Starting phenix.real_space_refine on Sat Mar 7 01:18:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tay_10430/03_2026/6tay_10430_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tay_10430/03_2026/6tay_10430.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 { model { file = "/net/cci-nas-00/data/ceres_data/6tay_10430/03_2026/6tay_10430_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tay_10430/03_2026/6tay_10430_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6tay_10430/03_2026/6tay_10430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tay_10430/03_2026/6tay_10430.map" } 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= 0.003 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 208 5.16 5 C 22441 2.51 5 N 6059 2.21 5 O 6527 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s 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: 35241 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 35207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4417, 35207 Classifications: {'peptide': 4417} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 181, 'TRANS': 4235} 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 26230 SG CYS A3962 88.596 133.489 219.905 1.00121.06 S ATOM 26394 SG CYS A3982 86.094 131.351 222.600 1.00124.67 S ATOM 26419 SG CYS A3985 89.737 131.777 222.863 1.00127.04 S ATOM 26120 SG CYS A3947 79.329 126.208 217.232 0.50 96.21 S ATOM 26145 SG CYS A3950 76.707 123.355 216.016 1.00104.83 S ATOM 26273 SG CYS A3967 76.780 126.459 214.111 1.00111.70 S ATOM 26298 SG CYS A3970 75.210 126.926 217.834 1.00115.80 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: 7.37, per 1000 atoms: 0.21 Number of scatterers: 35241 At special positions: 0 Unit cell: (128.96, 153.92, 243.36, 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 208 16.00 P 3 15.00 Mg 1 11.99 O 6527 8.00 N 6059 7.00 C 22441 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=2.04 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: 2.96 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 A3982 " pdb="ZN ZN A5203 " - pdb=" SG CYS A3962 " pdb="ZN ZN A5203 " - pdb=" SG CYS A3985 " pdb=" ZN A5204 " pdb="ZN ZN A5204 " - pdb=" SG CYS A3967 " pdb="ZN ZN A5204 " - pdb=" SG CYS A3950 " pdb="ZN ZN A5204 " - pdb=" SG CYS A3947 " pdb="ZN ZN A5204 " - pdb=" SG CYS A3970 " Number of angles added : 9 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8460 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 17 sheets defined 62.1% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.71 Creating SS restraints... Processing helix chain 'A' and resid 477 through 491 removed outlier: 4.331A pdb=" N UNK A 481 " --> pdb=" O UNK A 477 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N UNK A 491 " --> pdb=" O UNK A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 511 Processing helix chain 'A' and resid 517 through 539 removed outlier: 3.671A pdb=" N UNK A 521 " --> pdb=" O UNK A 517 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N UNK A 522 " --> pdb=" O UNK A 518 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N UNK A 523 " --> pdb=" O UNK A 519 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N UNK A 539 " --> pdb=" O UNK A 535 " (cutoff:3.500A) 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: 3.597A pdb=" N LYS A 611 " --> pdb=" O THR A 608 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LYS A 612 " --> pdb=" O VAL A 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 608 through 612' Processing helix chain 'A' and resid 613 through 620 removed outlier: 3.759A pdb=" N CYS A 618 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR A 619 " --> pdb=" O ASP A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 635 removed outlier: 3.841A pdb=" N HIS A 632 " --> pdb=" O PRO A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 640 Processing helix chain 'A' and resid 643 through 656 Processing helix chain 'A' and resid 663 through 667 Processing helix chain 'A' and resid 669 through 673 Processing helix chain 'A' and resid 688 through 694 Processing helix chain 'A' and resid 699 through 704 removed outlier: 3.739A pdb=" N PHE A 703 " --> pdb=" O SER A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 720 Processing helix chain 'A' and resid 721 through 726 removed outlier: 3.565A pdb=" N ARG A 725 " --> pdb=" O ALA A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 738 Processing helix chain 'A' and resid 739 through 741 No H-bonds generated for 'chain 'A' and resid 739 through 741' Processing helix chain 'A' and resid 742 through 750 Processing helix chain 'A' and resid 750 through 757 removed outlier: 3.826A pdb=" N ASP A 756 " --> pdb=" O ASP A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 770 Processing helix chain 'A' and resid 780 through 801 removed outlier: 3.972A pdb=" N TYR A 801 " --> pdb=" O LEU A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 828 removed outlier: 3.553A pdb=" N TYR A 814 " --> pdb=" O LEU A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 851 removed outlier: 3.780A pdb=" N ILE A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 889 Processing helix chain 'A' and resid 907 through 917 Processing helix chain 'A' and resid 927 through 939 removed outlier: 3.619A pdb=" N LEU A 931 " --> pdb=" O LYS A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 949 Processing helix chain 'A' and resid 962 through 982 Processing helix chain 'A' and resid 994 through 1009 Processing helix chain 'A' and resid 1020 through 1031 removed outlier: 3.808A pdb=" N ILE A1024 " --> pdb=" O ASP A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1043 removed outlier: 4.162A pdb=" N GLN A1036 " --> pdb=" O PRO A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1051 removed outlier: 3.532A pdb=" N ASN A1050 " --> pdb=" O ILE A1047 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A1051 " --> pdb=" O ILE A1048 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1047 through 1051' Processing helix chain 'A' and resid 1052 through 1070 Processing helix chain 'A' and resid 1079 through 1088 Processing helix chain 'A' and resid 1089 through 1103 Processing helix chain 'A' and resid 1113 through 1141 Processing helix chain 'A' and resid 1154 through 1160 removed outlier: 3.505A pdb=" N ILE A1158 " --> pdb=" O ASN A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1171 Processing helix chain 'A' and resid 1190 through 1204 Processing helix chain 'A' and resid 1206 through 1219 Processing helix chain 'A' and resid 1234 through 1241 removed outlier: 3.808A pdb=" N LEU A1238 " --> pdb=" O LEU A1234 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLU A1239 " --> pdb=" O PRO A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1259 removed outlier: 3.806A pdb=" N CYS A1245 " --> pdb=" O LEU A1241 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER A1258 " --> pdb=" O GLU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1270 Processing helix chain 'A' and resid 1271 through 1273 No H-bonds generated for 'chain 'A' and resid 1271 through 1273' Processing helix chain 'A' and resid 1277 through 1289 Processing helix chain 'A' and resid 1298 through 1330 removed outlier: 3.848A pdb=" N ARG A1302 " --> pdb=" O TRP A1298 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY A1330 " --> pdb=" O ARG A1326 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1344 Processing helix chain 'A' and resid 1361 through 1368 removed outlier: 4.088A pdb=" N LYS A1365 " --> pdb=" O PRO A1361 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA A1366 " --> pdb=" O GLN A1362 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1387 removed outlier: 3.612A pdb=" N GLN A1387 " --> pdb=" O GLU A1383 " (cutoff:3.500A) Processing helix chain 'A' and resid 1387 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: 3.880A pdb=" N ASP A1409 " --> pdb=" O LYS A1405 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE A1413 " --> pdb=" O ASP A1409 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A1414 " --> pdb=" O LEU A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1435 removed outlier: 3.663A pdb=" N ASP A1423 " --> pdb=" O ASP A1419 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL A1425 " --> pdb=" O ASP A1421 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA A1426 " --> pdb=" O VAL A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1463 removed outlier: 3.856A pdb=" N PHE A1451 " --> pdb=" O ASN A1447 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU A1457 " --> pdb=" O ASN A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1467 through 1477 Processing helix chain 'A' and resid 1478 through 1484 Processing helix chain 'A' and resid 1495 through 1507 Processing helix chain 'A' and resid 1544 through 1557 Processing helix chain 'A' and resid 1563 through 1594 removed outlier: 3.589A pdb=" N ASN A1567 " --> pdb=" O ASP A1563 " (cutoff:3.500A) Processing helix chain 'A' and resid 1630 through 1660 Processing helix chain 'A' and resid 1661 through 1665 removed outlier: 3.752A pdb=" N PHE A1665 " --> pdb=" O TYR A1662 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1679 removed outlier: 4.465A pdb=" N ARG A1679 " --> pdb=" O SER A1675 " (cutoff:3.500A) Processing helix chain 'A' and resid 1684 through 1691 Processing helix chain 'A' and resid 1692 through 1694 No H-bonds generated for 'chain 'A' and resid 1692 through 1694' Processing helix chain 'A' and resid 1699 through 1709 removed outlier: 3.555A pdb=" N LEU A1703 " --> pdb=" O THR A1699 " (cutoff:3.500A) Processing helix chain 'A' and resid 1712 through 1732 removed outlier: 3.525A pdb=" N ARG A1716 " --> pdb=" O SER A1712 " (cutoff:3.500A) Proline residue: A1727 - end of helix Processing helix chain 'A' and resid 1735 through 1750 Processing helix chain 'A' and resid 1760 through 1772 Processing helix chain 'A' and resid 1801 through 1810 Processing helix chain 'A' and resid 1832 through 1844 removed outlier: 3.836A pdb=" N VAL A1836 " --> pdb=" O THR A1832 " (cutoff:3.500A) Processing helix chain 'A' and resid 1863 through 1880 Processing helix chain 'A' and resid 1893 through 1897 removed outlier: 4.012A pdb=" N GLU A1897 " --> pdb=" O ALA A1894 " (cutoff:3.500A) Processing helix chain 'A' and resid 1899 through 1906 Processing helix chain 'A' and resid 1907 through 1909 No H-bonds generated for 'chain 'A' and resid 1907 through 1909' Processing helix chain 'A' and resid 1917 through 1930 Processing helix chain 'A' and resid 1938 through 1942 removed outlier: 3.757A pdb=" N VAL A1941 " --> pdb=" O ALA A1938 " (cutoff:3.500A) Processing helix chain 'A' and resid 1959 through 1975 Processing helix chain 'A' and resid 1993 through 2006 removed outlier: 3.793A pdb=" N VAL A1997 " --> pdb=" O ASP A1993 " (cutoff:3.500A) Proline residue: A2003 - end of helix removed outlier: 3.517A pdb=" N LYS A2006 " --> pdb=" O LEU A2002 " (cutoff:3.500A) Processing helix chain 'A' and resid 2027 through 2037 removed outlier: 3.572A pdb=" N PHE A2031 " --> pdb=" O GLY A2027 " (cutoff:3.500A) Processing helix chain 'A' and resid 2084 through 2088 removed outlier: 3.717A pdb=" N PHE A2088 " --> pdb=" O LEU A2085 " (cutoff:3.500A) Processing helix chain 'A' and resid 2095 through 2101 removed outlier: 3.853A pdb=" N ILE A2100 " --> pdb=" O PRO A2096 