Starting phenix.real_space_refine on Fri Oct 30 18:43:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9t8i_55694/10_2026/9t8i_55694.cif Found real_map, /net/cci-nas-00/data/ceres_data/9t8i_55694/10_2026/9t8i_55694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9t8i_55694/10_2026/9t8i_55694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9t8i_55694/10_2026/9t8i_55694.map" model { file = "/net/cci-nas-00/data/ceres_data/9t8i_55694/10_2026/9t8i_55694.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9t8i_55694/10_2026/9t8i_55694.cif" } resolution = 3.1 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 3 5.49 5 S 225 5.16 5 C 23273 2.51 5 N 6272 2.21 5 O 6731 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.18s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 36506 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 36473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4533, 36473 Classifications: {'peptide': 4533} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 180, 'TRANS': 4349} Chain breaks: 34 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' ZN': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 31211 SG CYS B4451 59.625 59.172 152.518 1.00234.99 S ATOM 31275 SG CYS B4471 56.478 61.264 153.183 1.00206.39 S ATOM 31297 SG CYS B4474 57.819 60.932 149.634 1.00240.72 S ATOM 27582 SG CYS B3962 38.834 14.915 219.839 1.00250.01 S ATOM 27710 SG CYS B3982 40.914 16.867 222.320 1.00254.27 S ATOM 27735 SG CYS B3985 37.415 15.771 223.296 1.00260.37 S Time building chain proxies: 7.78, per 1000 atoms: 0.21 Number of scatterers: 36506 At special positions: 0 Unit cell: (126.588, 147.84, 240.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 225 16.00 P 3 15.00 O 6731 8.00 N 6272 7.00 C 23273 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.37 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B5302 " pdb="ZN ZN B5302 " - pdb=" ND1 HIS B4455 " pdb="ZN ZN B5302 " - pdb=" SG CYS B4471 " pdb="ZN ZN B5302 " - pdb=" SG CYS B4474 " pdb="ZN ZN B5302 " - pdb=" SG CYS B4451 " pdb=" ZN B5303 " pdb="ZN ZN B5303 " - pdb=" ND1 HIS B3964 " pdb="ZN ZN B5303 " - pdb=" SG CYS B3982 " pdb="ZN ZN B5303 " - pdb=" SG CYS B3962 " pdb="ZN ZN B5303 " - pdb=" SG CYS B3985 " Number of angles added : 6 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8684 Finding SS restraints... Secondary structure from input PDB file: 246 helices and 24 sheets defined 67.4% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.14 Creating SS restraints... Processing helix chain 'B' and resid 358 through 361 Processing helix chain 'B' and resid 375 through 378 Processing helix chain 'B' and resid 395 through 397 No H-bonds generated for 'chain 'B' and resid 395 through 397' Processing helix chain 'B' and resid 410 through 412 No H-bonds generated for 'chain 'B' and resid 410 through 412' Processing helix chain 'B' and resid 456 through 460 removed outlier: 4.248A pdb=" N GLY B 460 " --> pdb=" O THR B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 514 removed outlier: 3.837A pdb=" N LEU B 513 " --> pdb=" O ILE B 509 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLN B 514 " --> pdb=" O PHE B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 537 removed outlier: 3.974A pdb=" N GLU B 537 " --> pdb=" O SER B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 552 Processing helix chain 'B' and resid 554 through 575 Proline residue: B 572 - end of helix removed outlier: 3.549A pdb=" N GLU B 575 " --> pdb=" O ALA B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 582 Processing helix chain 'B' and resid 590 through 605 Processing helix chain 'B' and resid 610 through 622 Processing helix chain 'B' and resid 627 through 640 Proline residue: B 637 - end of helix removed outlier: 4.097A pdb=" N ARG B 640 " --> pdb=" O SER B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 659 removed outlier: 3.566A pdb=" N TRP B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 674 Proline residue: B 669 - end of helix Processing helix chain 'B' and resid 680 through 684 Processing helix chain 'B' and resid 688 through 694 Processing helix chain 'B' and resid 711 through 720 removed outlier: 3.776A pdb=" N GLN B 715 " --> pdb=" O SER B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 726 Processing helix chain 'B' and resid 727 through 736 removed outlier: 4.351A pdb=" N PHE B 731 " --> pdb=" O ASP B 727 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ARG B 732 " --> pdb=" O GLU B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 741 No H-bonds generated for 'chain 'B' and resid 739 through 741' Processing helix chain 'B' and resid 742 through 750 Processing helix chain 'B' and resid 750 through 755 Processing helix chain 'B' and resid 757 through 759 No H-bonds generated for 'chain 'B' and resid 757 through 759' Processing helix chain 'B' and resid 760 through 770 removed outlier: 3.516A pdb=" N CYS B 764 " --> pdb=" O ARG B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 775 Processing helix chain 'B' and resid 780 through 802 Processing helix chain 'B' and resid 803 through 807 removed outlier: 3.950A pdb=" N GLY B 807 " --> pdb=" O ARG B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 829 Processing helix chain 'B' and resid 831 through 834 Processing helix chain 'B' and resid 835 through 852 Processing helix chain 'B' and resid 864 through 889 Processing helix chain 'B' and resid 907 through 917 Processing helix chain 'B' and resid 921 through 924 Processing helix chain 'B' and resid 925 through 940 removed outlier: 3.528A pdb=" N GLN B 940 " --> pdb=" O GLY B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 952 Processing helix chain 'B' and resid 962 through 983 Processing helix chain 'B' and resid 994 through 1010 Processing helix chain 'B' and resid 1020 through 1031 Processing helix chain 'B' and resid 1031 through 1044 removed outlier: 4.285A pdb=" N ARG B1035 " --> pdb=" O TRP B1031 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN B1036 " --> pdb=" O PRO B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1050 removed outlier: 3.973A pdb=" N ASP B1049 " --> pdb=" O GLU B1045 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN B1050 " --> pdb=" O LYS B1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1045 through 1050' Processing helix chain 'B' and resid 1052 through 1076 Processing helix chain 'B' and resid 1079 through 1089 Processing helix chain 'B' and resid 1089 through 1104 Processing helix chain 'B' and resid 1112 through 1144 removed outlier: 3.641A pdb=" N VAL B1144 " --> pdb=" O GLN B1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 1154 through 1161 Processing helix chain 'B' and resid 1167 through 1171 Processing helix chain 'B' and resid 1190 through 1204 Processing helix chain 'B' and resid 1206 through 1223 Processing helix chain 'B' and resid 1233 through 1241 Processing helix chain 'B' and resid 1241 through 1259 Processing helix chain 'B' and resid 1262 through 1270 Processing helix chain 'B' and resid 1271 through 1274 removed outlier: 3.833A pdb=" N VAL B1274 " --> pdb=" O LYS B1271 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1271 through 1274' Processing helix chain 'B' and resid 1276 through 1289 Processing helix chain 'B' and resid 1296 through 1330 removed outlier: 4.047A pdb=" N SER B1300 " --> pdb=" O LYS B1296 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU B1301 " --> pdb=" O GLY B1297 " (cutoff:3.500A) Processing helix chain 'B' and resid 1335 through 1337 No H-bonds generated for 'chain 'B' and resid 1335 through 1337' Processing helix chain 'B' and resid 1338 through 1352 removed outlier: 3.596A pdb=" N LEU B1342 " --> pdb=" O LEU B1338 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N GLU B1349 " --> pdb=" O ALA B1345 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ASP B1350 " --> pdb=" O ASP B1346 " (cutoff:3.500A) Processing helix chain 'B' and resid 1355 through 1359 Processing helix chain 'B' and resid 1361 through 1370 removed outlier: 4.083A pdb=" N LYS B1365 " --> pdb=" O PRO B1361 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA B1366 " --> pdb=" O GLN B1362 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B1370 " --> pdb=" O ALA B1366 " (cutoff:3.500A) Processing helix chain 'B' and resid 1374 through 1387 Processing helix chain 'B' and resid 1387 through 1398 Processing helix chain 'B' and resid 1400 through 1415 removed outlier: 3.862A pdb=" N LEU B1404 " --> pdb=" O ASP B1400 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS B1405 " --> pdb=" O ILE B1401 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL B1406 " --> pdb=" O ASN B1402 " (cutoff:3.500A) Processing helix chain 'B' and resid 1418 through 1440 removed outlier: 4.145A pdb=" N VAL B1425 " --> pdb=" O ASP B1421 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA B1426 " --> pdb=" O VAL B1422 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N SER B1437 " --> pdb=" O GLN B1433 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU B1438 " --> pdb=" O GLY B1434 " (cutoff:3.500A) Processing helix chain 'B' and resid 1447 through 1464 removed outlier: 3.892A pdb=" N ASN B1464 " --> pdb=" O ARG B1460 " (cutoff:3.500A) Processing helix chain 'B' and resid 1467 through 1478 Processing helix chain 'B' and resid 1478 through 1486 removed outlier: 4.214A pdb=" N LYS B1486 " --> pdb=" O LEU B1482 " (cutoff:3.500A) Processing helix chain 'B' and resid 1495 through 1507 Processing helix chain 'B' and resid 1521 through 1525 Processing helix chain 'B' and resid 1544 through 1558 Processing helix chain 'B' and resid 1563 through 1594 removed outlier: 3.553A pdb=" N ASN B1567 " --> pdb=" O ASP B1563 " (cutoff:3.500A) Processing helix chain 'B' and resid 1630 through 1660 Processing helix chain 'B' and resid 1661 through 1666 Processing helix chain 'B' and resid 1667 through 1679 removed outlier: 3.880A pdb=" N ARG B1679 " --> pdb=" O SER B1675 " (cutoff:3.500A) Processing helix chain 'B' and resid 1684 through 1692 Processing helix chain 'B' and resid 1699 through 1711 removed outlier: 3.693A pdb=" N GLU B1711 " --> pdb=" O THR B1707 " (cutoff:3.500A) Processing helix chain 'B' and resid 1712 through 1732 Proline residue: B1727 - end of helix Processing helix chain 'B' and resid 1735 through 1755 removed outlier: 7.418A pdb=" N SER B1752 " --> pdb=" O LEU B1748 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ALA B1753 " --> pdb=" O VAL B1749 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE B1754 " --> pdb=" O TYR B1750 " (cutoff:3.500A) Processing helix chain 'B' and resid 1760 through 1776 removed outlier: 4.149A pdb=" N GLY B1776 " --> pdb=" O ALA B1772 " (cutoff:3.500A) Processing helix chain 'B' and resid 1798 through 1800 No H-bonds generated for 'chain 'B' and resid 1798 through 1800' Processing helix chain 'B' and resid 1801 through 1812 removed outlier: 3.682A pdb=" N GLN B1812 " --> pdb=" O ALA B1808 " (cutoff:3.500A) Processing helix chain 'B' and resid 1832 through 1845 removed outlier: 3.560A pdb=" N VAL B1836 " --> pdb=" O THR B1832 " (cutoff:3.500A) Processing helix chain 'B' and resid 1859 through 1862 Processing helix chain 'B' and resid 1863 through 1880 Processing helix chain 'B' and resid 1895 through 1897 No H-bonds generated for 'chain 'B' and resid 1895 through 1897' Processing helix chain 'B' and resid 1899 through 1905 Processing helix chain 'B' and resid 1906 through 1909 Processing helix chain 'B' and resid 1917 through 1930 Processing helix chain 'B' and resid 1937 through 1942 removed outlier: 3.726A pdb=" N VAL B1941 " --> pdb=" O ALA B1938 " (cutoff:3.500A) Processing helix chain 'B' and resid 1959 through 1976 Processing helix chain 'B' and resid 1993 through 2002 removed outlier: 3.790A pdb=" N VAL B1997 " --> pdb=" O ASP B1993 " (cutoff:3.500A) Processing helix chain 'B' and resid 2003 through 2005 No H-bonds generated for 'chain 'B' and resid 2003 through 2005' Processing helix chain 'B' and resid 2006 through 2011 Processing helix chain 'B' and resid 2027 through 2037 Processing helix chain 'B' and resid 2080 through 2086 Processing helix chain 'B' and resid 2095 through 2103 Processing helix chain 'B' and resid 2116 through 2122 Processing helix chain 'B' and resid 2122 through 2137 Proline residue: B2128 - end of helix removed outlier: 3.792A pdb=" N GLN B2137 " --> pdb=" O LYS B2133 " (cutoff:3.500A) Processing helix chain 'B' and resid 2154 through 2166 Processing helix chain 'B' and resid 2172 through 2193 Processing helix chain 'B' and resid 2207 through 2224 removed outlier: 4.009A pdb=" N ASP B2222 " --> pdb=" O LEU B2218 