Starting phenix.real_space_refine on Fri Oct 30 18:02:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/33hm_59444/10_2026/33hm_59444.cif Found real_map, /net/cci-nas-00/data/ceres_data/33hm_59444/10_2026/33hm_59444.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 { model { file = "/net/cci-nas-00/data/ceres_data/33hm_59444/10_2026/33hm_59444.cif" } default_model = "/net/cci-nas-00/data/ceres_data/33hm_59444/10_2026/33hm_59444.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/33hm_59444/10_2026/33hm_59444.map" default_real_map = "/net/cci-nas-00/data/ceres_data/33hm_59444/10_2026/33hm_59444.map" } 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 23262 2.51 5 N 6271 2.21 5 O 6727 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.16s 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: 36490 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 36457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4532, 36457 Classifications: {'peptide': 4532} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 180, 'TRANS': 4348} 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 31195 SG CYS B4451 69.836 67.390 90.183 1.00226.39 S ATOM 31259 SG CYS B4471 72.927 69.400 89.075 1.00214.37 S ATOM 31281 SG CYS B4474 71.607 69.766 92.638 1.00221.24 S ATOM 27566 SG CYS B3962 88.970 14.877 27.973 1.00188.27 S ATOM 27694 SG CYS B3982 86.940 17.069 25.553 1.00186.88 S ATOM 27719 SG CYS B3985 90.393 15.753 24.523 1.00202.40 S Time building chain proxies: 7.25, per 1000 atoms: 0.20 Number of scatterers: 36490 At special positions: 0 Unit cell: (131.442, 169.463, 247.676, 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 6727 8.00 N 6271 7.00 C 23262 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: 3.10 Conformation dependent library (CDL) restraints added in 1.6 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 B4474 " pdb="ZN ZN B5302 " - pdb=" SG CYS B4471 " 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 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8682 Finding SS restraints... Secondary structure from input PDB file: 248 helices and 26 sheets defined 67.2% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'B' and resid 375 through 378 removed outlier: 3.632A pdb=" N GLY B 378 " --> pdb=" O GLU B 375 " (cutoff:3.500A) No H-bonds generated for '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 489 through 512 Processing helix chain 'B' and resid 517 through 536 Processing helix chain 'B' and resid 549 through 552 Processing helix chain 'B' and resid 554 through 571 Processing helix chain 'B' and resid 572 through 576 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 636 Processing helix chain 'B' and resid 637 through 640 removed outlier: 3.992A pdb=" N ARG B 640 " --> pdb=" O PRO B 637 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 637 through 640' Processing helix chain 'B' and resid 641 through 659 removed outlier: 3.641A pdb=" N TRP B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 674 removed outlier: 3.512A pdb=" N ILE B 667 " --> pdb=" O ARG B 663 " (cutoff:3.500A) Proline residue: B 669 - end of helix removed outlier: 3.510A pdb=" N CYS B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 684 removed outlier: 3.647A pdb=" N SER B 684 " --> pdb=" O LYS B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 694 Processing helix chain 'B' and resid 700 through 705 removed outlier: 3.924A pdb=" N ASP B 705 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 720 removed outlier: 3.538A 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: 4.420A pdb=" N PHE B 731 " --> pdb=" O ASP B 727 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ARG B 732 " --> pdb=" O GLU B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 750 removed outlier: 4.429A pdb=" N SER B 744 " --> pdb=" O LEU B 740 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N SER B 745 " --> pdb=" O GLU B 741 " (cutoff:3.500A) 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: 3.600A 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: 3.986A 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: 3.580A 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: 4.444A pdb=" N ARG B1035 " --> pdb=" O TRP B1031 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN B1036 " --> pdb=" O PRO B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1051 removed outlier: 3.881A pdb=" N ILE B1051 " --> pdb=" O ILE B1048 " (cutoff:3.500A) 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: 3.617A 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 removed outlier: 3.814A pdb=" N CYS B1245 " --> pdb=" O LEU B1241 " (cutoff:3.500A) Processing helix chain 'B' and resid 1262 through 1270 Processing helix chain 'B' and resid 1271 through 1274 removed outlier: 3.772A 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 1295 through 1330 removed outlier: 4.094A pdb=" N ILE B1299 " --> pdb=" O GLN B1295 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER B1300 " --> pdb=" O LYS B1296 " (cutoff:3.500A) removed outlier: 3.752A 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: 3.610A pdb=" N LEU B1342 " --> pdb=" O LEU B1338 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLU B1349 " --> pdb=" O ALA B1345 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ASP B1350 " --> pdb=" O ASP B1346 " (cutoff:3.500A) Processing helix chain 'B' and resid 1361 through 1370 removed outlier: 4.467A pdb=" N LYS B1365 " --> pdb=" O PRO B1361 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ALA B1366 " --> pdb=" O GLN B1362 " (cutoff:3.500A) Processing helix chain 'B' and resid 1374 through 1387 Processing helix chain 'B' and resid 1387 through 1398 removed outlier: 3.765A pdb=" N VAL B1391 " --> pdb=" O GLN B1387 " (cutoff:3.500A) Processing helix chain 'B' and resid 1402 through 1415 removed outlier: 4.491A pdb=" N VAL B1406 " --> pdb=" O ASN B1402 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE B1413 " --> pdb=" O ASP B1409 " (cutoff:3.500A) Processing helix chain 'B' and resid 1418 through 1440 removed outlier: 4.268A pdb=" N VAL B1425 " --> pdb=" O ASP B1421 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA B1426 " --> pdb=" O VAL B1422 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N SER B1437 " --> pdb=" O GLN B1433 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N LEU B1438 " --> pdb=" O GLY B1434 " (cutoff:3.500A) Processing helix chain 'B' and resid 1447 through 1465 removed outlier: 3.535A 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 1485 removed outlier: 3.532A pdb=" N THR B1484 " --> pdb=" O GLU B1480 " (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 1593 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: 3.963A 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 Processing helix chain 'B' and resid 1712 through 1733 Proline residue: B1727 - end of helix removed outlier: 3.653A pdb=" N GLU B1733 " --> pdb=" O GLN B1729 " (cutoff:3.500A) Processing helix chain 'B' and resid 1735 through 1750 Processing helix chain 'B' and resid 1750 through 1755 removed outlier: 3.856A pdb=" N PHE B1754 " --> pdb=" O TYR B1750 " (cutoff:3.500A) Processing helix chain 'B' and resid 1760 through 1776 removed outlier: 4.227A 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 1811 Processing helix chain 'B' and resid 1832 through 1845 removed outlier: 3.569A 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 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 1941 removed outlier: 3.667A pdb=" N THR B1940 " --> pdb=" O SER B1937 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL B1941 " --> pdb=" O ALA B1938 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1937 through 1941' Processing helix chain 'B' and resid 1959 through 1976 Processing helix chain 'B' and resid 1993 through 2002 removed outlier: 3.742A 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 removed outlier: 3.503A pdb=" N LYS B2011 " --> pdb=" O GLU B2007 " (cutoff:3.500A) 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: 3.774A 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: 4.110A pdb=" N ASP B2222 " --> pdb=" O LEU B2218 " (cutoff:3.500A) removed outlier: 3.753A 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: 3.737A pdb=" N THR B2453 " --> pdb=" O ALA B2450 " (cutoff:3.500A) removed outlier: 5.971A 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: 3.836A 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 2538 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: 3.898A 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: 3.855A 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: 3.864A 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 2736 through 2747 Processing helix chain 'B' and resid 2748 through 2752 Processing helix chain 'B' and resid 2754 through 2759 removed outlier: 3.725A pdb=" N CYS B2759 " --> pdb=" O GLU B2755 " (cutoff:3.500A) Processing helix chain 'B' and resid 2775 through 2791 removed outlier: 3.505A pdb=" N ILE B2779 " --> pdb=" O THR B2775 " (cutoff:3.500A) Processing helix chain 'B' and resid 2806 through 2811 removed outlier: 3.918A pdb=" N ALA B2810 " --> pdb=" O GLU B2806 " (cutoff:3.500A) removed outlier: 3.529A 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 Processing helix chain 'B' and resid 2820 through 2828 Processing helix chain 'B' and resid 2835 through 2839 Processing helix chain 'B' and resid 2852 through 2856 removed outlier: 3.551A 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 2883 through 2890 Processing helix chain 'B' and resid 2892 through 2907 Processing helix chain 'B' and resid 2913 through 2932 Processing helix chain 'B' and resid 2936 through 2948 Processing helix chain 'B' and resid 2955 through 2963 removed outlier: 4.183A 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 3018 Processing helix chain 'B' and resid 3037 through 3056 Processing helix chain 'B' and resid 3063 through 3077 removed outlier: 3.636A pdb=" N LEU B3067 " --> pdb=" O ASN B3063 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLU B3069 " --> pdb=" O GLN B3065 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N SER B3070 " --> pdb=" O ASN B3066 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ASP B3073 " --> pdb=" O GLU B3069 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ALA B3074 " --> pdb=" O SER B3070 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN B3076 " --> pdb=" O TYR B3072 " (cutoff:3.500A) removed outlier: 3.798A 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: 3.853A 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: 3.546A pdb=" N SER B3187 " --> pdb=" O ASP B3183 " (cutoff:3.500A) removed outlier: 3.599A 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: 4.178A 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 3313 through 3327 Processing helix chain 'B' and resid 3345 through 3365 removed outlier: 3.751A pdb=" N LEU B3349 " --> pdb=" O ARG B3345 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ALA B3351 " --> pdb=" O ALA B3347 " (cutoff:3.500A) removed outlier: 4.632A 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: 3.860A pdb=" N LEU B3417 " --> pdb=" O ASP B3413 " (cutoff:3.500A) Processing helix chain 'B' and resid 3421 through 3426 removed outlier: 3.975A pdb=" N PHE B3426 " --> pdb=" O ILE B3422 " (cutoff:3.500A) Processing helix chain 'B' and resid 3470 through 3475 Processing helix chain 'B' and resid 3476 through 3491 removed outlier: 4.293A pdb=" N GLN B3486 " --> pdb=" O GLN B3482 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLY B3487 " --> pdb=" O SER B3483 " (cutoff:3.500A) Processing helix chain 'B' and resid 3496 through 3500 removed outlier: 3.780A pdb=" N ALA B3500 " --> pdb=" O GLU B3497 " (cutoff:3.500A) Processing helix chain 'B' and resid 3501 through 3513 Processing helix chain 'B' and resid 3517 through 3541 removed outlier: 4.167A 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 3556 Processing helix chain 'B' and resid 3556 through 3564 Processing helix chain 'B' and resid 3565 through 3589 Proline residue: B3580 - end of helix Processing helix chain 'B' and resid 3590 through 3592 No H-bonds generated for 'chain 'B' and resid 3590 through 3592' Processing helix chain 'B' and resid 3593 through 3600 removed outlier: 4.202A pdb=" N LEU B3597 " --> pdb=" O GLY B3593 " (cutoff:3.500A) removed outlier: 4.140A 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 3677 