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP A2101 " --> pdb=" O LYS A2097 " (cutoff:3.500A) Processing helix chain 'A' and resid 2116 through 2121 Processing helix chain 'A' and resid 2126 through 2137 removed outlier: 4.042A pdb=" N ARG A2134 " --> pdb=" O GLN A2130 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN A2137 " --> pdb=" O LYS A2133 " (cutoff:3.500A) Processing helix chain 'A' and resid 2154 through 2166 removed outlier: 3.839A pdb=" N TYR A2165 " --> pdb=" O HIS A2161 " (cutoff:3.500A) Processing helix chain 'A' and resid 2172 through 2192 removed outlier: 3.732A 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: 3.572A pdb=" N PHE A2211 " --> pdb=" O GLY A2207 " (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 2386 through 2400 Processing helix chain 'A' and resid 2417 through 2440 removed outlier: 3.568A pdb=" N ILE A2421 " --> pdb=" O THR A2417 " (cutoff:3.500A) Processing helix chain 'A' and resid 2455 through 2464 removed outlier: 3.680A pdb=" N ILE A2459 " --> pdb=" O ALA A2455 " (cutoff:3.500A) Processing helix chain 'A' and resid 2492 through 2500 Processing helix chain 'A' and resid 2536 through 2538 No H-bonds generated for 'chain 'A' and resid 2536 through 2538' Processing helix chain 'A' and resid 2548 through 2563 removed outlier: 5.008A pdb=" N TYR A2554 " --> pdb=" O ALA A2550 " (cutoff:3.500A) Processing helix chain 'A' and resid 2569 through 2589 removed outlier: 3.525A pdb=" N THR A2573 " --> pdb=" O ASN A2569 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A2589 " --> pdb=" O MET A2585 " (cutoff:3.500A) Processing helix chain 'A' and resid 2598 through 2615 removed outlier: 3.561A pdb=" N VAL A2602 " --> pdb=" O SER A2598 " (cutoff:3.500A) Processing helix chain 'A' and resid 2618 through 2631 Processing helix chain 'A' and resid 2642 through 2654 Processing helix chain 'A' and resid 2660 through 2669 removed outlier: 3.611A pdb=" N TYR A2664 " --> pdb=" O GLU A2660 " (cutoff:3.500A) Processing helix chain 'A' and resid 2673 through 2677 removed outlier: 3.855A pdb=" N ASN A2677 " --> pdb=" O LYS A2674 " (cutoff:3.500A) Processing helix chain 'A' and resid 2678 through 2696 removed outlier: 3.735A pdb=" N ILE A2682 " --> pdb=" O SER A2678 " (cutoff:3.500A) Processing helix chain 'A' and resid 2706 through 2722 removed outlier: 3.531A pdb=" N LYS A2710 " --> pdb=" O ASN A2706 " (cutoff:3.500A) Processing helix chain 'A' and resid 2737 through 2747 Processing helix chain 'A' and resid 2775 through 2791 removed outlier: 4.256A pdb=" N ILE A2779 " --> pdb=" O THR A2775 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A2780 " --> pdb=" O PRO A2776 " (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 2827 removed outlier: 3.565A pdb=" N LEU A2824 " --> pdb=" O THR A2820 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU A2826 " --> pdb=" O HIS A2822 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP A2827 " --> pdb=" O PRO A2823 " (cutoff:3.500A) Processing helix chain 'A' and resid 2851 through 2856 removed outlier: 3.774A 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 2882 through 2890 Processing helix chain 'A' and resid 2892 through 2907 Processing helix chain 'A' and resid 2913 through 2932 removed outlier: 3.746A 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 2964 removed outlier: 3.791A pdb=" N SER A2963 " --> pdb=" O ILE A2959 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU A2964 " --> pdb=" O PHE A2960 " (cutoff:3.500A) Processing helix chain 'A' and resid 2974 through 2984 Processing helix chain 'A' and resid 3010 through 3019 Processing helix chain 'A' and resid 3037 through 3056 Processing helix chain 'A' and resid 3063 through 3068 removed outlier: 3.723A pdb=" N LEU A3067 " --> pdb=" O ASN A3063 " (cutoff:3.500A) Processing helix chain 'A' and resid 3071 through 3076 removed outlier: 3.542A pdb=" N ASN A3076 " --> pdb=" O TYR A3072 " (cutoff:3.500A) Processing helix chain 'A' and resid 3113 through 3119 Processing helix chain 'A' and resid 3121 through 3126 Processing helix chain 'A' and resid 3140 through 3159 Processing helix chain 'A' and resid 3172 through 3177 removed outlier: 3.553A pdb=" N VAL A3176 " --> pdb=" O SER A3172 " (cutoff:3.500A) Processing helix chain 'A' and resid 3185 through 3197 removed outlier: 3.508A pdb=" N GLY A3197 " --> pdb=" O VAL A3193 " (cutoff:3.500A) Processing helix chain 'A' and resid 3203 through 3219 removed outlier: 3.677A pdb=" N ARG A3207 " --> pdb=" O GLU A3203 " (cutoff:3.500A) removed outlier: 3.881A 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 3234 through 3248 removed outlier: 4.295A pdb=" N THR A3238 " --> pdb=" O LEU A3234 " (cutoff:3.500A) Processing helix chain 'A' and resid 3254 through 3264 removed outlier: 3.940A pdb=" N ARG A3264 " --> pdb=" O GLN A3260 " (cutoff:3.500A) Processing helix chain 'A' and resid 3286 through 3296 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: 3.579A pdb=" N PHE A3317 " --> pdb=" O THR A3313 " (cutoff:3.500A) Processing helix chain 'A' and resid 3349 through 3365 Processing helix chain 'A' and resid 3383 through 3388 Processing helix chain 'A' and resid 3413 through 3420 removed outlier: 3.640A pdb=" N LEU A3417 " --> pdb=" O ASP A3413 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL A3420 " --> pdb=" O LYS A3416 " (cutoff:3.500A) Processing helix chain 'A' and resid 3422 through 3427 Processing helix chain 'A' and resid 3476 through 3490 removed outlier: 4.935A pdb=" N GLN A3486 " --> pdb=" O GLN A3482 " (cutoff:3.500A) removed outlier: 4.788A 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 3518 through 3542 removed outlier: 4.280A pdb=" N ASN A3541 " --> pdb=" O LYS A3537 " (cutoff:3.500A) Processing helix chain 'A' and resid 3543 through 3548 removed outlier: 3.544A pdb=" N GLU A3548 " --> pdb=" O ARG A3544 " (cutoff:3.500A) Processing helix chain 'A' and resid 3548 through 3555 removed outlier: 3.525A pdb=" N ALA A3555 " --> pdb=" O THR A3551 " (cutoff:3.500A) Processing helix chain 'A' and resid 3556 through 3564 Processing helix chain 'A' and resid 3565 through 3590 removed outlier: 3.637A pdb=" N THR A3569 " --> pdb=" O THR A3565 " (cutoff:3.500A) Proline residue: A3580 - end of helix removed outlier: 3.895A pdb=" N HIS A3588 " --> pdb=" O SER A3584 " (cutoff:3.500A) Processing helix chain 'A' and resid 3594 through 3600 removed outlier: 3.888A pdb=" N LEU A3598 " --> pdb=" O ASN A3594 " (cutoff:3.500A) Processing helix chain 'A' and resid 3604 through 3616 removed outlier: 3.602A pdb=" N GLN A3608 " --> pdb=" O PRO A3604 " (cutoff:3.500A) Processing helix chain 'A' and resid 3657 through 3676 Processing helix chain 'A' and resid 3680 through 3691 Processing helix chain 'A' and resid 3692 through 3699 Processing helix chain 'A' and resid 3702 through 3722 removed outlier: 3.601A pdb=" N LYS A3708 " --> pdb=" O ALA A3704 " (cutoff:3.500A) Processing helix chain 'A' and resid 3727 through 3745 Processing helix chain 'A' and resid 3761 through 3771 removed outlier: 4.129A pdb=" N HIS A3765 " --> pdb=" O LEU A3761 " (cutoff:3.500A) Processing helix chain 'A' and resid 3771 through 3785 Processing helix chain 'A' and resid 3787 through 3800 removed outlier: 3.991A pdb=" N SER A3791 " --> pdb=" O GLN A3787 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU A3797 " --> pdb=" O SER A3793 " (cutoff:3.500A) Processing helix chain 'A' and resid 3807 through 3823 Processing helix chain 'A' and resid 3828 through 3839 removed outlier: 3.914A pdb=" N LEU A3833 " --> pdb=" O PRO A3829 " (cutoff:3.500A) Processing helix chain 'A' and resid 3839 through 3847 Processing helix chain 'A' and resid 3856 through 3883 removed outlier: 3.573A pdb=" N ARG A3860 " --> pdb=" O GLY A3856 " (cutoff:3.500A) Processing helix chain 'A' and resid 3883 through 3890 Processing helix chain 'A' and resid 3894 through 3910 removed outlier: 3.542A pdb=" N THR A3900 " --> pdb=" O PRO A3896 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER A3903 " --> pdb=" O THR A3899 " (cutoff:3.500A) Processing helix chain 'A' and resid 3917 through 3941 removed outlier: 3.970A pdb=" N PHE A3921 " --> pdb=" O THR A3917 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG A3941 " --> pdb=" O LYS A3937 " (cutoff:3.500A) Processing helix chain 'A' and resid 3968 through 3975 Processing helix chain 'A' and resid 4000 through 4026 Processing helix chain 'A' and resid 4035 through 4045 Processing helix chain 'A' and resid 4082 through 4089 Processing helix chain 'A' and resid 4092 through 4095 Processing helix chain 'A' and resid 4096 through 4111 removed outlier: 3.606A pdb=" N ILE A4100 " --> pdb=" O VAL A4096 " (cutoff:3.500A) Processing helix chain 'A' and resid 4117 through 4138 removed outlier: 3.519A pdb=" N TYR A4121 " --> pdb=" O LYS A4117 " (cutoff:3.500A) Processing helix chain 'A' and resid 4142 through 4155 Processing helix chain 'A' and resid 4171 through 4196 removed outlier: 3.759A pdb=" N GLU A4194 " --> pdb=" O ASP A4190 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN A4196 " --> pdb=" O LEU A4192 " (cutoff:3.500A) Processing helix chain 'A' and resid 4203 through 4219 removed outlier: 3.794A pdb=" N ARG A4207 " --> pdb=" O GLU A4203 " (cutoff:3.500A) Processing helix chain 'A' and resid 4222 through 4236 Processing helix chain 'A' and resid 4237 through 4243 Processing helix chain 'A' and resid 4251 through 4255 removed outlier: 3.545A pdb=" N VAL A4254 " --> pdb=" O CYS A4251 " (cutoff:3.500A) Processing helix chain 'A' and resid 4279 through 4293 removed outlier: 3.574A pdb=" N VAL A4283 " --> pdb=" O GLU A4279 " (cutoff:3.500A) Processing helix chain 'A' and resid 4297 through 4305 Processing helix chain 'A' and resid 4309 through 4331 removed outlier: 3.703A pdb=" N SER A4331 " --> pdb=" O ALA A4327 " (cutoff:3.500A) Processing helix chain 'A' and resid 4342 through 4353 removed outlier: 3.688A pdb=" N VAL A4346 " --> pdb=" O GLN A4342 " (cutoff:3.500A) Processing helix chain 'A' and resid 4354 through 4357 Processing helix chain 'A' and resid 4361 through 4370 Processing helix chain 'A' and resid 4384 through 4403 removed outlier: 3.515A pdb=" N THR A4388 " --> pdb=" O ILE A4384 " (cutoff:3.500A) Processing helix chain 'A' and resid 4408 through 4416 Processing helix chain 'A' and resid 4522 through 4544 removed outlier: 3.648A pdb=" N HIS A4543 " --> pdb=" O VAL A4539 " (cutoff:3.500A) Processing helix chain 'A' and resid 4544 through 4552 removed outlier: 4.090A 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 4634 through 4648 removed outlier: 3.728A pdb=" N ASN A4638 " --> pdb=" O HIS A4634 " (cutoff:3.500A) Proline residue: A4640 - end of helix Processing helix chain 'A' and resid 4655 through 4660 Processing helix chain 'A' and resid 4691 through 4702 removed outlier: 3.603A pdb=" N LEU A4695 " --> pdb=" O THR A4691 " (cutoff:3.500A) Processing helix chain 'A' and resid 4703 through 4708 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 4784 through 4789 Processing helix chain 'A' and resid 4808 through 4813 removed outlier: 3.501A pdb=" N ILE A4812 " --> pdb=" O PHE A4809 " (cutoff:3.500A) Processing helix chain 'A' and resid 4820 through 4845 removed outlier: 3.984A pdb=" N THR A4824 " --> pdb=" O GLY A4820 " (cutoff:3.500A) Processing helix chain 'A' and resid 4854 