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE B2223 " --> pdb=" O MET B2219 " (cutoff:3.500A) Processing helix chain 'B' and resid 2250 through 2255 Processing helix chain 'B' and resid 2309 through 2318 Processing helix chain 'B' and resid 2325 through 2329 Processing helix chain 'B' and resid 2330 through 2343 Processing helix chain 'B' and resid 2357 through 2374 Processing helix chain 'B' and resid 2386 through 2400 Processing helix chain 'B' and resid 2417 through 2440 Processing helix chain 'B' and resid 2450 through 2454 removed outlier: 3.739A pdb=" N THR B2453 " --> pdb=" O ALA B2450 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N GLU B2454 " --> pdb=" O ASN B2451 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2450 through 2454' Processing helix chain 'B' and resid 2455 through 2464 removed outlier: 3.765A pdb=" N ILE B2459 " --> pdb=" O ALA B2455 " (cutoff:3.500A) Processing helix chain 'B' and resid 2492 through 2501 Processing helix chain 'B' and resid 2523 through 2525 No H-bonds generated for 'chain 'B' and resid 2523 through 2525' Processing helix chain 'B' and resid 2533 through 2540 Proline residue: B2538 - end of helix Processing helix chain 'B' and resid 2547 through 2563 Processing helix chain 'B' and resid 2569 through 2589 Processing helix chain 'B' and resid 2598 through 2615 removed outlier: 3.989A pdb=" N VAL B2602 " --> pdb=" O SER B2598 " (cutoff:3.500A) Processing helix chain 'B' and resid 2615 through 2630 Processing helix chain 'B' and resid 2632 through 2636 removed outlier: 3.631A pdb=" N HIS B2635 " --> pdb=" O ASP B2632 " (cutoff:3.500A) Processing helix chain 'B' and resid 2640 through 2654 Processing helix chain 'B' and resid 2660 through 2670 removed outlier: 3.851A pdb=" N ARG B2670 " --> pdb=" O THR B2666 " (cutoff:3.500A) Processing helix chain 'B' and resid 2678 through 2697 Processing helix chain 'B' and resid 2706 through 2723 Processing helix chain 'B' and resid 2735 through 2747 removed outlier: 3.530A pdb=" N ALA B2739 " --> pdb=" O SER B2735 " (cutoff:3.500A) Processing helix chain 'B' and resid 2748 through 2752 Processing helix chain 'B' and resid 2754 through 2759 removed outlier: 3.702A pdb=" N CYS B2759 " --> pdb=" O GLU B2755 " (cutoff:3.500A) Processing helix chain 'B' and resid 2775 through 2791 removed outlier: 3.556A pdb=" N ILE B2779 " --> pdb=" O THR B2775 " (cutoff:3.500A) Processing helix chain 'B' and resid 2806 through 2811 removed outlier: 3.955A pdb=" N ALA B2810 " --> pdb=" O GLU B2806 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU B2811 " --> pdb=" O VAL B2807 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2806 through 2811' Processing helix chain 'B' and resid 2816 through 2819 removed outlier: 3.509A pdb=" N LYS B2819 " --> pdb=" O MET B2816 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2816 through 2819' Processing helix chain 'B' and resid 2820 through 2828 Processing helix chain 'B' and resid 2835 through 2839 removed outlier: 3.583A pdb=" N LYS B2839 " --> pdb=" O PRO B2836 " (cutoff:3.500A) Processing helix chain 'B' and resid 2851 through 2856 removed outlier: 3.540A pdb=" N ASN B2856 " --> pdb=" O ALA B2853 " (cutoff:3.500A) Processing helix chain 'B' and resid 2867 through 2880 Processing helix chain 'B' and resid 2882 through 2890 Processing helix chain 'B' and resid 2892 through 2907 Processing helix chain 'B' and resid 2913 through 2932 removed outlier: 3.584A pdb=" N TYR B2917 " --> pdb=" O GLY B2913 " (cutoff:3.500A) Processing helix chain 'B' and resid 2936 through 2949 Processing helix chain 'B' and resid 2955 through 2963 removed outlier: 4.051A pdb=" N SER B2963 " --> pdb=" O ILE B2959 " (cutoff:3.500A) Processing helix chain 'B' and resid 2964 through 2968 Processing helix chain 'B' and resid 2974 through 2984 Processing helix chain 'B' and resid 3010 through 3019 Processing helix chain 'B' and resid 3037 through 3056 Processing helix chain 'B' and resid 3063 through 3077 removed outlier: 3.883A pdb=" N LEU B3067 " --> pdb=" O ASN B3063 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLU B3069 " --> pdb=" O GLN B3065 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N SER B3070 " --> pdb=" O ASN B3066 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASP B3073 " --> pdb=" O GLU B3069 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ALA B3074 " --> pdb=" O SER B3070 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN B3076 " --> pdb=" O TYR B3072 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN B3077 " --> pdb=" O ASP B3073 " (cutoff:3.500A) Processing helix chain 'B' and resid 3113 through 3119 Processing helix chain 'B' and resid 3121 through 3128 removed outlier: 3.651A pdb=" N LEU B3128 " --> pdb=" O LEU B3124 " (cutoff:3.500A) Processing helix chain 'B' and resid 3134 through 3139 Processing helix chain 'B' and resid 3140 through 3159 Processing helix chain 'B' and resid 3172 through 3177 Processing helix chain 'B' and resid 3183 through 3197 removed outlier: 3.560A pdb=" N SER B3187 " --> pdb=" O ASP B3183 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY B3197 " --> pdb=" O VAL B3193 " (cutoff:3.500A) Processing helix chain 'B' and resid 3202 through 3219 Processing helix chain 'B' and resid 3222 through 3229 Processing helix chain 'B' and resid 3230 through 3232 No H-bonds generated for 'chain 'B' and resid 3230 through 3232' Processing helix chain 'B' and resid 3234 through 3249 removed outlier: 4.306A pdb=" N THR B3238 " --> pdb=" O LEU B3234 " (cutoff:3.500A) Processing helix chain 'B' and resid 3254 through 3265 Processing helix chain 'B' and resid 3285 through 3296 Processing helix chain 'B' and resid 3309 through 3311 No H-bonds generated for 'chain 'B' and resid 3309 through 3311' Processing helix chain 'B' and resid 3313 through 3327 removed outlier: 3.571A pdb=" N PHE B3317 " --> pdb=" O THR B3313 " (cutoff:3.500A) Processing helix chain 'B' and resid 3345 through 3365 removed outlier: 3.701A pdb=" N LEU B3349 " --> pdb=" O ARG B3345 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ALA B3351 " --> pdb=" O ALA B3347 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N SER B3352 " --> pdb=" O GLN B3348 " (cutoff:3.500A) Processing helix chain 'B' and resid 3383 through 3388 Processing helix chain 'B' and resid 3413 through 3419 removed outlier: 4.083A pdb=" N LEU B3417 " --> pdb=" O ASP B3413 " (cutoff:3.500A) Processing helix chain 'B' and resid 3421 through 3426 removed outlier: 3.825A pdb=" N PHE B3426 " --> pdb=" O ILE B3422 " (cutoff:3.500A) Processing helix chain 'B' and resid 3471 through 3475 removed outlier: 3.934A pdb=" N LEU B3475 " --> pdb=" O CYS B3471 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3471 through 3475' Processing helix chain 'B' and resid 3476 through 3491 removed outlier: 4.380A pdb=" N GLN B3486 " --> pdb=" O GLN B3482 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLY B3487 " --> pdb=" O SER B3483 " (cutoff:3.500A) Processing helix chain 'B' and resid 3501 through 3513 Processing helix chain 'B' and resid 3517 through 3541 removed outlier: 4.102A pdb=" N ASN B3541 " --> pdb=" O LYS B3537 " (cutoff:3.500A) Processing helix chain 'B' and resid 3543 through 3548 Processing helix chain 'B' and resid 3548 through 3555 Processing helix chain 'B' and resid 3556 through 3564 Processing helix chain 'B' and resid 3565 through 3590 Proline residue: B3580 - end of helix Processing helix chain 'B' and resid 3591 through 3593 No H-bonds generated for 'chain 'B' and resid 3591 through 3593' Processing helix chain 'B' and resid 3594 through 3600 removed outlier: 4.245A pdb=" N LEU B3598 " --> pdb=" O ASN B3594 " (cutoff:3.500A) Processing helix chain 'B' and resid 3604 through 3616 Processing helix chain 'B' and resid 3657 through 3676 Processing helix chain 'B' and resid 3680 through 3692 Processing helix chain 'B' and resid 3692 through 3700 Processing helix chain 'B' and resid 3702 through 3722 Processing helix chain 'B' and resid 3726 through 3748 removed outlier: 4.136A pdb=" N SER B3748 " --> pdb=" O LEU B3744 " (cutoff:3.500A) Processing helix chain 'B' and resid 3761 through 3771 removed outlier: 4.110A pdb=" N HIS B3765 " --> pdb=" O LEU B3761 " (cutoff:3.500A) Processing helix chain 'B' and resid 3771 through 3785 Processing helix chain 'B' and resid 3787 through 3795 removed outlier: 3.635A pdb=" N SER B3791 " --> pdb=" O GLN B3787 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN B3794 " --> pdb=" O SER B3790 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA B3795 " --> pdb=" O SER B3791 " (cutoff:3.500A) Processing helix chain 'B' and resid 3807 through 3823 Processing helix chain 'B' and resid 3828 through 3848 removed outlier: 4.257A pdb=" N THR B3841 " --> pdb=" O LYS B3837 " (cutoff:3.500A) Proline residue: B3842 - end of helix Processing helix chain 'B' and resid 3856 through 3883 Processing helix chain 'B' and resid 3883 through 3891 Processing helix chain 'B' and resid 3894 through 3911 removed outlier: 3.595A pdb=" N SER B3903 " --> pdb=" O THR B3899 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU B3911 " --> pdb=" O LYS B3907 " (cutoff:3.500A) Processing helix chain 'B' and resid 3917 through 3940 Processing helix chain 'B' and resid 3968 through 3974 Processing helix chain 'B' and resid 3998 through 4026 Processing helix chain 'B' and resid 4035 through 4047 removed outlier: 3.535A pdb=" N PHE B4047 " --> pdb=" O LEU B4043 " (cutoff:3.500A) Processing helix chain 'B' and resid 4082 through 4090 Processing helix chain 'B' and resid 4092 through 4111 removed outlier: 5.333A pdb=" N ASP B4098 " --> pdb=" O HIS B4094 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N TYR B4099 " --> pdb=" O GLU B4095 " (cutoff:3.500A) Processing helix chain 'B' and resid 4117 through 4139 Processing helix chain 'B' and resid 4142 through 4157 Processing helix chain 'B' and resid 4171 through 4197 removed outlier: 3.905A pdb=" N GLU B4197 " --> pdb=" O SER B4193 " (cutoff:3.500A) Processing helix chain 'B' and resid 4202 through 4219 Processing helix chain 'B' and resid 4222 through 4245 removed outlier: 7.424A pdb=" N MET B4238 " --> pdb=" O SER B4234 " (cutoff:3.500A) removed outlier: 9.597A pdb=" N GLU B4239 " --> pdb=" O GLN B4235 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE B4240 " --> pdb=" O ARG B4236 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL B4241 " --> pdb=" O GLY B4237 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE B4244 " --> pdb=" O PHE B4240 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER B4245 " --> pdb=" O VAL B4241 " (cutoff:3.500A) Processing helix chain 'B' and resid 4249 through 4255 removed outlier: 4.446A pdb=" N TRP B4253 " --> pdb=" O PRO B4250 " (cutoff:3.500A) Processing helix chain 'B' and resid 4256 through 4263 removed outlier: 3.843A pdb=" N ILE B4260 " --> pdb=" O PRO B4256 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA B4261 " --> pdb=" O ARG B4257 " (cutoff:3.500A) Processing helix chain 'B' and resid 4271 through 4276 Processing helix chain 'B' and resid 4277 through 4294 Processing helix chain 'B' and resid 4296 through 4306 Processing helix chain 'B' and resid 4309 through 4330 removed outlier: 4.068A pdb=" N ALA B4327 " --> pdb=" O THR B4323 " (cutoff:3.500A) Processing helix chain 'B' and resid 4342 through 4353 Processing helix chain 'B' and resid 4358 through 4370 Processing helix chain 'B' and resid 4373 through 4378 Processing helix chain 'B' and resid 4382 through 4403 Processing helix chain 'B' and resid 4405 through 4407 No H-bonds generated for 'chain 'B' and resid 4405 through 4407' Processing helix chain 'B' and resid 4408 through 4416 Processing helix chain 'B' and resid 4417 through 4422 Processing helix chain 'B' and resid 4522 through 4544 Processing helix chain 'B' and resid 4544 through 4552 removed outlier: 3.756A pdb=" N LEU B4548 " --> pdb=" O ASN B4544 " (cutoff:3.500A) Processing helix chain 'B' and resid 4558 through 4579 Processing helix chain 'B' and resid 4581 through 4599 Processing helix chain 'B' and resid 4613 through 4634 removed outlier: 4.045A pdb=" N HIS B4634 " --> pdb=" O ARG B4630 " (cutoff:3.500A) Processing helix chain 'B' and resid 4634 through 4648 Proline residue: B4640 - end of helix Processing helix chain 'B' and resid 4649 through 4654 removed outlier: 4.475A pdb=" N SER B4654 " --> pdb=" O GLU B4650 " (cutoff:3.500A) Processing helix chain 'B' and resid 4655 through 4662 Processing helix chain 'B' and resid 4665 through 4669 removed outlier: 4.503A pdb=" N PHE B4668 " --> pdb=" O PRO B4665 " (cutoff:3.500A) Processing helix chain 'B' and resid 4691 through 4702 