87 47.13 0 5.00e+00 4.00e-02 8.88e+01 dihedral pdb=" CA GLU A4165 " pdb=" C GLU A4165 " pdb=" N PRO A4166 " pdb=" CA PRO A4166 " ideal model delta harmonic sigma weight residual -180.00 -136.64 -43.36 0 5.00e+00 4.00e-02 7.52e+01 ... (remaining 21909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 4550 0.080 - 0.159: 860 0.159 - 0.239: 88 0.239 - 0.318: 7 0.318 - 0.398: 6 Chirality restraints: 5511 Sorted by residual: chirality pdb=" CB ILE A1373 " pdb=" CA ILE A1373 " pdb=" CG1 ILE A1373 " pdb=" CG2 ILE A1373 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" CB ILE A 896 " pdb=" CA ILE A 896 " pdb=" CG1 ILE A 896 " pdb=" CG2 ILE A 896 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CB VAL A4048 " pdb=" CA VAL A4048 " pdb=" CG1 VAL A4048 " pdb=" CG2 VAL A4048 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 5508 not shown) Planarity restraints: 6228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A3122 " -0.075 5.00e-02 4.00e+02 1.14e-01 2.08e+01 pdb=" N PRO A3123 " 0.197 5.00e-02 4.00e+02 pdb=" CA PRO A3123 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO A3123 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 687 " -0.061 5.00e-02 4.00e+02 9.23e-02 1.36e+01 pdb=" N PRO A 688 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO A 688 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 688 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A5023 " -0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C GLN A5023 " 0.063 2.00e-02 2.50e+03 pdb=" O GLN A5023 " -0.024 2.00e-02 2.50e+03 pdb=" N PHE A5024 " -0.021 2.00e-02 2.50e+03 ... (remaining 6225 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 380 2.63 - 3.20: 31347 3.20 - 3.77: 55725 3.77 - 4.33: 75767 4.33 - 4.90: 123466 Nonbonded interactions: 286685 Sorted by model distance: nonbonded pdb=" OG SER A1961 " pdb="MG MG A5202 " model vdw 2.065 2.170 nonbonded pdb=" OG1 THR A1820 " pdb=" OD1 ASP A1822 " model vdw 2.225 3.040 nonbonded pdb=" OH TYR A1666 " pdb=" O MET A1690 " model vdw 2.264 3.040 nonbonded pdb=" OH TYR A3664 " pdb=" OG1 THR A3692 " model vdw 2.273 3.040 nonbonded pdb=" O LEU A2945 " pdb=" OG SER A2949 " model vdw 2.274 3.040 ... (remaining 286680 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 2.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 39.300 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.060 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 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 : 0.010 0.516 35965 Z= 0.403 Angle : 1.164 53.393 48676 Z= 0.610 Chirality : 0.063 0.398 5511 Planarity : 0.008 0.114 6228 Dihedral : 11.276 83.492 13448 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.49 % Favored : 90.32 % Rotamer: Outliers : 0.46 % Allowed : 2.82 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.81 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.10 (0.10), residues: 4319 helix: -2.34 (0.08), residues: 2479 sheet: -1.45 (0.31), residues: 232 loop : -3.35 (0.13), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A2127 TYR 0.048 0.004 TYR A2057 PHE 0.058 0.004 PHE A2960 TRP 0.033 0.004 TRP A5135 HIS 0.023 0.003 HIS A2688 Details of bonding type rmsd covalent geometry : bond 0.00911 (35955) covalent geometry : angle 1.12727 (48663) SS BOND : bond 0.00328 ( 2) SS BOND : angle 3.11467 ( 4) hydrogen bonds : bond 0.13884 ( 1800) hydrogen bonds : angle 6.75277 ( 5283) metal coordination : bond 0.24871 ( 8) metal coordination : angle 21.32586 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 473 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 643 GLN cc_start: 0.7687 (mm-40) cc_final: 0.7354 (mm110) REVERT: A 874 LEU cc_start: 0.8139 (tt) cc_final: 0.7901 (mt) REVERT: A 1256 LEU cc_start: 0.8957 (mt) cc_final: 0.8581 (mt) REVERT: A 1275 ASP cc_start: 0.7833 (t0) cc_final: 0.7608 (t0) REVERT: A 1277 TYR cc_start: 0.7987 (m-80) cc_final: 0.7773 (m-10) REVERT: A 1378 GLN cc_start: 0.7237 (tt0) cc_final: 0.6789 (tt0) REVERT: A 1521 SER cc_start: 0.8542 (m) cc_final: 0.8305 (p) REVERT: A 2164 ILE cc_start: 0.8434 (tt) cc_final: 0.8167 (pt) REVERT: A 2215 PHE cc_start: 0.7836 (t80) cc_final: 0.7585 (t80) REVERT: A 2216 MET cc_start: 0.7092 (mmt) cc_final: 0.6593 (mmt) REVERT: A 2304 LYS cc_start: 0.8395 (mttp) cc_final: 0.8162 (mmmm) REVERT: A 2420 MET cc_start: 0.8342 (mtt) cc_final: 0.8117 (mtt) REVERT: A 2476 ASP cc_start: 0.6899 (p0) cc_final: 0.6683 (p0) REVERT: A 2801 VAL cc_start: 0.9141 (OUTLIER) cc_final: 0.8889 (m) REVERT: A 2923 MET cc_start: 0.8421 (mtp) cc_final: 0.8098 (mtt) REVERT: A 3644 HIS cc_start: 0.7174 (m170) cc_final: 0.6126 (m-70) REVERT: A 3675 ILE cc_start: 0.8101 (mt) cc_final: 0.7730 (tt) REVERT: A 3984 TYR cc_start: 0.8607 (t80) cc_final: 0.8400 (t80) REVERT: A 4003 LYS cc_start: 0.8771 (mmmt) cc_final: 0.8529 (tppt) REVERT: A 4007 LYS cc_start: 0.8607 (mtmt) cc_final: 0.8243 (pttt) REVERT: A 4316 TYR cc_start: 0.7157 (m-10) cc_final: 0.6780 (m-10) REVERT: A 4356 LEU cc_start: 0.8718 (pt) cc_final: 0.8476 (pp) REVERT: A 4507 SER cc_start: 0.8272 (m) cc_final: 0.8071 (t) REVERT: A 4600 GLN cc_start: 0.7003 (mp-120) cc_final: 0.6749 (mp10) REVERT: A 4668 PHE cc_start: 0.7427 (p90) cc_final: 0.7119 (p90) REVERT: A 4856 SER cc_start: 0.7697 (m) cc_final: 0.7450 (p) REVERT: A 4941 MET cc_start: 0.7240 (mtp) cc_final: 0.6997 (mtp) REVERT: A 5084 LEU cc_start: 0.8590 (mt) cc_final: 0.8359 (mp) REVERT: A 5107 MET cc_start: 0.6979 (tmm) cc_final: 0.6284 (tmm) REVERT: A 5127 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8229 (tm) REVERT: A 5146 GLN cc_start: 0.7617 (pt0) cc_final: 0.7288 (tm-30) outliers start: 18 outliers final: 5 residues processed: 489 average time/residue: 0.2825 time to fit residues: 207.6500 Evaluate side-chains 307 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 300 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 2801 VAL Chi-restraints excluded: chain A residue 2957 LEU Chi-restraints excluded: chain A residue 3376 VAL Chi-restraints excluded: chain A residue 3965 VAL Chi-restraints excluded: chain A residue 4858 VAL Chi-restraints excluded: chain A residue 5127 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 432 optimal weight: 0.8980 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 4.9990 chunk 424 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 781 GLN A 822 HIS A 827 ASN A 831 ASN A1186 HIS A1378 GLN A1429 HIS A1453 ASN A1579 ASN A1595 ASN A1660 HIS A1770 HIS A1816 GLN A1920 ASN A1930 GLN A2139 GLN A2161 HIS A2270 ASN A2273 HIS A2413 HIS A2480 HIS A2790 GLN ** A2847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2942 HIS A2981 GLN ** A3017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3095 HIS A3252 HIS A3337 GLN A3542 GLN ** A3608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3644 HIS A3705 GLN A3914 ASN A4008 HIS A4176 GLN A4196 GLN A4242 GLN A4249 HIS A4382 ASN A4420 ASN A4543 HIS A4560 GLN ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4587 HIS A4679 HIS A4697 HIS A4757 HIS A4834 HIS A4842 GLN ** A4846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4873 ASN A4886 GLN A4892 GLN ** A4909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4932 HIS A4957 GLN A5017 HIS A5028 HIS A5056 HIS A5146 GLN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.085225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.070252 restraints weight = 114740.831| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.95 r_work: 0.3221 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 35965 Z= 0.147 Angle : 0.689 12.502 48676 Z= 0.353 Chirality : 0.043 0.269 5511 Planarity : 0.005 0.086 6228 Dihedral : 6.566 88.635 4806 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.43 % Favored : 91.50 % Rotamer: Outliers : 1.15 % Allowed : 6.77 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.12), residues: 4319 helix: -0.54 (0.10), residues: 2482 sheet: -1.26 (0.32), residues: 233 loop : -2.97 (0.14), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A4155 