through 4858 removed outlier: 4.031A pdb=" N VAL A4858 " --> pdb=" O ILE A4855 " (cutoff:3.500A) Processing helix chain 'A' and resid 4871 through 4878 removed outlier: 3.624A pdb=" N LEU A4875 " --> pdb=" O ASP A4871 " (cutoff:3.500A) Processing helix chain 'A' and resid 4895 through 4907 Processing helix chain 'A' and resid 4929 through 4941 removed outlier: 4.057A pdb=" N LEU A4933 " --> pdb=" O ASN A4929 " (cutoff:3.500A) Processing helix chain 'A' and resid 4947 through 4958 removed outlier: 3.638A pdb=" N SER A4952 " --> pdb=" O ASN A4948 " (cutoff:3.500A) Processing helix chain 'A' and resid 4960 through 4980 removed outlier: 3.522A pdb=" N ALA A4964 " --> pdb=" O SER A4960 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR A4980 " --> pdb=" O GLY A4976 " (cutoff:3.500A) Processing helix chain 'A' and resid 5003 through 5010 removed outlier: 3.766A pdb=" N LEU A5007 " --> pdb=" O THR A5003 " (cutoff:3.500A) Processing helix chain 'A' and resid 5011 through 5013 No H-bonds generated for 'chain 'A' and resid 5011 through 5013' Processing helix chain 'A' and resid 5018 through 5036 Processing helix chain 'A' and resid 5053 through 5066 removed outlier: 4.405A pdb=" N GLU A5066 " --> pdb=" O THR A5062 " (cutoff:3.500A) Processing helix chain 'A' and resid 5068 through 5084 removed outlier: 4.070A pdb=" N LEU A5074 " --> pdb=" O ASP A5070 " (cutoff:3.500A) Processing helix chain 'A' and resid 5098 through 5109 Processing helix chain 'A' and resid 5113 through 5122 removed outlier: 5.368A pdb=" N VAL A5118 " --> pdb=" O LEU A5115 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N GLU A5119 " --> pdb=" O SER A5116 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER A5120 " --> pdb=" O GLU A5117 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A5122 " --> pdb=" O GLU A5119 " (cutoff:3.500A) Processing helix chain 'A' and resid 5127 through 5129 No H-bonds generated for 'chain 'A' and resid 5127 through 5129' Processing helix chain 'A' and resid 5130 through 5149 Processing sheet with id=AA1, first strand: chain 'A' and resid 894 through 895 removed outlier: 3.509A pdb=" N ARG A 902 " --> pdb=" O SER A 895 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1149 through 1151 removed outlier: 6.548A pdb=" N GLN A1149 " --> pdb=" O VAL A1232 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 1540 through 1543 removed outlier: 3.758A pdb=" N GLY A1612 " --> pdb=" O TYR A1606 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1792 through 1796 removed outlier: 6.051A pdb=" N ASN A1793 " --> pdb=" O ILE A1890 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N CYS A1892 " --> pdb=" O ASN A1793 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE A1795 " --> pdb=" O CYS A1892 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N TYR A1854 " --> pdb=" O VAL A1889 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU A1891 " --> pdb=" O TYR A1854 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU A1856 " --> pdb=" O LEU A1891 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1982 through 1987 removed outlier: 6.296A pdb=" N LYS A1983 " --> pdb=" O HIS A2017 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASP A2019 " --> pdb=" O LYS A1983 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE A1985 " --> pdb=" O ASP A2019 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N PHE A2016 " --> pdb=" O LEU A2058 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N GLU A2060 " --> pdb=" O PHE A2016 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE A2018 " --> pdb=" O GLU A2060 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ILE A2020 " --> pdb=" O PRO A2062 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER A1953 " --> pdb=" O ILE A2061 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N VAL A2091 " --> pdb=" O VAL A1948 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE A1950 " --> pdb=" O VAL A2091 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2040 through 2042 Processing sheet with id=AA7, first strand: chain 'A' and resid 2266 through 2269 Processing sheet with id=AA8, first strand: chain 'A' and resid 2282 through 2285 removed outlier: 3.707A pdb=" N MET A2307 " --> pdb=" O VAL A2291 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2407 through 2411 removed outlier: 6.491A pdb=" N VAL A2377 " --> pdb=" O ALA A2483 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N CYS A2485 " --> pdb=" O VAL A2377 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE A2379 " --> pdb=" O CYS A2485 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP A2541 " --> pdb=" O ILE A2378 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2467 through 2468 Processing sheet with id=AB2, first strand: chain 'A' and resid 2763 through 2768 removed outlier: 6.627A pdb=" N LEU A2726 " --> pdb=" O GLY A2844 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N SER A2846 " --> pdb=" O LEU A2726 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU A2728 " --> pdb=" O SER A2846 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N PHE A2727 " --> pdb=" O VAL A2861 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 3026 through 3028 removed outlier: 3.511A pdb=" N VAL A3060 " --> pdb=" O GLU A3026 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3080 through 3082 removed outlier: 4.541A pdb=" N LYS A3086 " --> pdb=" O VAL A3101 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3304 through 3307 removed outlier: 6.833A pdb=" N LYS A3332 " --> pdb=" O PHE A3372 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N TYR A3374 " --> pdb=" O LYS A3332 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU A3334 " --> pdb=" O TYR A3374 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N VAL A3376 " --> pdb=" O LEU A3334 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE A3336 " --> pdb=" O VAL A3376 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LYS A3378 " --> pdb=" O ILE A3336 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ALA A3338 " --> pdb=" O LYS A3378 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3492 through 3493 Processing sheet with id=AB7, first strand: chain 'A' and resid 3957 through 3959 Processing sheet with id=AB8, first strand: chain 'A' and resid 4880 through 4883 1824 hydrogen bonds defined for protein. 5349 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: 11.39 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11182 1.34 - 1.46: 7801 1.46 - 1.58: 16668 1.58 - 1.70: 5 1.70 - 1.83: 305 Bond restraints: 35961 Sorted by residual: bond pdb=" C4 ATP A5201 " pdb=" C5 ATP A5201 " ideal model delta sigma weight residual 1.388 1.449 -0.061 1.00e-02 1.00e+04 3.77e+01 bond pdb=" C5 ATP A5201 " pdb=" N7 ATP A5201 " ideal model delta sigma weight residual 1.387 1.326 0.061 1.00e-02 1.00e+04 3.66e+01 bond pdb=" C4 ATP A5201 " pdb=" N9 ATP A5201 " ideal model delta sigma weight residual 1.374 1.316 0.058 1.00e-02 1.00e+04 3.38e+01 bond pdb=" C5 ATP A5201 " pdb=" C6 ATP A5201 " ideal model delta sigma weight residual 1.409 1.460 -0.051 1.00e-02 1.00e+04 2.58e+01 bond pdb=" C4' ATP A5201 " pdb=" O4' ATP A5201 " ideal model delta sigma weight residual 1.444 1.401 0.043 1.10e-02 8.26e+03 1.51e+01 ... (remaining 35956 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 47656 3.45 - 6.90: 896 6.90 - 10.35: 97 10.35 - 13.80: 17 13.80 - 17.25: 4 Bond angle restraints: 48670 Sorted by residual: angle pdb=" PB ATP A5201 " pdb=" O3B ATP A5201 " pdb=" PG ATP A5201 " ideal model delta sigma weight residual 139.87 122.62 17.25 1.00e+00 1.00e+00 2.97e+02 angle pdb=" PA ATP A5201 " pdb=" O3A ATP A5201 " pdb=" PB ATP A5201 " ideal model delta sigma weight residual 136.83 124.15 12.68 1.00e+00 1.00e+00 1.61e+02 angle pdb=" C5 ATP A5201 " pdb=" C4 ATP A5201 " pdb=" N3 ATP A5201 " ideal model delta sigma weight residual 126.80 118.87 7.93 1.00e+00 1.00e+00 6.28e+01 angle pdb=" N3 ATP A5201 " pdb=" C4 ATP A5201 " pdb=" N9 ATP A5201 " ideal model delta sigma weight residual 127.04 135.53 -8.49 1.15e+00 7.59e-01 5.47e+01 angle pdb=" N VAL A 759 " pdb=" CA VAL A 759 " pdb=" C VAL A 759 " ideal model delta sigma weight residual 113.20 106.79 6.41 9.60e-01 1.09e+00 4.45e+01 ... (remaining 48665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 20598 16.85 - 33.70: 1056 33.70 - 50.54: 212 50.54 - 67.39: 18 67.39 - 84.24: 33 Dihedral angle restraints: 21917 sinusoidal: 8928 harmonic: 12989 Sorted by residual: dihedral pdb=" CA ILE A1373 " pdb=" C ILE A1373 " pdb=" N SER A1374 " pdb=" CA SER A1374 " ideal model delta harmonic sigma weight residual 180.00 129.84 50.16 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CA THR A2225 " pdb=" C THR A2225 " pdb=" N PRO A2226 " pdb=" CA PRO A2226 " ideal model delta harmonic sigma weight residual 180.00 147.68 32.32 0 5.00e+00 4.00e-02 4.18e+01 dihedral pdb=" CA SER A 779 " pdb=" C SER A 779 " pdb=" N ASN A 780 " pdb=" CA ASN A 780 " ideal model delta harmonic sigma weight residual 180.00 148.94 31.06 0 5.00e+00 4.00e-02 3.86e+01 ... (remaining 21914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 4342 0.074 - 0.147: 1016 0.147 - 0.221: 129 0.221 - 0.295: 16 0.295 - 0.368: 9 Chirality restraints: 5512 Sorted by residual: 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 2.28 0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CB VAL A3010 " pdb=" CA VAL A3010 " pdb=" CG1 VAL A3010 " pdb=" CG2 VAL A3010 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CB ILE A2378 " pdb=" CA ILE A2378 " pdb=" CG1 ILE A2378 " pdb=" CG2 ILE A2378 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.87e+00 ... (remaining 5509 not shown) Planarity restraints: 6228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A2783 " -0.023 2.00e-02 2.50e+03 2.75e-02 1.32e+01 pdb=" CG PHE A2783 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A2783 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE A2783 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A2783 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE A2783 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE A2783 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A2960 " -0.024 2.00e-02 2.50e+03 2.68e-02 1.25e+01 pdb=" CG PHE A2960 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A2960 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE A2960 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A2960 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A2960 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A2960 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A4323 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C THR A4323 " 0.059 2.00e-02 2.50e+03 pdb=" O THR A4323 " -0.022 2.00e-02 2.50e+03 pdb=" N GLU A4324 " -0.020 2.00e-02 2.50e+03 ... (remaining 6225 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 368 2.63 - 3.20: 30985 3.20 - 3.77: 55531 3.77 - 4.33: 76544 4.33 - 4.90: 125503 Nonbonded interactions: 288931 Sorted by model distance: nonbonded pdb=" OE2 GLU A2060 " pdb="MG MG A5202 " model vdw 2.066 2.170 nonbonded pdb=" OG SER A1961 " pdb="MG MG A5202 " model vdw 2.069 2.170 nonbonded pdb=" O GLU A1375 " pdb=" NH1 ARG A1379 " model vdw 2.171 3.120 nonbonded pdb=" OH TYR A3664 " pdb=" OG1 THR A3692 " model vdw 2.233 3.040 nonbonded pdb=" O LEU A 848 " pdb=" OG SER A 852 " model