through 3679 No H-bonds generated for 'chain 'B' and resid 3677 through 3679' 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: 3.825A pdb=" N SER B3748 " --> pdb=" O LEU B3744 " (cutoff:3.500A) Processing helix chain 'B' and resid 3761 through 3771 removed outlier: 4.015A 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 3793 removed outlier: 3.797A pdb=" N SER B3791 " --> pdb=" O GLN B3787 " (cutoff:3.500A) Processing helix chain 'B' and resid 3807 through 3823 Processing helix chain 'B' and resid 3828 through 3848 removed outlier: 4.231A pdb=" N THR B3841 " --> pdb=" O LYS B3837 " (cutoff:3.500A) Proline residue: B3842 - end of helix Processing helix chain 'B' and resid 3849 through 3853 removed outlier: 3.601A pdb=" N CYS B3853 " --> pdb=" O GLY B3850 " (cutoff:3.500A) 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: 3.519A pdb=" N SER B3903 " --> pdb=" O THR B3899 " (cutoff:3.500A) removed outlier: 3.727A 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 4046 Processing helix chain 'B' and resid 4082 through 4090 Processing helix chain 'B' and resid 4092 through 4111 removed outlier: 5.143A pdb=" N ASP B4098 " --> pdb=" O HIS B4094 " (cutoff:3.500A) removed outlier: 5.323A 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: 3.650A 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: 7.420A pdb=" N MET B4238 " --> pdb=" O SER B4234 " (cutoff:3.500A) removed outlier: 9.614A pdb=" N GLU B4239 " --> pdb=" O GLN B4235 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE B4240 " --> pdb=" O ARG B4236 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B4241 " --> pdb=" O GLY B4237 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE B4244 " --> pdb=" O PHE B4240 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER B4245 " --> pdb=" O VAL B4241 " (cutoff:3.500A) Processing helix chain 'B' and resid 4251 through 4255 removed outlier: 3.661A pdb=" N VAL B4254 " --> pdb=" O CYS B4251 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE B4255 " --> pdb=" O GLN B4252 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4251 through 4255' Processing helix chain 'B' and resid 4256 through 4263 removed outlier: 3.853A pdb=" N ILE B4260 " --> pdb=" O PRO B4256 " (cutoff:3.500A) removed outlier: 3.851A 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: 4.158A 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 4354 through 4357 Processing helix chain 'B' and resid 4358 through 4371 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: 3.844A 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 4633 Processing helix chain 'B' and resid 4634 through 4649 Proline residue: B4640 - end of helix Processing helix chain 'B' and resid 4655 through 4662 Processing helix chain 'B' and resid 4665 through 4669 removed outlier: 4.293A 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: 4.970A pdb=" N ARG B4784 " --> pdb=" O ASN B4780 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N SER B4785 " --> pdb=" O ALA B4781 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR B4788 " --> pdb=" O ARG B4784 " (cutoff:3.500A) Processing helix chain 'B' and resid 4797 through 4801 removed outlier: 4.472A pdb=" N SER B4801 " --> pdb=" O TYR B4798 " (cutoff:3.500A) Processing helix chain 'B' and resid 4808 through 4812 removed outlier: 3.542A pdb=" N ILE B4812 " --> pdb=" O PHE B4809 " (cutoff:3.500A) 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: 3.514A pdb=" N THR B4824 " --> pdb=" O GLY B4820 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR B4840 " --> pdb=" O ASN B4836 " (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 removed outlier: 3.551A pdb=" N ASN B4879 " --> pdb=" O LEU B4875 " (cutoff:3.500A) Processing helix chain 'B' and resid 4895 through 4908 Processing helix chain 'B' and resid 4929 through 4941 removed outlier: 3.780A 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: 3.548A pdb=" N GLY B4976 " --> pdb=" O GLU B4972 " (cutoff:3.500A) removed outlier: 3.739A 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 5011 through 5013 No H-bonds generated for 'chain 'B' and resid 5011 through 5013' 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: 3.731A pdb=" N ALA B5027 " --> pdb=" O GLN B5023 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER B5030 " --> pdb=" O SER B5026 " (cutoff:3.500A) Processing helix chain 'B' and resid 5045 through 5049 Processing helix chain 'B' and resid 5053 through 5067 removed outlier: 4.204A pdb=" N GLU B5066 " --> pdb=" O THR B5062 " (cutoff:3.500A) Processing helix chain 'B' and resid 5068 through 5084 Processing helix chain 'B' and resid 5098 through 5109 Processing helix chain 'B' and resid 5114 through 5122 removed outlier: 3.757A 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 389 through 393 removed outlier: 5.865A pdb=" N CYS B 390 " --> pdb=" O GLU B 402 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLU B 402 " --> pdb=" O CYS B 390 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN B 392 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N TRP B 464 " --> pdb=" O THR B 347 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR B 349 " --> pdb=" O TRP B 464 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLN B 466 " --> pdb=" O THR B 349 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N TYR B 351 " --> pdb=" O GLN B 466 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ASP B 468 " --> pdb=" O TYR B 351 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N HIS B 353 " --> pdb=" O ASP B 468 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE B 470 " --> pdb=" O HIS B 353 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ILE B 355 " --> pdb=" O ILE B 470 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 368 through 373 Processing sheet with id=AA3, first strand: chain 'B' and resid 368 through 373 removed outlier: 3.622A pdb=" N ASN B 449 " --> pdb=" O HIS B 541 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N CYS B 451 " --> pdb=" O MET B 539 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N MET B 539 " --> pdb=" O CYS B 451 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 894 through 895 Processing sheet with id=AA5, first strand: chain 'B' and resid 1149 through 1150 removed outlier: 7.055A pdb=" N GLN B1149 " --> pdb=" O VAL B1232 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 1173 through 1174 Processing sheet with id=AA7, first strand: chain 'B' and resid 1540 through 1543 removed outlier: 3.824A pdb=" N GLY B1612 " --> pdb=" O TYR B1606 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1794 through 1797 removed outlier: 6.354A pdb=" N ILE B1795 " --> pdb=" O CYS B1892 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1982 through 1987 removed outlier: 6.509A pdb=" N VAL B2014 " --> pdb=" O LEU B2056 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU B2058 " --> pdb=" O VAL B2014 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N PHE B2016 " --> pdb=" O LEU B2058 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLU B2060 " --> pdb=" O PHE B2016 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE B2018 " --> pdb=" O GLU B2060 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ILE B2020 " --> pdb=" O PRO B2062 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER B1953 " --> pdb=" O ILE B2061 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 2040 through 2042 Processing sheet with id=AB2, first strand: chain 'B' and resid 2266 through 2270 removed outlier: 3.614A pdb=" N THR B2275 " --> pdb=" O ASN B2270 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 2282 through 2285 removed outlier: 7.540A pdb=" N ALA B2293 " --> pdb=" O ASP B2305 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ASP B2305 " --> pdb=" O ALA B2293 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 2407 through 2411 removed outlier: 6.507A pdb=" N LYS B2408 " --> pdb=" O PHE B2446 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ASP B2448 " --> pdb=" O LYS B2408 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL B2410 " --> pdb=" O ASP B2448 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL B2377 " --> pdb=" O ALA B2483 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N CYS B2485 " --> pdb=" O VAL B2377 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE B2379 " --> pdb=" O CYS B2485 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 2467 through 2468 Processing sheet with id=AB6, first strand: chain 'B' and resid 2516 through 2517 removed outlier: 3.547A pdb=" N ILE B2520 " --> pdb=" O LEU B2517 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 2762 through 2769 removed outlier: 6.003A pdb=" N GLN B2762 " --> pdb=" O VAL B2799 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N VAL B2801 " --> pdb=" O GLN B2762 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N HIS B2764 " --> pdb=" O VAL B2801 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL B2803 " --> pdb=" O HIS B2764 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL B2766 " --> pdb=" O VAL B2803 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ASP B2805 " --> pdb=" O VAL B2766 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE B2768 " --> pdb=" O ASP B2805 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU B2726 " --> pdb=" O GLY B2844 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N SER B2846 " --> pdb=" O LEU B2726 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU B2728 " --> pdb=" O SER B2846 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE B2727 " --> pdb=" O VAL B2861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 3026 through 3028 removed outlier: 6.493A pdb=" N VAL B3059 " --> pdb=" O ILE B3108 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ILE B3110 " --> pdb=" O VAL B3059 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU B3061 " --> pdb=" O ILE B3110 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N GLU B3112 " --> pdb=" O LEU B3061 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU B3002 " --> pdb=" O VAL B3109 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N GLU B3111 " --> pdb=" O LEU B3002 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL B3004 " --> pdb=" O GLU B3111 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 3080 through 3081 removed outlier: 4.552A pdb=" N LYS B3086 " --> pdb=" O VAL B3101 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B3101 " --> pdb=" O LYS B3086 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 3304 through 3307 removed outlier: 6.706A pdb=" N LYS B3332 " --> pdb=" O PHE B3372 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N TYR B3374 " --> pdb=" O LYS B3332 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU B3334 " --> pdb=" O TYR B3374 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL B3376 " --> pdb=" O LEU B3334 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ILE B3336 " --> pdb=" O VAL B3376 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LYS B3378 " --> pdb=" O ILE B3336 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ALA B3338 " --> pdb=" O LYS B3378 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 3492 through 3494 removed outlier: 7.006A pdb=" N ARG B3493 " --> pdb=" O VAL B3641 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 3636 through 3637 removed outlier: 4.493A pdb=" N MET B3636 " --> pdb=" O TRP B4928 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 3957 through 3960 removed outlier: 3.929A pdb=" N HIS B3964 " --> pdb=" O LEU B3960 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 4047 through 4048 removed outlier: 3.926A pdb=" N HIS B4063 " --> pdb=" O VAL B4048 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 4079 through 4081 Processing sheet with id=AC7, first strand: chain 'B' and resid 4449 through 4450 Processing sheet with id=AC8, first strand: chain 'B' and resid 4852 through 4854 removed outlier: 6.700A pdb=" N VAL B4853 " --> pdb=" O THR B4915 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 2114 hydrogen bonds defined for protein. 