TYR 0.030 0.002 TYR A3901 PHE 0.034 0.002 PHE A2371 TRP 0.017 0.002 TRP A5022 HIS 0.009 0.001 HIS A4587 Details of bonding type rmsd covalent geometry : bond 0.00325 (35955) covalent geometry : angle 0.68441 (48663) SS BOND : bond 0.00080 ( 2) SS BOND : angle 1.58308 ( 4) hydrogen bonds : bond 0.04143 ( 1800) hydrogen bonds : angle 4.77430 ( 5283) metal coordination : bond 0.00759 ( 8) metal coordination : angle 5.55427 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 324 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 643 GLN cc_start: 0.7932 (mm-40) cc_final: 0.7637 (mm110) REVERT: A 644 ARG cc_start: 0.8261 (mtm110) cc_final: 0.7539 (mtm110) REVERT: A 648 TYR cc_start: 0.7115 (m-10) cc_final: 0.6870 (m-80) REVERT: A 1149 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7833 (mp10) REVERT: A 1166 LYS cc_start: 0.8297 (mttt) cc_final: 0.8043 (ttmt) REVERT: A 1275 ASP cc_start: 0.8424 (t0) cc_final: 0.8134 (t0) REVERT: A 1313 HIS cc_start: 0.8237 (OUTLIER) cc_final: 0.8035 (t-90) REVERT: A 1521 SER cc_start: 0.8343 (m) cc_final: 0.7980 (p) REVERT: A 1905 PHE cc_start: 0.7861 (m-10) cc_final: 0.7580 (m-80) REVERT: A 2164 ILE cc_start: 0.8639 (tt) cc_final: 0.8350 (pt) REVERT: A 2215 PHE cc_start: 0.7692 (t80) cc_final: 0.7412 (t80) REVERT: A 2216 MET cc_start: 0.7418 (mmt) cc_final: 0.7020 (mmt) REVERT: A 2304 LYS cc_start: 0.8396 (mttp) cc_final: 0.7936 (mmmm) REVERT: A 2407 MET cc_start: 0.8658 (ttt) cc_final: 0.8293 (ttt) REVERT: A 2801 VAL cc_start: 0.8995 (OUTLIER) cc_final: 0.8771 (m) REVERT: A 2855 MET cc_start: 0.6734 (mpp) cc_final: 0.5440 (mpp) REVERT: A 2923 MET cc_start: 0.8605 (mtp) cc_final: 0.8343 (mtt) REVERT: A 3675 ILE cc_start: 0.8418 (mt) cc_final: 0.7932 (tt) REVERT: A 3731 MET cc_start: 0.7362 (tpp) cc_final: 0.6875 (tmm) REVERT: A 3814 MET cc_start: 0.8526 (ttm) cc_final: 0.8002 (tpp) REVERT: A 3984 TYR cc_start: 0.8601 (t80) cc_final: 0.8034 (t80) REVERT: A 4007 LYS cc_start: 0.8792 (mtmt) cc_final: 0.8346 (pttt) REVERT: A 4255 PHE cc_start: 0.7767 (m-10) cc_final: 0.7384 (m-10) REVERT: A 4262 GLN cc_start: 0.7619 (pt0) cc_final: 0.7291 (pt0) REVERT: A 4316 TYR cc_start: 0.7158 (m-10) cc_final: 0.6861 (m-10) REVERT: A 4356 LEU cc_start: 0.8928 (pt) cc_final: 0.8672 (pp) REVERT: A 4507 SER cc_start: 0.8375 (m) cc_final: 0.8001 (p) REVERT: A 4600 GLN cc_start: 0.7198 (mp-120) cc_final: 0.6990 (mp10) REVERT: A 4630 ARG cc_start: 0.7999 (ttm170) cc_final: 0.7749 (ttm110) REVERT: A 4668 PHE cc_start: 0.7554 (p90) cc_final: 0.7205 (p90) REVERT: A 4809 PHE cc_start: 0.8313 (t80) cc_final: 0.8082 (t80) REVERT: A 4856 SER cc_start: 0.8002 (m) cc_final: 0.7552 (p) REVERT: A 4908 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8244 (pt) REVERT: A 5084 LEU cc_start: 0.8569 (mt) cc_final: 0.8308 (mp) REVERT: A 5127 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8038 (tm) REVERT: A 5146 GLN cc_start: 0.7742 (pt0) cc_final: 0.7433 (tm-30) outliers start: 45 outliers final: 21 residues processed: 358 average time/residue: 0.2456 time to fit residues: 137.7152 Evaluate side-chains 313 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 287 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1149 GLN Chi-restraints excluded: chain A residue 1313 HIS Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 2143 THR Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2357 THR Chi-restraints excluded: chain A residue 2563 VAL Chi-restraints excluded: chain A residue 2801 VAL Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 2957 LEU Chi-restraints excluded: chain A residue 3598 LEU Chi-restraints excluded: chain A residue 3692 THR Chi-restraints excluded: chain A residue 3965 VAL Chi-restraints excluded: chain A residue 4083 VAL Chi-restraints excluded: chain A residue 4634 HIS Chi-restraints excluded: chain A residue 4858 VAL Chi-restraints excluded: chain A residue 4903 ILE Chi-restraints excluded: chain A residue 4908 LEU Chi-restraints excluded: chain A residue 5127 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 328 optimal weight: 0.0470 chunk 373 optimal weight: 6.9990 chunk 205 optimal weight: 0.0670 chunk 344 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 436 optimal weight: 3.9990 chunk 383 optimal weight: 0.9990 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 632 HIS ** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1757 HIS A2273 HIS A3017 GLN A3037 GLN A3267 HIS A3705 GLN A4176 GLN ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4623 HIS A4757 HIS ** A4846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4892 GLN ** A4909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.085912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.070924 restraints weight = 114893.900| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.65 r_work: 0.3261 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 35965 Z= 0.117 Angle : 0.620 11.158 48676 Z= 0.315 Chirality : 0.041 0.230 5511 Planarity : 0.005 0.095 6228 Dihedral : 6.002 87.793 4805 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.17 % Favored : 91.78 % Rotamer: Outliers : 1.44 % Allowed : 8.05 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.13), residues: 4319 helix: 0.27 (0.10), residues: 2500 sheet: -0.98 (0.31), residues: 246 loop : -2.76 (0.15), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A3772 TYR 0.022 0.001 TYR A1277 PHE 0.028 0.001 PHE A2371 TRP 0.014 0.001 TRP A2541 HIS 0.010 0.001 HIS A3644 Details of bonding type rmsd covalent geometry : bond 0.00254 (35955) covalent geometry : angle 0.61758 (48663) SS BOND : bond 0.00421 ( 2) SS BOND : angle 1.68150 ( 4) hydrogen bonds : bond 0.03530 ( 1800) hydrogen bonds : angle 4.28583 ( 5283) metal coordination : bond 0.00704 ( 8) metal coordination : angle 4.25245 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 308 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 643 GLN cc_start: 0.7918 (mm-40) cc_final: 0.7665 (mm110) REVERT: A 644 ARG cc_start: 0.8271 (mtm110) cc_final: 0.7580 (mtm110) REVERT: A 1166 LYS cc_start: 0.8285 (mttt) cc_final: 0.8073 (ttmt) REVERT: A 1275 ASP cc_start: 0.8401 (t0) cc_final: 0.8125 (t0) REVERT: A 1521 SER cc_start: 0.8312 (m) cc_final: 0.7965 (p) REVERT: A 1596 MET cc_start: 0.8065 (mmm) cc_final: 0.7463 (mmm) REVERT: A 1905 PHE cc_start: 0.7802 (m-80) cc_final: 0.7442 (m-80) REVERT: A 2164 ILE cc_start: 0.8600 (tt) cc_final: 0.8356 (pt) REVERT: A 2215 PHE cc_start: 0.7620 (t80) cc_final: 0.7329 (t80) REVERT: A 2304 LYS cc_start: 0.8284 (mttp) cc_final: 0.7981 (ttmm) REVERT: A 2855 MET cc_start: 0.6680 (mpp) cc_final: 0.5640 (mpp) REVERT: A 2923 MET cc_start: 0.8546 (mtp) cc_final: 0.8267 (mtt) REVERT: A 3659 TRP cc_start: 0.7161 (p-90) cc_final: 0.6779 (p-90) REVERT: A 3735 MET cc_start: 0.7217 (mtp) cc_final: 0.6800 (ptm) REVERT: A 4007 LYS cc_start: 0.8753 (mtmt) cc_final: 0.8551 (pttt) REVERT: A 4014 MET cc_start: 0.7492 (mtm) cc_final: 0.7207 (mtm) REVERT: A 4236 ARG cc_start: 0.7681 (mmm-85) cc_final: 0.7251 (mmm-85) REVERT: A 4244 PHE cc_start: 0.8011 (m-80) cc_final: 0.7691 (t80) REVERT: A 4255 PHE cc_start: 0.7829 (m-10) cc_final: 0.7256 (m-10) REVERT: A 4262 GLN cc_start: 0.7676 (pt0) cc_final: 0.7463 (pt0) REVERT: A 4316 TYR cc_start: 0.7127 (m-10) cc_final: 0.6830 (m-10) REVERT: A 4507 SER cc_start: 0.8286 (m) cc_final: 0.7949 (p) REVERT: A 4668 PHE cc_start: 0.7500 (p90) cc_final: 0.7226 (p90) REVERT: A 4739 LYS cc_start: 0.8244 (tmtt) cc_final: 0.7967 (tttm) REVERT: A 4809 PHE cc_start: 0.8269 (t80) cc_final: 0.8029 (t80) REVERT: A 4908 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8141 (pt) REVERT: A 5107 MET cc_start: 0.7520 (tmm) cc_final: 0.7210 (tpp) REVERT: A 5127 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8046 (tm) REVERT: A 5146 GLN cc_start: 0.7643 (pt0) cc_final: 0.7396 (tm-30) outliers start: 56 outliers final: 26 residues processed: 346 average time/residue: 0.2511 time to fit residues: 136.8996 Evaluate side-chains 