vdw 2.243 3.040 ... (remaining 288926 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: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.430 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 39.760 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 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 : 0.011 0.188 35971 Z= 0.445 Angle : 1.162 17.247 48683 Z= 0.616 Chirality : 0.064 0.368 5512 Planarity : 0.008 0.081 6228 Dihedral : 11.357 84.238 13451 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.91 % Favored : 90.97 % Rotamer: Outliers : 0.28 % Allowed : 3.44 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.07 % 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: -3.72 (0.10), residues: 4320 helix: -2.17 (0.08), residues: 2444 sheet: -0.85 (0.32), residues: 241 loop : -3.01 (0.13), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG A2523 TYR 0.051 0.004 TYR A2057 PHE 0.060 0.005 PHE A2960 TRP 0.036 0.005 TRP A5022 HIS 0.030 0.004 HIS A2688 Details of bonding type rmsd covalent geometry : bond 0.01071 (35961) covalent geometry : angle 1.15360 (48670) SS BOND : bond 0.00571 ( 2) SS BOND : angle 2.65003 ( 4) hydrogen bonds : bond 0.14005 ( 1824) hydrogen bonds : angle 6.43416 ( 5349) metal coordination : bond 0.13881 ( 8) metal coordination : angle 9.96629 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 519 time to evaluate : 1.322 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 663 ARG cc_start: 0.7767 (ttm-80) cc_final: 0.7535 (ttm110) REVERT: A 883 ASN cc_start: 0.8284 (m-40) cc_final: 0.8075 (m-40) REVERT: A 934 MET cc_start: 0.7527 (ttp) cc_final: 0.7314 (ttm) REVERT: A 940 GLN cc_start: 0.7315 (mt0) cc_final: 0.6794 (tm-30) REVERT: A 1120 ARG cc_start: 0.7719 (mmt-90) cc_final: 0.7499 (mmt180) REVERT: A 1134 VAL cc_start: 0.8523 (t) cc_final: 0.8238 (p) REVERT: A 1305 GLN cc_start: 0.7926 (tm-30) cc_final: 0.7455 (mt0) REVERT: A 1409 ASP cc_start: 0.7865 (m-30) cc_final: 0.7643 (m-30) REVERT: A 1433 GLN cc_start: 0.7962 (mt0) cc_final: 0.7622 (mt0) REVERT: A 1519 LYS cc_start: 0.8644 (mmpt) cc_final: 0.8360 (mmtm) REVERT: A 1864 TYR cc_start: 0.7949 (t80) cc_final: 0.7680 (t80) REVERT: A 2258 ARG cc_start: 0.6759 (pmt170) cc_final: 0.6430 (mtm110) REVERT: A 2259 TRP cc_start: 0.7742 (m100) cc_final: 0.7459 (m100) REVERT: A 2648 MET cc_start: 0.8754 (mmm) cc_final: 0.8205 (mmp) REVERT: A 3200 ASP cc_start: 0.7082 (p0) cc_final: 0.6871 (p0) REVERT: A 3537 LYS cc_start: 0.8592 (tmmt) cc_final: 0.8389 (tttp) REVERT: A 3619 LYS cc_start: 0.8722 (pmmt) cc_final: 0.8460 (ptpp) REVERT: A 3636 MET cc_start: 0.3772 (ptp) cc_final: 0.3352 (tpp) REVERT: A 3968 LEU cc_start: 0.8531 (tp) cc_final: 0.7866 (tp) REVERT: A 3980 MET cc_start: 0.8056 (tpp) cc_final: 0.7748 (tpp) REVERT: A 4001 HIS cc_start: 0.7428 (m-70) cc_final: 0.7190 (m-70) REVERT: A 4089 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8295 (mt) REVERT: A 4406 GLN cc_start: 0.7701 (tp40) cc_final: 0.7467 (tm-30) outliers start: 11 outliers final: 2 residues processed: 530 average time/residue: 0.2650 time to fit residues: 213.9682 Evaluate side-chains 339 residues out of total 3911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 336 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2741 ILE Chi-restraints excluded: chain A residue 3641 VAL Chi-restraints excluded: chain A residue 4089 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 0.0980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 0.1980 chunk 424 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 789 ASN A 822 HIS A 983 GLN A1014 ASN A1089 HIS A1186 HIS A1343 ASN A1429 HIS A1433 GLN A1567 ASN A1591 HIS A1595 ASN A1660 HIS A1770 HIS A1812 GLN A1816 GLN A1849 GLN ** A1882 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1920 ASN A1930 GLN A2413 HIS A2480 HIS A2493 GLN A2942 HIS A2981 GLN A3251 GLN A3337 GLN A3400 HIS A3496 ASN A3536 ASN A3542 GLN A3561 GLN A3568 HIS ** A3608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3777 ASN A3914 ASN A4001 HIS A4008 HIS A4060 HIS A4395 HIS A4413 ASN A4500 GLN A4543 HIS A4587 HIS A4590 HIS A4606 ASN ** A4634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4697 HIS A4759 HIS A4834 HIS ** A4900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4959 GLN A5002 GLN A5017 HIS A5028 HIS A5056 HIS A5146 GLN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.103902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.082984 restraints weight = 74595.082| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.33 r_work: 0.3019 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 35971 Z= 0.137 Angle : 0.653 13.821 48683 Z= 0.331 Chirality : 0.042 0.207 5512 Planarity : 0.005 0.073 6228 Dihedral : 6.334 81.654 4801 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.41 % Favored : 92.52 % Rotamer: Outliers : 1.08 % Allowed : 6.69 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.68 (0.12), residues: 4320 helix: -0.26 (0.10), residues: 2484 sheet: -0.40 (0.34), residues: 227 loop : -2.56 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A3228 TYR 0.029 0.002 TYR A 753 PHE 0.038 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 0.00303 (35961) covalent geometry : angle 0.65162 (48670) SS BOND : bond 0.00189 ( 2) SS BOND : angle 1.70829 ( 4) hydrogen bonds : bond 0.03921 ( 1824) hydrogen bonds : angle 4.39692 ( 5349) metal coordination : bond 0.00464 ( 8) metal coordination : angle 2.92964 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 379 time to evaluate : 1.160 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 934 MET cc_start: 0.7593 (ttp) cc_final: 0.7379 (ttm) REVERT: A 940 GLN cc_start: 0.7243 (mt0) cc_final: 0.6780 (tm-30) REVERT: A 1305 GLN cc_start: 0.7720 (tm-30) cc_final: 0.7503 (mt0) REVERT: A 1327 ARG cc_start: 0.7370 (ttm-80) cc_final: 0.7156 (tpm170) REVERT: A 1409 ASP cc_start: 0.8199 (m-30) cc_final: 0.7858 (m-30) REVERT: A 1433 GLN cc_start: 0.8014 (mt0) cc_final: 0.7809 (mt0) REVERT: A 2258 ARG cc_start: 0.7084 (pmt170) cc_final: 0.6525 (ptt-90) REVERT: A 2288 ASN cc_start: 0.8510 (p0) cc_final: 0.8147 (p0) REVERT: A 2324 ILE cc_start: 0.7596 (mt) cc_final: 0.7262 (mt) REVERT: A 2495 MET cc_start: 0.8587 (tpp) cc_final: 0.8139 (tpt) REVERT: A 2554 TYR cc_start: 0.7758 (m-80) cc_final: 0.7483 (m-80) REVERT: A 2648 MET cc_start: 0.8801 (mmm) cc_final: 0.8414 (mmt) REVERT: A 3331 ARG cc_start: 0.8382 (mtt90) cc_final: 0.7940 (mtm180) REVERT: A 3511 ASP cc_start: 0.8319 (m-30) cc_final: 0.7982 (m-30) REVERT: A 3537 LYS cc_start: 0.8756 (tmmt) cc_final: 0.8553 (tttp) REVERT: A 3552 ARG cc_start: 0.7996 (tpp-160) cc_final: 0.7608 (mmp-170) REVERT: A 3619 LYS cc_start: 0.8786 (pmmt) cc_final: 0.8535 (pttm) REVERT: A 3814 MET cc_start: 0.8288 (tpp) cc_final: 0.7992 (tpp) REVERT: A 4344 GLU cc_start: 0.7198 (mp0) cc_final: 0.6994 (mp0) REVERT: A 5059 LEU cc_start: 0.8491 (mt) cc_final: 0.8281 (mt) outliers start: 42 outliers final: 15 residues processed: 407 average time/residue: 0.2472 time to fit residues: 157.2545 Evaluate side-chains 336 residues out of total 3911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 321 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 2169 ILE Chi-restraints excluded: chain A residue 2574 CYS Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 3114 ASP Chi-restraints excluded: chain A residue 3641 VAL Chi-restraints excluded: chain A residue 3647 LEU Chi-restraints excluded: chain A residue 3858 MET Chi-restraints excluded: chain A residue 3919 ARG Chi-restraints excluded: chain A residue 4167 VAL Chi-restraints excluded: chain A residue 4671 HIS Chi-restraints excluded: chain A residue 4782 LEU Chi-restraints excluded: chain A residue 5056 HIS Chi-restraints excluded: chain A residue 5112 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 55 optimal weight: 0.8980 chunk 200 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 436 optimal weight: 10.0000 chunk 383 optimal weight: 0.8980 chunk 396 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 374 optimal weight: 0.9980 chunk 422 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 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 803 HIS A 827 ASN A1057 GLN ** A1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1214 GLN A1591 HIS ** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1882 HIS A2822 HIS ** A3348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3392 HIS ** A3608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4634 HIS A5014 GLN A5146 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.103784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.082971 restraints weight = 74417.694| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.09 r_work: 0.3038 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 35971 Z= 0.139 Angle : 0.623 12.144 48683 Z= 0.312 Chirality : 0.042 0.227 5512 Planarity : 0.005 0.131 6228 Dihedral : 5.894 89.509 4797 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.75 % Favored : 92.20 % Rotamer: Outliers : 1.51 % Allowed : 7.84 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.87 (0.13), residues: 4320 helix: 0.48 (0.10), residues: 2511 sheet: -0.22 (0.34), residues: 226 loop : -2.38 (0.15), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A3941 TYR 0.024 0.001 TYR A1717 PHE 0.038 0.002 PHE A2371 TRP 0.019 0.001 TRP A1298 HIS 0.012 0.001 HIS A5056 Details of bonding type rmsd covalent geometry : bond 0.00322 (35961) covalent geometry : angle 0.62169 (48670) SS BOND : bond 0.00259 ( 2) SS BOND : angle 1.37024 ( 4) hydrogen bonds : bond 0.03612 ( 1824) hydrogen bonds : angle 4.09328 ( 5349) metal coordination : bond 0.00903 ( 8) metal coordination : angle 2.50581 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 338 time to evaluate : 1.498 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 934 MET cc_start: 0.7662 (ttp) cc_final: 0.7412 (ttm) REVERT: A 940 GLN cc_start: 0.7549 (mt0) cc_final: 0.6873 (tm-30) REVERT: A 988 GLU cc_start: 0.7325 (pm20) cc_final: 0.7074 (mt-10) REVERT: A 1285 LYS cc_start: 0.7988 (mtmm) cc_final: 0.7733 (mmtt) REVERT: A 1305 GLN cc_start: 0.7759 (tm-30) cc_final: 0.7473 (mt0) REVERT: A 1327 ARG cc_start: 0.7363 (ttm-80) cc_final: 0.7086 (tpm170) REVERT: A 1373 ILE cc_start: 0.5938 (OUTLIER) cc_final: 0.5624 (mt) REVERT: A 1409 ASP cc_start: 0.8360 (m-30) cc_final: 0.8045 (m-30) REVERT: A 1936 LEU cc_start: 0.7864 (tt) cc_final: 0.7465 (tp) REVERT: A 2258 ARG cc_start: 0.7319 (pmt170) cc_final: 0.6728 (ptt-90) REVERT: A 2288 ASN cc_start: 0.8618 (p0) cc_final: 0.8260 (p0) REVERT: A 2495 MET cc_start: 0.8805 (tpp) cc_final: 0.8322 (tpt) REVERT: A 2554 TYR cc_start: 0.7981 (m-80) cc_final: 0.7697 (m-80) REVERT: A 2648 MET cc_start: 0.8887 (mmm) cc_final: 0.8560 (mmt) REVERT: A 3331 ARG cc_start: 0.8605 (mtt90) cc_final: 0.8131 (mtm180) REVERT: A 3345 ARG cc_start: 0.8279 (mtp180) cc_final: 0.8067 (mtp-110) REVERT: A 3370 PHE cc_start: 0.8692 (m-80) cc_final: 0.8332 (m-80) REVERT: A 3511 ASP cc_start: 0.8467 (m-30) cc_final: 0.8131 (m-30) REVERT: A 3537 LYS cc_start: 0.8832 (tmmt) cc_final: 0.8608 (tttp) REVERT: A 3552 ARG cc_start: 0.8247 (tpp-160) cc_final: 0.7870 (mmp-170) REVERT: A 3619 LYS cc_start: 0.8922 (pmmt) cc_final: 0.8720 (ptpp) REVERT: A 3636 MET cc_start: 0.3463 (tpp) cc_final: 0.2356 (ptt) REVERT: A 4406 GLN