6111 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: 13.85 Time building geometry restraints manager: 4.16 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: 11927 1.34 - 1.46: 7628 1.46 - 1.58: 17347 1.58 - 1.70: 2 1.70 - 1.82: 329 Bond restraints: 37233 Sorted by residual: bond pdb=" C ASP B3956 " pdb=" O ASP B3956 " ideal model delta sigma weight residual 1.233 1.241 -0.008 4.80e-03 4.34e+04 2.55e+00 bond pdb=" CA PRO B 942 " pdb=" C PRO B 942 " ideal model delta sigma weight residual 1.514 1.507 0.008 5.50e-03 3.31e+04 1.97e+00 bond pdb=" CA GLN B 410 " pdb=" C GLN B 410 " ideal model delta sigma weight residual 1.522 1.498 0.024 1.72e-02 3.38e+03 1.92e+00 bond pdb=" CB GLU B1620 " pdb=" CG GLU B1620 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.77e+00 bond pdb=" CB GLN B4509 " pdb=" CG GLN B4509 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.25e+00 ... (remaining 37228 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 49596 1.45 - 2.91: 528 2.91 - 4.36: 196 4.36 - 5.81: 16 5.81 - 7.27: 6 Bond angle restraints: 50342 Sorted by residual: angle pdb=" CB GLU B1620 " pdb=" CG GLU B1620 " pdb=" CD GLU B1620 " ideal model delta sigma weight residual 112.60 117.36 -4.76 1.70e+00 3.46e-01 7.84e+00 angle pdb=" CA LYS B3938 " pdb=" CB LYS B3938 " pdb=" CG LYS B3938 " ideal model delta sigma weight residual 114.10 119.64 -5.54 2.00e+00 2.50e-01 7.68e+00 angle pdb=" CB ARG B4257 " pdb=" CG ARG B4257 " pdb=" CD ARG B4257 " ideal model delta sigma weight residual 111.30 117.50 -6.20 2.30e+00 1.89e-01 7.28e+00 angle pdb=" CB MET B3503 " pdb=" CG MET B3503 " pdb=" SD MET B3503 " ideal model delta sigma weight residual 112.70 119.97 -7.27 3.00e+00 1.11e-01 5.87e+00 angle pdb=" CG MET B4935 " pdb=" SD MET B4935 " pdb=" CE MET B4935 " ideal model delta sigma weight residual 100.90 106.20 -5.30 2.20e+00 2.07e-01 5.80e+00 ... (remaining 50337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 19831 17.83 - 35.66: 2171 35.66 - 53.49: 541 53.49 - 71.31: 85 71.31 - 89.14: 30 Dihedral angle restraints: 22658 sinusoidal: 9341 harmonic: 13317 Sorted by residual: dihedral pdb=" CA ILE B4661 " pdb=" C ILE B4661 " pdb=" N TYR B4662 " pdb=" CA TYR B4662 " ideal model delta harmonic sigma weight residual -180.00 -161.05 -18.95 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA MET B2042 " pdb=" C MET B2042 " pdb=" N ASP B2043 " pdb=" CA ASP B2043 " ideal model delta harmonic sigma weight residual 180.00 162.70 17.30 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ILE B 918 " pdb=" C ILE B 918 " pdb=" N GLY B 919 " pdb=" CA GLY B 919 " ideal model delta harmonic sigma weight residual -180.00 -163.20 -16.80 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 22655 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 5086 0.057 - 0.114: 546 0.114 - 0.171: 50 0.171 - 0.228: 0 0.228 - 0.285: 3 Chirality restraints: 5685 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 -2.92 0.29 2.00e-01 2.50e+01 2.03e+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 -2.95 0.27 2.00e-01 2.50e+01 1.82e+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 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 5682 not shown) Planarity restraints: 6409 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 544 " -0.164 9.50e-02 1.11e+02 7.37e-02 3.77e+00 pdb=" NE ARG B 544 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG B 544 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 544 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 544 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B4165 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO B4166 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B4166 " -0.025 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 B2933 " -0.160 9.50e-02 1.11e+02 7.20e-02 3.55e+00 pdb=" NE ARG B2933 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG B2933 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG B2933 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B2933 " -0.002 2.00e-02 2.50e+03 ... (remaining 6406 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 6688 2.77 - 3.30: 37614 3.30 - 3.83: 60544 3.83 - 4.37: 74191 4.37 - 4.90: 124385 Nonbonded interactions: 303422 Sorted by model distance: nonbonded pdb=" O ASP B4370 " pdb=" OD1 ASP B4370 " model vdw 2.234 3.040 nonbonded pdb=" O ALA B4422 " pdb=" OD1 ASN B4423 " model vdw 2.300 3.040 nonbonded pdb=" O GLY B 378 " pdb=" OE1 GLN B 379 " model vdw 2.305 3.040 nonbonded pdb=" O2' ATP B5301 " pdb=" O3' ATP B5301 " model vdw 2.312 2.432 nonbonded pdb=" O ASP B1151 " pdb=" OD1 ASP B1151 " model vdw 2.347 3.040 ... (remaining 303417 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 44.240 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 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 0.044 37241 Z= 0.126 Angle : 0.455 7.265 50348 Z= 0.234 Chirality : 0.036 0.285 5685 Planarity : 0.004 0.074 6409 Dihedral : 15.704 89.142 13976 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.39 % Allowed : 15.65 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 1.80 (0.13), residues: 4462 helix: 1.97 (0.10), residues: 2648 sheet: -0.92 (0.29), residues: 284 loop : 0.36 (0.17), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 544 TYR 0.014 0.001 TYR B1750 PHE 0.011 0.001 PHE B 531 TRP 0.010 0.001 TRP B3870 HIS 0.004 0.001 HIS B1928 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (37233) covalent geometry : angle 0.45481 / 0.23 (50342) hydrogen bonds : bond 0.14773 / 9.67 ( 2108) hydrogen bonds : angle 5.88653 / 4.17 ( 6111) metal coordination : bond 0.00456 / 0.19 ( 8) metal coordination : angle 0.64077 / 0.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 4084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 272 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 368 LYS cc_start: 0.7642 (mmmt) cc_final: 0.7360 (mmtt) REVERT: B 388 MET cc_start: 0.7443 (mmm) cc_final: 0.6823 (mtp) REVERT: B 396 ASP cc_start: 0.7090 (p0) cc_final: 0.6680 (p0) REVERT: B 874 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8460 (tt) REVERT: B 1035 ARG cc_start: 0.8492 (ttp80) cc_final: 0.8135 (ttp80) REVERT: B 1183 ARG cc_start: 0.7915 (ptp-170) cc_final: 0.7651 (ptp-170) REVERT: B 1519 LYS cc_start: 0.8995 (mmmt) cc_final: 0.8763 (tptp) REVERT: B 1567 ASN cc_start: 0.8930 (m-40) cc_final: 0.8656 (m110) REVERT: B 1751 MET cc_start: 0.7945 (tmm) cc_final: 0.7457 (tmm) REVERT: B 2259 TRP cc_start: 0.8194 (m100) cc_final: 0.7924 (m100) REVERT: B 2495 MET cc_start: 0.8549 (tpp) cc_final: 0.8290 (tpp) REVERT: B 2747 MET cc_start: 0.8933 (mtt) cc_final: 0.8708 (mtm) REVERT: B 3072 TYR cc_start: 0.7764 (OUTLIER) cc_final: 0.7396 (p90) REVERT: B 3271 ARG cc_start: 0.8245 (mtp85) cc_final: 0.8025 (mmm-85) REVERT: B 3683 LYS cc_start: 0.8091 (mtmt) cc_final: 0.7820 (pttp) REVERT: B 4206 ARG cc_start: 0.8454 (ttp-110) cc_final: 0.8121 (ptp-170) REVERT: B 4262 GLN cc_start: 0.8330 (tm-30) cc_final: 0.8043 (pp30) REVERT: B 4348 LYS cc_start: 0.8796 (mmmt) cc_final: 0.8590 (mttt) REVERT: B 4532 LEU cc_start: 0.8826 (tt) cc_final: 0.8550 (mp) outliers start: 16 outliers final: 6 residues processed: 282 average time/residue: 0.2849 time to fit residues: 123.4696 Evaluate side-chains 263 residues out of total 4084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 255 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 541 HIS Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1420 ILE Chi-restraints excluded: chain B residue 2569 ASN Chi-restraints excluded: chain B residue 3072 TYR Chi-restraints excluded: chain B residue 3588 HIS 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: 6.9990 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.0770 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 0.9990 chunk 424 optimal weight: 1.9990 overall best weight: 0.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 809 ASN B1585 HIS B3671 GLN B3838 ASN ** B4001 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4534 HIS B4939 ASN B5121 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.073560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.061411 restraints weight = 114237.742| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.54 r_work: 0.3013 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 37241 Z= 0.165 Angle : 0.516 8.696 50348 Z= 0.267 Chirality : 0.040 0.153 5685 Planarity : 0.004 0.056 6409 Dihedral : 4.724 89.863 4934 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.71 % Allowed : 13.66 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 2.33 (0.13), residues: 4462 helix: 2.43 (0.10), residues: 2659 sheet: -0.59 (0.29), residues: 295 loop : 0.46 (0.17), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B3345 TYR 0.013 0.001 TYR B1810 PHE 0.015 0.001 PHE B3157 TRP 0.013 0.001 TRP B 926 HIS 0.006 0.001 HIS B 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (37233) covalent geometry : angle 0.51570 / 0.27 (50342) hydrogen bonds : bond 0.04415 / 2.91 ( 2108) hydrogen bonds : angle 4.30602 / 3.06 ( 6111) metal coordination : bond 0.00469 / 0.21 ( 8) metal coordination : angle 1.17225 / 0.67 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 4084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 282 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 368 LYS cc_start: 0.7652 (mmmt) cc_final: 0.7425 (mmtt) REVERT: B 388 MET cc_start: 0.7680 (mmm) cc_final: 0.6928 (mtp) REVERT: B 396 ASP cc_start: 0.7094 (p0) cc_final: 0.6795 (p0) REVERT: B 490 THR cc_start: 0.4846 (OUTLIER) cc_final: 0.3879 (p) REVERT: B 491 ARG cc_start: 0.5983 (OUTLIER) cc_final: 0.5279 (mmt180) REVERT: B 874 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8434 (tt) REVERT: B 1314 GLN cc_start: 0.7777 (pp30) cc_final: 0.7498 (pp30) REVERT: B 1519 LYS cc_start: 0.8946 (mmmt) cc_final: 0.8737 (tptp) REVERT: B 1567 ASN cc_start: 0.8770 (m-40) cc_final: 0.8390 (m110) REVERT: B 1751 MET cc_start: 0.7691 (tmm) cc_final: 0.7236 (tmm) REVERT: B 1752 SER cc_start: 0.8285 (OUTLIER) cc_final: 0.7981 (t) REVERT: B 1992 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8565 (tt) REVERT: B 2061 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8711 (tt) REVERT: B 2259 TRP cc_start: 0.8154 (m100) cc_final: 0.7946 (m100) REVERT: B 2495 MET cc_start: 0.8453 (tpp) cc_final: 0.8197 (tpp) REVERT: B 2585 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.8008 (mmt) REVERT: B 2747 MET cc_start: 0.8851 (mtt) cc_final: 0.8613 (mtm) REVERT: B 3072 TYR cc_start: 0.7571 (OUTLIER) cc_final: 0.7273 (p90) REVERT: B 3271 ARG cc_start: 0.8046 (mtp85) cc_final: 0.7820 (mmm-85) REVERT: B 3537 LYS cc_start: 0.9036 (ttmm) cc_final: 0.8825 (tptm) REVERT: B 3731 MET cc_start: 0.8605 (tpp) cc_final: 0.8390 (tpp) REVERT: B 3814 MET cc_start: 0.9041 (tpt) cc_final: 0.8612 (tpt) REVERT: B 3858 MET cc_start: 0.8175 (tpp) cc_final: 0.7886 (tpp) REVERT: B 3908 CYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8138 (p) REVERT: B 4129 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7835 (mt-10) REVERT: B 4291 VAL cc_start: 0.8768 (t) cc_final: 0.8566 (t) REVERT: B 4348 LYS cc_start: 0.8848 (mmmt) cc_final: 0.8551 (mttt) outliers start: 70 outliers final: 34 residues processed: 332 average time/residue: 0.2743 time to fit residues: 142.0890 Evaluate side-chains 302 residues out of total 4084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 258 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 541 HIS Chi-restraints excluded: chain B residue 556 LYS Chi-restraints excluded: chain B residue 560 THR 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 906 SER Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 1064 SER Chi-restraints excluded: chain B residue 1267 ASP Chi-restraints excluded: chain B residue 1313 HIS Chi-restraints excluded: chain B residue 1325 VAL Chi-restraints excluded: chain B residue 1326 ARG Chi-restraints excluded: chain B residue 1337 VAL Chi-restraints excluded: chain B residue 1342 LEU Chi-restraints excluded: chain B residue 1731 LEU Chi-restraints excluded: chain B residue 1752 SER Chi-restraints excluded: chain B residue 1951 VAL Chi-restraints excluded: chain B residue 1992 LEU Chi-restraints excluded: chain B residue 2061 ILE Chi-restraints excluded: chain B residue 2468 VAL Chi-restraints excluded: chain B residue 2569 ASN Chi-restraints excluded: chain B residue 2571 SER Chi-restraints excluded: chain B residue 2585 MET Chi-restraints excluded: chain B residue 2786 CYS Chi-restraints excluded: chain B residue 2924 VAL Chi-restraints excluded: chain B residue 3072 TYR Chi-restraints excluded: chain B residue 3265 MET Chi-restraints excluded: chain B residue 3485 VAL Chi-restraints excluded: chain B residue 3588 HIS Chi-restraints excluded: chain B residue 3703 VAL Chi-restraints excluded: chain B residue 3755 TYR Chi-restraints excluded: chain B residue 3833 LEU Chi-restraints excluded: chain B residue 3863 ILE Chi-restraints excluded: chain B residue 3891 ILE Chi-restraints excluded: chain B residue 3908 CYS Chi-restraints excluded: chain B residue 3924 VAL Chi-restraints excluded: chain B residue 4129 GLU Chi-restraints excluded: chain B residue 4131 SER Chi-restraints excluded: chain B residue 4378 ILE Chi-restraints excluded: chain B residue 4883 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: [441, 371, 337, 168, 184, 192, 143, 37, 298, 418, 76] chunk 441 optimal weight: 4.9990 chunk 371 optimal weight: 4.9990 chunk 337 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 298 optimal weight: 6.9990 chunk 418 optimal weight: 0.0010 chunk 76 optimal weight: 8.9990 overall best weight: 1.