295 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 267 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 2276 MET Chi-restraints excluded: chain A residue 2357 THR Chi-restraints excluded: chain A residue 2557 GLN Chi-restraints excluded: chain A residue 2563 VAL Chi-restraints excluded: chain A residue 2574 CYS Chi-restraints excluded: chain A residue 2716 MET Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 2957 LEU Chi-restraints excluded: chain A residue 3160 VAL Chi-restraints excluded: chain A residue 3692 THR Chi-restraints excluded: chain A residue 3965 VAL Chi-restraints excluded: chain A residue 4083 VAL Chi-restraints excluded: chain A residue 4362 ARG Chi-restraints excluded: chain A residue 4634 HIS Chi-restraints excluded: chain A residue 4858 VAL Chi-restraints excluded: chain A residue 4903 ILE Chi-restraints excluded: chain A residue 4908 LEU Chi-restraints excluded: chain A residue 4941 MET Chi-restraints excluded: chain A residue 5127 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 106 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 412 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 chunk 15 optimal weight: 0.0030 chunk 329 optimal weight: 20.0000 chunk 300 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 218 optimal weight: 0.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 632 HIS A1378 GLN A1453 ASN A2273 HIS ** A3644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4587 HIS A4757 HIS ** A4846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5014 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.085030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.069989 restraints weight = 114939.259| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.65 r_work: 0.3236 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35965 Z= 0.146 Angle : 0.625 10.641 48676 Z= 0.316 Chirality : 0.042 0.188 5511 Planarity : 0.004 0.093 6228 Dihedral : 5.875 87.513 4804 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.50 % Favored : 91.46 % Rotamer: Outliers : 1.74 % Allowed : 8.82 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.13), residues: 4319 helix: 0.55 (0.11), residues: 2506 sheet: -0.87 (0.31), residues: 256 loop : -2.64 (0.15), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A4598 TYR 0.021 0.002 TYR A2146 PHE 0.059 0.002 PHE A3939 TRP 0.013 0.001 TRP A4555 HIS 0.006 0.001 HIS A 832 Details of bonding type rmsd covalent geometry : bond 0.00338 (35955) covalent geometry : angle 0.62245 (48663) SS BOND : bond 0.00104 ( 2) SS BOND : angle 2.03062 ( 4) hydrogen bonds : bond 0.03571 ( 1800) hydrogen bonds : angle 4.18860 ( 5283) metal coordination : bond 0.00738 ( 8) metal coordination : angle 3.75958 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 278 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 643 GLN cc_start: 0.7744 (mm-40) cc_final: 0.7456 (mm-40) REVERT: A 717 MET cc_start: 0.8179 (mtm) cc_final: 0.7337 (mtt) REVERT: A 1166 LYS cc_start: 0.8333 (mttt) cc_final: 0.8091 (ttmt) REVERT: A 1275 ASP cc_start: 0.8396 (t0) cc_final: 0.8111 (t0) REVERT: A 1521 SER cc_start: 0.8366 (m) cc_final: 0.8063 (p) REVERT: A 1596 MET cc_start: 0.8110 (mmm) cc_final: 0.7566 (mmp) REVERT: A 1905 PHE cc_start: 0.7843 (m-80) cc_final: 0.7626 (m-80) REVERT: A 2024 VAL cc_start: 0.8042 (OUTLIER) cc_final: 0.7767 (t) REVERT: A 2164 ILE cc_start: 0.8570 (tt) cc_final: 0.8358 (pt) REVERT: A 2304 LYS cc_start: 0.8346 (mttp) cc_final: 0.8044 (tppt) REVERT: A 2316 ARG cc_start: 0.8316 (tpp80) cc_final: 0.8086 (tpp80) REVERT: A 2512 GLU cc_start: 0.8098 (pp20) cc_final: 0.7791 (pp20) REVERT: A 2855 MET cc_start: 0.6816 (mpp) cc_final: 0.5895 (mpp) REVERT: A 2923 MET cc_start: 0.8574 (mtp) cc_final: 0.8302 (mtt) REVERT: A 3731 MET cc_start: 0.7001 (tmm) cc_final: 0.6500 (tmm) REVERT: A 3806 MET cc_start: 0.8309 (tpt) cc_final: 0.7037 (tpt) REVERT: A 3814 MET cc_start: 0.8552 (ttm) cc_final: 0.8209 (tpp) REVERT: A 4007 LYS cc_start: 0.8797 (mtmt) cc_final: 0.8398 (pttt) REVERT: A 4206 ARG cc_start: 0.7762 (mmm-85) cc_final: 0.7490 (mpt90) REVERT: A 4255 PHE cc_start: 0.7869 (m-10) cc_final: 0.7335 (m-10) REVERT: A 4262 GLN cc_start: 0.7734 (pt0) cc_final: 0.7486 (pt0) REVERT: A 4289 LYS cc_start: 0.8323 (pttt) cc_final: 0.7911 (pttm) REVERT: A 4316 TYR cc_start: 0.7119 (m-10) cc_final: 0.6852 (m-10) REVERT: A 4507 SER cc_start: 0.8295 (m) cc_final: 0.7964 (p) REVERT: A 4668 PHE cc_start: 0.7535 (p90) cc_final: 0.7267 (p90) REVERT: A 4739 LYS cc_start: 0.8264 (tmtt) cc_final: 0.8016 (tttm) REVERT: A 4809 PHE cc_start: 0.8296 (t80) cc_final: 0.8087 (t80) REVERT: A 4908 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8277 (pt) REVERT: A 5107 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.6708 (tpp) REVERT: A 5127 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8052 (tm) REVERT: A 5128 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.7470 (tpt) REVERT: A 5146 GLN cc_start: 0.7706 (pt0) cc_final: 0.7458 (tm-30) outliers start: 68 outliers final: 40 residues processed: 328 average time/residue: 0.2355 time to fit residues: 121.9080 Evaluate side-chains 308 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 263 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 832 HIS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1420 ILE Chi-restraints excluded: chain A residue 1468 LEU Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 1948 VAL Chi-restraints excluded: chain A residue 2024 VAL Chi-restraints excluded: chain A residue 2151 VAL Chi-restraints excluded: chain A residue 2276 MET Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2357 THR Chi-restraints excluded: chain A residue 2563 VAL Chi-restraints excluded: chain A residue 2574 CYS Chi-restraints excluded: chain A residue 2628 HIS Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 2924 VAL Chi-restraints excluded: chain A residue 2957 LEU Chi-restraints excluded: chain A residue 3160 VAL Chi-restraints excluded: chain A residue 3243 SER Chi-restraints excluded: chain A residue 3395 LEU Chi-restraints excluded: chain A residue 3692 THR Chi-restraints excluded: chain A residue 3719 LEU Chi-restraints excluded: chain A residue 3759 LEU Chi-restraints excluded: chain A residue 3965 VAL Chi-restraints excluded: chain A residue 4083 VAL Chi-restraints excluded: chain A residue 4634 HIS Chi-restraints excluded: chain A residue 4658 THR Chi-restraints excluded: chain A residue 4747 VAL Chi-restraints excluded: chain A residue 4858 VAL Chi-restraints excluded: chain A residue 4903 ILE Chi-restraints excluded: chain A residue 4908 LEU Chi-restraints excluded: chain A residue 4941 MET Chi-restraints excluded: chain A residue 4999 MET Chi-restraints excluded: chain A residue 5107 MET Chi-restraints excluded: chain A residue 5127 LEU Chi-restraints excluded: chain A residue 5128 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 425 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 289 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 236 optimal weight: 3.9990 chunk 223 optimal weight: 0.7980 chunk 403 optimal weight: 0.7980 chunk 160 optimal weight: 0.9980 chunk 220 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 632 HIS A2273 HIS ** A3644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4249 HIS A4757 HIS ** A4846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.085308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.070467 restraints weight = 115411.645| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.75 r_work: 0.3242 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3243 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35965 Z= 0.127 Angle : 0.612 9.841 48676 Z= 0.309 Chirality : 0.042 0.417 5511 Planarity : 0.004 0.090 6228 Dihedral : 5.747 87.325 4804 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.43 % Favored : 91.55 % Rotamer: Outliers : 1.95 % Allowed : 9.44 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.13), residues: 