Processing helix chain 'B' and resid 4703 through 4708 Processing helix chain 'B' and resid 4708 through 4717 Processing helix chain 'B' and resid 4717 through 4722 Processing helix chain 'B' and resid 4723 through 4725 No H-bonds generated for 'chain 'B' and resid 4723 through 4725' Processing helix chain 'B' and resid 4726 through 4741 Processing helix chain 'B' and resid 4751 through 4758 Processing helix chain 'B' and resid 4761 through 4789 removed outlier: 5.115A pdb=" N ARG B4784 " --> pdb=" O ASN B4780 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N SER B4785 " --> pdb=" O ALA B4781 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THR B4788 " --> pdb=" O ARG B4784 " (cutoff:3.500A) Processing helix chain 'B' and resid 4797 through 4801 removed outlier: 4.497A pdb=" N SER B4801 " --> pdb=" O TYR B4798 " (cutoff:3.500A) Processing helix chain 'B' and resid 4808 through 4812 Processing helix chain 'B' and resid 4817 through 4819 No H-bonds generated for 'chain 'B' and resid 4817 through 4819' Processing helix chain 'B' and resid 4820 through 4845 removed outlier: 3.529A pdb=" N THR B4824 " --> pdb=" O GLY B4820 " (cutoff:3.500A) Processing helix chain 'B' and resid 4856 through 4858 No H-bonds generated for 'chain 'B' and resid 4856 through 4858' Processing helix chain 'B' and resid 4859 through 4863 Processing helix chain 'B' and resid 4871 through 4879 Processing helix chain 'B' and resid 4895 through 4907 Processing helix chain 'B' and resid 4929 through 4941 removed outlier: 3.699A pdb=" N LEU B4933 " --> pdb=" O ASN B4929 " (cutoff:3.500A) Processing helix chain 'B' and resid 4947 through 4958 Processing helix chain 'B' and resid 4960 through 4981 removed outlier: 3.579A pdb=" N GLY B4976 " --> pdb=" O GLU B4972 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE B4977 " --> pdb=" O ILE B4973 " (cutoff:3.500A) Processing helix chain 'B' and resid 4988 through 4995 Processing helix chain 'B' and resid 5003 through 5010 Processing helix chain 'B' and resid 5014 through 5016 No H-bonds generated for 'chain 'B' and resid 5014 through 5016' Processing helix chain 'B' and resid 5017 through 5036 removed outlier: 3.739A pdb=" N ALA B5027 " --> pdb=" O GLN B5023 " (cutoff:3.500A) Processing helix chain 'B' and resid 5045 through 5049 Processing helix chain 'B' and resid 5053 through 5065 Processing helix chain 'B' and resid 5068 through 5083 Processing helix chain 'B' and resid 5098 through 5109 Processing helix chain 'B' and resid 5114 through 5122 removed outlier: 3.671A pdb=" N SER B5120 " --> pdb=" O SER B5116 " (cutoff:3.500A) Processing helix chain 'B' and resid 5127 through 5129 No H-bonds generated for 'chain 'B' and resid 5127 through 5129' Processing helix chain 'B' and resid 5130 through 5148 Processing sheet with id=AA1, first strand: chain 'B' and resid 433 through 434 removed outlier: 4.149A pdb=" N VAL B 369 " --> pdb=" O MET B 388 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N CYS B 386 " --> pdb=" O VAL B 371 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N CYS B 386 " --> pdb=" O ASP B 406 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N ASP B 406 " --> pdb=" O CYS B 386 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N MET B 388 " --> pdb=" O LYS B 404 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N LYS B 404 " --> pdb=" O MET B 388 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N CYS B 390 " --> pdb=" O GLU B 402 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLU B 402 " --> pdb=" O CYS B 390 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN B 392 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ILE B 355 " --> pdb=" O ASP B 468 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE B 470 " --> pdb=" O ILE B 355 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 433 through 434 removed outlier: 4.080A pdb=" N CYS B 451 " --> pdb=" O MET B 539 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N MET B 539 " --> pdb=" O CYS B 451 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 894 through 895 Processing sheet with id=AA4, first strand: chain 'B' and resid 1149 through 1150 removed outlier: 6.796A pdb=" N GLN B1149 " --> pdb=" O VAL B1232 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 1173 through 1174 removed outlier: 3.510A pdb=" N ILE B1173 " --> pdb=" O ARG B1183 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1540 through 1543 removed outlier: 3.616A pdb=" N GLY B1612 " --> pdb=" O TYR B1606 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1794 through 1797 removed outlier: 6.439A pdb=" N ILE B1795 " --> pdb=" O CYS B1892 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1982 through 1987 removed outlier: 6.531A pdb=" N VAL B2014 " --> pdb=" O LEU B2056 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU B2058 " --> pdb=" O VAL B2014 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N PHE B2016 " --> pdb=" O LEU B2058 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLU B2060 " --> pdb=" O PHE B2016 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE B2018 " --> pdb=" O GLU B2060 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ILE B2020 " --> pdb=" O PRO B2062 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER B1953 " --> pdb=" O ILE B2061 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 2040 through 2042 Processing sheet with id=AB1, first strand: chain 'B' and resid 2266 through 2270 removed outlier: 3.598A pdb=" N THR B2275 " --> pdb=" O ASN B2270 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 2282 through 2285 removed outlier: 7.436A pdb=" N ALA B2293 " --> pdb=" O ASP B2305 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ASP B2305 " --> pdb=" O ALA B2293 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 2407 through 2411 removed outlier: 6.563A pdb=" N LYS B2408 " --> pdb=" O PHE B2446 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ASP B2448 " --> pdb=" O LYS B2408 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL B2410 " --> pdb=" O ASP B2448 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL B2377 " --> pdb=" O ALA B2483 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N CYS B2485 " --> pdb=" O VAL B2377 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE B2379 " --> pdb=" O CYS B2485 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TRP B2541 " --> pdb=" O ILE B2378 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 2467 through 2468 Processing sheet with id=AB5, first strand: chain 'B' and resid 2516 through 2517 removed outlier: 3.644A pdb=" N ILE B2520 " --> pdb=" O LEU B2517 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 2762 through 2769 removed outlier: 6.737A pdb=" N LEU B2726 " --> pdb=" O GLY B2844 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N SER B2846 " --> pdb=" O LEU B2726 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU B2728 " --> pdb=" O SER B2846 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N PHE B2727 " --> pdb=" O VAL B2861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 3026 through 3028 removed outlier: 6.423A pdb=" N VAL B3059 " --> pdb=" O ILE B3108 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE B3110 " --> pdb=" O VAL B3059 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU B3061 " --> pdb=" O ILE B3110 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N GLU B3112 " --> pdb=" O LEU B3061 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU B3002 " --> pdb=" O VAL B3109 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N GLU B3111 " --> pdb=" O LEU B3002 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N VAL B3004 " --> pdb=" O GLU B3111 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 3080 through 3081 removed outlier: 4.521A pdb=" N LYS B3086 " --> pdb=" O VAL B3101 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 3304 through 3307 removed outlier: 6.218A pdb=" N VAL B3304 " --> pdb=" O VAL B3335 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N GLN B3337 " --> pdb=" O VAL B3304 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU B3306 " --> pdb=" O GLN B3337 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N ASP B3339 " --> pdb=" O LEU B3306 " (cutoff:3.500A) removed outlier: 9.338A pdb=" N ARG B3397 " --> pdb=" O ALA B3272 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N PHE B3274 " --> pdb=" O ARG B3397 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N VAL B3399 " --> pdb=" O PHE B3274 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLU B3276 " --> pdb=" O VAL B3399 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 3492 through 3494 removed outlier: 6.888A pdb=" N ARG B3493 " --> pdb=" O VAL B3641 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 3636 through 3637 removed outlier: 3.834A pdb=" N MET B3636 " --> pdb=" O TRP B4928 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 3957 through 3960 removed outlier: 3.877A pdb=" N HIS B3964 " --> pdb=" O LEU B3960 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 4079 through 4081 Processing sheet with id=AC5, first strand: chain 'B' and resid 4449 through 4450 Processing sheet with id=AC6, first strand: chain 'B' and resid 4852 through 4854 2128 hydrogen bonds defined for protein. 6156 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: 15.58 Time building geometry restraints manager: 4.33 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: 11933 1.34 - 1.46: 8355 1.46 - 1.58: 16631 1.58 - 1.70: 2 1.70 - 1.82: 329 Bond restraints: 37250 Sorted by residual: bond pdb=" C1' ATP B5301 " pdb=" O4' ATP B5301 " ideal model delta sigma weight residual 1.416 1.400 0.016 1.30e-02 5.92e+03 1.49e+00 bond pdb=" CB LYS B4348 " pdb=" CG LYS B4348 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.19e+00 bond pdb=" C4' ATP B5301 " pdb=" O4' ATP B5301 " ideal model delta sigma weight residual 1.444 1.433 0.011 1.10e-02 8.26e+03 1.03e+00 bond pdb=" CB MET B1751 " pdb=" CG MET B1751 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.90e-01 bond pdb=" CB CYS B1710 " pdb=" SG CYS B1710 " ideal model delta sigma weight residual 1.808 1.782 0.026 3.30e-02 9.18e+02 6.30e-01 ... (remaining 37245 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 50017 2.12 - 4.23: 326 4.23 - 6.35: 17 6.35 - 8.46: 5 8.46 - 10.58: 1 Bond angle restraints: 50366 Sorted by residual: angle pdb=" CB MET B1751 " pdb=" CG MET B1751 " pdb=" SD MET B1751 " ideal model delta sigma weight residual 112.70 123.28 -10.58 3.00e+00 1.11e-01 1.24e+01 angle pdb=" CB LYS B4348 " pdb=" CG LYS B4348 " pdb=" CD LYS B4348 " ideal model delta sigma weight residual 111.30 118.15 -6.85 2.30e+00 1.89e-01 8.87e+00 angle pdb=" CB MET B3503 " pdb=" CG MET B3503 " pdb=" SD MET B3503 " ideal model delta sigma weight residual 112.70 120.81 -8.11 3.00e+00 1.11e-01 7.31e+00 angle pdb=" C3' ATP B5301 " pdb=" C4' ATP B5301 " pdb=" C5' ATP B5301 " ideal model delta sigma weight residual 115.19 110.65 4.54 1.76e+00 3.23e-01 6.65e+00 angle pdb=" CA LYS B4348 " pdb=" CB LYS B4348 " pdb=" CG LYS B4348 " ideal model delta sigma weight residual 114.10 119.15 -5.05 2.00e+00 2.50e-01 6.38e+00 ... (remaining 50361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 19987 17.69 - 35.37: 2072 35.37 - 53.06: 499 53.06 - 70.75: 86 70.75 - 88.44: 23 Dihedral angle restraints: 22667 sinusoidal: 9346 harmonic: 13321 Sorted by residual: dihedral pdb=" CA MET B2042 " pdb=" C MET B2042 " pdb=" N ASP B2043 " pdb=" CA ASP B2043 " ideal model delta harmonic sigma weight residual 180.00 162.79 17.21 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA TYR B3755 " pdb=" C TYR B3755 " pdb=" N LYS B3756 " pdb=" CA LYS B3756 " ideal model delta harmonic sigma weight residual 180.00 163.05 16.95 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA HIS B5017 " pdb=" C HIS B5017 " pdb=" N ILE B5018 " pdb=" CA ILE B5018 " ideal model delta harmonic sigma weight residual -180.00 -163.13 -16.87 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 22664 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 5045 0.056 - 0.112: 579 0.112 - 0.168: 59 0.168 - 0.223: 0 0.223 - 0.279: 3 Chirality restraints: 5686 Sorted by residual: chirality pdb=" C3' ATP B5301 " pdb=" C2' ATP B5301 " pdb=" C4' ATP B5301 " pdb=" O3' ATP B5301 " both_signs ideal model delta sigma weight residual False -2.63 -2.91 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C2' ATP B5301 " pdb=" C1' ATP B5301 " pdb=" C3' ATP B5301 " pdb=" O2' ATP B5301 " both_signs ideal model delta sigma weight residual False -2.68 -2.94 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" C4' ATP B5301 " pdb=" C3' ATP B5301 " pdb=" C5' ATP B5301 " pdb=" O4' ATP B5301 " both_signs ideal model delta sigma weight residual False -2.49 -2.75 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 5683 not shown) Planarity restraints: 6413 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B4165 " 0.031 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO B4166 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO B4166 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B4166 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B3727 " -0.139 9.50e-02 1.11e+02 6.25e-02 2.56e+00 pdb=" NE ARG B3727 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG B3727 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B3727 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B3727 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B4794 " -0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO B4795 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B4795 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B4795 " -0.022 5.00e-02 4.00e+02 ... (remaining 6410 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 12140 2.84 - 3.35: 38327 3.35 - 3.87: 62105 3.87 - 4.38: 73265 4.38 - 4.90: 121028 Nonbonded interactions: 306865 Sorted by model distance: nonbonded pdb=" O2' ATP B5301 " pdb=" O3' ATP B5301 " model vdw 2.321 2.432 nonbonded pdb=" O LEU B4297 " pdb=" OD1 ASN B4301 " model vdw 2.401 3.040 nonbonded pdb=" O TYR B5106 " pdb=" OG1 THR B5109 " model vdw 2.442 3.040 nonbonded pdb=" O GLY B 361 " pdb=" OD1 ASN B 363 " model vdw 2.460 3.040 nonbonded pdb=" N GLN B4509 " pdb=" OE1 GLN B4509 " model vdw 2.460 3.120 ... (remaining 306860 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.720 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 48.170 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.080 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 37258 Z= 0.123 Angle : 0.454 10.576 50372 Z= 0.234 Chirality : 0.036 0.279 5686 Planarity : 0.003 0.063 6413 Dihedral : 15.170 88.437 13983 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.44 % Allowed : 12.38 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % 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: 2.20 (0.13), residues: 4463 helix: 2.34 (0.10), residues: 2655 sheet: -0.70 (0.29), residues: 301 loop : 0.41 (0.17), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B3727 TYR 0.010 0.001 TYR B1277 PHE 0.014 0.001 PHE B 528 TRP 0.012 0.001 TRP B 559 HIS 0.014 0.001 HIS B4671 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (37250) covalent geometry : angle 0.45366 / 0.23 (50366) hydrogen bonds : bond 0.12270 / 7.96 ( 2126) hydrogen bonds : angle 5.77421 / 4.15 ( 6156) metal coordination : bond 0.00559 / 0.23 ( 8) metal coordination : angle 1.52808 / 0.82 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 174 time to evaluate : 1.474 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: B 360 PHE cc_start: 0.7569 (m-10) cc_final: 0.7303 (m-10) REVERT: B 474 ARG cc_start: 0.8053 (tpm170) cc_final: 0.7801 (tpm170) REVERT: B 852 SER cc_start: 0.8485 (OUTLIER) cc_final: 0.8284 (p) REVERT: B 864 LYS cc_start: 0.8891 (tppt) cc_final: 0.8505 (tppt) REVERT: B 874 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8958 (tt) REVERT: B 893 MET cc_start: 0.8801 (ttm) cc_final: 0.8591 (ttt) REVERT: B 902 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7957 (ptt-90) REVERT: B 2307 MET cc_start: 0.9007 (ptp) cc_final: 0.8563 (ptm) REVERT: B 2369 MET cc_start: 0.9074 (tpp) cc_final: 0.8569 (tpt) REVERT: B 3072 TYR cc_start: 0.8122 (OUTLIER) cc_final: 0.7582 (p90) REVERT: B 3863 ILE cc_start: 0.9436 (OUTLIER) cc_final: 0.9137 (tt) REVERT: B 4014 MET cc_start: 0.9097 (mtm) cc_final: 0.8887 (mtp) REVERT: B 4143 LEU cc_start: 0.9402 (tp) cc_final: 0.9108 (tp) REVERT: B 4328 LEU cc_start: 0.9181 (mt) cc_final: 0.8880 (tt) REVERT: B 4366 ARG cc_start: 0.9282 (OUTLIER) cc_final: 0.9056 (ptp-110) REVERT: B 4431 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7733 (mm-30) REVERT: B 4537 MET cc_start: 0.8977 (mtt) cc_final: 0.8769 (mtm) REVERT: B 4935 MET cc_start: 0.8624 (mmm) cc_final: 0.8334 (mmm) outliers start: 59 outliers final: 37 residues processed: 226 average time/residue: 0.2525 time to fit residues: 92.9546 Evaluate side-chains 213 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 169 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 365 GLU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 586 CYS Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 779 SER Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 902 ARG Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1420 ILE Chi-restraints excluded: chain B residue 1520 ILE Chi-restraints excluded: chain B residue 1602 THR Chi-restraints excluded: chain B residue 1944 ASP Chi-restraints excluded: chain B residue 2005 LEU Chi-restraints excluded: chain B residue 2039 GLN Chi-restraints excluded: chain B residue 2225 THR Chi-restraints excluded: chain B residue 2317 LEU Chi-restraints excluded: chain B residue 2468 VAL Chi-restraints excluded: chain B residue 2509 SER Chi-restraints excluded: chain B residue 2519 SER Chi-restraints excluded: chain B residue 2569 ASN Chi-restraints excluded: chain B residue 2672 PHE Chi-restraints excluded: chain B residue 2679 SER Chi-restraints excluded: chain B residue 2813 SER Chi-restraints excluded: chain B residue 2862 SER Chi-restraints excluded: chain B residue 2970 LYS Chi-restraints excluded: chain B residue 3072 TYR Chi-restraints excluded: chain B residue 3233 SER Chi-restraints excluded: chain B residue 3714 LEU Chi-restraints excluded: chain B residue 3722 MET Chi-restraints excluded: chain B residue 3863 ILE Chi-restraints excluded: chain B residue 3925 MET Chi-restraints excluded: chain B residue 3942 PHE Chi-restraints excluded: chain B residue 4001 HIS Chi-restraints excluded: chain B residue 4092 SER Chi-restraints excluded: chain B residue 4131 SER Chi-restraints excluded: chain B residue 4257 ARG Chi-restraints excluded: chain B residue 4366 ARG Chi-restraints excluded: chain B residue 4431 GLU Chi-restraints excluded: chain B residue 4645 LEU Chi-restraints excluded: chain B residue 4683 ILE Chi-restraints excluded: chain B residue 4789 ASN Chi-restraints excluded: chain B residue 5098 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: [432, 197, 388, 215, 20, 132, 261, 248, 207, 401, 424] chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 4.9990 chunk 424 optimal weight: 8.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 718 GLN B 749 ASN B 812 GLN B1140 GLN B2474 HIS B2790 GLN B3041 GLN B3095 HIS ** B4242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4423 ASN B5121 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.042379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.034901 restraints weight = 191288.239| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.86 r_work: 0.2718 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.0763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 37258 Z= 0.253 Angle : 0.533 10.262 50372 Z= 0.274 Chirality : 0.041 0.187 5686 Planarity : 0.004 0.051 6413 Dihedral : 5.811 74.353 5004 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.62 % Allowed : 12.33 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % 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: 2.48 (0.13), residues: 4463 helix: 2.55 (0.10), residues: 2662 sheet: -0.39 (0.29), residues: 312 loop : 0.50 (0.17), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B2857 TYR 0.013 0.001 TYR B1277 PHE 0.020 0.001 PHE B 703 TRP 0.021 0.001 TRP B4928 HIS 0.011 0.001 HIS B4671 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.25 (37250) covalent geometry : angle 0.53317 / 0.27 (50366) hydrogen bonds : bond 0.04308 / 2.90 ( 2126) hydrogen bonds : angle 4.33646 / 3.12 ( 6156) metal coordination : bond 0.00489 / 0.23 ( 8) metal coordination : angle 1.30712 / 0.70 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 179 time to evaluate : 1.609 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: B 473 MET cc_start: 0.7799 (ppp) cc_final: 0.7567 (ppp) REVERT: B 474 ARG cc_start: 0.8179 (tpm170) cc_final: 0.7487 (tpm170) REVERT: B 537 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7738 (pm20) REVERT: B 757 VAL cc_start: 0.9430 (OUTLIER) cc_final: 0.9209 (p) REVERT: B 864 LYS cc_start: 0.8767 (tppt) cc_final: 0.8419 (tppt) REVERT: B 874 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8895 (tt) REVERT: B 893 MET cc_start: 0.8784 (ttm) cc_final: 0.8572 (ttt) REVERT: B 2307 MET cc_start: 0.8856 (ptp) cc_final: 0.8450 (ptm) REVERT: B 2340 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8824 (mm) REVERT: B 2369 MET cc_start: 0.8945 (tpp) cc_final: 0.8419 (tpt) REVERT: B 2600 ARG cc_start: 0.8673 (mtp180) cc_final: 0.8440 (mtp-110) REVERT: B 3072 TYR cc_start: 0.7942 (OUTLIER) cc_final: 0.7408 (p90) REVERT: B 4014 MET cc_start: 0.9022 (mtm) cc_final: 0.8811 (mtp) REVERT: B 4143 LEU cc_start: 0.9336 (tp) cc_final: 0.9039 (tp) REVERT: B 4328 LEU cc_start: 0.9112 (mt) cc_final: 0.8805 (tt) REVERT: B 4935 MET cc_start: 0.8640 (mmm) cc_final: 0.8326 (mmm) REVERT: B 5128 MET cc_start: 0.8950 (mmm) cc_final: 0.8720 (mmm) outliers start: 66 outliers final: 37 residues processed: 234 average time/residue: 0.2487 time to fit residues: 94.4114 Evaluate side-chains 214 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 172 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 906 SER Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1064 SER Chi-restraints excluded: chain B residue 1085 LEU Chi-restraints excluded: chain B residue 1237 VAL Chi-restraints excluded: chain B residue 1317 SER Chi-restraints excluded: chain B residue 1420 ILE Chi-restraints excluded: chain B residue 1540 LEU Chi-restraints excluded: chain B residue 1615 MET Chi-restraints excluded: chain B residue 1676 SER Chi-restraints excluded: chain B residue 1708 SER Chi-restraints excluded: chain B residue 1737 MET Chi-restraints excluded: chain B residue 1846 SER Chi-restraints excluded: chain B residue 1936 LEU Chi-restraints excluded: chain B residue 2005 LEU Chi-restraints excluded: chain B residue 2193 SER Chi-restraints excluded: chain B residue 2267 VAL Chi-restraints excluded: chain B residue 2340 LEU Chi-restraints excluded: chain B residue 2468 VAL Chi-restraints excluded: chain B residue 2569 ASN Chi-restraints excluded: chain B residue 2775 THR Chi-restraints excluded: chain B residue 3044 ARG Chi-restraints excluded: chain B residue 3072 TYR Chi-restraints excluded: chain B residue 3256 VAL Chi-restraints excluded: chain B residue 3259 LEU Chi-restraints excluded: chain B residue 3316 SER Chi-restraints excluded: chain B residue 3421 THR Chi-restraints excluded: chain B residue 3624 SER Chi-restraints excluded: chain B residue 3722 MET Chi-restraints excluded: chain B residue 3841 THR Chi-restraints excluded: chain B residue 3925 MET Chi-restraints excluded: chain B residue 3942 PHE Chi-restraints excluded: chain B residue 4195 LEU Chi-restraints excluded: chain B residue 4257 ARG Chi-restraints excluded: chain B residue 4789 ASN Chi-restraints excluded: chain B residue 5107 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: [446, 235, 47, 329, 223, 354, 13, 377, 211, 110, 112] chunk 446 optimal weight: 6.9990 chunk 235 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 329 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 354 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 377 optimal weight: 9.9990 chunk 211 optimal weight: 0.1980 chunk 110 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 632 HIS B1221 ASN B2628 HIS B3126 ASN ** B3838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4094 HIS B4196 GLN ** B4242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4769 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.042678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.035187 restraints weight = 189815.393| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.88 r_work: 0.2730 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 37258 Z= 0.171 Angle : 0.485 9.442 50372 Z= 0.249 Chirality : 0.039 0.171 5686 Planarity : 0.003 0.053 6413 Dihedral : 4.857 77.912 4948 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.86 % Allowed : 12.48 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % 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: 2.62 (0.13), residues: 4463 helix: 2.66 (0.10), residues: 2672 sheet: -0.23 (0.29), residues: 314 loop : 0.53 (0.17), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B3919 TYR 0.012 0.001 TYR B3315 PHE 0.021 0.001 PHE B 360 TRP 0.021 0.001 