cc_start: 0.8405 (tp40) cc_final: 0.8136 (tp40) outliers start: 59 outliers final: 27 residues processed: 386 average time/residue: 0.2428 time to fit residues: 147.5662 Evaluate side-chains 344 residues out of total 3911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 316 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1155 ILE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1373 ILE Chi-restraints excluded: chain A residue 1427 CYS Chi-restraints excluded: chain A residue 2169 ILE Chi-restraints excluded: chain A residue 2194 ILE Chi-restraints excluded: chain A residue 2574 CYS Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 2881 SER Chi-restraints excluded: chain A residue 2964 LEU Chi-restraints excluded: chain A residue 3023 GLN Chi-restraints excluded: chain A residue 3114 ASP Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3524 LEU Chi-restraints excluded: chain A residue 3647 LEU Chi-restraints excluded: chain A residue 3858 MET Chi-restraints excluded: chain A residue 3919 ARG Chi-restraints excluded: chain A residue 4167 VAL Chi-restraints excluded: chain A residue 4635 LEU Chi-restraints excluded: chain A residue 4671 HIS Chi-restraints excluded: chain A residue 4782 LEU Chi-restraints excluded: chain A residue 4941 MET Chi-restraints excluded: chain A residue 5112 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 218 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 377 optimal weight: 7.9990 chunk 182 optimal weight: 0.5980 chunk 235 optimal weight: 0.1980 chunk 90 optimal weight: 6.9990 chunk 290 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 393 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1092 GLN ** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3575 GLN ** A3608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4134 GLN A4883 GLN ** A5121 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 = 0.3640 r_free = 0.3640 target = 0.103565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.082721 restraints weight = 74046.170| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.10 r_work: 0.3025 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 35971 Z= 0.145 Angle : 0.606 10.049 48683 Z= 0.304 Chirality : 0.042 0.206 5512 Planarity : 0.004 0.113 6228 Dihedral : 5.667 82.982 4796 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 1.31 % Allowed : 9.10 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.41 (0.13), residues: 4320 helix: 0.88 (0.10), residues: 2511 sheet: -0.18 (0.34), residues: 226 loop : -2.24 (0.16), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3493 TYR 0.024 0.001 TYR A1717 PHE 0.037 0.002 PHE A2371 TRP 0.018 0.001 TRP A1298 HIS 0.006 0.001 HIS A 832 Details of bonding type rmsd covalent geometry : bond 0.00343 (35961) covalent geometry : angle 0.60576 (48670) SS BOND : bond 0.00265 ( 2) SS BOND : angle 1.22583 ( 4) hydrogen bonds : bond 0.03484 ( 1824) hydrogen bonds : angle 3.94464 ( 5349) metal coordination : bond 0.00410 ( 8) metal coordination : angle 1.94468 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 340 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 677 LYS cc_start: 0.7437 (mmtp) cc_final: 0.7092 (mtmm) REVERT: A 934 MET cc_start: 0.7528 (ttp) cc_final: 0.7309 (ttm) REVERT: A 940 GLN cc_start: 0.7558 (mt0) cc_final: 0.6869 (tm-30) REVERT: A 1247 ASP cc_start: 0.8620 (m-30) cc_final: 0.8310 (m-30) REVERT: A 1285 LYS cc_start: 0.8034 (mtmm) cc_final: 0.7776 (mmtt) REVERT: A 1305 GLN cc_start: 0.7826 (tm-30) cc_final: 0.7621 (mt0) REVERT: A 1327 ARG cc_start: 0.7451 (ttm-80) cc_final: 0.7106 (tpp-160) REVERT: A 1373 ILE cc_start: 0.5967 (OUTLIER) cc_final: 0.5676 (mt) REVERT: A 1409 ASP cc_start: 0.8376 (m-30) cc_final: 0.8069 (m-30) REVERT: A 1414 SER cc_start: 0.8503 (t) cc_final: 0.8268 (m) REVERT: A 1936 LEU cc_start: 0.7640 (tt) cc_final: 0.7426 (tp) REVERT: A 2258 ARG cc_start: 0.7303 (pmt170) cc_final: 0.6528 (mtm110) REVERT: A 2495 MET cc_start: 0.8866 (tpp) cc_final: 0.8422 (tpt) REVERT: A 2543 PHE cc_start: 0.7887 (OUTLIER) cc_final: 0.7541 (m-80) REVERT: A 2554 TYR cc_start: 0.7889 (m-80) cc_final: 0.7630 (m-80) REVERT: A 2648 MET cc_start: 0.8893 (mmm) cc_final: 0.8545 (mmp) REVERT: A 2753 PHE cc_start: 0.8089 (m-80) cc_final: 0.7705 (m-80) REVERT: A 3331 ARG cc_start: 0.8640 (mtt90) cc_final: 0.8215 (mtm180) REVERT: A 3345 ARG cc_start: 0.8309 (mtp180) cc_final: 0.8082 (mtp-110) REVERT: A 3370 PHE cc_start: 0.8666 (m-80) cc_final: 0.8162 (m-80) REVERT: A 3536 ASN cc_start: 0.8626 (OUTLIER) cc_final: 0.8313 (t0) REVERT: A 3537 LYS cc_start: 0.8841 (tmmt) cc_final: 0.8619 (tttp) REVERT: A 3552 ARG cc_start: 0.8348 (tpp-160) cc_final: 0.7972 (mmp-170) REVERT: A 3636 MET cc_start: 0.2776 (tpp) cc_final: 0.1913 (ptt) REVERT: A 3835 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8626 (mp) REVERT: A 3981 MET cc_start: 0.7908 (ttp) cc_final: 0.7693 (ptm) REVERT: A 4406 GLN cc_start: 0.8400 (tp40) cc_final: 0.8172 (tp40) REVERT: A 5042 ARG cc_start: 0.7981 (ttp-110) cc_final: 0.7781 (mtm-85) outliers start: 51 outliers final: 33 residues processed: 376 average time/residue: 0.2425 time to fit residues: 143.2503 Evaluate side-chains 356 residues out of total 3911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 319 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1155 ILE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1373 ILE Chi-restraints excluded: chain A residue 1427 CYS Chi-restraints excluded: chain A residue 2169 ILE Chi-restraints excluded: chain A residue 2338 LEU Chi-restraints excluded: chain A residue 2543 PHE Chi-restraints excluded: chain A residue 2574 CYS Chi-restraints excluded: chain A residue 2628 HIS Chi-restraints excluded: chain A residue 2707 LEU Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 2964 LEU Chi-restraints excluded: chain A residue 3023 GLN Chi-restraints excluded: chain A residue 3114 ASP Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3524 LEU Chi-restraints excluded: chain A residue 3536 ASN Chi-restraints excluded: chain A residue 3647 LEU Chi-restraints excluded: chain A residue 3722 MET Chi-restraints excluded: chain A residue 3835 LEU Chi-restraints excluded: chain A residue 3858 MET Chi-restraints excluded: chain A residue 3919 ARG Chi-restraints excluded: chain A residue 4167 VAL Chi-restraints excluded: chain A residue 4297 LEU Chi-restraints excluded: chain A residue 4635 LEU Chi-restraints excluded: chain A residue 4671 HIS Chi-restraints excluded: chain A residue 4782 LEU Chi-restraints excluded: chain A residue 4853 VAL Chi-restraints excluded: chain A residue 4941 MET Chi-restraints excluded: chain A residue 5112 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 71 optimal weight: 9.9990 chunk 294 optimal weight: 2.9990 chunk 428 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 286 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 411 optimal weight: 2.9990 chunk 352 optimal weight: 0.9980 chunk 404 optimal weight: 0.6980 chunk 228 optimal weight: 0.5980 chunk 14 optimal weight: 0.0770 overall best weight: 1.0740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 796 HIS A1378 GLN ** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2136 HIS ** A3348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4900 GLN ** A5121 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 = 0.3609 r_free = 0.3609 target = 0.099455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.077546 restraints weight = 74541.230| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.35 r_work: 0.2982 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 35971 Z= 0.153 Angle : 0.607 10.372 48683 Z= 0.303 Chirality : 0.042 0.207 5512 Planarity : 0.004 0.095 6228 Dihedral : 5.557 78.922 4796 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 1.67 % Allowed : 9.66 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.18 (0.13), residues: 4320 helix: 1.09 (0.11), residues: 2519 sheet: -0.18 (0.34), residues: 226 loop : -2.17 (0.16), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A2933 TYR 0.024 0.001 TYR A1717 PHE 0.034 0.002 PHE A2371 TRP 0.021 0.001 TRP A1298 HIS 0.007 0.001 HIS A 832 Details of bonding type rmsd covalent geometry : bond 0.00364 (35961) covalent geometry : angle 0.60594 (48670) SS BOND : bond 0.00328 ( 2) SS BOND : angle 1.17680 ( 4) hydrogen bonds : bond 0.03458 ( 1824) hydrogen bonds : angle 3.87442 ( 5349) metal coordination : bond 0.00595 ( 8) metal coordination : angle 2.23109 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 341 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 934 MET cc_start: 0.7469 (ttp) cc_final: 0.7265 (ttm) REVERT: A 940 GLN cc_start: 0.7417 (mt0) cc_final: 0.6849 (tm-30) REVERT: A 1247 ASP cc_start: 0.8532 (m-30) cc_final: 0.8212 (m-30) REVERT: A 1305 GLN cc_start: 0.7813 (tm-30) cc_final: 0.7611 (mt0) REVERT: A 1327 ARG cc_start: 0.7414 (ttm-80) cc_final: 0.7060 (tpp-160) REVERT: A 1409 ASP cc_start: 0.8234 (m-30) cc_final: 0.7980 (m-30) REVERT: A 1414 SER cc_start: 0.8401 (t) cc_final: 0.8198 (m) REVERT: A 2258 ARG cc_start: 0.7002 (pmt170) cc_final: 0.6366 (mtm110) REVERT: A 2324 ILE cc_start: 0.7760 (mt) cc_final: 0.7488 (mt) REVERT: A 2543 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.7404 (m-80) REVERT: A 2554 TYR cc_start: 0.7789 (m-80) cc_final: 0.7540 (m-80) REVERT: A 2648 MET cc_start: 0.8740 (mmm) cc_final: 0.8446 (mmp) REVERT: A 3331 ARG cc_start: 0.8484 (mtt90) cc_final: 0.8105 (mtm-85) REVERT: A 3370 PHE cc_start: 0.8505 (m-80) cc_final: 0.8048 (m-80) REVERT: A 3511 ASP cc_start: 0.8432 (m-30) cc_final: 0.8093 (m-30) REVERT: A 3536 ASN cc_start: 0.8541 (OUTLIER) cc_final: 0.8280 (t0) REVERT: A 3537 LYS cc_start: 0.8739 (tmmt) cc_final: 0.8505 (tttp) REVERT: A 3552 ARG cc_start: 0.8262 (tpp-160) cc_final: 0.7839 (mmp-170) REVERT: A 3636 MET cc_start: 0.2699 (tpp) cc_final: 0.1898 (ptt) REVERT: A 4987 MET cc_start: 0.5778 (tpt) cc_final: 0.5560 (tpt) outliers start: 65 outliers final: 43 residues processed: 390 average time/residue: 0.2454 time to fit residues: 150.3304 Evaluate side-chains 367 residues out of total 3911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 322 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1155 ILE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1427 CYS Chi-restraints excluded: chain A residue 1631 VAL Chi-restraints excluded: chain A residue 1820 THR Chi-restraints excluded: chain A residue 2151 VAL Chi-restraints excluded: chain A residue 2169 ILE Chi-restraints excluded: chain A residue 2338 LEU Chi-restraints excluded: chain A residue 2371 PHE Chi-restraints excluded: chain A residue 2543 PHE Chi-restraints excluded: chain A residue 2574 CYS Chi-restraints excluded: chain A residue 2628 HIS Chi-restraints excluded: chain A residue 2707 LEU Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 2924 VAL Chi-restraints excluded: chain A residue 2964 LEU Chi-restraints excluded: chain A residue 3023 GLN Chi-restraints excluded: chain A residue 3114 ASP Chi-restraints excluded: chain A residue 3245 GLU Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3536 ASN Chi-restraints excluded: chain A residue 3581 ILE Chi-restraints excluded: chain A residue 3647 LEU Chi-restraints excluded: chain A residue 3722 MET Chi-restraints excluded: chain A residue 3858 MET Chi-restraints excluded: chain A residue 3919 ARG Chi-restraints excluded: chain A residue 3944 ILE Chi-restraints excluded: chain A residue 4048 VAL Chi-restraints excluded: chain A residue 4074 VAL Chi-restraints excluded: chain A residue 4297 LEU Chi-restraints excluded: chain A residue 4513 VAL Chi-restraints excluded: chain A residue 4519 ARG Chi-restraints excluded: chain A residue 4635 LEU Chi-restraints excluded: chain A residue 4671 HIS Chi-restraints excluded: chain A residue 4782 LEU Chi-restraints excluded: chain A residue 4853 VAL Chi-restraints excluded: chain A residue 4941 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 397 optimal weight: 0.4980 chunk 181 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 341 optimal weight: 0.9990 chunk 96 optimal weight: 0.4980 chunk 144 optimal weight: 1.9990 chunk 336 optimal weight: 0.9980 chunk 418 optimal weight: 0.0970 chunk 241 optimal weight: 0.6980 chunk 277 optimal weight: 1.9990 chunk 195 optimal weight: 5.