4319 helix: 0.77 (0.11), residues: 2512 sheet: -0.79 (0.31), residues: 256 loop : -2.54 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1327 TYR 0.028 0.001 TYR A 729 PHE 0.041 0.001 PHE A3939 TRP 0.018 0.001 TRP A4555 HIS 0.007 0.001 HIS A 832 Details of bonding type rmsd covalent geometry : bond 0.00287 (35955) covalent geometry : angle 0.61021 (48663) SS BOND : bond 0.00018 ( 2) SS BOND : angle 1.34759 ( 4) hydrogen bonds : bond 0.03416 ( 1800) hydrogen bonds : angle 4.08291 ( 5283) metal coordination : bond 0.00670 ( 8) metal coordination : angle 3.23472 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 281 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 643 GLN cc_start: 0.7728 (mm-40) cc_final: 0.7463 (mm-40) REVERT: A 717 MET cc_start: 0.8035 (mtm) cc_final: 0.7572 (mtt) REVERT: A 795 MET cc_start: 0.7868 (mtm) cc_final: 0.7650 (mtm) REVERT: A 1166 LYS cc_start: 0.8349 (mttt) cc_final: 0.8085 (ttmt) REVERT: A 1263 PHE cc_start: 0.7579 (m-10) cc_final: 0.7304 (m-80) REVERT: A 1275 ASP cc_start: 0.8424 (t0) cc_final: 0.8142 (t0) REVERT: A 1521 SER cc_start: 0.8350 (m) cc_final: 0.8046 (p) REVERT: A 1596 MET cc_start: 0.8058 (mmm) cc_final: 0.7516 (mmp) REVERT: A 1690 MET cc_start: 0.8964 (mtp) cc_final: 0.8731 (mtm) REVERT: A 1823 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.4086 (mp0) REVERT: A 1905 PHE cc_start: 0.7821 (m-80) cc_final: 0.7422 (m-80) REVERT: A 2024 VAL cc_start: 0.8049 (OUTLIER) cc_final: 0.7769 (t) REVERT: A 2164 ILE cc_start: 0.8635 (tt) cc_final: 0.8389 (pt) REVERT: A 2304 LYS cc_start: 0.8425 (mttp) cc_final: 0.8065 (mtpp) REVERT: A 2316 ARG cc_start: 0.8322 (tpp80) cc_final: 0.8117 (tpp80) REVERT: A 2512 GLU cc_start: 0.8088 (pp20) cc_final: 0.7790 (pp20) REVERT: A 2855 MET cc_start: 0.6771 (mpp) cc_final: 0.5904 (mpp) REVERT: A 2923 MET cc_start: 0.8552 (mtp) cc_final: 0.8269 (mtt) REVERT: A 3806 MET cc_start: 0.8310 (tpt) cc_final: 0.6950 (tpt) REVERT: A 3814 MET cc_start: 0.8547 (ttm) cc_final: 0.8177 (tpp) REVERT: A 4002 ARG cc_start: 0.8039 (tpp-160) cc_final: 0.7660 (tpp-160) REVERT: A 4007 LYS cc_start: 0.8780 (mtmt) cc_final: 0.8371 (pttt) REVERT: A 4244 PHE cc_start: 0.8105 (m-80) cc_final: 0.7645 (t80) REVERT: A 4255 PHE cc_start: 0.7847 (m-10) cc_final: 0.7299 (m-10) REVERT: A 4316 TYR cc_start: 0.7134 (m-10) cc_final: 0.6899 (m-10) REVERT: A 4507 SER cc_start: 0.8285 (m) cc_final: 0.7935 (p) REVERT: A 4600 GLN cc_start: 0.7186 (mp10) cc_final: 0.6984 (mp10) REVERT: A 4668 PHE cc_start: 0.7492 (p90) cc_final: 0.7197 (p90) REVERT: A 4739 LYS cc_start: 0.8296 (tmtt) cc_final: 0.8066 (tttm) REVERT: A 4809 PHE cc_start: 0.8317 (t80) cc_final: 0.8078 (t80) REVERT: A 4872 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8218 (mt) REVERT: A 4908 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8355 (pt) REVERT: A 5107 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.6778 (tpp) REVERT: A 5127 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8099 (tm) REVERT: A 5128 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7526 (tpt) outliers start: 76 outliers final: 47 residues processed: 337 average time/residue: 0.2266 time to fit residues: 123.0670 Evaluate side-chains 319 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 265 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 832 HIS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1313 HIS Chi-restraints excluded: chain A residue 1332 THR Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1420 ILE Chi-restraints excluded: chain A residue 1823 GLU Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 1948 VAL Chi-restraints excluded: chain A residue 2024 VAL Chi-restraints excluded: chain A residue 2151 VAL Chi-restraints excluded: chain A residue 2276 MET Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2557 GLN Chi-restraints excluded: chain A residue 2563 VAL Chi-restraints excluded: chain A residue 2628 HIS Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 2924 VAL Chi-restraints excluded: chain A residue 2957 LEU Chi-restraints excluded: chain A residue 3128 LEU Chi-restraints excluded: chain A residue 3160 VAL Chi-restraints excluded: chain A residue 3376 VAL Chi-restraints excluded: chain A residue 3395 LEU Chi-restraints excluded: chain A residue 3399 VAL Chi-restraints excluded: chain A residue 3652 TYR Chi-restraints excluded: chain A residue 3675 ILE Chi-restraints excluded: chain A residue 3692 THR Chi-restraints excluded: chain A residue 3711 GLN Chi-restraints excluded: chain A residue 3719 LEU Chi-restraints excluded: chain A residue 3759 LEU Chi-restraints excluded: chain A residue 3781 ILE Chi-restraints excluded: chain A residue 3965 VAL Chi-restraints excluded: chain A residue 4083 VAL Chi-restraints excluded: chain A residue 4634 HIS Chi-restraints excluded: chain A residue 4658 THR Chi-restraints excluded: chain A residue 4747 VAL Chi-restraints excluded: chain A residue 4858 VAL Chi-restraints excluded: chain A residue 4872 LEU Chi-restraints excluded: chain A residue 4903 ILE Chi-restraints excluded: chain A residue 4908 LEU Chi-restraints excluded: chain A residue 4941 MET Chi-restraints excluded: chain A residue 4991 VAL Chi-restraints excluded: chain A residue 4999 MET Chi-restraints excluded: chain A residue 5107 MET Chi-restraints excluded: chain A residue 5127 LEU Chi-restraints excluded: chain A residue 5128 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 407 optimal weight: 0.9980 chunk 281 optimal weight: 2.9990 chunk 336 optimal weight: 0.3980 chunk 264 optimal weight: 0.4980 chunk 347 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 239 optimal weight: 0.6980 chunk 184 optimal weight: 0.6980 chunk 286 optimal weight: 2.9990 chunk 208 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 632 HIS A 749 ASN A2273 HIS A3538 GLN ** A3644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3979 GLN A4757 HIS ** A4846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.085804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.070748 restraints weight = 115498.997| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.65 r_work: 0.3260 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35965 Z= 0.118 Angle : 0.609 12.295 48676 Z= 0.305 Chirality : 0.041 0.230 5511 Planarity : 0.004 0.088 6228 Dihedral : 5.625 86.424 4804 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.17 % Favored : 91.80 % Rotamer: Outliers : 1.90 % Allowed : 9.62 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.13), residues: 4319 helix: 0.95 (0.11), residues: 2507 sheet: -0.74 (0.33), residues: 238 loop : -2.42 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A4362 TYR 0.019 0.001 TYR A 729 PHE 0.035 0.001 PHE A3939 TRP 0.021 0.001 TRP A4555 HIS 0.007 0.001 HIS A 832 Details of bonding type rmsd covalent geometry : bond 0.00266 (35955) covalent geometry : angle 0.60779 (48663) SS BOND : bond 0.00186 ( 2) SS BOND : angle 2.15012 ( 4) hydrogen bonds : bond 0.03322 ( 1800) hydrogen bonds : angle 3.99893 ( 5283) metal coordination : bond 0.00554 ( 8) metal coordination : angle 2.59869 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 277 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 643 GLN cc_start: 0.7765 (mm-40) cc_final: 0.7527 (mm-40) REVERT: A 665 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8141 (mp) REVERT: A 795 MET cc_start: 0.7891 (mtm) cc_final: 0.7665 (mtm) REVERT: A 1166 LYS cc_start: 0.8343 (mttt) cc_final: 0.7955 (ttmt) REVERT: A 1263 PHE cc_start: 0.7588 (m-10) cc_final: 0.7317 (m-80) REVERT: A 1275 ASP cc_start: 0.8270 (t0) cc_final: 0.8021 (t0) REVERT: A 1521 SER cc_start: 0.8358 (m) cc_final: 0.8074 (p) REVERT: A 1596 MET cc_start: 0.7990 (mmm) cc_final: 0.7481 (mmp) REVERT: A 1690 MET cc_start: 0.8952 (mtp) cc_final: 0.8713 (mtm) REVERT: A 1823 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.4078 (mp0) REVERT: A 1905 PHE cc_start: 0.7764 (m-80) cc_final: 0.7365 (m-80) REVERT: A 2024 