TRP B4928 HIS 0.013 0.001 HIS B4671 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (37250) covalent geometry : angle 0.48455 / 0.25 (50366) hydrogen bonds : bond 0.03872 / 2.60 ( 2126) hydrogen bonds : angle 4.07482 / 2.94 ( 6156) metal coordination : bond 0.00327 / 0.17 ( 8) metal coordination : angle 1.27902 / 0.70 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 178 time to evaluate : 1.475 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: B 474 ARG cc_start: 0.8199 (tpm170) cc_final: 0.7502 (tpm170) REVERT: B 547 LYS cc_start: 0.8605 (tptt) cc_final: 0.8306 (tptt) REVERT: B 667 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.9002 (mt) REVERT: B 864 LYS cc_start: 0.8772 (tppt) cc_final: 0.8435 (tppt) REVERT: B 874 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8885 (tt) REVERT: B 893 MET cc_start: 0.8788 (ttm) cc_final: 0.8537 (ttt) REVERT: B 902 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7716 (ptt-90) REVERT: B 1288 CYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8795 (m) REVERT: B 2307 MET cc_start: 0.8831 (ptp) cc_final: 0.8426 (ptm) REVERT: B 2369 MET cc_start: 0.8916 (tpp) cc_final: 0.8400 (tpt) REVERT: B 2600 ARG cc_start: 0.8665 (mtp180) cc_final: 0.8424 (mtm110) REVERT: B 2855 MET cc_start: 0.8540 (ptp) cc_final: 0.8193 (ptt) REVERT: B 3072 TYR cc_start: 0.7917 (OUTLIER) cc_final: 0.7400 (p90) REVERT: B 3097 VAL cc_start: 0.8888 (OUTLIER) cc_final: 0.8673 (m) REVERT: B 3863 ILE cc_start: 0.9409 (OUTLIER) cc_final: 0.9128 (tt) REVERT: B 4014 MET cc_start: 0.8998 (mtm) cc_final: 0.8792 (mtp) REVERT: B 4328 LEU cc_start: 0.9029 (mt) cc_final: 0.8712 (tt) REVERT: B 4537 MET cc_start: 0.8944 (mtm) cc_final: 0.8708 (mtm) REVERT: B 4652 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8635 (tp) REVERT: B 4935 MET cc_start: 0.8651 (mmm) cc_final: 0.8348 (mmm) REVERT: B 5128 MET cc_start: 0.8938 (mmm) cc_final: 0.8690 (mmm) outliers start: 76 outliers final: 43 residues processed: 239 average time/residue: 0.2498 time to fit residues: 96.7130 Evaluate side-chains 221 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 170 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 612 LYS Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 902 ARG Chi-restraints excluded: chain B residue 906 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1064 SER Chi-restraints excluded: chain B residue 1181 TYR Chi-restraints excluded: chain B residue 1237 VAL Chi-restraints excluded: chain B residue 1288 CYS Chi-restraints excluded: chain B residue 1317 SER Chi-restraints excluded: chain B residue 1540 LEU Chi-restraints excluded: chain B residue 1615 MET Chi-restraints excluded: chain B residue 1676 SER Chi-restraints excluded: chain B residue 1737 MET Chi-restraints excluded: chain B residue 1828 THR Chi-restraints excluded: chain B residue 1936 LEU Chi-restraints excluded: chain B residue 2005 LEU Chi-restraints excluded: chain B residue 2039 GLN Chi-restraints excluded: chain B residue 2143 THR Chi-restraints excluded: chain B residue 2267 VAL Chi-restraints excluded: chain B residue 2317 LEU Chi-restraints excluded: chain B residue 2434 SER Chi-restraints excluded: chain B residue 2569 ASN Chi-restraints excluded: chain B residue 2775 THR Chi-restraints excluded: chain B residue 3044 ARG Chi-restraints excluded: chain B residue 3072 TYR Chi-restraints excluded: chain B residue 3097 VAL Chi-restraints excluded: chain B residue 3259 LEU Chi-restraints excluded: chain B residue 3299 LEU Chi-restraints excluded: chain B residue 3316 SER Chi-restraints excluded: chain B residue 3421 THR Chi-restraints excluded: chain B residue 3624 SER Chi-restraints excluded: chain B residue 3722 MET Chi-restraints excluded: chain B residue 3841 THR Chi-restraints excluded: chain B residue 3863 ILE Chi-restraints excluded: chain B residue 3925 MET Chi-restraints excluded: chain B residue 3942 PHE Chi-restraints excluded: chain B residue 4171 SER Chi-restraints excluded: chain B residue 4195 LEU Chi-restraints excluded: chain B residue 4257 ARG Chi-restraints excluded: chain B residue 4297 LEU Chi-restraints excluded: chain B residue 4433 LEU Chi-restraints excluded: chain B residue 4576 LYS Chi-restraints excluded: chain B residue 4652 ILE Chi-restraints excluded: chain B residue 4683 ILE Chi-restraints excluded: chain B residue 4789 ASN Chi-restraints excluded: chain B residue 5107 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: [197, 247, 187, 330, 67, 246, 3, 426, 418, 386, 289] chunk 197 optimal weight: 3.9990 chunk 247 optimal weight: 6.9990 chunk 187 optimal weight: 0.0870 chunk 330 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 246 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 426 optimal weight: 2.9990 chunk 418 optimal weight: 10.0000 chunk 386 optimal weight: 6.9990 chunk 289 optimal weight: 5.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B3348 GLN ** B3838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4094 HIS ** B4263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.042572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.035059 restraints weight = 190121.562| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.89 r_work: 0.2731 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 37258 Z= 0.181 Angle : 0.488 10.493 50372 Z= 0.249 Chirality : 0.039 0.169 5686 Planarity : 0.003 0.055 6413 Dihedral : 4.806 80.301 4945 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.98 % Allowed : 12.75 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % 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: 2.65 (0.13), residues: 4463 helix: 2.68 (0.10), residues: 2673 sheet: -0.16 (0.28), residues: 314 loop : 0.53 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B3727 TYR 0.012 0.001 TYR B3901 PHE 0.018 0.001 PHE B 703 TRP 0.023 0.001 TRP B4928 HIS 0.005 0.001 HIS B4671 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (37250) covalent geometry : angle 0.48813 / 0.25 (50366) hydrogen bonds : bond 0.03764 / 2.54 ( 2126) hydrogen bonds : angle 3.99403 / 2.88 ( 6156) metal coordination : bond 0.00327 / 0.17 ( 8) metal coordination : angle 1.20587 / 0.65 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 174 time to evaluate : 1.545 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: B 360 PHE cc_start: 0.7256 (m-10) cc_final: 0.7045 (m-10) REVERT: B 547 LYS cc_start: 0.8620 (tptt) cc_final: 0.8349 (tptt) REVERT: B 667 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8990 (mt) REVERT: B 864 LYS cc_start: 0.8777 (tppt) cc_final: 0.8436 (tppt) REVERT: B 874 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8917 (tt) REVERT: B 893 MET cc_start: 0.8776 (ttm) cc_final: 0.8538 (ttt) REVERT: B 1288 CYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8784 (m) REVERT: B 1723 MET cc_start: 0.8505 (mmt) cc_final: 0.8105 (mmt) REVERT: B 2307 MET cc_start: 0.8840 (ptp) cc_final: 0.8446 (ptm) REVERT: B 2369 MET cc_start: 0.8908 (tpp) cc_final: 0.8396 (tpt) REVERT: B 2600 ARG cc_start: 0.8678 (mtp180) cc_final: 0.8436 (mtm110) REVERT: B 2855 MET cc_start: 0.8512 (ptp) cc_final: 0.8186 (ptt) REVERT: B 3072 TYR cc_start: 0.7931 (OUTLIER) cc_final: 0.7403 (p90) REVERT: B 3097 VAL cc_start: 0.8892 (OUTLIER) cc_final: 0.8679 (m) REVERT: B 3863 ILE cc_start: 0.9415 (OUTLIER) cc_final: 0.9133 (tt) REVERT: B 4014 MET cc_start: 0.9015 (mtm) cc_final: 0.8802 (mtp) REVERT: B 4328 LEU cc_start: 0.8981 (mt) cc_final: 0.8681 (tt) REVERT: B 4537 MET cc_start: 0.8981 (mtm) cc_final: 0.8756 (mtm) REVERT: B 4935 MET cc_start: 0.8678 (mmm) cc_final: 0.8366 (mmm) REVERT: B 5128 MET cc_start: 0.8939 (mmm) cc_final: 0.8655 (mmm) outliers start: 81 outliers final: 52 residues processed: 241 average time/residue: 0.2457 time to fit residues: 95.7245 Evaluate side-chains 228 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 170 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 612 LYS Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 906 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1064 SER Chi-restraints excluded: chain B residue 1181 TYR Chi-restraints excluded: chain B residue 1196 MET Chi-restraints excluded: chain B residue 1237 VAL Chi-restraints excluded: chain B residue 1288 CYS Chi-restraints excluded: chain B residue 1317 SER Chi-restraints excluded: chain B residue 1337 VAL Chi-restraints excluded: chain B residue 1540 LEU Chi-restraints excluded: chain B residue 1558 MET Chi-restraints excluded: chain B residue 1615 MET Chi-restraints excluded: chain B residue 1676 SER Chi-restraints excluded: chain B residue 1737 MET Chi-restraints excluded: chain B residue 1828 THR Chi-restraints excluded: chain B residue 1846 SER Chi-restraints excluded: chain B residue 1936 LEU Chi-restraints excluded: chain B residue 2005 LEU Chi-restraints excluded: chain B residue 2039 GLN Chi-restraints excluded: chain B residue 2143 THR Chi-restraints excluded: chain B residue 2267 VAL Chi-restraints excluded: chain B residue 2317 LEU Chi-restraints excluded: chain B residue 2434 SER Chi-restraints excluded: chain B residue 2468 VAL Chi-restraints excluded: chain B residue 2509 SER Chi-restraints excluded: chain B residue 2569 ASN Chi-restraints excluded: chain B residue 2775 THR Chi-restraints excluded: chain B residue 3044 ARG Chi-restraints excluded: chain B residue 3072 TYR Chi-restraints excluded: chain B residue 3097 VAL Chi-restraints excluded: chain B residue 3099 CYS Chi-restraints excluded: chain B residue 3259 LEU Chi-restraints excluded: chain B residue 3262 HIS Chi-restraints excluded: chain B residue 3299 LEU Chi-restraints excluded: chain B residue 3316 SER Chi-restraints excluded: chain B residue 3421 THR Chi-restraints excluded: chain B residue 3624 SER Chi-restraints excluded: chain B residue 3722 MET Chi-restraints excluded: chain B residue 3841 THR Chi-restraints excluded: chain B residue 3863 ILE Chi-restraints excluded: chain B residue 3925 MET Chi-restraints excluded: chain B residue 3942 PHE Chi-restraints excluded: chain B residue 4171 SER Chi-restraints excluded: chain B residue 4195 LEU Chi-restraints excluded: chain B residue 4548 LEU Chi-restraints excluded: chain B residue 4576 LYS Chi-restraints excluded: chain B residue 4594 SER Chi-restraints excluded: chain B residue 4645 LEU Chi-restraints excluded: chain B residue 4683 ILE Chi-restraints excluded: chain B residue 4789 ASN Chi-restraints excluded: chain B residue 5107 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: [2, 69, 5, 322, 37, 180, 97, 177, 134, 68, 25] chunk 2 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 322 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 180 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 177 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B3126 ASN ** B3838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4094 HIS ** B4242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.042395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.034887 restraints weight = 190090.157| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.86 r_work: 0.2724 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 37258 Z= 0.212 Angle : 0.502 10.742 50372 Z= 0.255 Chirality : 0.039 0.167 5686 Planarity : 0.004 0.056 6413 Dihedral : 4.768 80.848 4941 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.18 % Allowed : 12.78 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % 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: 2.65 (0.13), residues: 4463 helix: 2.67 (0.10), residues: 2680 sheet: -0.08 (0.28), residues: 314 loop : 0.52 (0.17), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B3727 TYR 0.016 0.001 TYR B3315 PHE 0.018 0.001 PHE B 703 TRP 0.014 0.001 TRP B 559 HIS 0.004 0.001 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 (37250) covalent geometry : angle 0.50148 / 0.26 (50366) hydrogen bonds : bond 0.03792 / 2.56 ( 2126) hydrogen bonds : angle 3.97565 / 2.87 ( 6156) metal coordination : bond 0.00472 / 0.23 ( 8) metal coordination : angle 1.23433 / 0.66 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 175 time to evaluate : 1.489 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: B 359 HIS cc_start: 0.8316 (OUTLIER) cc_final: 0.8114 (t70) REVERT: B 473 MET cc_start: 0.8049 (tmm) cc_final: 0.7818 (tmm) REVERT: B 547 LYS cc_start: 0.8643 (tptt) cc_final: 0.8330 (tptt) REVERT: B 667 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8993 (mt) REVERT: B 864 LYS cc_start: 0.8773 (tppt) cc_final: 0.8439 (tppt) REVERT: B 874 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8907 (tt) REVERT: B 893 MET cc_start: 0.8781 (ttm) cc_final: 0.8545 (ttt) REVERT: B 902 