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 803 HIS A1595 ASN A3600 GLN ** A3608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4249 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.104648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.083502 restraints weight = 73910.843| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.11 r_work: 0.3048 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35971 Z= 0.114 Angle : 0.576 9.919 48683 Z= 0.287 Chirality : 0.040 0.187 5512 Planarity : 0.004 0.066 6228 Dihedral : 5.320 82.352 4796 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.55 % Favored : 92.43 % Rotamer: Outliers : 1.72 % Allowed : 9.66 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 4320 helix: 1.36 (0.11), residues: 2509 sheet: -0.07 (0.34), residues: 223 loop : -2.05 (0.16), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 646 TYR 0.025 0.001 TYR A1717 PHE 0.031 0.001 PHE A2371 TRP 0.012 0.001 TRP A1601 HIS 0.009 0.001 HIS A 803 Details of bonding type rmsd covalent geometry : bond 0.00258 (35961) covalent geometry : angle 0.57535 (48670) SS BOND : bond 0.00216 ( 2) SS BOND : angle 1.08953 ( 4) hydrogen bonds : bond 0.03143 ( 1824) hydrogen bonds : angle 3.75378 ( 5349) metal coordination : bond 0.00325 ( 8) metal coordination : angle 1.78870 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 338 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 613 ASP cc_start: 0.6755 (m-30) cc_final: 0.6467 (m-30) REVERT: A 934 MET cc_start: 0.7507 (ttp) cc_final: 0.7300 (ttm) REVERT: A 940 GLN cc_start: 0.7483 (mt0) cc_final: 0.6870 (tm-30) REVERT: A 988 GLU cc_start: 0.7369 (pm20) cc_final: 0.6941 (mp0) REVERT: A 1247 ASP cc_start: 0.8742 (m-30) cc_final: 0.8423 (m-30) REVERT: A 1260 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7828 (tptp) REVERT: A 1409 ASP cc_start: 0.8190 (m-30) cc_final: 0.7928 (m-30) REVERT: A 1519 LYS cc_start: 0.8789 (mmmt) cc_final: 0.8326 (mmtm) REVERT: A 1589 LYS cc_start: 0.9112 (mttt) cc_final: 0.8867 (mtmm) REVERT: A 1823 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6905 (pt0) REVERT: A 2258 ARG cc_start: 0.7216 (pmt170) cc_final: 0.6350 (mtm110) REVERT: A 2324 ILE cc_start: 0.7840 (mt) cc_final: 0.7434 (mt) REVERT: A 2543 PHE cc_start: 0.7759 (OUTLIER) cc_final: 0.7454 (m-80) REVERT: A 2554 TYR cc_start: 0.7942 (m-80) cc_final: 0.7647 (m-80) REVERT: A 2648 MET cc_start: 0.8796 (mmm) cc_final: 0.8474 (mmt) REVERT: A 3345 ARG cc_start: 0.8265 (mtp180) cc_final: 0.7933 (mtp-110) REVERT: A 3370 PHE cc_start: 0.8634 (m-80) cc_final: 0.8134 (m-80) REVERT: A 3511 ASP cc_start: 0.8494 (m-30) cc_final: 0.8087 (m-30) REVERT: A 3537 LYS cc_start: 0.8805 (tmmt) cc_final: 0.8561 (tttp) REVERT: A 3552 ARG cc_start: 0.8261 (tpp-160) cc_final: 0.7893 (mmp-170) REVERT: A 3636 MET cc_start: 0.2620 (tpp) cc_final: 0.1784 (ptt) REVERT: A 3858 MET cc_start: 0.7017 (OUTLIER) cc_final: 0.6729 (ttm) outliers start: 67 outliers final: 44 residues processed: 385 average time/residue: 0.2438 time to fit residues: 147.7928 Evaluate side-chains 363 residues out of total 3911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 315 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain A residue 803 HIS Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1260 LYS Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1427 CYS Chi-restraints excluded: chain A residue 1631 VAL Chi-restraints excluded: chain A residue 1823 GLU Chi-restraints excluded: chain A residue 2151 VAL Chi-restraints excluded: chain A residue 2169 ILE Chi-restraints excluded: chain A residue 2338 LEU Chi-restraints excluded: chain A residue 2371 PHE Chi-restraints excluded: chain A residue 2543 PHE Chi-restraints excluded: chain A residue 2574 CYS Chi-restraints excluded: chain A residue 2628 HIS Chi-restraints excluded: chain A residue 2707 LEU Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 2924 VAL Chi-restraints excluded: chain A residue 2964 LEU Chi-restraints excluded: chain A residue 3023 GLN Chi-restraints excluded: chain A residue 3114 ASP Chi-restraints excluded: chain A residue 3245 GLU Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3524 LEU Chi-restraints excluded: chain A residue 3536 ASN Chi-restraints excluded: chain A residue 3641 VAL Chi-restraints excluded: chain A residue 3647 LEU Chi-restraints excluded: chain A residue 3722 MET Chi-restraints excluded: chain A residue 3858 MET Chi-restraints excluded: chain A residue 3919 ARG Chi-restraints excluded: chain A residue 3944 ILE Chi-restraints excluded: chain A residue 3997 VAL Chi-restraints excluded: chain A residue 4048 VAL Chi-restraints excluded: chain A residue 4267 VAL Chi-restraints excluded: chain A residue 4297 LEU Chi-restraints excluded: chain A residue 4635 LEU Chi-restraints excluded: chain A residue 4671 HIS Chi-restraints excluded: chain A residue 4782 LEU Chi-restraints excluded: chain A residue 4853 VAL Chi-restraints excluded: chain A residue 4984 ASP Chi-restraints excluded: chain A residue 5040 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 29 optimal weight: 2.9990 chunk 368 optimal weight: 0.8980 chunk 191 optimal weight: 3.9990 chunk 371 optimal weight: 4.9990 chunk 217 optimal weight: 0.7980 chunk 210 optimal weight: 3.9990 chunk 388 optimal weight: 0.9990 chunk 343 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 393 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 632 HIS A 803 HIS A 996 GLN A1595 ASN A1741 GLN A1907 GLN A2273 HIS ** A3608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.103861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.082290 restraints weight = 74241.860| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.27 r_work: 0.3013 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35971 Z= 0.135 Angle : 0.591 11.698 48683 Z= 0.295 Chirality : 0.041 0.194 5512 Planarity : 0.004 0.066 6228 Dihedral : 5.293 82.150 4796 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 1.79 % Allowed : 10.02 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.24 (0.13), residues: 4320 helix: 1.44 (0.11), residues: 2508 sheet: -0.05 (0.34), residues: 222 loop : -1.99 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2933 TYR 0.038 0.001 TYR A 753 PHE 0.032 0.001 PHE A2371 TRP 0.013 0.001 TRP A1601 HIS 0.018 0.001 HIS A 803 Details of bonding type rmsd covalent geometry : bond 0.00318 (35961) covalent geometry : angle 0.59007 (48670) SS BOND : bond 0.00638 ( 2) SS BOND : angle 2.25709 ( 4) hydrogen bonds : bond 0.03270 ( 1824) hydrogen bonds : angle 3.75242 ( 5349) metal coordination : bond 0.00330 ( 8) metal coordination : angle 2.14020 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 329 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 677 LYS cc_start: 0.7391 (mmtp) cc_final: 0.6981 (mtmm) REVERT: A 934 MET cc_start: 0.7634 (ttp) cc_final: 0.7419 (ttm) REVERT: A 940 GLN cc_start: 0.7522 (mt0) cc_final: 0.6912 (tm-30) REVERT: A 988 GLU cc_start: 0.7353 (pm20) cc_final: 0.7078 (mp0) REVERT: A 1247 ASP cc_start: 0.8735 (m-30) cc_final: 0.8430 (m-30) REVERT: A 1260 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7746 (tptp) REVERT: A 1394 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8391 (mp) REVERT: A 1409 ASP cc_start: 0.8221 (m-30) cc_final: 0.7966 (m-30) REVERT: A 1452 MET cc_start: 0.6717 (mmm) cc_final: 0.6516 (mmm) REVERT: A 1519 LYS cc_start: 0.8739 (mmmt) cc_final: 0.8292 (mmtm) REVERT: A 1596 MET cc_start: 0.8682 (mmm) cc_final: 0.8475 (mmm) REVERT: A 2258 ARG cc_start: 0.7254 (pmt170) cc_final: 0.6385 (mtm110) REVERT: A 2324 ILE cc_start: 0.7885 (mt) cc_final: 0.7590 (mt) REVERT: A 2543 PHE cc_start: 0.7816 (OUTLIER) cc_final: 0.7470 (m-80) REVERT: A 2554 TYR cc_start: 0.7929 (m-80) cc_final: 0.7623 (m-80) REVERT: A 2648 MET cc_start: 0.8815 (mmm) cc_final: 0.8601 (mmp) REVERT: A 2691 ASP cc_start: 0.8922 (m-30) cc_final: 0.8523 (m-30) REVERT: A 3370 PHE cc_start: 0.8712 (m-80) cc_final: 0.8243 (m-80) REVERT: A 3511 ASP cc_start: 0.8545 (m-30) cc_final: 0.8222 (m-30) REVERT: A 3537 LYS cc_start: 0.8826 (tmmt) cc_final: 0.8576 (tttp) REVERT: A 3552 ARG cc_start: 0.8381 (tpp-160) cc_final: 0.7993 (mmp-170) REVERT: A 3636 MET cc_start: 0.2381 (tpp) cc_final: 0.1341 (ptt) REVERT: A 3638 PHE cc_start: 0.6949 (OUTLIER) cc_final: 0.6648 (t80) REVERT: A 3858 MET cc_start: 0.7108 (OUTLIER) cc_final: 0.6833 (ttm) REVERT: A 3948 PHE cc_start: 0.6338 (t80) cc_final: 0.6128 (t80) REVERT: A 4348 LYS cc_start: 0.8324 (tptp) cc_final: 0.8096 (tptp) REVERT: A 4519 ARG cc_start: 0.6333 (OUTLIER) cc_final: 0.6059 (pmm150) outliers start: 70 outliers final: 52 residues processed: 378 average time/residue: 0.2364 time to fit residues: 141.3049 Evaluate side-chains 372 residues out of total 3911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 314 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain A residue 803 HIS Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1260 LYS Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1394 LEU Chi-restraints excluded: chain A residue 1427 CYS Chi-restraints excluded: chain A residue 1595 ASN Chi-restraints excluded: chain A residue 1750 TYR Chi-restraints excluded: chain A residue 2151 VAL Chi-restraints excluded: chain A residue 2169 ILE Chi-restraints excluded: chain A residue 2273 HIS Chi-restraints excluded: chain A residue 2306 VAL Chi-restraints excluded: chain A residue 2338 LEU Chi-restraints excluded: chain A residue 2371 PHE Chi-restraints excluded: chain A residue 2543 PHE Chi-restraints excluded: chain A residue 2574 CYS Chi-restraints excluded: chain A residue 2628 HIS Chi-restraints excluded: chain A residue 2707 LEU Chi-restraints excluded: chain A residue 2773 HIS Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 2924 VAL Chi-restraints excluded: chain A residue 2964 LEU Chi-restraints excluded: chain A residue 3023 GLN Chi-restraints excluded: chain A residue 3114 ASP Chi-restraints excluded: chain A residue 3245 GLU Chi-restraints excluded: chain A residue 3367 THR Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3524 LEU Chi-restraints excluded: chain A residue 3536 ASN Chi-restraints excluded: chain A residue 3638 PHE Chi-restraints excluded: chain A residue 3641 VAL Chi-restraints excluded: chain A residue 3647 LEU Chi-restraints excluded: chain A residue 3722 