VAL cc_start: 0.7976 (OUTLIER) cc_final: 0.7670 (t) REVERT: A 2164 ILE cc_start: 0.8604 (tt) cc_final: 0.8380 (pt) REVERT: A 2304 LYS cc_start: 0.8395 (mttp) cc_final: 0.8055 (mtpp) REVERT: A 2316 ARG cc_start: 0.8264 (tpp80) cc_final: 0.8063 (tpp80) REVERT: A 2512 GLU cc_start: 0.7987 (pp20) cc_final: 0.7739 (pp20) REVERT: A 2855 MET cc_start: 0.6669 (mpp) cc_final: 0.5817 (mpp) REVERT: A 3806 MET cc_start: 0.8292 (tpt) cc_final: 0.6961 (tpt) REVERT: A 4002 ARG cc_start: 0.8036 (tpp-160) cc_final: 0.7515 (tpp-160) REVERT: A 4007 LYS cc_start: 0.8759 (mtmt) cc_final: 0.8279 (pttt) REVERT: A 4244 PHE cc_start: 0.8072 (m-80) cc_final: 0.7733 (t80) REVERT: A 4255 PHE cc_start: 0.7842 (m-80) cc_final: 0.7107 (m-10) REVERT: A 4316 TYR cc_start: 0.7067 (m-10) cc_final: 0.6816 (m-10) REVERT: A 4507 SER cc_start: 0.8241 (m) cc_final: 0.7919 (p) REVERT: A 4600 GLN cc_start: 0.7077 (mp10) cc_final: 0.6822 (mp10) REVERT: A 4668 PHE cc_start: 0.7559 (p90) cc_final: 0.7347 (p90) REVERT: A 4739 LYS cc_start: 0.8249 (tmtt) cc_final: 0.8041 (tttm) REVERT: A 4795 PRO cc_start: 0.8342 (Cg_exo) cc_final: 0.8111 (Cg_endo) REVERT: A 4809 PHE cc_start: 0.8319 (t80) cc_final: 0.8089 (t80) REVERT: A 4872 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8217 (mt) REVERT: A 4908 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8245 (pt) REVERT: A 5107 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.6921 (tpp) REVERT: A 5127 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8066 (tm) REVERT: A 5128 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7553 (tpt) outliers start: 74 outliers final: 52 residues processed: 332 average time/residue: 0.2313 time to fit residues: 123.5311 Evaluate side-chains 319 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 259 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 729 TYR Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 832 HIS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1313 HIS Chi-restraints excluded: chain A residue 1332 THR Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1468 LEU Chi-restraints excluded: chain A residue 1823 GLU Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 1948 VAL Chi-restraints excluded: chain A residue 2024 VAL Chi-restraints excluded: chain A residue 2151 VAL Chi-restraints excluded: chain A residue 2276 MET Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2357 THR Chi-restraints excluded: chain A residue 2557 GLN Chi-restraints excluded: chain A residue 2563 VAL Chi-restraints excluded: chain A residue 2574 CYS Chi-restraints excluded: chain A residue 2628 HIS Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 2924 VAL Chi-restraints excluded: chain A residue 2957 LEU Chi-restraints excluded: chain A residue 3128 LEU Chi-restraints excluded: chain A residue 3160 VAL Chi-restraints excluded: chain A residue 3243 SER Chi-restraints excluded: chain A residue 3395 LEU Chi-restraints excluded: chain A residue 3399 VAL Chi-restraints excluded: chain A residue 3519 ARG Chi-restraints excluded: chain A residue 3692 THR Chi-restraints excluded: chain A residue 3711 GLN Chi-restraints excluded: chain A residue 3719 LEU Chi-restraints excluded: chain A residue 3757 PHE Chi-restraints excluded: chain A residue 3759 LEU Chi-restraints excluded: chain A residue 3781 ILE Chi-restraints excluded: chain A residue 3965 VAL Chi-restraints excluded: chain A residue 4083 VAL Chi-restraints excluded: chain A residue 4270 MET Chi-restraints excluded: chain A residue 4291 VAL Chi-restraints excluded: chain A residue 4378 ILE Chi-restraints excluded: chain A residue 4634 HIS Chi-restraints excluded: chain A residue 4658 THR Chi-restraints excluded: chain A residue 4747 VAL Chi-restraints excluded: chain A residue 4858 VAL Chi-restraints excluded: chain A residue 4872 LEU Chi-restraints excluded: chain A residue 4908 LEU Chi-restraints excluded: chain A residue 4941 MET Chi-restraints excluded: chain A residue 4991 VAL Chi-restraints excluded: chain A residue 4999 MET Chi-restraints excluded: chain A residue 5107 MET Chi-restraints excluded: chain A residue 5127 LEU Chi-restraints excluded: chain A residue 5128 MET Chi-restraints excluded: chain A residue 5132 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 140 optimal weight: 0.8980 chunk 265 optimal weight: 0.5980 chunk 108 optimal weight: 0.8980 chunk 193 optimal weight: 0.0570 chunk 414 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 196 optimal weight: 9.9990 chunk 411 optimal weight: 0.0050 chunk 102 optimal weight: 0.7980 chunk 199 optimal weight: 0.0070 chunk 98 optimal weight: 2.9990 overall best weight: 0.2930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 632 HIS A1295 GLN A1595 ASN A2273 HIS A3799 HIS A4262 GLN A4757 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.086796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.071818 restraints weight = 115214.327| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.66 r_work: 0.3288 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 35965 Z= 0.105 Angle : 0.597 11.424 48676 Z= 0.298 Chirality : 0.040 0.209 5511 Planarity : 0.004 0.086 6228 Dihedral : 5.486 85.384 4804 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.78 % Favored : 92.17 % Rotamer: Outliers : 1.77 % Allowed : 10.13 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.13), residues: 4319 helix: 1.09 (0.11), residues: 2507 sheet: -0.64 (0.33), residues: 238 loop : -2.35 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1114 TYR 0.017 0.001 TYR A2146 PHE 0.029 0.001 PHE A3939 TRP 0.016 0.001 TRP A4555 HIS 0.007 0.001 HIS A 832 Details of bonding type rmsd covalent geometry : bond 0.00224 (35955) covalent geometry : angle 0.59618 (48663) SS BOND : bond 0.00047 ( 2) SS BOND : angle 1.53670 ( 4) hydrogen bonds : bond 0.03120 ( 1800) hydrogen bonds : angle 3.91015 ( 5283) metal coordination : bond 0.00430 ( 8) metal coordination : angle 2.24549 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 275 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 643 GLN cc_start: 0.7770 (mm-40) cc_final: 0.7502 (mm-40) REVERT: A 665 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8165 (mp) REVERT: A 795 MET cc_start: 0.7871 (mtm) cc_final: 0.7631 (mtm) REVERT: A 1059 MET cc_start: 0.7368 (mtt) cc_final: 0.7086 (tmm) REVERT: A 1263 PHE cc_start: 0.7550 (m-10) cc_final: 0.7301 (m-80) REVERT: A 1275 ASP cc_start: 0.8258 (t0) cc_final: 0.8002 (t0) REVERT: A 1442 MET cc_start: 0.6892 (mmp) cc_final: 0.6488 (mmp) REVERT: A 1521 SER cc_start: 0.8323 (m) cc_final: 0.8038 (p) REVERT: A 1596 MET cc_start: 0.7914 (mmm) cc_final: 0.7468 (mmt) REVERT: A 1690 MET cc_start: 0.8947 (mtp) cc_final: 0.8711 (mtm) REVERT: A 1823 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.4054 (mp0) REVERT: A 1905 PHE cc_start: 0.7739 (m-80) cc_final: 0.7371 (m-80) REVERT: A 1944 ASP cc_start: 0.7566 (m-30) cc_final: 0.7289 (t0) REVERT: A 2164 ILE cc_start: 0.8602 (tt) cc_final: 0.8368 (pt) REVERT: A 2205 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6842 (tt) REVERT: A 2206 ARG cc_start: 0.7258 (pmt-80) cc_final: 0.7033 (ptt90) REVERT: A 2304 LYS cc_start: 0.8305 (mttp) cc_final: 0.7967 (mtpp) REVERT: A 2512 GLU cc_start: 0.7965 (pp20) cc_final: 0.7727 (pp20) REVERT: A 2855 MET cc_start: 0.6599 (mpp) cc_final: 0.5736 (mpp) REVERT: A 3806 MET cc_start: 0.8237 (tpt) cc_final: 0.6999 (tpt) REVERT: A 3814 MET cc_start: 0.8497 (ttm) cc_final: 0.8115 (tpp) REVERT: A 4002 ARG cc_start: 0.8105 (tpp-160) cc_final: 0.7671 (tpp-160) REVERT: A 4007 LYS cc_start: 0.8770 (mtmt) cc_final: 0.8497 (mttm) REVERT: A 4244 PHE cc_start: 0.7994 (m-80) cc_final: 0.7757 (t80) REVERT: A 4255 PHE cc_start: 0.7569 (m-80) cc_final: 0.7115 (m-10) REVERT: A 4378 ILE cc_start: 0.7059 (OUTLIER) cc_final: 0.6609 (tp) REVERT: A 4600 GLN cc_start: 0.7051 (mp10) cc_final: 0.6836 (mp10) REVERT: A 4795 PRO cc_start: 0.8339 (Cg_exo) cc_final: 0.8118 (Cg_endo) REVERT: A 4809 PHE cc_start: 