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7721 (ptt-90) REVERT: B 1288 CYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8785 (m) REVERT: B 2307 MET cc_start: 0.8786 (ptp) cc_final: 0.8381 (ptm) REVERT: B 2369 MET cc_start: 0.8918 (tpp) cc_final: 0.8455 (tpt) REVERT: B 2600 ARG cc_start: 0.8668 (mtp180) cc_final: 0.8437 (mtm110) REVERT: B 3072 TYR cc_start: 0.7936 (OUTLIER) cc_final: 0.7393 (p90) REVERT: B 3097 VAL cc_start: 0.8894 (OUTLIER) cc_final: 0.8686 (m) REVERT: B 3863 ILE cc_start: 0.9419 (OUTLIER) cc_final: 0.9142 (tt) REVERT: B 4014 MET cc_start: 0.9012 (mtm) cc_final: 0.8799 (mtp) REVERT: B 4328 LEU cc_start: 0.8955 (mt) cc_final: 0.8662 (tt) REVERT: B 4537 MET cc_start: 0.8994 (mtm) cc_final: 0.8782 (mtm) REVERT: B 4935 MET cc_start: 0.8723 (mmm) cc_final: 0.8405 (mmm) REVERT: B 5128 MET cc_start: 0.8970 (mmm) cc_final: 0.8655 (mmm) outliers start: 89 outliers final: 63 residues processed: 250 average time/residue: 0.2476 time to fit residues: 99.3948 Evaluate side-chains 241 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 170 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 359 HIS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 612 LYS Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 902 ARG Chi-restraints excluded: chain B residue 906 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1064 SER Chi-restraints excluded: chain B residue 1181 TYR Chi-restraints excluded: chain B residue 1186 HIS Chi-restraints excluded: chain B residue 1196 MET Chi-restraints excluded: chain B residue 1237 VAL Chi-restraints excluded: chain B residue 1288 CYS Chi-restraints excluded: chain B residue 1317 SER Chi-restraints excluded: chain B residue 1325 VAL Chi-restraints excluded: chain B residue 1337 VAL Chi-restraints excluded: chain B residue 1450 ASP Chi-restraints excluded: chain B residue 1540 LEU Chi-restraints excluded: chain B residue 1558 MET Chi-restraints excluded: chain B residue 1602 THR Chi-restraints excluded: chain B residue 1615 MET Chi-restraints excluded: chain B residue 1676 SER Chi-restraints excluded: chain B residue 1704 VAL Chi-restraints excluded: chain B residue 1737 MET Chi-restraints excluded: chain B residue 1828 THR Chi-restraints excluded: chain B residue 1846 SER Chi-restraints excluded: chain B residue 1936 LEU Chi-restraints excluded: chain B residue 2005 LEU Chi-restraints excluded: chain B residue 2039 GLN Chi-restraints excluded: chain B residue 2143 THR Chi-restraints excluded: chain B residue 2267 VAL Chi-restraints excluded: chain B residue 2276 MET Chi-restraints excluded: chain B residue 2317 LEU Chi-restraints excluded: chain B residue 2434 SER Chi-restraints excluded: chain B residue 2468 VAL Chi-restraints excluded: chain B residue 2509 SER Chi-restraints excluded: chain B residue 2569 ASN Chi-restraints excluded: chain B residue 2775 THR Chi-restraints excluded: chain B residue 2807 VAL Chi-restraints excluded: chain B residue 3044 ARG Chi-restraints excluded: chain B residue 3072 TYR Chi-restraints excluded: chain B residue 3097 VAL Chi-restraints excluded: chain B residue 3256 VAL Chi-restraints excluded: chain B residue 3259 LEU Chi-restraints excluded: chain B residue 3262 HIS Chi-restraints excluded: chain B residue 3268 HIS Chi-restraints excluded: chain B residue 3299 LEU Chi-restraints excluded: chain B residue 3316 SER Chi-restraints excluded: chain B residue 3371 VAL Chi-restraints excluded: chain B residue 3421 THR Chi-restraints excluded: chain B residue 3624 SER Chi-restraints excluded: chain B residue 3722 MET Chi-restraints excluded: chain B residue 3841 THR Chi-restraints excluded: chain B residue 3863 ILE Chi-restraints excluded: chain B residue 3925 MET Chi-restraints excluded: chain B residue 3942 PHE Chi-restraints excluded: chain B residue 4171 SER Chi-restraints excluded: chain B residue 4195 LEU Chi-restraints excluded: chain B residue 4433 LEU Chi-restraints excluded: chain B residue 4576 LYS Chi-restraints excluded: chain B residue 4594 SER Chi-restraints excluded: chain B residue 4676 SER Chi-restraints excluded: chain B residue 4683 ILE Chi-restraints excluded: chain B residue 4789 ASN Chi-restraints excluded: chain B residue 5107 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: [277, 288, 88, 128, 150, 31, 340, 67, 115, 359, 317] chunk 277 optimal weight: 0.6980 chunk 288 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 150 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 340 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 359 optimal weight: 9.9990 chunk 317 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B3838 ASN B4094 HIS ** B4242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.043141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.035652 restraints weight = 189251.572| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.90 r_work: 0.2751 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 37258 Z= 0.111 Angle : 0.465 11.215 50372 Z= 0.236 Chirality : 0.038 0.155 5686 Planarity : 0.003 0.055 6413 Dihedral : 4.689 89.802 4941 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.57 % Allowed : 13.53 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % 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: 2.75 (0.13), residues: 4463 helix: 2.74 (0.10), residues: 2679 sheet: 0.01 (0.29), residues: 312 loop : 0.57 (0.17), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B3727 TYR 0.013 0.001 TYR B1750 PHE 0.020 0.001 PHE B 703 TRP 0.013 0.001 TRP B 559 HIS 0.004 0.001 HIS B2822 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (37250) covalent geometry : angle 0.46530 / 0.24 (50366) hydrogen bonds : bond 0.03457 / 2.33 ( 2126) hydrogen bonds : angle 3.83759 / 2.77 ( 6156) metal coordination : bond 0.00302 / 0.14 ( 8) metal coordination : angle 1.19181 / 0.65 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 175 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 547 LYS cc_start: 0.8636 (tptt) cc_final: 0.8321 (tptt) REVERT: B 667 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8977 (mt) REVERT: B 864 LYS cc_start: 0.8765 (tppt) cc_final: 0.8406 (tppt) REVERT: B 874 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8907 (tt) REVERT: B 893 MET cc_start: 0.8758 (ttm) cc_final: 0.8521 (ttt) REVERT: B 902 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7720 (ptt-90) REVERT: B 1288 CYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8738 (m) REVERT: B 1723 MET cc_start: 0.8579 (mmt) cc_final: 0.8140 (mmt) REVERT: B 2082 PHE cc_start: 0.7917 (m-80) cc_final: 0.7647 (m-80) REVERT: B 2307 MET cc_start: 0.8775 (ptp) cc_final: 0.8398 (ptm) REVERT: B 2369 MET cc_start: 0.8879 (tpp) cc_final: 0.8413 (tpt) REVERT: B 2462 ILE cc_start: 0.9324 (OUTLIER) cc_final: 0.9067 (mm) REVERT: B 2658 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8682 (mp) REVERT: B 3072 TYR cc_start: 0.7875 (OUTLIER) cc_final: 0.7379 (p90) REVERT: B 3097 VAL cc_start: 0.8891 (OUTLIER) cc_final: 0.8690 (m) REVERT: B 3299 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8934 (tp) REVERT: B 3410 MET cc_start: 0.8791 (mtm) cc_final: 0.8499 (ttm) REVERT: B 3727 ARG cc_start: 0.8341 (tpt90) cc_final: 0.8140 (tpt90) REVERT: B 3863 ILE cc_start: 0.9393 (OUTLIER) cc_final: 0.9103 (tt) REVERT: B 4014 MET cc_start: 0.8991 (mtm) cc_final: 0.8789 (mtp) REVERT: B 4328 LEU cc_start: 0.8862 (mt) cc_final: 0.8563 (tt) REVERT: B 4537 MET cc_start: 0.8945 (mtm) cc_final: 0.8731 (mtm) REVERT: B 4935 MET cc_start: 0.8725 (mmm) cc_final: 0.8387 (mmm) REVERT: B 5128 MET cc_start: 0.8965 (mmm) cc_final: 0.8650 (mmm) outliers start: 64 outliers final: 38 residues processed: 229 average time/residue: 0.2554 time to fit residues: 94.5358 Evaluate side-chains 216 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 168 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 612 LYS Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 902 ARG Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1085 LEU Chi-restraints excluded: chain B residue 1237 VAL Chi-restraints excluded: chain B residue 1288 CYS Chi-restraints excluded: chain B residue 1317 SER Chi-restraints excluded: chain B residue 1337 VAL Chi-restraints excluded: chain B residue 1540 LEU Chi-restraints excluded: chain B residue 1558 MET Chi-restraints excluded: chain B residue 1676 SER Chi-restraints excluded: chain B residue 1737 MET Chi-restraints excluded: chain B residue 1846 SER Chi-restraints excluded: chain B residue 1936 LEU Chi-restraints excluded: chain B residue 2005 LEU Chi-restraints excluded: chain B residue 2039 GLN Chi-restraints excluded: chain B residue 2267 VAL Chi-restraints excluded: chain B residue 2276 MET Chi-restraints excluded: chain B residue 2462 ILE Chi-restraints excluded: chain B residue 2509 SER Chi-restraints excluded: chain B residue 2569 ASN Chi-restraints excluded: chain B residue 2658 LEU Chi-restraints excluded: chain B residue 2807 VAL Chi-restraints excluded: chain B residue 3044 ARG Chi-restraints excluded: chain B residue 3072 TYR Chi-restraints excluded: chain B residue 3097 VAL Chi-restraints excluded: chain B residue 3099 CYS Chi-restraints excluded: chain B residue 3259 LEU Chi-restraints excluded: chain B residue 3262 HIS Chi-restraints excluded: chain B residue 3299 LEU Chi-restraints excluded: chain B residue 3316 SER Chi-restraints excluded: chain B residue 3841 THR Chi-restraints excluded: chain B residue 3863 ILE Chi-restraints excluded: chain B residue 3925 MET Chi-restraints excluded: chain B residue 3942 PHE Chi-restraints excluded: chain B residue 4001 HIS Chi-restraints excluded: chain B residue 4195 LEU Chi-restraints excluded: chain B residue 4576 LYS Chi-restraints excluded: chain B residue 4683 ILE Chi-restraints excluded: chain B residue 4789 ASN Chi-restraints excluded: chain B residue 5107 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: [29, 397, 276, 206, 136, 241, 374, 68, 358, 410, 264] chunk 29 optimal weight: 0.9980 chunk 397 optimal weight: 8.9990 chunk 276 optimal weight: 3.9990 chunk 206 optimal weight: 0.0270 chunk 136 optimal weight: 2.9990 chunk 241 optimal weight: 7.9990 chunk 374 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 358 optimal weight: 10.0000 chunk 410 optimal weight: 3.9990 chunk 264 optimal weight: 1.9990 overall best weight: 2.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 423 HIS ** B4242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.042665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.035189 restraints weight = 189728.637| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.88 r_work: 0.2736 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 37258 Z= 0.177 Angle : 0.485 11.664 50372 Z= 0.244 Chirality : 0.038 0.163 5686 Planarity : 0.003 0.056 6413 Dihedral : 4.649 88.131 4938 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.81 % Allowed : 13.46 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % 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: 2.75 (0.13), residues: 4463 helix: 2.74 (0.10), residues: 2680 sheet: 0.02 (0.28), residues: 318 loop : 0.58 (0.17), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B3727 TYR 0.013 0.001 TYR B3901 PHE 0.018 0.001 PHE B3948 TRP 0.013 0.001 TRP B 559 HIS 0.006 0.001 HIS B4094 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (37250) covalent geometry : angle 0.48464 / 0.24 (50366) hydrogen bonds : bond 0.03572 / 2.41 ( 2126) hydrogen bonds : angle 3.85874 / 2.78 ( 6156) metal coordination : bond 0.00387 / 0.20 ( 8) metal coordination : angle 1.21170 / 0.66 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 174 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 547 LYS cc_start: 0.8633 (tptt) cc_final: 0.8326 (tptt) REVERT: B 667 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8985 (mt) REVERT: B 864 LYS cc_start: 0.8787 (tppt) cc_final: 0.8435 (tppt) REVERT: B 874 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8933 (tt) REVERT: B 893 MET cc_start: 0.8774 (ttm) cc_final: 0.8533 (ttt) REVERT: B 902 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7722 (ptt-90) REVERT: B 1288 CYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8758 (m) REVERT: B 1723 MET cc_start: 0.8598 (mmt) cc_final: 0.8077 (mmt) REVERT: B 2115 MET cc_start: 0.9244 (ttp) cc_final: 0.8993 (ttp) REVERT: B 2307 MET cc_start: 0.8786 (ptp) cc_final: 0.8409 (ptm) REVERT: B 2369 MET cc_start: 0.8903 (tpp) cc_final: 0.8449 (tpt) REVERT: B 2462 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.9077 (mm) REVERT: B 3072 TYR cc_start: 0.7913 (OUTLIER) cc_final: 0.7383 (p90) REVERT: B 3097 VAL cc_start: 0.8885 (OUTLIER) cc_final: 0.8684 (m) REVERT: B 3299 