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1585 HIS B1793 ASN B3711 GLN B4001 HIS B4196 GLN ** B4242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4939 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.072735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.060596 restraints weight = 114523.940| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.55 r_work: 0.2989 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 37241 Z= 0.228 Angle : 0.537 11.178 50348 Z= 0.275 Chirality : 0.041 0.152 5685 Planarity : 0.004 0.068 6409 Dihedral : 4.756 87.292 4930 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.25 % Allowed : 14.03 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 4462 helix: 2.34 (0.10), residues: 2668 sheet: -0.48 (0.29), residues: 295 loop : 0.35 (0.17), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B3345 TYR 0.016 0.001 TYR B3901 PHE 0.017 0.002 PHE B3157 TRP 0.014 0.002 TRP B3153 HIS 0.007 0.001 HIS B 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.23 (37233) covalent geometry : angle 0.53651 / 0.27 (50342) hydrogen bonds : bond 0.04466 / 2.95 ( 2108) hydrogen bonds : angle 4.22104 / 3.00 ( 6111) metal coordination : bond 0.00514 / 0.24 ( 8) metal coordination : angle 0.83708 / 0.47 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 4084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 268 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 368 LYS cc_start: 0.7865 (mmmt) cc_final: 0.7649 (mmtt) REVERT: B 388 MET cc_start: 0.7947 (mmm) cc_final: 0.7076 (mtp) REVERT: B 396 ASP cc_start: 0.7115 (p0) cc_final: 0.6818 (p0) REVERT: B 410 GLN cc_start: 0.5691 (OUTLIER) cc_final: 0.3930 (mp10) REVERT: B 490 THR cc_start: 0.4811 (p) cc_final: 0.3999 (p) REVERT: B 491 ARG cc_start: 0.6191 (OUTLIER) cc_final: 0.5281 (mmt180) REVERT: B 874 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8494 (tt) REVERT: B 1267 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7887 (t0) REVERT: B 1519 LYS cc_start: 0.8965 (mmmt) cc_final: 0.8712 (tptp) REVERT: B 1567 ASN cc_start: 0.8736 (m-40) cc_final: 0.8342 (m110) REVERT: B 1724 LYS cc_start: 0.8523 (mmtm) cc_final: 0.8224 (mmtt) REVERT: B 1751 MET cc_start: 0.7848 (tmm) cc_final: 0.7288 (tmm) REVERT: B 1752 SER cc_start: 0.8381 (OUTLIER) cc_final: 0.8080 (t) REVERT: B 1992 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8542 (tt) REVERT: B 2495 MET cc_start: 0.8442 (tpp) cc_final: 0.8145 (tpp) REVERT: B 2553 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.9000 (tt) REVERT: B 2561 ARG cc_start: 0.8354 (mtt180) cc_final: 0.7931 (mtt90) REVERT: B 2585 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7971 (mmt) REVERT: B 2747 MET cc_start: 0.8863 (mtt) cc_final: 0.8604 (mtm) REVERT: B 3072 TYR cc_start: 0.7647 (OUTLIER) cc_final: 0.7291 (p90) REVERT: B 3271 ARG cc_start: 0.8061 (mtp85) cc_final: 0.7840 (mmm-85) REVERT: B 3537 LYS cc_start: 0.9047 (ttmm) cc_final: 0.8844 (tptm) REVERT: B 3636 MET cc_start: 0.8357 (ppp) cc_final: 0.7553 (ppp) REVERT: B 3714 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8970 (tt) REVERT: B 3814 MET cc_start: 0.9053 (tpt) cc_final: 0.8662 (tpt) REVERT: B 3858 MET cc_start: 0.8248 (tpp) cc_final: 0.7920 (tpp) REVERT: B 3908 CYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8177 (p) REVERT: B 3980 MET cc_start: 0.6373 (mpp) cc_final: 0.6155 (mpp) REVERT: B 4129 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7833 (mt-10) REVERT: B 4148 ARG cc_start: 0.8340 (ttp-110) cc_final: 0.8136 (ttp-110) REVERT: B 4206 ARG cc_start: 0.8314 (ttp-110) cc_final: 0.7775 (mtm110) REVERT: B 4348 LYS cc_start: 0.8939 (mmmt) cc_final: 0.8733 (mttt) REVERT: B 4596 LEU cc_start: 0.8633 (tp) cc_final: 0.8418 (tp) outliers start: 92 outliers final: 43 residues processed: 342 average time/residue: 0.2598 time to fit residues: 139.1180 Evaluate side-chains 314 residues out of total 4084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 259 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 541 HIS Chi-restraints excluded: chain B residue 556 LYS Chi-restraints excluded: chain B residue 560 THR 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 906 SER Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 1064 SER Chi-restraints excluded: chain B residue 1214 GLN Chi-restraints excluded: chain B residue 1267 ASP Chi-restraints excluded: chain B residue 1313 HIS Chi-restraints excluded: chain B residue 1325 VAL Chi-restraints excluded: chain B residue 1326 ARG Chi-restraints excluded: chain B residue 1337 VAL Chi-restraints excluded: chain B residue 1420 ILE Chi-restraints excluded: chain B residue 1731 LEU Chi-restraints excluded: chain B residue 1752 SER Chi-restraints excluded: chain B residue 1846 SER Chi-restraints excluded: chain B residue 1855 SER Chi-restraints excluded: chain B residue 1951 VAL Chi-restraints excluded: chain B residue 1992 LEU Chi-restraints excluded: chain B residue 2184 ASN Chi-restraints excluded: chain B residue 2468 VAL Chi-restraints excluded: chain B residue 2553 LEU Chi-restraints excluded: chain B residue 2569 ASN Chi-restraints excluded: chain B residue 2571 SER Chi-restraints excluded: chain B residue 2585 MET Chi-restraints excluded: chain B residue 2786 CYS Chi-restraints excluded: chain B residue 2813 SER Chi-restraints excluded: chain B residue 2887 ASP Chi-restraints excluded: chain B residue 2924 VAL Chi-restraints excluded: chain B residue 3044 ARG Chi-restraints excluded: chain B residue 3072 TYR Chi-restraints excluded: chain B residue 3265 MET Chi-restraints excluded: chain B residue 3287 ASN Chi-restraints excluded: chain B residue 3294 SER Chi-restraints excluded: chain B residue 3485 VAL Chi-restraints excluded: chain B residue 3703 VAL Chi-restraints excluded: chain B residue 3714 LEU Chi-restraints excluded: chain B residue 3761 LEU Chi-restraints excluded: chain B residue 3833 LEU Chi-restraints excluded: chain B residue 3859 THR Chi-restraints excluded: chain B residue 3863 ILE Chi-restraints excluded: chain B residue 3891 ILE Chi-restraints excluded: chain B residue 3908 CYS Chi-restraints excluded: chain B residue 3924 VAL Chi-restraints excluded: chain B residue 4129 GLU Chi-restraints excluded: chain B residue 4131 SER Chi-restraints excluded: chain B residue 4378 ILE Chi-restraints excluded: chain B residue 4507 SER Chi-restraints excluded: chain B residue 4883 GLN Chi-restraints excluded: chain B residue 4891 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: [355, 271, 175, 73, 166, 334, 129, 428, 182, 418, 423] chunk 355 optimal weight: 2.9990 chunk 271 optimal weight: 3.9990 chunk 175 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 334 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 428 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 418 optimal weight: 0.5980 chunk 423 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1585 HIS B1930 GLN B2790 GLN ** B4242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4395 HIS B4939 ASN B5056 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.072482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.059938 restraints weight = 114045.277| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.74 r_work: 0.2979 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 37241 Z= 0.211 Angle : 0.529 11.762 50348 Z= 0.270 Chirality : 0.040 0.167 5685 Planarity : 0.004 0.072 6409 Dihedral : 4.717 88.518 4927 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.67 % Allowed : 14.40 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 2.19 (0.13), residues: 4462 helix: 2.33 (0.10), residues: 2669 sheet: -0.46 (0.28), residues: 296 loop : 0.33 (0.17), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 544 TYR 0.015 0.001 TYR B1924 PHE 0.017 0.001 PHE B3157 TRP 0.014 0.001 TRP B3153 HIS 0.005 0.001 HIS B4395 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.21 (37233) covalent geometry : angle 0.52939 / 0.27 (50342) hydrogen bonds : bond 0.04240 / 2.80 ( 2108) hydrogen bonds : angle 4.12329 / 2.93 ( 6111) metal coordination : bond 0.00413 / 0.19 ( 8) metal coordination : angle 0.69537 / 0.37 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 4084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 268 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 368 LYS cc_start: 0.7986 (mmmt) cc_final: 0.7765 (mmtt) REVERT: B 396 ASP cc_start: 0.7207 (p0) cc_final: 0.6884 (p0) REVERT: B 410 GLN cc_start: 0.5659 (OUTLIER) cc_final: 0.3903 (mp10) REVERT: B 473 MET cc_start: 0.7426 (ppp) cc_final: 0.7181 (ppp) REVERT: B 490 THR cc_start: 0.4791 (OUTLIER) cc_final: 0.3182 (m) REVERT: B 491 ARG cc_start: 0.6225 (OUTLIER) cc_final: 0.5490 (mmt-90) REVERT: B 591 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8230 (ttmt) REVERT: B 1267 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7890 (t0) REVERT: B 1290 MET cc_start: 0.8021 (ttp) cc_final: 0.7779 (mtp) REVERT: B 1519 LYS cc_start: 0.8923 (mmmt) cc_final: 0.8694 (tptp) REVERT: B 1567 ASN cc_start: 0.8722 (m-40) cc_final: 0.8329 (m110) REVERT: B 1751 MET cc_start: 0.7849 (tmm) cc_final: 0.7250 (tmm) REVERT: B 1752 SER cc_start: 0.8352 (OUTLIER) cc_final: 0.8031 (t) REVERT: B 1992 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8532 (tt) REVERT: B 2292 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7240 (m-30) REVERT: B 2462 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8671 (mm) REVERT: B 2495 MET cc_start: 0.8451 (tpp) cc_final: 0.8146 (tpp) REVERT: B 2553 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8986 (tt) REVERT: B 2561 ARG cc_start: 0.8357 (mtt180) cc_final: 0.7898 (mtt90) REVERT: B 2585 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7962 (mmt) REVERT: B 2747 MET cc_start: 0.8856 (mtt) cc_final: 0.8583 (mtm) REVERT: B 3072 TYR cc_start: 0.7710 (OUTLIER) cc_final: 0.7345 (p90) REVERT: B 3271 ARG cc_start: 0.8085 (mtp85) cc_final: 0.7876 (mmm-85) REVERT: B 3636 MET cc_start: 0.8452 (ppp) cc_final: 0.8049 (ppp) REVERT: B 3714 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8944 (tt) REVERT: B 3814 MET cc_start: 0.9055 (tpt) cc_final: 0.8680 (tpt) REVERT: B 3858 MET cc_start: 0.8276 (tpp) cc_final: 0.7934 (tpp) REVERT: B 3908 CYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8096 (p) REVERT: B 3980 MET cc_start: 0.6576 (mpp) cc_final: 0.6344 (mpp) REVERT: B 4129 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7849 (mt-10) REVERT: B 4370 ASP cc_start: 0.8688 (t0) cc_final: 0.8384 (t0) outliers start: 109 outliers final: 65 residues processed: 355 average time/residue: 0.2769 time to fit residues: 153.8424 Evaluate side-chains 334 residues out of total 4084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 254 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 541 HIS Chi-restraints excluded: chain B residue 556 LYS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 633 SER 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 906 SER Chi-restraints excluded: chain B residue 961 HIS Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 1064 SER Chi-restraints excluded: chain B residue 1146 HIS Chi-restraints excluded: chain B residue 1214 GLN Chi-restraints excluded: chain B residue 1267 ASP Chi-restraints excluded: chain B residue 1313 HIS Chi-restraints excluded: chain B residue 1325 VAL Chi-restraints excluded: chain B residue 1326 ARG Chi-restraints excluded: chain B residue 1342 LEU Chi-restraints excluded: chain B residue 1420 ILE Chi-restraints excluded: chain B residue 1442 MET Chi-restraints excluded: chain B residue 1602 THR Chi-restraints excluded: chain B residue 1626 THR Chi-restraints