0.8305 (t80) cc_final: 0.8063 (t80) REVERT: A 4872 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8182 (mt) REVERT: A 5107 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.7050 (tpp) REVERT: A 5127 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8058 (tm) REVERT: A 5128 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7444 (tpt) outliers start: 69 outliers final: 44 residues processed: 328 average time/residue: 0.2317 time to fit residues: 121.6183 Evaluate side-chains 310 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 258 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 729 TYR Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 832 HIS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1313 HIS Chi-restraints excluded: chain A residue 1332 THR Chi-restraints excluded: chain A residue 1468 LEU Chi-restraints excluded: chain A residue 1823 GLU Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 1948 VAL Chi-restraints excluded: chain A residue 2151 VAL Chi-restraints excluded: chain A residue 2205 LEU Chi-restraints excluded: chain A residue 2276 MET Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2357 THR Chi-restraints excluded: chain A residue 2557 GLN Chi-restraints excluded: chain A residue 2563 VAL Chi-restraints excluded: chain A residue 2628 HIS Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 2924 VAL Chi-restraints excluded: chain A residue 2957 LEU Chi-restraints excluded: chain A residue 3160 VAL Chi-restraints excluded: chain A residue 3243 SER Chi-restraints excluded: chain A residue 3376 VAL Chi-restraints excluded: chain A residue 3399 VAL Chi-restraints excluded: chain A residue 3519 ARG Chi-restraints excluded: chain A residue 3598 LEU Chi-restraints excluded: chain A residue 3692 THR Chi-restraints excluded: chain A residue 3711 GLN Chi-restraints excluded: chain A residue 3757 PHE Chi-restraints excluded: chain A residue 3759 LEU Chi-restraints excluded: chain A residue 3781 ILE Chi-restraints excluded: chain A residue 3965 VAL Chi-restraints excluded: chain A residue 4083 VAL Chi-restraints excluded: chain A residue 4378 ILE Chi-restraints excluded: chain A residue 4634 HIS Chi-restraints excluded: chain A residue 4658 THR Chi-restraints excluded: chain A residue 4747 VAL Chi-restraints excluded: chain A residue 4858 VAL Chi-restraints excluded: chain A residue 4872 LEU Chi-restraints excluded: chain A residue 4991 VAL Chi-restraints excluded: chain A residue 5107 MET Chi-restraints excluded: chain A residue 5127 LEU Chi-restraints excluded: chain A residue 5128 MET Chi-restraints excluded: chain A residue 5132 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 279 optimal weight: 5.9990 chunk 394 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 352 optimal weight: 0.5980 chunk 207 optimal weight: 6.9990 chunk 241 optimal weight: 1.9990 chunk 21 optimal weight: 0.0370 chunk 168 optimal weight: 10.0000 chunk 203 optimal weight: 0.0370 chunk 202 optimal weight: 0.9980 chunk 225 optimal weight: 2.9990 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 632 HIS A 940 GLN A2145 GLN A4262 GLN A4757 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.086672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.071630 restraints weight = 114916.787| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.66 r_work: 0.3280 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 35965 Z= 0.110 Angle : 0.598 11.348 48676 Z= 0.299 Chirality : 0.041 0.341 5511 Planarity : 0.004 0.087 6228 Dihedral : 5.410 87.373 4804 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.03 % Favored : 91.94 % Rotamer: Outliers : 1.59 % Allowed : 10.72 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.13), residues: 4319 helix: 1.20 (0.11), residues: 2502 sheet: -0.54 (0.33), residues: 238 loop : -2.28 (0.15), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2319 TYR 0.018 0.001 TYR A2146 PHE 0.026 0.001 PHE A3939 TRP 0.015 0.001 TRP A4555 HIS 0.007 0.001 HIS A 832 Details of bonding type rmsd covalent geometry : bond 0.00244 (35955) covalent geometry : angle 0.59702 (48663) SS BOND : bond 0.00071 ( 2) SS BOND : angle 1.25942 ( 4) hydrogen bonds : bond 0.03105 ( 1800) hydrogen bonds : angle 3.88258 ( 5283) metal coordination : bond 0.00459 ( 8) metal coordination : angle 2.16143 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 270 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 643 GLN cc_start: 0.7723 (mm-40) cc_final: 0.7480 (mm-40) REVERT: A 665 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8167 (mp) REVERT: A 795 MET cc_start: 0.7884 (mtm) cc_final: 0.7651 (mtm) REVERT: A 939 LYS cc_start: 0.8610 (mmmt) cc_final: 0.8256 (mtmt) REVERT: A 1059 MET cc_start: 0.7364 (mtt) cc_final: 0.7102 (tmm) REVERT: A 1263 PHE cc_start: 0.7572 (m-10) cc_final: 0.7332 (m-80) REVERT: A 1275 ASP cc_start: 0.8233 (t0) cc_final: 0.7981 (t0) REVERT: A 1690 MET cc_start: 0.8946 (mtp) cc_final: 0.8725 (mtm) REVERT: A 1823 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.4091 (mp0) REVERT: A 1905 PHE cc_start: 0.7736 (m-80) cc_final: 0.7375 (m-80) REVERT: A 1944 ASP cc_start: 0.7546 (m-30) cc_final: 0.7286 (t0) REVERT: A 2164 ILE cc_start: 0.8616 (tt) cc_final: 0.8378 (pt) REVERT: A 2205 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6782 (tt) REVERT: A 2304 LYS cc_start: 0.8325 (mttp) cc_final: 0.7985 (mtpp) REVERT: A 2512 GLU cc_start: 0.7995 (pp20) cc_final: 0.7742 (pp20) REVERT: A 3519 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7571 (ptt180) REVERT: A 3731 MET cc_start: 0.6982 (tmm) cc_final: 0.6472 (tmm) REVERT: A 3806 MET cc_start: 0.8220 (tpt) cc_final: 0.7102 (tpt) REVERT: A 3814 MET cc_start: 0.8499 (ttm) cc_final: 0.8112 (tpp) REVERT: A 4003 LYS cc_start: 0.8812 (mmmt) cc_final: 0.8591 (mmtm) REVERT: A 4007 LYS cc_start: 0.8776 (mtmt) cc_final: 0.8495 (mttm) REVERT: A 4291 VAL cc_start: 0.6506 (OUTLIER) cc_final: 0.6295 (t) REVERT: A 4378 ILE cc_start: 0.7046 (OUTLIER) cc_final: 0.6597 (tp) REVERT: A 4795 PRO cc_start: 0.8360 (Cg_exo) cc_final: 0.8137 (Cg_endo) REVERT: A 4809 PHE cc_start: 0.8285 (t80) cc_final: 0.8056 (t80) REVERT: A 4870 ARG cc_start: 0.8308 (ttp80) cc_final: 0.7977 (ttp-110) REVERT: A 4872 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8167 (mt) REVERT: A 5107 MET cc_start: 0.7562 (OUTLIER) cc_final: 0.6781 (tmm) REVERT: A 5127 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7803 (tp) REVERT: A 5128 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7430 (tpt) outliers start: 62 outliers final: 44 residues processed: 319 average time/residue: 0.2392 time to fit residues: 121.9512 Evaluate side-chains 310 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 256 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 729 TYR Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 832 HIS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1313 HIS Chi-restraints excluded: chain A residue 1332 THR Chi-restraints excluded: chain A residue 1468 LEU Chi-restraints excluded: chain A residue 1823 GLU Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 1948 VAL Chi-restraints excluded: chain A residue 2151 VAL Chi-restraints excluded: chain A residue 2205 LEU Chi-restraints excluded: chain A residue 2276 MET Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2306 VAL Chi-restraints excluded: chain A residue 2357 THR Chi-restraints excluded: chain A residue 2557 GLN Chi-restraints excluded: chain A residue 2563 VAL Chi-restraints excluded: chain A residue 2574 CYS Chi-restraints excluded: chain A residue 2628 HIS Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 2957 LEU Chi-restraints excluded: chain A residue 3160 VAL Chi-restraints excluded: chain A residue 3243 SER Chi-restraints excluded: chain A residue 3376 VAL Chi-restraints excluded: chain A residue 3399 VAL Chi-restraints excluded: chain A residue 3519 ARG Chi-restraints excluded: chain A residue 3598 LEU Chi-restraints excluded: chain A residue 