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8944 (tp) REVERT: B 3410 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8403 (ttm) REVERT: B 3863 ILE cc_start: 0.9404 (OUTLIER) cc_final: 0.9113 (tt) REVERT: B 4014 MET cc_start: 0.9013 (mtm) cc_final: 0.8809 (mtp) REVERT: B 4257 ARG cc_start: 0.8001 (ptp-170) cc_final: 0.7660 (ptt-90) REVERT: B 4262 GLN cc_start: 0.8974 (tm-30) cc_final: 0.8746 (tm-30) REVERT: B 4328 LEU cc_start: 0.8874 (mt) cc_final: 0.8565 (tt) REVERT: B 4537 MET cc_start: 0.8985 (mtm) cc_final: 0.8777 (mtm) REVERT: B 4935 MET cc_start: 0.8760 (mmm) cc_final: 0.8424 (mmm) REVERT: B 5128 MET cc_start: 0.8987 (mmm) cc_final: 0.8641 (mmm) outliers start: 74 outliers final: 54 residues processed: 236 average time/residue: 0.2464 time to fit residues: 95.0863 Evaluate side-chains 234 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 170 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 612 LYS Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 902 ARG Chi-restraints excluded: chain B residue 906 SER Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1064 SER Chi-restraints excluded: chain B residue 1085 LEU Chi-restraints excluded: chain B residue 1181 TYR Chi-restraints excluded: chain B residue 1196 MET Chi-restraints excluded: chain B residue 1237 VAL Chi-restraints excluded: chain B residue 1288 CYS Chi-restraints excluded: chain B residue 1317 SER Chi-restraints excluded: chain B residue 1337 VAL Chi-restraints excluded: chain B residue 1447 ASN Chi-restraints excluded: chain B residue 1540 LEU Chi-restraints excluded: chain B residue 1558 MET Chi-restraints excluded: chain B residue 1602 THR Chi-restraints excluded: chain B residue 1676 SER Chi-restraints excluded: chain B residue 1737 MET Chi-restraints excluded: chain B residue 1846 SER Chi-restraints excluded: chain B residue 1936 LEU Chi-restraints excluded: chain B residue 2005 LEU Chi-restraints excluded: chain B residue 2039 GLN Chi-restraints excluded: chain B residue 2143 THR Chi-restraints excluded: chain B residue 2267 VAL Chi-restraints excluded: chain B residue 2276 MET Chi-restraints excluded: chain B residue 2434 SER Chi-restraints excluded: chain B residue 2462 ILE Chi-restraints excluded: chain B residue 2468 VAL Chi-restraints excluded: chain B residue 2509 SER Chi-restraints excluded: chain B residue 2569 ASN Chi-restraints excluded: chain B residue 2775 THR Chi-restraints excluded: chain B residue 2807 VAL Chi-restraints excluded: chain B residue 3044 ARG Chi-restraints excluded: chain B residue 3072 TYR Chi-restraints excluded: chain B residue 3097 VAL Chi-restraints excluded: chain B residue 3099 CYS Chi-restraints excluded: chain B residue 3259 LEU Chi-restraints excluded: chain B residue 3262 HIS Chi-restraints excluded: chain B residue 3299 LEU Chi-restraints excluded: chain B residue 3316 SER Chi-restraints excluded: chain B residue 3371 VAL Chi-restraints excluded: chain B residue 3410 MET Chi-restraints excluded: chain B residue 3421 THR Chi-restraints excluded: chain B residue 3624 SER Chi-restraints excluded: chain B residue 3722 MET Chi-restraints excluded: chain B residue 3841 THR Chi-restraints excluded: chain B residue 3863 ILE Chi-restraints excluded: chain B residue 3925 MET Chi-restraints excluded: chain B residue 3942 PHE Chi-restraints excluded: chain B residue 4001 HIS Chi-restraints excluded: chain B residue 4171 SER Chi-restraints excluded: chain B residue 4195 LEU Chi-restraints excluded: chain B residue 4576 LYS Chi-restraints excluded: chain B residue 4676 SER Chi-restraints excluded: chain B residue 4683 ILE Chi-restraints excluded: chain B residue 4789 ASN Chi-restraints excluded: chain B residue 5107 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: [365, 431, 407, 425, 164, 283, 91, 56, 449, 233, 73] chunk 365 optimal weight: 1.9990 chunk 431 optimal weight: 0.8980 chunk 407 optimal weight: 2.9990 chunk 425 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 283 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 449 optimal weight: 5.9990 chunk 233 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B4094 HIS ** B4242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.042927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.035456 restraints weight = 188658.446| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.88 r_work: 0.2748 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 37258 Z= 0.132 Angle : 0.478 12.001 50372 Z= 0.240 Chirality : 0.038 0.156 5686 Planarity : 0.003 0.055 6413 Dihedral : 4.614 88.363 4938 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.76 % Allowed : 13.71 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % 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: 2.76 (0.13), residues: 4463 helix: 2.72 (0.10), residues: 2689 sheet: 0.08 (0.28), residues: 317 loop : 0.61 (0.17), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B3727 TYR 0.012 0.001 TYR B3901 PHE 0.019 0.001 PHE B 703 TRP 0.013 0.001 TRP B4928 HIS 0.004 0.001 HIS B2822 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (37250) covalent geometry : angle 0.47795 / 0.24 (50366) hydrogen bonds : bond 0.03431 / 2.31 ( 2126) hydrogen bonds : angle 3.80351 / 2.74 ( 6156) metal coordination : bond 0.00304 / 0.15 ( 8) metal coordination : angle 1.16445 / 0.63 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 175 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 547 LYS cc_start: 0.8629 (tptt) cc_final: 0.8302 (tptt) REVERT: B 667 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8976 (mt) REVERT: B 864 LYS cc_start: 0.8770 (tppt) cc_final: 0.8413 (tppt) REVERT: B 874 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8924 (tt) REVERT: B 902 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7719 (ptt-90) REVERT: B 1288 CYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8738 (m) REVERT: B 1723 MET cc_start: 0.8569 (mmt) cc_final: 0.8033 (mmt) REVERT: B 1934 ARG cc_start: 0.8914 (mtm110) cc_final: 0.8694 (ptt-90) REVERT: B 2082 PHE cc_start: 0.7942 (m-80) cc_final: 0.7631 (m-80) REVERT: B 2115 MET cc_start: 0.9240 (ttp) cc_final: 0.9019 (ttp) REVERT: B 2292 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7370 (m-30) REVERT: B 2307 MET cc_start: 0.8784 (ptp) cc_final: 0.8410 (ptm) REVERT: B 2369 MET cc_start: 0.8882 (tpp) cc_final: 0.8418 (tpt) REVERT: B 2462 ILE cc_start: 0.9322 (OUTLIER) cc_final: 0.9060 (mm) REVERT: B 2658 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8686 (mp) REVERT: B 3072 TYR cc_start: 0.7890 (OUTLIER) cc_final: 0.7364 (p90) REVERT: B 3299 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8937 (tp) REVERT: B 3410 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8462 (ttm) REVERT: B 3727 ARG cc_start: 0.8535 (mmm160) cc_final: 0.8134 (tpm170) REVERT: B 3772 ARG cc_start: 0.8963 (ttp-110) cc_final: 0.8720 (ttp-110) REVERT: B 3863 ILE cc_start: 0.9386 (OUTLIER) cc_final: 0.9081 (tt) REVERT: B 4257 ARG cc_start: 0.7973 (ptp-170) cc_final: 0.7633 (ptt-90) REVERT: B 4262 GLN cc_start: 0.8963 (tm-30) cc_final: 0.8733 (tm-30) REVERT: B 4328 LEU cc_start: 0.8840 (mt) cc_final: 0.8506 (tt) REVERT: B 4537 MET cc_start: 0.8948 (mtm) cc_final: 0.8741 (mtm) REVERT: B 4935 MET cc_start: 0.8787 (mmm) cc_final: 0.8449 (mmm) REVERT: B 5128 MET cc_start: 0.8967 (mmm) cc_final: 0.8622 (mmm) outliers start: 72 outliers final: 50 residues processed: 236 average time/residue: 0.2594 time to fit residues: 99.4669 Evaluate side-chains 232 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 171 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 586 CYS Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 612 LYS Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 902 ARG Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1064 SER Chi-restraints excluded: chain B residue 1085 LEU Chi-restraints excluded: chain B residue 1181 TYR Chi-restraints excluded: chain B residue 1237 VAL Chi-restraints excluded: chain B residue 1288 CYS Chi-restraints excluded: chain B residue 1317 SER Chi-restraints excluded: chain B residue 1337 VAL Chi-restraints excluded: chain B residue 1540 LEU Chi-restraints excluded: chain B residue 1558 MET Chi-restraints excluded: chain B residue 1602 THR Chi-restraints excluded: chain B residue 1676 SER Chi-restraints excluded: chain B residue 1737 MET Chi-restraints excluded: chain B residue 1846 SER Chi-restraints excluded: chain B residue 1936 LEU Chi-restraints excluded: chain B residue 2005 LEU Chi-restraints excluded: chain B residue 2039 GLN Chi-restraints excluded: chain B residue 2143 THR Chi-restraints excluded: chain B residue 2267 VAL Chi-restraints excluded: chain B residue 2276 MET Chi-restraints excluded: chain B residue 2292 ASP Chi-restraints excluded: chain B residue 2434 SER Chi-restraints excluded: chain B residue 2462 ILE Chi-restraints excluded: chain B residue 2468 VAL Chi-restraints excluded: chain B residue 2509 SER Chi-restraints excluded: chain B residue 2569 ASN Chi-restraints excluded: chain B residue 2658 LEU Chi-restraints excluded: chain B residue 2775 THR Chi-restraints excluded: chain B residue 2807 VAL Chi-restraints excluded: chain B residue 3044 ARG Chi-restraints excluded: chain B residue 3072 TYR Chi-restraints excluded: chain B residue 3099 CYS Chi-restraints excluded: chain B residue 3259 LEU Chi-restraints excluded: chain B residue 3262 HIS Chi-restraints excluded: chain B residue 3268 HIS Chi-restraints excluded: chain B residue 3299 LEU Chi-restraints excluded: chain B residue 3316 SER Chi-restraints excluded: chain B residue 3371 VAL Chi-restraints excluded: chain B residue 3410 MET Chi-restraints excluded: chain B residue 3841 THR Chi-restraints excluded: chain B residue 3863 ILE Chi-restraints excluded: chain B residue 3925 MET Chi-restraints excluded: chain B residue 3942 PHE Chi-restraints excluded: chain B residue 4001 HIS Chi-restraints excluded: chain B residue 4171 SER Chi-restraints excluded: chain B residue 4195 LEU Chi-restraints excluded: chain B residue 4548 LEU Chi-restraints excluded: chain B residue 4576 LYS Chi-restraints excluded: chain B residue 4683 ILE Chi-restraints excluded: chain B residue 4789 ASN Chi-restraints excluded: chain B residue 5107 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: [392, 41, 70, 306, 406, 421, 139, 239, 195, 158, 122] chunk 392 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 306 optimal weight: 1.9990 chunk 406 optimal weight: 3.9990 chunk 421 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 239 optimal weight: 0.8980 chunk 195 optimal weight: 8.9990 chunk 158 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B4094 HIS ** B4242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.042947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.035463 restraints weight = 190240.343| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.90 r_work: 0.2749 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 37258 Z= 0.132 Angle : 0.479 12.238 50372 Z= 0.240 Chirality : 0.038 0.159 5686 Planarity : 0.003 0.055 6413 Dihedral : 4.594 87.083 4938 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.69 % Allowed : 13.78 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % 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: 2.78 (0.13), residues: 4463 helix: 2.73 (0.10), residues: 2688 sheet: 0.09 (0.28), residues: 317 loop : 0.63 (0.18), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B3727 TYR 0.013 0.001 TYR B 900 PHE 0.019 0.001 PHE B 703 TRP 0.013 0.001 TRP B4928 HIS 0.004 0.001 HIS B2822 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (37250) covalent geometry : angle 0.47936 / 0.24 (50366) hydrogen bonds : bond 0.03395 / 2.28 ( 2126) hydrogen bonds : angle 3.78471 / 2.73 ( 6156) metal coordination : bond 0.00310 / 0.15 ( 8) metal coordination : angle 1.12045 / 0.60 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 174 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 359 HIS cc_start: 0.8247 (OUTLIER) cc_final: 0.7813 (t70) REVERT: B 547 LYS cc_start: 0.8626 (tptt) cc_final: 0.8308 (tptt) REVERT: B 667 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8976 (mt) REVERT: B 864 LYS cc_start: 0.8787 (tppt) cc_final: 0.8457 (tppt) REVERT: B 874 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8917 (tt) REVERT: B 902 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7727 (ptt-90) REVERT: B 1288 CYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8731 (m) REVERT: B 1723 MET cc_start: 0.8599 (mmt) cc_final: 0.8235 (mmt) REVERT: B 1934 ARG cc_start: 0.8918 (mtm110) cc_final: 0.8710 (ptt-90) REVERT: B 2082 PHE cc_start: 0.7950 (m-80) cc_final: 0.7651 (m-80) REVERT: B 2115 MET cc_start: 0.9203 (ttp) cc_final: 0.8967 (ttp) REVERT: B 2292 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7360 (m-30) REVERT: B 2307 MET cc_start: 0.8781 (ptp) cc_final: 0.8397 (ptm) REVERT: B 2369 MET cc_start: 0.8867 (tpp) cc_final: 0.8418 (tpt) REVERT: B 2462 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.9057 (mm) REVERT: B 2658 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8688 (mp) REVERT: B 3072 TYR cc_start: 0.7876 (OUTLIER) cc_final: 0.7360 (p90) REVERT: B 3299 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8953 (tp) REVERT: B 3410 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8452 (ttm) REVERT: B 3727 ARG cc_start: 0.8521 (mmm160) cc_final: 0.8111 (tpm170) REVERT: B 3772 ARG cc_start: 0.8959 (ttp-110) cc_final: 0.8706 (ttp-110) REVERT: B 3863 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.9095 (tt) REVERT: B 3974 TRP cc_start: 0.7567 (t-100) cc_final: 0.7326 (t-100) REVERT: B 4257 ARG cc_start: 0.7963 (ptp-170) cc_final: 0.7622 (ptt-90) REVERT: B 4262 GLN cc_start: 0.8957 (tm-30) cc_final: 0.8727 (tm-30) REVERT: B 4328 LEU cc_start: 0.8830 (mt) cc_final: 0.8497 (tt) REVERT: B 4537 MET cc_start: 0.8944 (mtm) cc_final: 0.8735 (mtm) REVERT: B 4935 MET cc_start: 0.8794 (mmm) cc_final: 0.8451 (mmm) REVERT: B 5079 MET cc_start: 0.9287 (ttm) cc_final: 0.9014 (ttp) REVERT: B 5107 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8474 (mpp) REVERT: B 5128 MET cc_start: 0.8958 (mmm) cc_final: 0.8553 (mmm) outliers start: 69 outliers final: 51 residues processed: 233 average time/residue: 0.2488 time to fit residues: 94.5452 Evaluate side-chains 237 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 173 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 359 HIS Chi-restraints excluded: chain B residue 586 CYS Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 612 LYS Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 902 ARG Chi-restraints excluded: chain B residue 906 SER Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1064 SER Chi-restraints excluded: chain B residue 1085 LEU Chi-restraints excluded: chain B residue 1181 TYR Chi-restraints excluded: chain B residue 1237 VAL Chi-restraints excluded: chain B residue 1288 CYS Chi-restraints excluded: chain B residue 1317 SER Chi-restraints excluded: chain B residue 1337 VAL Chi-restraints excluded: chain B residue 1540 LEU Chi-restraints excluded: chain B residue 1558 MET Chi-restraints excluded: chain B residue 1602 THR Chi-restraints excluded: chain B residue 1676 SER Chi-restraints excluded: chain B residue 1737 MET Chi-restraints excluded: chain B residue 1846 SER Chi-restraints excluded: chain B residue 1936 LEU Chi-restraints excluded: chain B residue 2005 LEU Chi-restraints excluded: chain B residue 2039 GLN Chi-restraints excluded: chain B residue 2143 THR Chi-restraints excluded: chain B residue 2267 VAL Chi-restraints excluded: chain B residue 2276 MET Chi-restraints excluded: chain B residue 2292 ASP Chi-restraints excluded: chain B residue 2317 LEU Chi-restraints excluded: chain B residue 2434 SER Chi-restraints excluded: chain B residue 2462 ILE Chi-restraints excluded: chain B residue 2468 VAL Chi-restraints excluded: chain B residue 2509 SER Chi-restraints excluded: chain B residue 2569 ASN Chi-restraints excluded: chain B residue 2650 ILE Chi-restraints excluded: chain B residue 2658 LEU Chi-restraints excluded: chain B residue 2775 THR Chi-restraints excluded: chain B residue 2807 VAL Chi-restraints excluded: chain B residue 3044 ARG Chi-restraints excluded: chain B residue 3072 TYR Chi-restraints excluded: chain B residue 3259 LEU Chi-restraints excluded: chain B residue 3262 HIS Chi-restraints excluded: chain B residue 3299 LEU Chi-restraints excluded: chain B residue 3316 SER Chi-restraints excluded: chain B residue 3371 VAL Chi-restraints excluded: chain B residue 3410 MET Chi-restraints excluded: chain B residue 3722 MET Chi-restraints excluded: chain B residue 3841 THR Chi-restraints excluded: chain B residue 3863 ILE Chi-restraints excluded: chain B residue 3925 MET Chi-restraints excluded: chain B residue 3942 PHE Chi-restraints excluded: chain B residue 4001 HIS Chi-restraints excluded: chain B residue 4171 SER Chi-restraints excluded: chain B residue 4195 LEU Chi-restraints excluded: chain B residue 4548 LEU Chi-restraints excluded: chain B residue 4576 LYS Chi-restraints excluded: chain B residue 4676 SER Chi-restraints excluded: chain B residue 4683 ILE Chi-restraints excluded: chain B residue 5107 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: [145, 264, 363, 104, 3, 450, 253, 218, 94, 60, 26] chunk 145 optimal weight: 3.9990 chunk 264 optimal weight: 0.9990 chunk 363 optimal weight: 8.9990 chunk 104 optimal weight: 0.9980 chunk 3 optimal weight: 0.0070 chunk 450 optimal weight: 3.9990 chunk 253 optimal weight: 1.9990 chunk 218 optimal weight: 7.9990 chunk 94 optimal weight: 0.0060 chunk 60 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 overall best weight: 0.5816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B4094 HIS ** B4242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4879 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.043558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.036084 restraints weight = 188765.567| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.91 r_work: 0.2770 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 37258 Z= 0.097 Angle : 0.470 11.853 50372 Z= 0.234 Chirality : 0.037 0.152 5686 Planarity : 0.003 0.054 6413 Dihedral : 4.485 81.443 4936 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.32 % Allowed : 14.24 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % 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: 2.86 (0.13), residues: 4463 helix: 2.79 (0.10), residues: 2683 sheet: 0.18 (0.28), residues: 316 loop : 0.67 (0.18), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B4379 TYR 0.012 0.001 TYR B1750 PHE 0.021 0.001 PHE B 703 TRP 0.013 0.001 TRP B4928 HIS 0.004 0.000 HIS B2822 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (37250) covalent geometry : angle 0.46962 / 0.23 (50366) hydrogen bonds : bond 0.03186 / 2.13 ( 2126) hydrogen bonds : angle 3.70958 / 2.67 ( 6156) metal coordination : bond 0.00332 / 0.14 ( 8) metal coordination : angle 1.00405 / 0.53 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 173 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 359 HIS cc_start: 0.8254 (OUTLIER) cc_final: 0.7815 (t-90) REVERT: B 547 LYS cc_start: 0.8624 (tptt) cc_final: 0.8281 (tptt) REVERT: B 667 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8963 (mt) REVERT: B 864 LYS cc_start: 0.8767 (tppt) cc_final: 0.8444 (tppt) REVERT: B 874 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8928 (tt) REVERT: B 902 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7526 (ptt-90) REVERT: B 1288 CYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8715 (m) REVERT: B 1723 MET cc_start: 0.8595 (mmt) cc_final: 0.8266 (mmt) REVERT: B 1741 GLN cc_start: 0.9085 (tm-30) cc_final: 0.8663 (pp30) REVERT: B 2082 PHE cc_start: 0.7935 (m-80) cc_final: 0.7654 (m-80) REVERT: B 2115 MET cc_start: 0.9176 (ttp) cc_final: 0.8975 (ttp) REVERT: B 2292 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7347 (m-30) REVERT: B 2307 MET cc_start: 0.8778 (ptp) cc_final: 0.8397 (ptm) REVERT: B 2369 MET cc_start: 0.8804 (tpp) cc_final: 0.8308 (tpt) REVERT: B 2658 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8655 (mp) REVERT: B 2855 MET cc_start: 0.8453 (ptp) cc_final: 0.8194 (ptt) REVERT: B 3072 TYR cc_start: 0.7835 (OUTLIER) cc_final: 0.7339 (p90) REVERT: B 3410 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8527 (ttm) REVERT: B 3727 ARG cc_start: 0.8536 (mmm160) cc_final: 0.8082 (tpm170) REVERT: B 3772 ARG cc_start: 0.8952 (ttp-110) cc_final: 0.8713 (ttp-110) REVERT: B 3863 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.9092 (tt) REVERT: B 3974 TRP cc_start: 0.7600 (t-100) cc_final: 0.7369 (t-100) REVERT: B 4257 ARG cc_start: 0.7951 (ptp-170) cc_final: 0.7632 (ptt-90) REVERT: B 4537 MET cc_start: 0.8913 (mtm) cc_final: 0.8703 (mtm) REVERT: B 4935 MET cc_start: 0.8789 (mmm) cc_final: 0.8447 (mmm) REVERT: B 4987 MET cc_start: 0.9026 (ttt) cc_final: 0.8732 (ttp) REVERT: B 5079 MET cc_start: 0.9241 (ttm) cc_final: 0.8934 (ttm) REVERT: B 5107 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8473 (mpp) REVERT: B 5128 MET cc_start: 0.8966 (mmm) cc_final: 0.8597 (mmm) outliers start: 54 outliers final: 39 residues processed: 219 average time/residue: 0.2430 time to fit residues: 86.6012 Evaluate side-chains 221 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 171 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 359 HIS Chi-restraints excluded: chain B residue 586 CYS Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 902 ARG Chi-restraints excluded: chain B residue 906 SER Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1064 SER Chi-restraints excluded: chain B residue 1181 TYR Chi-restraints excluded: chain B residue 1237 VAL Chi-restraints excluded: chain B residue 1288 CYS Chi-restraints excluded: chain B residue 1317 SER Chi-restraints excluded: chain B residue 1337 VAL Chi-restraints excluded: chain B residue 1540 LEU Chi-restraints excluded: chain B residue 1558 MET Chi-restraints excluded: chain B residue 1602 THR Chi-restraints excluded: chain B residue 1676 SER Chi-restraints excluded: chain B residue 1737 MET Chi-restraints excluded: chain B residue 2005 LEU Chi-restraints excluded: chain B residue 2143 THR Chi-restraints excluded: chain B residue 2267 VAL Chi-restraints excluded: chain B residue 2276 MET Chi-restraints excluded: chain B residue 2292 ASP Chi-restraints excluded: chain B residue 2434 SER Chi-restraints excluded: chain B residue 2468 VAL Chi-restraints excluded: chain B residue 2509 SER Chi-restraints excluded: chain B residue 2569 ASN Chi-restraints excluded: chain B residue 2650 ILE Chi-restraints excluded: chain B residue 2658 LEU Chi-restraints excluded: chain B residue 2807 VAL Chi-restraints excluded: chain B residue 3072 TYR Chi-restraints excluded: chain B residue 3259 LEU Chi-restraints excluded: chain B residue 3262 HIS Chi-restraints excluded: chain B residue 3316 SER Chi-restraints excluded: chain B residue 3371 VAL Chi-restraints excluded: chain B residue 3410 MET Chi-restraints excluded: chain B residue 3722 MET Chi-restraints excluded: chain B residue 3863 ILE Chi-restraints excluded: chain B residue 3942 PHE Chi-restraints excluded: chain B residue 4001 HIS Chi-restraints excluded: chain B residue 4171 SER Chi-restraints excluded: chain B residue 4195 LEU Chi-restraints excluded: chain B residue 4548 LEU Chi-restraints excluded: chain B residue 4683 ILE Chi-restraints excluded: chain B residue 5107 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: [78, 184, 338, 68, 141, 386, 431, 442, 112, 308, 165] chunk 78 optimal weight: 7.9990 chunk 184 optimal weight: 1.9990 chunk 338 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 chunk 386 optimal weight: 2.9990 chunk 431 optimal weight: 0.7980 chunk 442 optimal weight: 4.9990 chunk 112 optimal weight: 0.0970 chunk 308 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1757 HIS B4094 HIS ** B4242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.043264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.035795 restraints weight = 188741.865| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.90 r_work: 0.2764 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 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 0.037 37258 Z= 0.110 Angle : 0.469 12.014 50372 Z= 0.233 Chirality : 0.037 0.155 5686 Planarity : 0.003 0.055 6413 Dihedral : 4.396 82.106 4933 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.35 % Allowed : 14.22 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % 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: 2.89 (0.13), residues: 4463 helix: 2.80 (0.10), residues: 2688 sheet: 0.21 (0.28), residues: 316 loop : 0.68 (0.18), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B3727 TYR 0.015 0.001 TYR B 900 PHE 0.019 0.001 PHE B3948 TRP 0.012 0.001 TRP B4928 HIS 0.004 0.000 HIS B2822 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (37250) covalent geometry : angle 0.46938 / 0.23 (50366) hydrogen bonds : bond 0.03204 / 2.15 ( 2126) hydrogen bonds : angle 3.70071 / 2.67 ( 6156) metal coordination : bond 0.00336 / 0.15 ( 8) metal coordination : angle 0.92405 / 0.49 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7510.24 seconds wall clock time: 129 minutes 57.95 seconds (7797.95 seconds total)