excluded: chain B residue 1731 LEU Chi-restraints excluded: chain B residue 1752 SER Chi-restraints excluded: chain B residue 1846 SER Chi-restraints excluded: chain B residue 1855 SER Chi-restraints excluded: chain B residue 1931 VAL Chi-restraints excluded: chain B residue 1951 VAL Chi-restraints excluded: chain B residue 1992 LEU Chi-restraints excluded: chain B residue 2061 ILE Chi-restraints excluded: chain B residue 2184 ASN Chi-restraints excluded: chain B residue 2225 THR Chi-restraints excluded: chain B residue 2275 THR Chi-restraints excluded: chain B residue 2292 ASP Chi-restraints excluded: chain B residue 2427 GLU 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 2553 LEU Chi-restraints excluded: chain B residue 2569 ASN Chi-restraints excluded: chain B residue 2571 SER Chi-restraints excluded: chain B residue 2585 MET Chi-restraints excluded: chain B residue 2628 HIS Chi-restraints excluded: chain B residue 2652 VAL Chi-restraints excluded: chain B residue 2786 CYS Chi-restraints excluded: chain B residue 2790 GLN Chi-restraints excluded: chain B residue 2813 SER Chi-restraints excluded: chain B residue 2924 VAL Chi-restraints excluded: chain B residue 2952 ASP Chi-restraints excluded: chain B residue 3044 ARG Chi-restraints excluded: chain B residue 3072 TYR Chi-restraints excluded: chain B residue 3265 MET Chi-restraints excluded: chain B residue 3287 ASN Chi-restraints excluded: chain B residue 3485 VAL Chi-restraints excluded: chain B residue 3545 SER Chi-restraints excluded: chain B residue 3703 VAL Chi-restraints excluded: chain B residue 3714 LEU Chi-restraints excluded: chain B residue 3761 LEU Chi-restraints excluded: chain B residue 3775 LEU Chi-restraints excluded: chain B residue 3808 LEU Chi-restraints excluded: chain B residue 3833 LEU Chi-restraints excluded: chain B residue 3859 THR Chi-restraints excluded: chain B residue 3863 ILE Chi-restraints excluded: chain B residue 3891 ILE Chi-restraints excluded: chain B residue 3908 CYS Chi-restraints excluded: chain B residue 3924 VAL Chi-restraints excluded: chain B residue 4032 THR Chi-restraints excluded: chain B residue 4092 SER Chi-restraints excluded: chain B residue 4129 GLU Chi-restraints excluded: chain B residue 4131 SER Chi-restraints excluded: chain B residue 4507 SER Chi-restraints excluded: chain B residue 4772 ILE Chi-restraints excluded: chain B residue 4857 GLU Chi-restraints excluded: chain B residue 4883 GLN Chi-restraints excluded: chain B residue 4891 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: [424, 144, 118, 347, 150, 394, 430, 52, 59, 265, 132] chunk 424 optimal weight: 0.6980 chunk 144 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 chunk 347 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 394 optimal weight: 0.9980 chunk 430 optimal weight: 0.9980 chunk 52 optimal weight: 0.0980 chunk 59 optimal weight: 0.9980 chunk 265 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 HIS B1090 GLN B1585 HIS B2790 GLN ** B4242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4939 ASN ** B5055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.073186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.060876 restraints weight = 113182.283| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.53 r_work: 0.3010 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37241 Z= 0.130 Angle : 0.489 9.609 50348 Z= 0.250 Chirality : 0.038 0.142 5685 Planarity : 0.004 0.068 6409 Dihedral : 4.610 86.147 4927 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.35 % Allowed : 14.74 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 2.37 (0.13), residues: 4462 helix: 2.47 (0.10), residues: 2678 sheet: -0.31 (0.29), residues: 296 loop : 0.39 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B4815 TYR 0.013 0.001 TYR B3901 PHE 0.016 0.001 PHE B3157 TRP 0.014 0.001 TRP B 926 HIS 0.004 0.001 HIS B 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (37233) covalent geometry : angle 0.48869 / 0.25 (50342) hydrogen bonds : bond 0.03841 / 2.54 ( 2108) hydrogen bonds : angle 3.99424 / 2.84 ( 6111) metal coordination : bond 0.00366 / 0.15 ( 8) metal coordination : angle 0.69017 / 0.35 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 4084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 262 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: 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 368 LYS cc_start: 0.8071 (mmmt) cc_final: 0.7794 (mmtt) REVERT: B 396 ASP cc_start: 0.7095 (p0) cc_final: 0.6763 (p0) REVERT: B 410 GLN cc_start: 0.5522 (OUTLIER) cc_final: 0.4019 (mp10) REVERT: B 473 MET cc_start: 0.7136 (ppp) cc_final: 0.6895 (ppp) REVERT: B 490 THR cc_start: 0.4589 (OUTLIER) cc_final: 0.4087 (p) REVERT: B 491 ARG cc_start: 0.6025 (mmt180) cc_final: 0.5622 (mmp-170) REVERT: B 591 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8185 (ttmt) REVERT: B 998 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.7973 (t80) REVERT: B 1035 ARG cc_start: 0.8340 (ttp80) cc_final: 0.8037 (ttp80) REVERT: B 1214 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8110 (mp10) REVERT: B 1267 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7828 (t0) REVERT: B 1290 MET cc_start: 0.8010 (ttp) cc_final: 0.7776 (mtp) REVERT: B 1519 LYS cc_start: 0.8899 (mmmt) cc_final: 0.8679 (tptp) REVERT: B 1751 MET cc_start: 0.7827 (tmm) cc_final: 0.7212 (tmm) REVERT: B 1752 SER cc_start: 0.8319 (OUTLIER) cc_final: 0.8011 (t) REVERT: B 1915 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8469 (pp30) REVERT: B 1992 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8535 (tt) REVERT: B 2292 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7454 (m-30) REVERT: B 2462 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8657 (mm) REVERT: B 2495 MET cc_start: 0.8415 (tpp) cc_final: 0.8117 (tpp) REVERT: B 2585 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7969 (mmt) REVERT: B 2747 MET cc_start: 0.8830 (mtt) cc_final: 0.8566 (mtm) REVERT: B 2869 LYS cc_start: 0.8977 (tppt) cc_final: 0.8757 (tppt) REVERT: B 3072 TYR cc_start: 0.7648 (OUTLIER) cc_final: 0.7312 (p90) REVERT: B 3271 ARG cc_start: 0.8059 (mtp85) cc_final: 0.7849 (mmm-85) REVERT: B 3636 MET cc_start: 0.8449 (ppp) cc_final: 0.8061 (ppp) REVERT: B 3714 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8949 (tt) REVERT: B 3858 MET cc_start: 0.8188 (tpp) cc_final: 0.7951 (tpp) REVERT: B 3908 CYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8011 (p) REVERT: B 4129 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7806 (mt-10) REVERT: B 4148 ARG cc_start: 0.8206 (ttp-110) cc_final: 0.7863 (ttm110) REVERT: B 4370 ASP cc_start: 0.8626 (t0) cc_final: 0.8391 (t0) outliers start: 96 outliers final: 50 residues processed: 340 average time/residue: 0.2679 time to fit residues: 142.5021 Evaluate side-chains 316 residues out of total 4084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 250 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 556 LYS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 779 SER Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 906 SER Chi-restraints excluded: chain B residue 961 HIS Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 998 PHE Chi-restraints excluded: chain B residue 1059 MET Chi-restraints excluded: chain B residue 1064 SER Chi-restraints excluded: chain B residue 1214 GLN Chi-restraints excluded: chain B residue 1267 ASP Chi-restraints excluded: chain B residue 1313 HIS Chi-restraints excluded: chain B residue 1326 ARG Chi-restraints excluded: chain B residue 1342 LEU Chi-restraints excluded: chain B residue 1626 THR Chi-restraints excluded: chain B residue 1731 LEU Chi-restraints excluded: chain B residue 1752 SER Chi-restraints excluded: chain B residue 1846 SER Chi-restraints excluded: chain B residue 1915 GLN Chi-restraints excluded: chain B residue 1992 LEU Chi-restraints excluded: chain B residue 2061 ILE Chi-restraints excluded: chain B residue 2184 ASN Chi-restraints excluded: chain B residue 2273 HIS Chi-restraints excluded: chain B residue 2275 THR Chi-restraints excluded: chain B residue 2292 ASP Chi-restraints excluded: chain B residue 2462 ILE Chi-restraints excluded: chain B residue 2468 VAL Chi-restraints excluded: chain B residue 2569 ASN Chi-restraints excluded: chain B residue 2571 SER Chi-restraints excluded: chain B residue 2585 MET Chi-restraints excluded: chain B residue 2597 VAL Chi-restraints excluded: chain B residue 2628 HIS Chi-restraints excluded: chain B residue 2786 CYS Chi-restraints excluded: chain B residue 2807 VAL Chi-restraints excluded: chain B residue 2813 SER Chi-restraints excluded: chain B residue 2924 VAL Chi-restraints excluded: chain B residue 3044 ARG Chi-restraints excluded: chain B residue 3072 TYR Chi-restraints excluded: chain B residue 3265 MET Chi-restraints excluded: chain B residue 3485 VAL Chi-restraints excluded: chain B residue 3545 SER Chi-restraints excluded: chain B residue 3703 VAL Chi-restraints excluded: chain B residue 3714 LEU Chi-restraints excluded: chain B residue 3808 LEU Chi-restraints excluded: chain B residue 3833 LEU Chi-restraints excluded: chain B residue 3859 THR Chi-restraints excluded: chain B residue 3863 ILE Chi-restraints excluded: chain B residue 3891 ILE Chi-restraints excluded: chain B residue 3908 CYS Chi-restraints excluded: chain B residue 3924 VAL Chi-restraints excluded: chain B residue 4129 GLU Chi-restraints excluded: chain B residue 4131 SER Chi-restraints excluded: chain B residue 4260 ILE Chi-restraints excluded: chain B residue 4507 SER Chi-restraints excluded: chain B residue 4857 GLU Chi-restraints excluded: chain B residue 4883 GLN Chi-restraints excluded: chain B residue 4891 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: [414, 125, 147, 440, 48, 214, 159, 348, 256, 101, 153] chunk 414 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 440 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 214 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 348 optimal weight: 0.8980 chunk 256 optimal weight: 0.0000 chunk 101 optimal weight: 0.9990 chunk 153 optimal weight: 3.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1585 HIS B2790 GLN ** B4242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4262 GLN B4939 ASN ** B5055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.073359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.061011 restraints weight = 113842.416| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.55 r_work: 0.3011 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 37241 Z= 0.134 Angle : 0.488 10.210 50348 Z= 0.248 Chirality : 0.038 0.141 5685 Planarity : 0.004 0.066 6409 Dihedral : 4.536 84.471 4925 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.18 % Allowed : 14.86 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 2.45 (0.13), residues: 4462 helix: 2.53 (0.10), residues: 2679 sheet: -0.21 (0.29), residues: 296 loop : 0.40 (0.17), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 544 TYR 0.013 0.001 TYR B1924 PHE 0.019 0.001 PHE B 703 TRP 0.014 0.001 TRP B 926 HIS 0.003 0.001 HIS B 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (37233) covalent geometry : angle 0.48773 / 0.25 (50342) hydrogen bonds : bond 0.03708 / 2.45 ( 2108) hydrogen bonds : angle 3.93264 / 2.80 ( 6111) metal coordination : bond 0.00350 / 0.15 ( 8) metal coordination : angle 0.68419 / 0.34 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 4084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 262 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 368 LYS cc_start: 0.8063 (mmmt) cc_final: 0.7823 (mmtt) REVERT: B 396 ASP cc_start: 0.7133 (p0) cc_final: 0.6793 (p0) REVERT: B 405 MET cc_start: 0.7500 (ppp) cc_final: 0.7027 (ppp) REVERT: B 410 GLN cc_start: 0.5490 (OUTLIER) cc_final: 0.3971 (mp10) REVERT: B 473 MET cc_start: 0.6933 (ppp) cc_final: 0.6389 (ppp) REVERT: B 490 THR cc_start: 0.4710 (OUTLIER) cc_final: 0.3398 (m) REVERT: B 491 ARG cc_start: 0.5944 (mmt180) cc_final: 0.5467 (mmt-90) REVERT: B 591 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8362 (ttmt) REVERT: B 998 PHE cc_start: 0.8553 (OUTLIER) cc_final: 0.8034 (t80) REVERT: B 1035 ARG cc_start: 0.8339 (ttp80) cc_final: 0.8047 (ttp80) REVERT: B 1214 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8115 (mp10) REVERT: B 1267 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7827 (t0) REVERT: B 1287 MET cc_start: 0.8363 (ttt) cc_final: 0.8126 (mtp) REVERT: B 1290 MET cc_start: 0.7970 (ttp) cc_final: 0.7717 (mtp) REVERT: B 1519 LYS cc_start: 0.8890 (mmmt) cc_final: 0.8677 (tptp) REVERT: B 1751 MET cc_start: 0.7782 (tmm) cc_final: 0.7188 (tmm) REVERT: B 1752 SER cc_start: 0.8302 (OUTLIER) cc_final: 0.7974 (t) REVERT: B 1992 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8541 (tt) REVERT: B 2462 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8649 (mm) REVERT: B 2495 MET cc_start: 0.8404 (tpp) cc_final: 0.8104 (tpp) REVERT: B 2561 ARG cc_start: 0.8360 (mtt90) cc_final: 0.7672 (mtt90) REVERT: B 2585 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7977 (mmt) REVERT: B 2600 ARG cc_start: 0.7891 (mtm-85) cc_final: 0.7498 (mpt180) REVERT: B 2747 MET cc_start: 0.8821 (mtt) cc_final: 0.8548 (mtm) REVERT: B 2869 LYS cc_start: 0.8955 (tppt) cc_final: 0.8691 (tppt) REVERT: B 3072 TYR cc_start: 0.7623 (OUTLIER) cc_final: 0.7302 (p90) REVERT: B 3636 MET cc_start: 0.8432 (ppp) cc_final: 0.8134 (ppp) REVERT: B 3714 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8958 (tt) REVERT: B 3858 MET cc_start: 0.8160 (tpp) cc_final: 0.7919 (tpp) REVERT: B 3908 CYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8008 (p) REVERT: B 4129 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7814 (mt-10) REVERT: B 4206 ARG cc_start: 0.8290 (ttp-110) cc_final: 0.7893 (ptp-170) REVERT: B 4370 ASP cc_start: 0.8608 (t0) cc_final: 0.8339 (t0) REVERT: B 5128 MET cc_start: 0.8104 (tpp) cc_final: 0.7191 (mpp) outliers start: 89 outliers final: 58 residues processed: 334 average time/residue: 0.2719 time to fit residues: 142.1018 Evaluate side-chains 324 residues out of total 4084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 252 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 556 LYS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 779 SER Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 961 HIS Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 998 PHE Chi-restraints excluded: chain B residue 1064 SER Chi-restraints excluded: chain B residue 1214 GLN Chi-restraints excluded: chain B residue 1267 ASP Chi-restraints excluded: chain B residue 1313 HIS Chi-restraints excluded: chain B residue 1325 VAL Chi-restraints excluded: chain B residue 1326 ARG Chi-restraints excluded: chain B residue 1342 LEU Chi-restraints excluded: chain B residue 1420 ILE Chi-restraints excluded: chain B residue 1565 ASN Chi-restraints excluded: chain B residue 1626 THR Chi-restraints excluded: chain B residue 1752 SER Chi-restraints excluded: chain B residue 1846 SER Chi-restraints excluded: chain B residue 1931 VAL Chi-restraints excluded: chain B residue 1992 LEU Chi-restraints excluded: chain B residue 2061 ILE Chi-restraints excluded: chain B residue 2184 ASN Chi-restraints excluded: chain B residue 2273 HIS Chi-restraints excluded: chain B residue 2275 THR 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 2571 SER Chi-restraints excluded: chain B residue 2585 MET Chi-restraints excluded: chain B residue 2597 VAL Chi-restraints excluded: chain B residue 2628 HIS Chi-restraints excluded: chain B residue 2786 CYS Chi-restraints excluded: chain B residue 2790 GLN Chi-restraints excluded: chain B residue 2807 VAL Chi-restraints excluded: chain B residue 2813 SER Chi-restraints excluded: chain B residue 2924 VAL Chi-restraints excluded: chain B residue 2952 ASP Chi-restraints excluded: chain B residue 3044 ARG Chi-restraints excluded: chain B residue 3072 TYR Chi-restraints excluded: chain B residue 3265 MET Chi-restraints excluded: chain B residue 3287 ASN Chi-restraints excluded: chain B residue 3485 VAL Chi-restraints excluded: chain B residue 3545 SER Chi-restraints excluded: chain B residue 3588 HIS Chi-restraints excluded: chain B residue 3703 VAL Chi-restraints excluded: chain B residue 3714 LEU Chi-restraints excluded: chain B residue 3808 LEU Chi-restraints excluded: chain B residue 3833 LEU Chi-restraints excluded: chain B residue 3859 THR Chi-restraints excluded: chain B residue 3863 ILE Chi-restraints excluded: chain B residue 3891 ILE Chi-restraints excluded: chain B residue 3908 CYS Chi-restraints excluded: chain B residue 3924 VAL Chi-restraints excluded: chain B residue 4129 GLU Chi-restraints excluded: chain B residue 4131 SER Chi-restraints excluded: chain B residue 4143 LEU Chi-restraints excluded: chain B residue 4260 ILE Chi-restraints excluded: chain B residue 4507 SER Chi-restraints excluded: chain B residue 4857 GLU Chi-restraints excluded: chain B residue 4883 GLN Chi-restraints excluded: chain B residue 4891 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: [372, 368, 221, 141, 449, 350, 408, 409, 208, 86, 435] chunk 372 optimal weight: 2.9990 chunk 368 optimal weight: 0.5980 chunk 221 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 449 optimal weight: 3.9990 chunk 350 optimal weight: 0.8980 chunk 408 optimal weight: 0.9990 chunk 409 optimal weight: 1.9990 chunk 208 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 435 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1075 ASN B1585 HIS B2790 GLN ** B4242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4939 ASN B5055 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.073324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.061296 restraints weight = 113905.013| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.52 r_work: 0.3012 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 37241 Z= 0.131 Angle : 0.483 9.145 50348 Z= 0.247 Chirality : 0.038 0.141 5685 Planarity : 0.004 0.066 6409 Dihedral : 4.506 83.553 4925 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.28 % Allowed : 15.16 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 4462 helix: 2.56 (0.10), residues: 2680 sheet: -0.17 (0.29), residues: 296 loop : 0.39 (0.17), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 544 TYR 0.015 0.001 TYR B3374 PHE 0.015 0.001 PHE B3157 TRP 0.013 0.001 TRP B 926 HIS 0.003 0.001 HIS B3400 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (37233) covalent geometry : angle 0.48326 / 0.25 (50342) hydrogen bonds : bond 0.03660 / 2.42 ( 2108) hydrogen bonds : angle 3.90562 / 2.78 ( 6111) metal coordination : bond 0.00364 / 0.15 ( 8) metal coordination : angle 0.72477 / 0.36 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 4084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 257 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 396 ASP cc_start: 0.7110 (p0) cc_final: 0.6762 (p0) REVERT: B 410 GLN cc_start: 0.5448 (OUTLIER) cc_final: 0.3914 (mp10) REVERT: B 473 MET cc_start: 0.6865 (ppp) cc_final: 0.6319 (ppp) REVERT: B 490 THR cc_start: 0.4753 (OUTLIER) cc_final: 0.3386 (m) REVERT: B 491 ARG cc_start: 0.5849 (mmt180) cc_final: 0.5410 (mmt-90) REVERT: B 591 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8353 (ttmt) REVERT: B 998 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.8020 (t80) REVERT: B 1035 ARG cc_start: 0.8327 (ttp80) cc_final: 0.8065 (ttp80) REVERT: B 1214 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8175 (mp10) REVERT: B 1267 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7790 (t0) REVERT: B 1287 MET cc_start: 0.8390 (ttt) cc_final: 0.8161 (mtp) REVERT: B 1290 MET cc_start: 0.7993 (ttp) cc_final: 0.7750 (mtp) REVERT: B 1724 LYS cc_start: 0.8638 (mmtm) cc_final: 0.8328 (mmtt) REVERT: B 1751 MET cc_start: 0.7822 (tmm) cc_final: 0.7221 (tmm) REVERT: B 1752 SER cc_start: 0.8306 (OUTLIER) cc_final: 0.7986 (t) REVERT: B 1992 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8582 (tt) REVERT: B 2292 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7480 (m-30) REVERT: B 2462 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8694 (mm) REVERT: B 2495 MET cc_start: 0.8419 (tpp) cc_final: 0.8149 (tpp) REVERT: B 2561 ARG cc_start: 0.8342 (mtt90) cc_final: 0.7600 (mtt90) REVERT: B 2585 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.8037 (mmt) REVERT: B 2600 ARG cc_start: 0.7868 (mtm-85) cc_final: 0.7069 (mpt180) REVERT: B 2747 MET cc_start: 0.8829 (mtt) cc_final: 0.8568 (mtm) REVERT: B 3072 TYR cc_start: 0.7612 (OUTLIER) cc_final: 0.7355 (p90) REVERT: B 3636 MET cc_start: 0.8411 (ppp) cc_final: 0.8101 (ppp) REVERT: B 3714 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9020 (tt) REVERT: B 3858 MET cc_start: 0.8085 (tpp) cc_final: 0.7866 (tpp) REVERT: B 3908 CYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8015 (p) REVERT: B 4129 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7808 (mt-10) REVERT: B 5128 MET cc_start: 0.8211 (tpp) cc_final: 0.7396 (mpp) outliers start: 93 outliers final: 61 residues processed: 338 average time/residue: 0.2735 time to fit residues: 144.8576 Evaluate side-chains 327 residues out of total 4084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 251 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 556 LYS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 779 SER Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 906 SER Chi-restraints excluded: chain B residue 961 HIS Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 998 PHE Chi-restraints excluded: chain B residue 1064 SER Chi-restraints excluded: chain B residue 1214 GLN Chi-restraints excluded: chain B residue 1267 ASP Chi-restraints excluded: chain B residue 1313 HIS Chi-restraints excluded: chain B residue 1325 VAL Chi-restraints excluded: chain B residue 1342 LEU Chi-restraints excluded: chain B residue 1420 ILE Chi-restraints excluded: chain B residue 1626 THR Chi-restraints excluded: chain B residue 1676 SER Chi-restraints excluded: chain B residue 1752 SER Chi-restraints excluded: chain B residue 1846 SER Chi-restraints excluded: chain B residue 1915 GLN Chi-restraints excluded: chain B residue 1931 VAL Chi-restraints excluded: chain B residue 1951 VAL Chi-restraints excluded: chain B residue 1992 LEU Chi-restraints excluded: chain B residue 2061 ILE Chi-restraints excluded: chain B residue 2184 ASN Chi-restraints excluded: chain B residue 2275 THR Chi-restraints excluded: chain B residue 2292 ASP 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 2571 SER Chi-restraints excluded: chain B residue 2585 MET Chi-restraints excluded: chain B residue 2597 VAL Chi-restraints excluded: chain B residue 2628 HIS Chi-restraints excluded: chain B residue 2786 CYS Chi-restraints excluded: chain B residue 2790 GLN Chi-restraints excluded: chain B residue 2807 VAL Chi-restraints excluded: chain B residue 2813 SER Chi-restraints excluded: chain B residue 2924 VAL Chi-restraints excluded: chain B residue 2952 ASP Chi-restraints excluded: chain B residue 3044 ARG Chi-restraints excluded: chain B residue 3072 TYR Chi-restraints excluded: chain B residue 3265 MET Chi-restraints excluded: chain B residue 3485 VAL Chi-restraints excluded: chain B residue 3545 SER Chi-restraints excluded: chain B residue 3588 HIS Chi-restraints excluded: chain B residue 3703 VAL Chi-restraints excluded: chain B residue 3714 LEU Chi-restraints excluded: chain B residue 3808 LEU Chi-restraints excluded: chain B residue 3833 LEU Chi-restraints excluded: chain B residue 3859 THR Chi-restraints excluded: chain B residue 3863 ILE Chi-restraints excluded: chain B residue 3891 ILE Chi-restraints excluded: chain B residue 3908 CYS Chi-restraints excluded: chain B residue 3924 VAL Chi-restraints excluded: chain B residue 4014 MET Chi-restraints excluded: chain B residue 4068 SER Chi-restraints excluded: chain B residue 4129 GLU Chi-restraints excluded: chain B residue 4131 SER Chi-restraints excluded: chain B residue 4143 LEU Chi-restraints excluded: chain B residue 4260 ILE Chi-restraints excluded: chain B residue 4507 SER Chi-restraints excluded: chain B residue 4591 LEU Chi-restraints excluded: chain B residue 4883 GLN Chi-restraints excluded: chain B residue 4891 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: [97, 421, 340, 263, 211, 289, 81, 300, 74, 246, 366] chunk 97 optimal weight: 0.0470 chunk 421 optimal weight: 3.9990 chunk 340 optimal weight: 0.7980 chunk 263 optimal weight: 1.9990 chunk 211 optimal weight: 8.9990 chunk 289 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 300 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 chunk 366 optimal weight: 4.9990 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1585 HIS B2790 GLN ** B2947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4939 ASN ** B5055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.072982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.060708 restraints weight = 113422.575| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.48 r_work: 0.3009 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 37241 Z= 0.167 Angle : 0.511 8.755 50348 Z= 0.260 Chirality : 0.039 0.146 5685 Planarity : 0.004 0.068 6409 Dihedral : 4.557 85.783 4925 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.30 % Allowed : 15.21 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 2.42 (0.13), residues: 4462 helix: 2.51 (0.10), residues: 2680 sheet: -0.14 (0.29), residues: 290 loop : 0.36 (0.17), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 956 TYR 0.015 0.001 TYR B1924 PHE 0.015 0.001 PHE B3157 TRP 0.012 0.001 TRP B 926 HIS 0.004 0.001 HIS B3102 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (37233) covalent geometry : angle 0.51089 / 0.26 (50342) hydrogen bonds : bond 0.03815 / 2.52 ( 2108) hydrogen bonds : angle 3.93461 / 2.80 ( 6111) metal coordination : bond 0.00394 / 0.17 ( 8) metal coordination : angle 0.66252 / 0.