MET Chi-restraints excluded: chain A residue 3858 MET Chi-restraints excluded: chain A residue 3919 ARG Chi-restraints excluded: chain A residue 3968 LEU Chi-restraints excluded: chain A residue 3997 VAL Chi-restraints excluded: chain A residue 4048 VAL Chi-restraints excluded: chain A residue 4267 VAL Chi-restraints excluded: chain A residue 4297 LEU Chi-restraints excluded: chain A residue 4513 VAL Chi-restraints excluded: chain A residue 4519 ARG Chi-restraints excluded: chain A residue 4635 LEU Chi-restraints excluded: chain A residue 4671 HIS Chi-restraints excluded: chain A residue 4782 LEU Chi-restraints excluded: chain A residue 4853 VAL Chi-restraints excluded: chain A residue 4941 MET Chi-restraints excluded: chain A residue 4984 ASP Chi-restraints excluded: chain A residue 5040 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 338 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 115 optimal weight: 0.2980 chunk 305 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 267 optimal weight: 2.9990 chunk 330 optimal weight: 5.9990 chunk 388 optimal weight: 0.9980 chunk 155 optimal weight: 0.6980 chunk 233 optimal weight: 0.3980 chunk 404 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 789 ASN A 796 HIS A 803 HIS A1595 ASN ** A2677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4590 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.104447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.082435 restraints weight = 74483.835| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.32 r_work: 0.3014 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35971 Z= 0.116 Angle : 0.581 13.991 48683 Z= 0.288 Chirality : 0.040 0.184 5512 Planarity : 0.004 0.066 6228 Dihedral : 5.230 86.464 4796 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 1.72 % Allowed : 9.92 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.36 (0.13), residues: 4320 helix: 1.55 (0.11), residues: 2508 sheet: -0.05 (0.34), residues: 222 loop : -1.94 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A3345 TYR 0.024 0.001 TYR A1717 PHE 0.030 0.001 PHE A2371 TRP 0.029 0.001 TRP A1298 HIS 0.014 0.001 HIS A 803 Details of bonding type rmsd covalent geometry : bond 0.00265 (35961) covalent geometry : angle 0.58057 (48670) SS BOND : bond 0.00258 ( 2) SS BOND : angle 1.81393 ( 4) hydrogen bonds : bond 0.03152 ( 1824) hydrogen bonds : angle 3.71290 ( 5349) metal coordination : bond 0.00304 ( 8) metal coordination : angle 2.04375 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 327 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 613 ASP cc_start: 0.6601 (m-30) cc_final: 0.6317 (m-30) REVERT: A 677 LYS cc_start: 0.7356 (mmtp) cc_final: 0.6953 (mtmm) REVERT: A 934 MET cc_start: 0.7606 (ttp) cc_final: 0.7405 (ttm) REVERT: A 940 GLN cc_start: 0.7357 (mt0) cc_final: 0.6841 (tm-30) REVERT: A 1048 ILE cc_start: 0.8272 (tp) cc_final: 0.7879 (tp) REVERT: A 1247 ASP cc_start: 0.8601 (m-30) cc_final: 0.8306 (m-30) REVERT: A 1260 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7728 (tptp) REVERT: A 1386 ARG cc_start: 0.7848 (mtm-85) cc_final: 0.7464 (mtm-85) REVERT: A 1394 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8294 (mp) REVERT: A 1409 ASP cc_start: 0.8059 (m-30) cc_final: 0.7824 (m-30) REVERT: A 1452 MET cc_start: 0.6658 (mmm) cc_final: 0.6457 (mmm) REVERT: A 1519 LYS cc_start: 0.8718 (mmmt) cc_final: 0.8315 (mmtm) REVERT: A 1823 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.6811 (pt0) REVERT: A 2248 GLU cc_start: 0.7675 (pm20) cc_final: 0.7428 (pm20) REVERT: A 2258 ARG cc_start: 0.6944 (pmt170) cc_final: 0.6299 (mtm110) REVERT: A 2324 ILE cc_start: 0.7769 (mt) cc_final: 0.7461 (mt) REVERT: A 2543 PHE cc_start: 0.7659 (OUTLIER) cc_final: 0.7347 (m-80) REVERT: A 2554 TYR cc_start: 0.7692 (m-80) cc_final: 0.7408 (m-80) REVERT: A 2648 MET cc_start: 0.8623 (mmm) cc_final: 0.8363 (mmt) REVERT: A 2691 ASP cc_start: 0.8634 (m-30) cc_final: 0.8264 (m-30) REVERT: A 2850 LEU cc_start: 0.8465 (mt) cc_final: 0.8170 (mt) REVERT: A 3370 PHE cc_start: 0.8508 (m-80) cc_final: 0.8032 (m-80) REVERT: A 3511 ASP cc_start: 0.8405 (m-30) cc_final: 0.8108 (m-30) REVERT: A 3537 LYS cc_start: 0.8714 (tmmt) cc_final: 0.8455 (tttp) REVERT: A 3552 ARG cc_start: 0.8162 (tpp-160) cc_final: 0.7782 (mmp-170) REVERT: A 3636 MET cc_start: 0.2182 (tpp) cc_final: 0.1118 (ptt) REVERT: A 3858 MET cc_start: 0.6797 (OUTLIER) cc_final: 0.6525 (ttm) REVERT: A 4348 LYS cc_start: 0.8185 (tptp) cc_final: 0.7962 (tptp) REVERT: A 4519 ARG cc_start: 0.6060 (OUTLIER) cc_final: 0.5279 (pmm150) REVERT: A 5085 LYS cc_start: 0.7784 (mmtm) cc_final: 0.7493 (mmmt) outliers start: 67 outliers final: 55 residues processed: 371 average time/residue: 0.2437 time to fit residues: 143.6410 Evaluate side-chains 380 residues out of total 3911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 319 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain A residue 803 HIS Chi-restraints excluded: chain A residue 832 HIS Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1260 LYS Chi-restraints excluded: chain A residue 1280 LEU Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1394 LEU Chi-restraints excluded: chain A residue 1427 CYS Chi-restraints excluded: chain A residue 1595 ASN Chi-restraints excluded: chain A residue 1631 VAL Chi-restraints excluded: chain A residue 1750 TYR Chi-restraints excluded: chain A residue 1823 GLU Chi-restraints excluded: chain A residue 2151 VAL Chi-restraints excluded: chain A residue 2169 ILE Chi-restraints excluded: chain A residue 2306 VAL Chi-restraints excluded: chain A residue 2338 LEU Chi-restraints excluded: chain A residue 2371 PHE Chi-restraints excluded: chain A residue 2543 PHE Chi-restraints excluded: chain A residue 2574 CYS Chi-restraints excluded: chain A residue 2628 HIS Chi-restraints excluded: chain A residue 2707 LEU Chi-restraints excluded: chain A residue 2773 HIS Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 2924 VAL Chi-restraints excluded: chain A residue 2964 LEU Chi-restraints excluded: chain A residue 3023 GLN Chi-restraints excluded: chain A residue 3114 ASP Chi-restraints excluded: chain A residue 3245 GLU Chi-restraints excluded: chain A residue 3367 THR Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3524 LEU Chi-restraints excluded: chain A residue 3536 ASN Chi-restraints excluded: chain A residue 3641 VAL Chi-restraints excluded: chain A residue 3647 LEU Chi-restraints excluded: chain A residue 3722 MET Chi-restraints excluded: chain A residue 3858 MET Chi-restraints excluded: chain A residue 3919 ARG Chi-restraints excluded: chain A residue 3968 LEU Chi-restraints excluded: chain A residue 3997 VAL Chi-restraints excluded: chain A residue 4048 VAL Chi-restraints excluded: chain A residue 4267 VAL Chi-restraints excluded: chain A residue 4297 LEU Chi-restraints excluded: chain A residue 4392 MET Chi-restraints excluded: chain A residue 4513 VAL Chi-restraints excluded: chain A residue 4519 ARG Chi-restraints excluded: chain A residue 4635 LEU Chi-restraints excluded: chain A residue 4671 HIS Chi-restraints excluded: chain A residue 4782 LEU Chi-restraints excluded: chain A residue 4853 VAL Chi-restraints excluded: chain A residue 4941 MET Chi-restraints excluded: chain A residue 4984 ASP Chi-restraints excluded: chain A residue 5040 LEU Chi-restraints excluded: chain A residue 5112 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 424 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 316 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 251 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 153 optimal weight: 0.8980 chunk 329 optimal weight: 0.8980 chunk 330 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 803 HIS A1595 ASN A1907 GLN A2273 HIS ** A2677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3608 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 = 0.3650 r_free = 0.3650 target = 0.104131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.082989 restraints weight = 74009.704| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.10 r_work: 0.3033 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35971 Z= 0.133 Angle : 0.592 12.521 48683 Z= 0.294 Chirality : 0.041 0.189 5512 Planarity : 0.004 0.065 6228 Dihedral : 5.228 86.418 4796 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 1.72 % Allowed : 10.33 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.38 (0.13), residues: 4320 helix: 1.57 (0.11), residues: 2509 sheet: 0.05 (0.34), residues: 219 loop : -1.96 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A3345 TYR 0.025 0.001 TYR A 753 PHE 0.031 0.001 PHE A2371 TRP 0.021 0.001 TRP A1298 HIS 0.014 0.001 HIS A 803 Details of bonding type rmsd covalent geometry : bond 0.00314 (35961) covalent geometry : angle 0.59175 (48670) SS BOND : bond 0.00321 ( 2) SS BOND : angle 1.62026 ( 4) hydrogen bonds : bond 0.03223 ( 1824) hydrogen bonds : angle 3.72506 ( 5349) metal coordination : bond 0.00351 ( 8) metal coordination : angle 2.01968 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 326 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 613 ASP cc_start: 0.6725 (m-30) cc_final: 0.6412 (m-30) REVERT: A 677 LYS cc_start: 0.7459 (mmtp) cc_final: 0.7067 (mtmm) REVERT: A 770 TYR cc_start: 0.8569 (OUTLIER) cc_final: 0.8019 (m-80) REVERT: A 934 MET cc_start: 0.7689 (ttp) cc_final: 0.7468 (ttm) REVERT: A 940 GLN cc_start: 0.7455 (mt0) cc_final: 0.6941 (tm-30) REVERT: A 1048 ILE cc_start: 0.8306 (tp) cc_final: 0.7907 (tp) REVERT: A 1247 ASP cc_start: 0.8676 (m-30) cc_final: 0.8348 (m-30) REVERT: A 1260 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7739 (tptp) REVERT: A 1386 ARG cc_start: 0.7964 (mtm-85) cc_final: 0.7620 (mtm180) REVERT: A 1394 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8429 (mp) REVERT: A 1409 ASP cc_start: 0.8207 (m-30) cc_final: 0.7961 (m-30) REVERT: A 1452 MET cc_start: 0.6809 (mmm) cc_final: 0.6605 (mmm) REVERT: A 1823 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.6973 (pt0) REVERT: A 2248 GLU cc_start: 0.7855 (pm20) cc_final: 0.7643 (pm20) REVERT: A 2258 ARG cc_start: 0.7223 (pmt170) cc_final: 0.6439 (mtm110) REVERT: A 2324 ILE cc_start: 0.7891 (mt) cc_final: 0.7582 (mt) REVERT: A 2543 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.7453 (m-80) REVERT: A 2554 TYR cc_start: 0.7799 (m-80) cc_final: 0.7521 (m-80) REVERT: A 2629 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7586 (pt0) REVERT: A 2648 MET cc_start: 0.8744 (mmm) cc_final: 0.8526 (mmt) REVERT: A 2691 ASP cc_start: 0.8831 (m-30) cc_final: 0.8471 (m-30) REVERT: A 3370 PHE cc_start: 0.8698 (m-80) cc_final: 0.8242 (m-80) REVERT: A 3536 ASN cc_start: 0.8600 (OUTLIER) cc_final: 0.8306 (t0) REVERT: A 3537 LYS cc_start: 0.8811 (tmmt) cc_final: 0.8553 (tttp) REVERT: A 3552 ARG cc_start: 0.8325 (tpp-160) cc_final: 0.7945 (mmp-170) REVERT: A 3636 MET cc_start: 0.2209 (tpp) cc_final: 0.1166 (ptt) REVERT: A 3858 MET cc_start: 0.7087 (OUTLIER) cc_final: 0.6815 (ttm) REVERT: A 3948 PHE cc_start: 0.6057 (t80) cc_final: 0.5856 (t80) REVERT: A 4348 LYS cc_start: 0.8319 (tptp) cc_final: 0.8096 (tptp) REVERT: A 4519 ARG cc_start: 0.6285 (OUTLIER) cc_final: 0.5561 (pmm150) outliers start: 67 outliers final: 55 residues processed: 370 average time/residue: 0.2295 time to fit residues: 135.3336 Evaluate