3692 THR Chi-restraints excluded: chain A residue 3711 GLN Chi-restraints excluded: chain A residue 3757 PHE Chi-restraints excluded: chain A residue 3759 LEU Chi-restraints excluded: chain A residue 3781 ILE Chi-restraints excluded: chain A residue 3965 VAL Chi-restraints excluded: chain A residue 4083 VAL Chi-restraints excluded: chain A residue 4291 VAL Chi-restraints excluded: chain A residue 4378 ILE Chi-restraints excluded: chain A residue 4634 HIS Chi-restraints excluded: chain A residue 4658 THR Chi-restraints excluded: chain A residue 4747 VAL Chi-restraints excluded: chain A residue 4858 VAL Chi-restraints excluded: chain A residue 4872 LEU Chi-restraints excluded: chain A residue 4991 VAL Chi-restraints excluded: chain A residue 5107 MET Chi-restraints excluded: chain A residue 5127 LEU Chi-restraints excluded: chain A residue 5128 MET Chi-restraints excluded: chain A residue 5132 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 385 optimal weight: 3.9990 chunk 326 optimal weight: 6.9990 chunk 302 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 237 optimal weight: 0.9990 chunk 352 optimal weight: 8.9990 chunk 379 optimal weight: 0.9980 chunk 140 optimal weight: 0.5980 chunk 262 optimal weight: 2.9990 chunk 349 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 632 HIS A1395 HIS A2273 HIS ** A2592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2613 HIS A2822 HIS A4262 GLN ** A4600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4757 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.085252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.070050 restraints weight = 114744.643| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.65 r_work: 0.3240 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 35965 Z= 0.156 Angle : 0.640 11.437 48676 Z= 0.320 Chirality : 0.043 0.323 5511 Planarity : 0.004 0.087 6228 Dihedral : 5.483 82.587 4804 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.17 % Favored : 91.80 % Rotamer: Outliers : 1.74 % Allowed : 10.90 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.13), residues: 4319 helix: 1.14 (0.11), residues: 2515 sheet: -0.66 (0.33), residues: 246 loop : -2.27 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A4362 TYR 0.020 0.002 TYR A2146 PHE 0.033 0.002 PHE A2371 TRP 0.017 0.002 TRP A1459 HIS 0.006 0.001 HIS A 832 Details of bonding type rmsd covalent geometry : bond 0.00367 (35955) covalent geometry : angle 0.63931 (48663) SS BOND : bond 0.00150 ( 2) SS BOND : angle 1.30471 ( 4) hydrogen bonds : bond 0.03414 ( 1800) hydrogen bonds : angle 3.98225 ( 5283) metal coordination : bond 0.01032 ( 8) metal coordination : angle 2.54414 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 268 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 643 GLN cc_start: 0.7787 (mm-40) cc_final: 0.7553 (mm110) REVERT: A 665 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8157 (mp) REVERT: A 1059 MET cc_start: 0.7319 (mtt) cc_final: 0.7047 (tmm) REVERT: A 1263 PHE cc_start: 0.7638 (m-10) cc_final: 0.7382 (m-80) REVERT: A 1275 ASP cc_start: 0.8226 (t0) cc_final: 0.7980 (t0) REVERT: A 1327 ARG cc_start: 0.7918 (ttp80) cc_final: 0.7639 (tmm160) REVERT: A 1442 MET cc_start: 0.6850 (mmp) cc_final: 0.6383 (mmp) REVERT: A 1521 SER cc_start: 0.8410 (m) cc_final: 0.8138 (p) REVERT: A 1690 MET cc_start: 0.8964 (mtp) cc_final: 0.8740 (mtm) REVERT: A 1815 ARG cc_start: 0.8095 (mmp-170) cc_final: 0.7879 (mmm160) REVERT: A 1823 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.4116 (mp0) REVERT: A 1905 PHE cc_start: 0.7806 (m-80) cc_final: 0.7511 (m-80) REVERT: A 1908 TYR cc_start: 0.7379 (m-80) cc_final: 0.6977 (m-80) REVERT: A 1944 ASP cc_start: 0.7631 (m-30) cc_final: 0.7319 (t0) REVERT: A 2100 ILE cc_start: 0.8472 (tp) cc_final: 0.8176 (tp) REVERT: A 2164 ILE cc_start: 0.8549 (tt) cc_final: 0.8330 (pt) REVERT: A 2205 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6752 (tt) REVERT: A 2304 LYS cc_start: 0.8434 (mttp) cc_final: 0.8090 (mtpp) REVERT: A 2512 GLU cc_start: 0.8022 (pp20) cc_final: 0.7751 (pp20) REVERT: A 2560 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7852 (mp10) REVERT: A 2855 MET cc_start: 0.6653 (mpp) cc_final: 0.5744 (mpp) REVERT: A 3806 MET cc_start: 0.8236 (tpt) cc_final: 0.7065 (tpt) REVERT: A 3814 MET cc_start: 0.8507 (ttm) cc_final: 0.8109 (tpp) REVERT: A 4003 LYS cc_start: 0.8842 (mmmt) cc_final: 0.8592 (mmtm) REVERT: A 4007 LYS cc_start: 0.8750 (mtmt) cc_final: 0.8494 (pttt) REVERT: A 4255 PHE cc_start: 0.7521 (m-10) cc_final: 0.7208 (m-10) REVERT: A 4316 TYR cc_start: 0.7069 (m-10) cc_final: 0.6807 (m-10) REVERT: A 4795 PRO cc_start: 0.8384 (Cg_exo) cc_final: 0.8168 (Cg_endo) REVERT: A 4809 PHE cc_start: 0.8286 (t80) cc_final: 0.8079 (t80) REVERT: A 4870 ARG cc_start: 0.8350 (ttp80) cc_final: 0.8018 (ttp-110) REVERT: A 4872 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8132 (mt) REVERT: A 5107 MET cc_start: 0.7585 (OUTLIER) cc_final: 0.6839 (tmm) REVERT: A 5127 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8057 (tm) REVERT: A 5128 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7612 (tpt) outliers start: 68 outliers final: 48 residues processed: 323 average time/residue: 0.2236 time to fit residues: 116.0554 Evaluate side-chains 318 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 262 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 832 HIS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1313 HIS Chi-restraints excluded: chain A residue 1468 LEU Chi-restraints excluded: chain A residue 1823 GLU Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 1948 VAL Chi-restraints excluded: chain A residue 2151 VAL Chi-restraints excluded: chain A residue 2205 LEU Chi-restraints excluded: chain A residue 2276 MET Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2306 VAL Chi-restraints excluded: chain A residue 2357 THR Chi-restraints excluded: chain A residue 2371 PHE Chi-restraints excluded: chain A residue 2557 GLN Chi-restraints excluded: chain A residue 2560 GLN Chi-restraints excluded: chain A residue 2563 VAL Chi-restraints excluded: chain A residue 2574 CYS Chi-restraints excluded: chain A residue 2628 HIS Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 2924 VAL Chi-restraints excluded: chain A residue 2957 LEU Chi-restraints excluded: chain A residue 3160 VAL Chi-restraints excluded: chain A residue 3243 SER Chi-restraints excluded: chain A residue 3376 VAL Chi-restraints excluded: chain A residue 3395 LEU Chi-restraints excluded: chain A residue 3399 VAL Chi-restraints excluded: chain A residue 3519 ARG Chi-restraints excluded: chain A residue 3598 LEU Chi-restraints excluded: chain A residue 3692 THR Chi-restraints excluded: chain A residue 3711 GLN Chi-restraints excluded: chain A residue 3757 PHE Chi-restraints excluded: chain A residue 3759 LEU Chi-restraints excluded: chain A residue 3781 ILE Chi-restraints excluded: chain A residue 3965 VAL Chi-restraints excluded: chain A residue 4083 VAL Chi-restraints excluded: chain A residue 4378 ILE Chi-restraints excluded: chain A residue 4658 THR Chi-restraints excluded: chain A residue 4744 VAL Chi-restraints excluded: chain A residue 4747 VAL Chi-restraints excluded: chain A residue 4858 VAL Chi-restraints excluded: chain A residue 4872 LEU Chi-restraints excluded: chain A residue 4941 MET Chi-restraints excluded: chain A residue 4991 VAL Chi-restraints excluded: chain A residue 5107 MET Chi-restraints excluded: chain A residue 5127 LEU Chi-restraints excluded: chain A residue 5128 MET Chi-restraints excluded: chain A residue 5132 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 45 optimal weight: 6.9990 chunk 156 optimal weight: 0.6980 chunk 314 optimal weight: 1.9990 chunk 197 optimal weight: 4.9990 chunk 332 optimal weight: 0.0570 chunk 375 optimal weight: 4.9990 chunk 289 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 257 optimal weight: 1.9990 chunk 185 optimal weight: 0.9980 chunk 224 optimal weight: 5.