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 4084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 261 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 396 ASP cc_start: 0.7156 (p0) cc_final: 0.6821 (p0) REVERT: B 405 MET cc_start: 0.7562 (ppp) cc_final: 0.7081 (ppp) REVERT: B 410 GLN cc_start: 0.5558 (OUTLIER) cc_final: 0.3943 (mp10) REVERT: B 473 MET cc_start: 0.6925 (ppp) cc_final: 0.6292 (ppp) REVERT: B 490 THR cc_start: 0.4761 (OUTLIER) cc_final: 0.1990 (m) REVERT: B 491 ARG cc_start: 0.5908 (OUTLIER) cc_final: 0.5264 (mmp-170) REVERT: B 591 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8357 (ttpt) REVERT: B 718 GLN cc_start: 0.7865 (mt0) cc_final: 0.7551 (mp10) REVERT: B 998 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.8033 (t80) REVERT: B 1035 ARG cc_start: 0.8326 (ttp80) cc_final: 0.8063 (ttp80) REVERT: B 1267 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7759 (t0) REVERT: B 1287 MET cc_start: 0.8403 (ttt) cc_final: 0.8141 (mtp) REVERT: B 1290 MET cc_start: 0.8015 (ttp) cc_final: 0.7783 (mtp) REVERT: B 1724 LYS cc_start: 0.8638 (mmtm) cc_final: 0.8324 (mmtt) REVERT: B 1751 MET cc_start: 0.7825 (tmm) cc_final: 0.7199 (tmm) REVERT: B 1752 SER cc_start: 0.8328 (OUTLIER) cc_final: 0.7994 (t) REVERT: B 1992 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8570 (tt) REVERT: B 2462 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8725 (mm) REVERT: B 2495 MET cc_start: 0.8412 (tpp) cc_final: 0.8138 (tpp) REVERT: B 2561 ARG cc_start: 0.8351 (mtt90) cc_final: 0.7575 (mtt90) REVERT: B 2585 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.8012 (mmt) REVERT: B 2600 ARG cc_start: 0.7873 (mtm-85) cc_final: 0.7061 (mpt180) REVERT: B 2747 MET cc_start: 0.8835 (mtt) cc_final: 0.8569 (mtm) REVERT: B 3072 TYR cc_start: 0.7609 (OUTLIER) cc_final: 0.7349 (p90) REVERT: B 3636 MET cc_start: 0.8442 (ppp) cc_final: 0.8109 (ppp) REVERT: B 3714 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9007 (tt) REVERT: B 3858 MET cc_start: 0.8056 (tpp) cc_final: 0.7828 (tpp) REVERT: B 3942 PHE cc_start: 0.7482 (p90) cc_final: 0.7107 (p90) REVERT: B 4129 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7801 (mt-10) REVERT: B 4348 LYS cc_start: 0.8758 (mttp) cc_final: 0.8493 (mptt) REVERT: B 4941 MET cc_start: 0.7965 (mtm) cc_final: 0.7730 (mpp) REVERT: B 5128 MET cc_start: 0.8185 (tpp) cc_final: 0.7445 (mpp) outliers start: 94 outliers final: 71 residues processed: 339 average time/residue: 0.2774 time to fit residues: 147.5808 Evaluate side-chains 338 residues out of total 4084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 254 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 556 LYS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 779 SER Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 906 SER Chi-restraints excluded: chain B residue 961 HIS Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 998 PHE Chi-restraints excluded: chain B residue 1059 MET Chi-restraints excluded: chain B residue 1064 SER Chi-restraints excluded: chain B residue 1214 GLN Chi-restraints excluded: chain B residue 1267 ASP Chi-restraints excluded: chain B residue 1313 HIS Chi-restraints excluded: chain B residue 1325 VAL Chi-restraints excluded: chain B residue 1326 ARG Chi-restraints excluded: chain B residue 1342 LEU Chi-restraints excluded: chain B residue 1371 GLN Chi-restraints excluded: chain B residue 1420 ILE Chi-restraints excluded: chain B residue 1626 THR Chi-restraints excluded: chain B residue 1676 SER Chi-restraints excluded: chain B residue 1752 SER Chi-restraints excluded: chain B residue 1846 SER Chi-restraints excluded: chain B residue 1855 SER Chi-restraints excluded: chain B residue 1915 GLN Chi-restraints excluded: chain B residue 1931 VAL Chi-restraints excluded: chain B residue 1951 VAL Chi-restraints excluded: chain B residue 1992 LEU Chi-restraints excluded: chain B residue 2061 ILE Chi-restraints excluded: chain B residue 2184 ASN Chi-restraints excluded: chain B residue 2225 THR Chi-restraints excluded: chain B residue 2275 THR Chi-restraints excluded: chain B residue 2427 GLU 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 2571 SER Chi-restraints excluded: chain B residue 2585 MET Chi-restraints excluded: chain B residue 2597 VAL Chi-restraints excluded: chain B residue 2628 HIS Chi-restraints excluded: chain B residue 2786 CYS Chi-restraints excluded: chain B residue 2807 VAL Chi-restraints excluded: chain B residue 2813 SER Chi-restraints excluded: chain B residue 2924 VAL Chi-restraints excluded: chain B residue 2952 ASP Chi-restraints excluded: chain B residue 3044 ARG Chi-restraints excluded: chain B residue 3072 TYR Chi-restraints excluded: chain B residue 3265 MET Chi-restraints excluded: chain B residue 3485 VAL Chi-restraints excluded: chain B residue 3545 SER Chi-restraints excluded: chain B residue 3603 SER Chi-restraints excluded: chain B residue 3703 VAL Chi-restraints excluded: chain B residue 3714 LEU Chi-restraints excluded: chain B residue 3808 LEU Chi-restraints excluded: chain B residue 3833 LEU Chi-restraints excluded: chain B residue 3859 THR Chi-restraints excluded: chain B residue 3863 ILE Chi-restraints excluded: chain B residue 3891 ILE Chi-restraints excluded: chain B residue 3908 CYS Chi-restraints excluded: chain B residue 3924 VAL Chi-restraints excluded: chain B residue 4014 MET Chi-restraints excluded: chain B residue 4068 SER Chi-restraints excluded: chain B residue 4129 GLU Chi-restraints excluded: chain B residue 4131 SER Chi-restraints excluded: chain B residue 4143 LEU Chi-restraints excluded: chain B residue 4260 ILE Chi-restraints excluded: chain B residue 4507 SER Chi-restraints excluded: chain B residue 4576 LYS Chi-restraints excluded: chain B residue 4591 LEU Chi-restraints excluded: chain B residue 4606 ASN Chi-restraints excluded: chain B residue 4681 SER Chi-restraints excluded: chain B residue 4883 GLN Chi-restraints excluded: chain B residue 4891 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: [327, 126, 103, 77, 354, 403, 37, 420, 138, 250, 319] chunk 327 optimal weight: 8.9990 chunk 126 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 354 optimal weight: 2.9990 chunk 403 optimal weight: 0.8980 chunk 37 optimal weight: 0.4980 chunk 420 optimal weight: 0.5980 chunk 138 optimal weight: 0.9980 chunk 250 optimal weight: 0.9980 chunk 319 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1585 HIS B2790 GLN ** B4242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4939 ASN ** B5055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.073289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.061041 restraints weight = 113718.492| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.49 r_work: 0.3018 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 37241 Z= 0.134 Angle : 0.496 9.256 50348 Z= 0.253 Chirality : 0.038 0.141 5685 Planarity : 0.004 0.065 6409 Dihedral : 4.515 83.165 4925 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.11 % Allowed : 15.55 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 2.47 (0.13), residues: 4462 helix: 2.54 (0.10), residues: 2684 sheet: -0.08 (0.29), residues: 290 loop : 0.37 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B4206 TYR 0.014 0.001 TYR B1924 PHE 0.021 0.001 PHE B 703 TRP 0.014 0.001 TRP B 926 HIS 0.004 0.001 HIS B1186 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (37233) covalent geometry : angle 0.49627 / 0.25 (50342) hydrogen bonds : bond 0.03638 / 2.40 ( 2108) hydrogen bonds : angle 3.88909 / 2.77 ( 6111) metal coordination : bond 0.00367 / 0.15 ( 8) metal coordination : angle 0.68715 / 0.33 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 4084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 259 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 396 ASP cc_start: 0.7154 (p0) cc_final: 0.6823 (p0) REVERT: B 405 MET cc_start: 0.7514 (ppp) cc_final: 0.7075 (ppp) REVERT: B 410 GLN cc_start: 0.5589 (OUTLIER) cc_final: 0.4050 (mp10) REVERT: B 473 MET cc_start: 0.6814 (ppp) cc_final: 0.6265 (ppp) REVERT: B 490 THR cc_start: 0.4652 (OUTLIER) cc_final: 0.1954 (m) REVERT: B 491 ARG cc_start: 0.5758 (mmt180) cc_final: 0.5105 (mmp-170) REVERT: B 591 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8363 (ttmt) REVERT: B 718 GLN cc_start: 0.7828 (mt0) cc_final: 0.7513 (mp10) REVERT: B 902 ARG cc_start: 0.7854 (ptt90) cc_final: 0.7601 (ptt90) REVERT: B 998 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.8046 (t80) REVERT: B 1035 ARG cc_start: 0.8309 (ttp80) cc_final: 0.8050 (ttp80) REVERT: B 1214 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.8164 (mp10) REVERT: B 1267 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7767 (t0) REVERT: B 1287 MET cc_start: 0.8400 (ttt) cc_final: 0.8135 (mtp) REVERT: B 1290 MET cc_start: 0.8006 (ttp) cc_final: 0.7774 (mtp) REVERT: B 1314 GLN cc_start: 0.7939 (pp30) cc_final: 0.7694 (pp30) REVERT: B 1751 MET cc_start: 0.7820 (tmm) cc_final: 0.7291 (tmm) REVERT: B 1752 SER cc_start: 0.8296 (OUTLIER) cc_final: 0.7877 (p) REVERT: B 1992 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8577 (tt) REVERT: B 2275 THR cc_start: 0.7812 (OUTLIER) cc_final: 0.7602 (p) REVERT: B 2317 LEU cc_start: 0.9440 (tt) cc_final: 0.9111 (mp) REVERT: B 2462 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8720 (mm) REVERT: B 2495 MET cc_start: 0.8409 (tpp) cc_final: 0.8136 (tpp) REVERT: B 2561 ARG cc_start: 0.8354 (mtt90) cc_final: 0.7623 (mtt90) REVERT: B 2585 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.8032 (mmt) REVERT: B 2600 ARG cc_start: 0.7861 (mtm-85) cc_final: 0.7043 (mpt180) REVERT: B 2747 MET cc_start: 0.8816 (mtt) cc_final: 0.8549 (mtm) REVERT: B 3072 TYR cc_start: 0.7586 (OUTLIER) cc_final: 0.7329 (p90) REVERT: B 3636 MET cc_start: 0.8419 (ppp) cc_final: 0.8089 (ppp) REVERT: B 3691 LYS cc_start: 0.8735 (mmtm) cc_final: 0.8423 (mmtm) REVERT: B 3714 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9026 (tt) REVERT: B 3858 MET cc_start: 0.8013 (tpp) cc_final: 0.7756 (tpp) REVERT: B 3942 PHE cc_start: 0.7469 (p90) cc_final: 0.7136 (p90) REVERT: B 4129 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7800 (mt-10) REVERT: B 4148 ARG cc_start: 0.8118 (ttp-110) cc_final: 0.7702 (ptm-80) REVERT: B 4206 ARG cc_start: 0.8302 (ttp-110) cc_final: 0.7710 (mtm110) REVERT: B 5058 ARG cc_start: 0.8565 (mtm110) cc_final: 0.8177 (mtt180) REVERT: B 5128 MET cc_start: 0.8236 (tpp) cc_final: 0.7478 (mpp) outliers start: 86 outliers final: 67 residues processed: 334 average time/residue: 0.2610 time to fit residues: 136.5019 Evaluate side-chains 337 residues out of total 4084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 256 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 556 LYS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 779 SER Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 906 SER Chi-restraints excluded: chain B residue 961 HIS Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 998 PHE Chi-restraints excluded: chain B residue 1059 MET Chi-restraints excluded: chain B residue 1064 SER Chi-restraints excluded: chain B residue 1214 GLN Chi-restraints excluded: chain B residue 1267 ASP Chi-restraints excluded: chain B residue 1313 HIS Chi-restraints excluded: chain B residue 1325 VAL Chi-restraints excluded: chain B residue 1326 ARG Chi-restraints excluded: chain B residue 1342 