side-chains 378 residues out of total 3911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 315 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain A residue 803 HIS Chi-restraints excluded: chain A residue 832 HIS Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1260 LYS Chi-restraints excluded: chain A residue 1280 LEU Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1394 LEU Chi-restraints excluded: chain A residue 1427 CYS Chi-restraints excluded: chain A residue 1595 ASN Chi-restraints excluded: chain A residue 1631 VAL Chi-restraints excluded: chain A residue 1719 LEU Chi-restraints excluded: chain A residue 1750 TYR Chi-restraints excluded: chain A residue 1823 GLU Chi-restraints excluded: chain A residue 2151 VAL Chi-restraints excluded: chain A residue 2169 ILE Chi-restraints excluded: chain A residue 2273 HIS Chi-restraints excluded: chain A residue 2306 VAL Chi-restraints excluded: chain A residue 2338 LEU Chi-restraints excluded: chain A residue 2371 PHE Chi-restraints excluded: chain A residue 2543 PHE Chi-restraints excluded: chain A residue 2574 CYS Chi-restraints excluded: chain A residue 2628 HIS Chi-restraints excluded: chain A residue 2707 LEU Chi-restraints excluded: chain A residue 2773 HIS Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 2924 VAL Chi-restraints excluded: chain A residue 2964 LEU Chi-restraints excluded: chain A residue 3023 GLN Chi-restraints excluded: chain A residue 3114 ASP Chi-restraints excluded: chain A residue 3245 GLU Chi-restraints excluded: chain A residue 3367 THR Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3524 LEU Chi-restraints excluded: chain A residue 3536 ASN Chi-restraints excluded: chain A residue 3641 VAL Chi-restraints excluded: chain A residue 3647 LEU Chi-restraints excluded: chain A residue 3722 MET Chi-restraints excluded: chain A residue 3858 MET Chi-restraints excluded: chain A residue 3919 ARG Chi-restraints excluded: chain A residue 3944 ILE Chi-restraints excluded: chain A residue 3968 LEU Chi-restraints excluded: chain A residue 3997 VAL Chi-restraints excluded: chain A residue 4048 VAL Chi-restraints excluded: chain A residue 4267 VAL Chi-restraints excluded: chain A residue 4297 LEU Chi-restraints excluded: chain A residue 4392 MET Chi-restraints excluded: chain A residue 4513 VAL Chi-restraints excluded: chain A residue 4519 ARG Chi-restraints excluded: chain A residue 4635 LEU Chi-restraints excluded: chain A residue 4671 HIS Chi-restraints excluded: chain A residue 4782 LEU Chi-restraints excluded: chain A residue 4853 VAL Chi-restraints excluded: chain A residue 4941 MET Chi-restraints excluded: chain A residue 4984 ASP Chi-restraints excluded: chain A residue 5040 LEU Chi-restraints excluded: chain A residue 5112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 252 optimal weight: 0.8980 chunk 9 optimal weight: 0.0050 chunk 42 optimal weight: 0.3980 chunk 260 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 390 optimal weight: 1.9990 chunk 402 optimal weight: 4.9990 chunk 254 optimal weight: 0.8980 chunk 174 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 803 HIS A1595 ASN A1907 GLN A2273 HIS ** A2677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3608 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 = 0.3656 r_free = 0.3656 target = 0.104381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.082326 restraints weight = 74333.731| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.33 r_work: 0.3014 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35971 Z= 0.121 Angle : 0.588 12.638 48683 Z= 0.292 Chirality : 0.041 0.191 5512 Planarity : 0.004 0.066 6228 Dihedral : 5.195 89.686 4796 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 1.67 % Allowed : 10.69 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.43 (0.13), residues: 4320 helix: 1.61 (0.11), residues: 2509 sheet: 0.06 (0.34), residues: 219 loop : -1.94 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A3493 TYR 0.024 0.001 TYR A1717 PHE 0.030 0.001 PHE A2371 TRP 0.023 0.001 TRP A1298 HIS 0.021 0.001 HIS A 803 Details of bonding type rmsd covalent geometry : bond 0.00279 (35961) covalent geometry : angle 0.58716 (48670) SS BOND : bond 0.00286 ( 2) SS BOND : angle 1.50854 ( 4) hydrogen bonds : bond 0.03158 ( 1824) hydrogen bonds : angle 3.71335 ( 5349) metal coordination : bond 0.00334 ( 8) metal coordination : angle 1.90310 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 320 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 613 ASP cc_start: 0.6583 (m-30) cc_final: 0.6275 (m-30) REVERT: A 677 LYS cc_start: 0.7382 (mmtp) cc_final: 0.7000 (mtmm) REVERT: A 770 TYR cc_start: 0.8441 (OUTLIER) cc_final: 0.7877 (m-80) REVERT: A 883 ASN cc_start: 0.8449 (m-40) cc_final: 0.8221 (m-40) REVERT: A 934 MET cc_start: 0.7661 (ttp) cc_final: 0.7456 (ttm) REVERT: A 940 GLN cc_start: 0.7281 (mt0) cc_final: 0.6836 (tm-30) REVERT: A 1048 ILE cc_start: 0.8251 (tp) cc_final: 0.7875 (tp) REVERT: A 1247 ASP cc_start: 0.8595 (m-30) cc_final: 0.8252 (m-30) REVERT: A 1260 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7667 (tptp) REVERT: A 1386 ARG cc_start: 0.7830 (mtm-85) cc_final: 0.7476 (mtm180) REVERT: A 1394 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8304 (mp) REVERT: A 1409 ASP cc_start: 0.8063 (m-30) cc_final: 0.7823 (m-30) REVERT: A 1452 MET cc_start: 0.6667 (mmm) cc_final: 0.6458 (mmm) REVERT: A 1519 LYS cc_start: 0.8671 (mmmt) cc_final: 0.8239 (mmtm) REVERT: A 1558 MET cc_start: 0.9126 (ptt) cc_final: 0.8905 (ptm) REVERT: A 1631 VAL cc_start: 0.8890 (OUTLIER) cc_final: 0.8589 (t) REVERT: A 1823 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.6763 (pt0) REVERT: A 2248 GLU cc_start: 0.7744 (pm20) cc_final: 0.7543 (pm20) REVERT: A 2258 ARG cc_start: 0.6941 (pmt170) cc_final: 0.6296 (mtm110) REVERT: A 2288 ASN cc_start: 0.8434 (p0) cc_final: 0.8146 (p0) REVERT: A 2324 ILE cc_start: 0.7768 (mt) cc_final: 0.7458 (mt) REVERT: A 2543 PHE cc_start: 0.7662 (OUTLIER) cc_final: 0.7348 (m-80) REVERT: A 2554 TYR cc_start: 0.7671 (m-80) cc_final: 0.7352 (m-80) REVERT: A 2691 ASP cc_start: 0.8641 (m-30) cc_final: 0.8275 (m-30) REVERT: A 3370 PHE cc_start: 0.8517 (m-80) cc_final: 0.8048 (m-80) REVERT: A 3536 ASN cc_start: 0.8495 (OUTLIER) cc_final: 0.8243 (t0) REVERT: A 3537 LYS cc_start: 0.8715 (tmmt) cc_final: 0.8453 (tttp) REVERT: A 3552 ARG cc_start: 0.8162 (tpp-160) cc_final: 0.7781 (mmp-170) REVERT: A 3636 MET cc_start: 0.1866 (tpp) cc_final: 0.0957 (ptt) REVERT: A 3858 MET cc_start: 0.6838 (OUTLIER) cc_final: 0.6587 (ttm) REVERT: A 4348 LYS cc_start: 0.8178 (tptp) cc_final: 0.7953 (tptp) REVERT: A 4519 ARG cc_start: 0.6079 (OUTLIER) cc_final: 0.5319 (pmm150) outliers start: 65 outliers final: 53 residues processed: 362 average time/residue: 0.2296 time to fit residues: 132.4326 Evaluate side-chains 376 residues out of total 3911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 314 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain A residue 803 HIS Chi-restraints excluded: chain A residue 832 HIS Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1260 LYS Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1394 LEU Chi-restraints excluded: chain A residue 1401 ILE Chi-restraints excluded: chain A residue 1427 CYS Chi-restraints excluded: chain A residue 1595 ASN Chi-restraints excluded: chain A residue 1631 VAL Chi-restraints excluded: chain A residue 1719 LEU Chi-restraints excluded: chain A residue 1823 GLU Chi-restraints excluded: chain A residue 2025 GLN Chi-restraints excluded: chain A residue 2151 VAL Chi-restraints excluded: chain A residue 2169 ILE Chi-restraints excluded: chain A residue 2273 HIS Chi-restraints excluded: chain A residue 2306 VAL Chi-restraints excluded: chain A residue 2338 LEU Chi-restraints excluded: chain A residue 2371 PHE Chi-restraints excluded: chain A residue 2543 PHE Chi-restraints excluded: chain A residue 2574 CYS Chi-restraints excluded: chain A residue 2628 HIS Chi-restraints excluded: chain A residue 2707 LEU Chi-restraints excluded: chain A residue 2773 HIS Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 2924 VAL Chi-restraints excluded: chain A residue 2964 LEU Chi-restraints excluded: chain A residue 3023 GLN Chi-restraints excluded: chain A residue 3114 ASP Chi-restraints excluded: chain A residue 3245 GLU Chi-restraints excluded: chain A residue 3367 THR Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3524 LEU Chi-restraints excluded: chain A residue 3536 ASN Chi-restraints excluded: chain A residue 3641 VAL Chi-restraints excluded: chain A residue 3647 LEU Chi-restraints excluded: chain A residue 3722 MET Chi-restraints excluded: chain A residue 3858 MET Chi-restraints excluded: chain A residue 3919 ARG Chi-restraints excluded: chain A residue 3944 ILE Chi-restraints excluded: chain A residue 3968 LEU Chi-restraints excluded: chain A residue 3997 VAL Chi-restraints excluded: chain A residue 4038 VAL Chi-restraints excluded: chain A residue 4048 VAL Chi-restraints excluded: chain A residue 4267 VAL Chi-restraints excluded: chain A residue 4297 LEU Chi-restraints excluded: chain A residue 4392 MET Chi-restraints excluded: chain A residue 4513 VAL Chi-restraints excluded: chain A residue 4519 ARG Chi-restraints excluded: chain A residue 4635 LEU Chi-restraints excluded: chain A residue 4671 HIS Chi-restraints excluded: chain A residue 4782 LEU Chi-restraints excluded: chain A residue 4941 MET Chi-restraints excluded: chain A residue 4984 ASP Chi-restraints excluded: chain A residue 5040 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 324 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 10 optimal weight: 0.0980 chunk 401 optimal weight: 0.9980 chunk 383 optimal weight: 0.9990 chunk 223 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 90 optimal weight: 0.0170 chunk 125 optimal weight: 1.9990 chunk 235 optimal weight: 0.7980 chunk 159 optimal weight: 0.4980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 803 HIS A1595 ASN A2273 HIS ** A2677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.102067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.081588 restraints weight = 73802.255| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.06 r_work: 0.3062 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 35971 Z= 0.110 Angle : 0.580 12.488 48683 Z= 0.288 Chirality : 0.040 0.175 5512 Planarity : 0.004 0.065 6228 Dihedral : 5.102 88.463 4796 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 1.64 % Allowed : 10.64 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.52 (0.13), residues: 4320 helix: 1.68 (0.11), residues: 2510 sheet: 0.09 (0.34), residues: 219 loop : -1.91 (0.16), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A3525 TYR 0.028 0.001 TYR A 753 PHE 0.027 0.001 PHE A2371 TRP 0.026 0.001 TRP A1298 HIS 0.021 0.001 HIS A 803 Details of bonding type rmsd covalent geometry : bond 0.00248 (35961) covalent geometry : angle 0.57960 (48670) SS BOND : bond 0.00238 ( 2) SS BOND : angle 1.43801 ( 4) hydrogen bonds : bond 0.03059 ( 1824) hydrogen bonds : angle 3.68306 ( 5349) metal coordination : bond 0.00326 ( 8) metal coordination : angle 1.91328 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8745.94 seconds wall clock time: 150 minutes 25.16 seconds (9025.16 seconds total)