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 632 HIS A 827 ASN A 940 GLN A2273 HIS A2592 ASN A4262 GLN ** A4600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4757 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.085748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.070598 restraints weight = 115122.010| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.66 r_work: 0.3250 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 35965 Z= 0.133 Angle : 0.634 11.554 48676 Z= 0.315 Chirality : 0.042 0.322 5511 Planarity : 0.004 0.086 6228 Dihedral : 5.471 82.956 4804 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.06 % Favored : 91.92 % Rotamer: Outliers : 1.56 % Allowed : 10.95 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.13), residues: 4319 helix: 1.15 (0.11), residues: 2508 sheet: -0.57 (0.33), residues: 240 loop : -2.22 (0.16), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2319 TYR 0.020 0.001 TYR A2146 PHE 0.054 0.001 PHE A3939 TRP 0.032 0.001 TRP A1459 HIS 0.007 0.001 HIS A 832 Details of bonding type rmsd covalent geometry : bond 0.00308 (35955) covalent geometry : angle 0.63303 (48663) SS BOND : bond 0.00332 ( 2) SS BOND : angle 2.87015 ( 4) hydrogen bonds : bond 0.03311 ( 1800) hydrogen bonds : angle 3.97549 ( 5283) metal coordination : bond 0.00818 ( 8) metal coordination : angle 2.38783 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 267 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 643 GLN cc_start: 0.7819 (mm-40) cc_final: 0.7570 (mm-40) REVERT: A 1059 MET cc_start: 0.7387 (mtt) cc_final: 0.7058 (tmm) REVERT: A 1263 PHE cc_start: 0.7628 (m-10) cc_final: 0.7370 (m-80) REVERT: A 1275 ASP cc_start: 0.8220 (t0) cc_final: 0.7967 (t0) REVERT: A 1327 ARG cc_start: 0.7883 (ttp80) cc_final: 0.7613 (tmm160) REVERT: A 1442 MET cc_start: 0.6819 (mmp) cc_final: 0.6389 (mmp) REVERT: A 1521 SER cc_start: 0.8384 (m) cc_final: 0.8116 (p) REVERT: A 1690 MET cc_start: 0.8962 (mtp) cc_final: 0.8737 (mtm) REVERT: A 1815 ARG cc_start: 0.8094 (mmp-170) cc_final: 0.7891 (mmm160) REVERT: A 1823 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.4164 (mp0) REVERT: A 1905 PHE cc_start: 0.7797 (m-80) cc_final: 0.7464 (m-80) REVERT: A 1908 TYR cc_start: 0.7406 (m-80) cc_final: 0.7015 (m-80) REVERT: A 1944 ASP cc_start: 0.7616 (m-30) cc_final: 0.7311 (t0) REVERT: A 2100 ILE cc_start: 0.8474 (tp) cc_final: 0.8176 (tp) REVERT: A 2164 ILE cc_start: 0.8536 (tt) cc_final: 0.8299 (pt) REVERT: A 2205 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6694 (tt) REVERT: A 2304 LYS cc_start: 0.8427 (mttp) cc_final: 0.8077 (mtpp) REVERT: A 2512 GLU cc_start: 0.8026 (pp20) cc_final: 0.7750 (pp20) REVERT: A 2560 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7883 (mp10) REVERT: A 2855 MET cc_start: 0.6634 (mpp) cc_final: 0.5780 (mpp) REVERT: A 3731 MET cc_start: 0.7012 (tmm) cc_final: 0.6573 (tmm) REVERT: A 3806 MET cc_start: 0.8227 (tpt) cc_final: 0.7022 (tpt) REVERT: A 3814 MET cc_start: 0.8494 (ttm) cc_final: 0.7991 (tpp) REVERT: A 3937 LYS cc_start: 0.7074 (mmtt) cc_final: 0.6853 (mtmm) REVERT: A 4007 LYS cc_start: 0.8799 (mtmt) cc_final: 0.8514 (mttm) REVERT: A 4255 PHE cc_start: 0.7516 (m-10) cc_final: 0.7188 (m-10) REVERT: A 4316 TYR cc_start: 0.7071 (m-10) cc_final: 0.6810 (m-10) REVERT: A 4795 PRO cc_start: 0.8387 (Cg_exo) cc_final: 0.8173 (Cg_endo) REVERT: A 4809 PHE cc_start: 0.8277 (t80) cc_final: 0.8063 (t80) REVERT: A 4872 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8141 (mt) REVERT: A 5107 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.6806 (tmm) REVERT: A 5127 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8057 (tm) REVERT: A 5128 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7607 (tpt) outliers start: 61 outliers final: 47 residues processed: 315 average time/residue: 0.2349 time to fit residues: 118.3205 Evaluate side-chains 315 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 261 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 832 HIS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1313 HIS Chi-restraints excluded: chain A residue 1468 LEU Chi-restraints excluded: chain A residue 1823 GLU Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 1948 VAL Chi-restraints excluded: chain A residue 2151 VAL Chi-restraints excluded: chain A residue 2205 LEU Chi-restraints excluded: chain A residue 2276 MET Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2306 VAL Chi-restraints excluded: chain A residue 2357 THR Chi-restraints excluded: chain A residue 2557 GLN Chi-restraints excluded: chain A residue 2560 GLN Chi-restraints excluded: chain A residue 2563 VAL Chi-restraints excluded: chain A residue 2574 CYS Chi-restraints excluded: chain A residue 2628 HIS Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 2924 VAL Chi-restraints excluded: chain A residue 2957 LEU Chi-restraints excluded: chain A residue 3160 VAL Chi-restraints excluded: chain A residue 3243 SER Chi-restraints excluded: chain A residue 3376 VAL Chi-restraints excluded: chain A residue 3395 LEU Chi-restraints excluded: chain A residue 3399 VAL Chi-restraints excluded: chain A residue 3519 ARG Chi-restraints excluded: chain A residue 3598 LEU Chi-restraints excluded: chain A residue 3692 THR Chi-restraints excluded: chain A residue 3711 GLN Chi-restraints excluded: chain A residue 3757 PHE Chi-restraints excluded: chain A residue 3781 ILE Chi-restraints excluded: chain A residue 3965 VAL Chi-restraints excluded: chain A residue 4083 VAL Chi-restraints excluded: chain A residue 4378 ILE Chi-restraints excluded: chain A residue 4658 THR Chi-restraints excluded: chain A residue 4744 VAL Chi-restraints excluded: chain A residue 4747 VAL Chi-restraints excluded: chain A residue 4858 VAL Chi-restraints excluded: chain A residue 4872 LEU Chi-restraints excluded: chain A residue 4941 MET Chi-restraints excluded: chain A residue 4991 VAL Chi-restraints excluded: chain A residue 4999 MET Chi-restraints excluded: chain A residue 5107 MET Chi-restraints excluded: chain A residue 5127 LEU Chi-restraints excluded: chain A residue 5128 MET Chi-restraints excluded: chain A residue 5132 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 189 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 231 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 152 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 403 optimal weight: 2.9990 chunk 361 optimal weight: 5.9990 chunk 356 optimal weight: 0.9980 chunk 394 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 632 HIS A2273 HIS A4262 GLN ** A4600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4757 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.086003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.070893 restraints weight = 114254.597| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.64 r_work: 0.3260 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35965 Z= 0.124 Angle : 0.627 11.473 48676 Z= 0.312 Chirality : 0.042 0.317 5511 Planarity : 0.004 0.086 6228 Dihedral : 5.436 83.083 4804 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.99 % Favored : 91.99 % Rotamer: Outliers : 1.46 % Allowed : 11.13 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.13), residues: 4319 helix: 1.20 (0.11), residues: 2503 sheet: -0.52 (0.33), residues: 240 loop : -2.22 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 644 TYR 0.019 0.001 TYR A2146 PHE 0.057 0.001 PHE A3939 TRP 0.029 0.001 TRP A1459 HIS 0.007 0.001 HIS A 832 Details of bonding type rmsd covalent geometry : bond 0.00283 (35955) covalent geometry : angle 0.62569 (48663) SS BOND : bond 0.00178 ( 2) SS BOND : angle 2.75085 ( 4) hydrogen bonds : bond 0.03260 ( 1800) hydrogen bonds : angle 3.95104 ( 5283) metal coordination : bond 0.00680 ( 8) metal coordination : angle 2.23883 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8269.07 seconds wall clock time: 142 minutes 29.44 seconds (8549.44 seconds total)