LEU Chi-restraints excluded: chain B residue 1371 GLN Chi-restraints excluded: chain B residue 1420 ILE Chi-restraints excluded: chain B residue 1626 THR Chi-restraints excluded: chain B residue 1676 SER Chi-restraints excluded: chain B residue 1752 SER Chi-restraints excluded: chain B residue 1846 SER Chi-restraints excluded: chain B residue 1855 SER Chi-restraints excluded: chain B residue 1915 GLN Chi-restraints excluded: chain B residue 1931 VAL Chi-restraints excluded: chain B residue 1951 VAL Chi-restraints excluded: chain B residue 1992 LEU Chi-restraints excluded: chain B residue 2061 ILE Chi-restraints excluded: chain B residue 2184 ASN Chi-restraints excluded: chain B residue 2225 THR Chi-restraints excluded: chain B residue 2275 THR Chi-restraints excluded: chain B residue 2427 GLU 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 2571 SER Chi-restraints excluded: chain B residue 2585 MET Chi-restraints excluded: chain B residue 2597 VAL Chi-restraints excluded: chain B residue 2628 HIS Chi-restraints excluded: chain B residue 2786 CYS Chi-restraints excluded: chain B residue 2807 VAL Chi-restraints excluded: chain B residue 2813 SER Chi-restraints excluded: chain B residue 2924 VAL Chi-restraints excluded: chain B residue 2952 ASP Chi-restraints excluded: chain B residue 3044 ARG Chi-restraints excluded: chain B residue 3072 TYR Chi-restraints excluded: chain B residue 3265 MET Chi-restraints excluded: chain B residue 3375 PHE Chi-restraints excluded: chain B residue 3485 VAL Chi-restraints excluded: chain B residue 3545 SER Chi-restraints excluded: chain B residue 3603 SER Chi-restraints excluded: chain B residue 3703 VAL Chi-restraints excluded: chain B residue 3714 LEU Chi-restraints excluded: chain B residue 3808 LEU Chi-restraints excluded: chain B residue 3833 LEU Chi-restraints excluded: chain B residue 3859 THR Chi-restraints excluded: chain B residue 3863 ILE Chi-restraints excluded: chain B residue 3891 ILE Chi-restraints excluded: chain B residue 3908 CYS Chi-restraints excluded: chain B residue 3924 VAL Chi-restraints excluded: chain B residue 4129 GLU Chi-restraints excluded: chain B residue 4131 SER Chi-restraints excluded: chain B residue 4143 LEU Chi-restraints excluded: chain B residue 4260 ILE Chi-restraints excluded: chain B residue 4507 SER Chi-restraints excluded: chain B residue 4576 LYS Chi-restraints excluded: chain B residue 4591 LEU Chi-restraints excluded: chain B residue 4681 SER Chi-restraints excluded: chain B residue 4883 GLN Chi-restraints excluded: chain B residue 4891 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: [425, 230, 385, 52, 277, 184, 118, 160, 393, 145, 412] chunk 425 optimal weight: 3.9990 chunk 230 optimal weight: 3.9990 chunk 385 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 277 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 393 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 412 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1585 HIS B2790 GLN ** B4242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4939 ASN ** B5055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.072699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.060658 restraints weight = 114059.955| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.52 r_work: 0.2991 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 37241 Z= 0.192 Angle : 0.535 9.960 50348 Z= 0.271 Chirality : 0.040 0.171 5685 Planarity : 0.004 0.069 6409 Dihedral : 4.609 88.016 4925 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.13 % Allowed : 15.74 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 2.37 (0.13), residues: 4462 helix: 2.45 (0.10), residues: 2685 sheet: -0.12 (0.29), residues: 290 loop : 0.34 (0.17), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B4206 TYR 0.017 0.001 TYR B1924 PHE 0.029 0.001 PHE B 703 TRP 0.020 0.001 TRP B4928 HIS 0.005 0.001 HIS B1928 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.19 (37233) covalent geometry : angle 0.53507 / 0.27 (50342) hydrogen bonds : bond 0.03955 / 2.62 ( 2108) hydrogen bonds : angle 3.96280 / 2.82 ( 6111) metal coordination : bond 0.00420 / 0.20 ( 8) metal coordination : angle 0.66458 / 0.33 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 4084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 264 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 396 ASP cc_start: 0.7122 (p0) cc_final: 0.6785 (p0) REVERT: B 405 MET cc_start: 0.7726 (ppp) cc_final: 0.7256 (ppp) REVERT: B 410 GLN cc_start: 0.5590 (OUTLIER) cc_final: 0.4136 (tm-30) REVERT: B 473 MET cc_start: 0.6917 (ppp) cc_final: 0.6386 (ppp) REVERT: B 490 THR cc_start: 0.4920 (OUTLIER) cc_final: 0.3542 (m) REVERT: B 491 ARG cc_start: 0.5829 (mmt180) cc_final: 0.5240 (mmt-90) REVERT: B 591 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8402 (ttpt) REVERT: B 718 GLN cc_start: 0.7868 (mt0) cc_final: 0.7536 (mp10) REVERT: B 956 ARG cc_start: 0.8090 (ttp80) cc_final: 0.7624 (ttp80) REVERT: B 998 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.8078 (t80) REVERT: B 1035 ARG cc_start: 0.8345 (ttp80) cc_final: 0.8089 (ttp80) REVERT: B 1102 ARG cc_start: 0.6894 (mtt90) cc_final: 0.6689 (mtm-85) REVERT: B 1267 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7799 (t0) REVERT: B 1287 MET cc_start: 0.8435 (ttt) cc_final: 0.8166 (mtp) REVERT: B 1290 MET cc_start: 0.8044 (ttp) cc_final: 0.7813 (mtp) REVERT: B 1724 LYS cc_start: 0.8657 (mmtm) cc_final: 0.8345 (mmtt) REVERT: B 1751 MET cc_start: 0.7884 (tmm) cc_final: 0.7370 (tmm) REVERT: B 1752 SER cc_start: 0.8294 (OUTLIER) cc_final: 0.7944 (p) REVERT: B 1992 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8581 (tt) REVERT: B 2292 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7290 (m-30) REVERT: B 2317 LEU cc_start: 0.9441 (tt) cc_final: 0.9155 (mp) REVERT: B 2420 MET cc_start: 0.8389 (mtp) cc_final: 0.8156 (mtm) REVERT: B 2462 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8750 (mm) REVERT: B 2495 MET cc_start: 0.8438 (tpp) cc_final: 0.8166 (tpp) REVERT: B 2561 ARG cc_start: 0.8368 (mtt90) cc_final: 0.7650 (mtt90) REVERT: B 2585 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.8048 (mmt) REVERT: B 2600 ARG cc_start: 0.7882 (mtm-85) cc_final: 0.7064 (mpt180) REVERT: B 2747 MET cc_start: 0.8853 (mtt) cc_final: 0.8595 (mtm) REVERT: B 3072 TYR cc_start: 0.7634 (OUTLIER) cc_final: 0.7375 (p90) REVERT: B 3636 MET cc_start: 0.8436 (ppp) cc_final: 0.8084 (ppp) REVERT: B 3691 LYS cc_start: 0.8783 (mmtm) cc_final: 0.8472 (mmtm) REVERT: B 3714 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.9024 (tt) REVERT: B 3858 MET cc_start: 0.8039 (tpp) cc_final: 0.7777 (tpp) REVERT: B 3942 PHE cc_start: 0.7464 (p90) cc_final: 0.7116 (p90) REVERT: B 4129 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7838 (mt-10) REVERT: B 4148 ARG cc_start: 0.8148 (ttp-110) cc_final: 0.7716 (ptm-80) REVERT: B 4206 ARG cc_start: 0.8305 (ttp-110) cc_final: 0.7737 (mtm110) REVERT: B 4348 LYS cc_start: 0.8779 (mttp) cc_final: 0.8478 (mptt) REVERT: B 5128 MET cc_start: 0.8320 (tpp) cc_final: 0.7577 (mpp) outliers start: 87 outliers final: 69 residues processed: 340 average time/residue: 0.2618 time to fit residues: 139.7967 Evaluate side-chains 339 residues out of total 4084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 257 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 556 LYS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 779 SER Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 906 SER Chi-restraints excluded: chain B residue 961 HIS Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 998 PHE Chi-restraints excluded: chain B residue 1059 MET Chi-restraints excluded: chain B residue 1064 SER Chi-restraints excluded: chain B residue 1214 GLN Chi-restraints excluded: chain B residue 1267 ASP Chi-restraints excluded: chain B residue 1313 HIS Chi-restraints excluded: chain B residue 1325 VAL Chi-restraints excluded: chain B residue 1326 ARG Chi-restraints excluded: chain B residue 1342 LEU Chi-restraints excluded: chain B residue 1371 GLN Chi-restraints excluded: chain B residue 1420 ILE Chi-restraints excluded: chain B residue 1626 THR Chi-restraints excluded: chain B residue 1676 SER Chi-restraints excluded: chain B residue 1752 SER Chi-restraints excluded: chain B residue 1846 SER Chi-restraints excluded: chain B residue 1855 SER Chi-restraints excluded: chain B residue 1915 GLN Chi-restraints excluded: chain B residue 1931 VAL Chi-restraints excluded: chain B residue 1951 VAL Chi-restraints excluded: chain B residue 1992 LEU Chi-restraints excluded: chain B residue 2061 ILE Chi-restraints excluded: chain B residue 2184 ASN Chi-restraints excluded: chain B residue 2225 THR Chi-restraints excluded: chain B residue 2292 ASP Chi-restraints excluded: chain B residue 2427 GLU 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 2571 SER Chi-restraints excluded: chain B residue 2585 MET Chi-restraints excluded: chain B residue 2597 VAL Chi-restraints excluded: chain B residue 2628 HIS Chi-restraints excluded: chain B residue 2786 CYS Chi-restraints excluded: chain B residue 2790 GLN Chi-restraints excluded: chain B residue 2807 VAL Chi-restraints excluded: chain B residue 2813 SER Chi-restraints excluded: chain B residue 2924 VAL Chi-restraints excluded: chain B residue 2952 ASP Chi-restraints excluded: chain B residue 3044 ARG Chi-restraints excluded: chain B residue 3072 TYR Chi-restraints excluded: chain B residue 3265 MET Chi-restraints excluded: chain B residue 3375 PHE Chi-restraints excluded: chain B residue 3485 VAL Chi-restraints excluded: chain B residue 3545 SER Chi-restraints excluded: chain B residue 3603 SER Chi-restraints excluded: chain B residue 3703 VAL Chi-restraints excluded: chain B residue 3714 LEU Chi-restraints excluded: chain B residue 3808 LEU Chi-restraints excluded: chain B residue 3833 LEU Chi-restraints excluded: chain B residue 3859 THR Chi-restraints excluded: chain B residue 3891 ILE Chi-restraints excluded: chain B residue 3908 CYS Chi-restraints excluded: chain B residue 3924 VAL Chi-restraints excluded: chain B residue 4014 MET Chi-restraints excluded: chain B residue 4129 GLU Chi-restraints excluded: chain B residue 4131 SER Chi-restraints excluded: chain B residue 4143 LEU Chi-restraints excluded: chain B residue 4260 ILE Chi-restraints excluded: chain B residue 4507 SER Chi-restraints excluded: chain B residue 4576 LYS Chi-restraints excluded: chain B residue 4591 LEU Chi-restraints excluded: chain B residue 4681 SER Chi-restraints excluded: chain B residue 4883 GLN Chi-restraints excluded: chain B residue 4891 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: [35, 452, 100, 95, 269, 68, 137, 186, 181, 422, 411] chunk 35 optimal weight: 1.9990 chunk 452 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 269 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 137 optimal weight: 0.0770 chunk 186 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 chunk 422 optimal weight: 2.9990 chunk 411 optimal weight: 2.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1585 HIS B2790 GLN ** B4242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4939 ASN ** B5055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.072655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.060454 restraints weight = 113206.297| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.63 r_work: 0.2990 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 37241 Z= 0.181 Angle : 0.532 10.415 50348 Z= 0.270 Chirality : 0.040 0.141 5685 Planarity : 0.004 0.069 6409 Dihedral : 4.615 87.327 4925 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.06 % Allowed : 15.72 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 2.35 (0.13), residues: 4462 helix: 2.43 (0.10), residues: 2691 sheet: -0.13 (0.29), residues: 290 loop : 0.36 (0.17), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B1102 TYR 0.016 0.001 TYR B1924 PHE 0.026 0.001 PHE B 703 TRP 0.015 0.001 TRP B4928 HIS 0.006 0.001 HIS B4671 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (37233) covalent geometry : angle 0.53175 / 0.27 (50342) hydrogen bonds : bond 0.03901 / 2.58 ( 2108) hydrogen bonds : angle 3.95930 / 2.82 ( 6111) metal coordination : bond 0.00391 / 0.18 ( 8) metal coordination : angle 0.66372 / 0.32 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8197.37 seconds wall clock time: 141 minutes 27.64 seconds (8487.64 seconds total)