Starting phenix.real_space_refine on Sun Feb 8 07:56:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pn0_71744/02_2026/9pn0_71744_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pn0_71744/02_2026/9pn0_71744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pn0_71744/02_2026/9pn0_71744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pn0_71744/02_2026/9pn0_71744.map" model { file = "/net/cci-nas-00/data/ceres_data/9pn0_71744/02_2026/9pn0_71744_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pn0_71744/02_2026/9pn0_71744_neut_trim.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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: 5 Type Number sf(0) Gaussians S 129 5.16 5 C 13081 2.51 5 N 3506 2.21 5 O 3686 1.98 5 H 20798 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 141 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41200 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 267 Unusual residues: {'ACE': 1} Classifications: {'peptide': 17, 'undetermined': 1} Modifications used: {'PEPT-D': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 16} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 308 Unusual residues: {'ACE': 1} Classifications: {'peptide': 17, 'undetermined': 1} Modifications used: {'PEPT-D': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 16} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 255 Unusual residues: {'ACE': 1} Classifications: {'peptide': 15, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 14} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 36566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2296, 36566 Classifications: {'peptide': 2296} Link IDs: {'PTRANS': 104, 'TRANS': 2191} Chain breaks: 24 Chain: "B" Number of atoms: 3801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 3801 Classifications: {'peptide': 250} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 233} Chain breaks: 2 Time building chain proxies: 7.78, per 1000 atoms: 0.19 Number of scatterers: 41200 At special positions: 0 Unit cell: (114.192, 134.688, 143.472, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 129 16.00 O 3686 8.00 N 3506 7.00 C 13081 6.00 H 20798 1.00 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.48 Conformation dependent library (CDL) restraints added in 1.2 seconds 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTY D 2 " pdb=" CB DTY C 2 " Number of C-beta restraints generated: 4960 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 2 sheets defined 76.1% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'D' and resid 3 through 8 Processing helix chain 'A' and resid 99 through 113 removed outlier: 3.849A pdb=" N VAL A 113 " --> pdb=" O CYS A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 138 Processing helix chain 'A' and resid 142 through 161 Processing helix chain 'A' and resid 164 through 178 Processing helix chain 'A' and resid 181 through 196 removed outlier: 4.215A pdb=" N ARG A 191 " --> pdb=" O ALA A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 199 No H-bonds generated for 'chain 'A' and resid 197 through 199' Processing helix chain 'A' and resid 200 through 219 removed outlier: 3.677A pdb=" N CYS A 204 " --> pdb=" O ARG A 200 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ARG A 205 " --> pdb=" O PRO A 201 " (cutoff:3.500A) Proline residue: A 206 - end of helix Proline residue: A 213 - end of helix removed outlier: 3.599A pdb=" N ARG A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 242 Proline residue: A 235 - end of helix removed outlier: 3.756A pdb=" N ALA A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 246 through 259 Processing helix chain 'A' and resid 265 through 282 removed outlier: 3.691A pdb=" N VAL A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 300 Processing helix chain 'A' and resid 309 through 324 Processing helix chain 'A' and resid 325 through 328 removed outlier: 3.521A pdb=" N GLN A 328 " --> pdb=" O PRO A 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 325 through 328' Processing helix chain 'A' and resid 352 through 367 Processing helix chain 'A' and resid 371 through 388 Processing helix chain 'A' and resid 390 through 399 removed outlier: 3.661A pdb=" N GLN A 395 " --> pdb=" O PRO A 391 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A 396 " --> pdb=" O GLU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 695 removed outlier: 4.074A pdb=" N HIS A 685 " --> pdb=" O ALA A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 728 removed outlier: 3.750A pdb=" N LEU A 727 " --> pdb=" O ALA A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 734 removed outlier: 3.613A pdb=" N SER A 734 " --> pdb=" O SER A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 761 removed outlier: 3.746A pdb=" N ASP A 760 " --> pdb=" O ASN A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 785 Processing helix chain 'A' and resid 788 through 801 Processing helix chain 'A' and resid 805 through 808 Processing helix chain 'A' and resid 809 through 818 removed outlier: 3.696A pdb=" N LYS A 818 " --> pdb=" O ARG A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 842 removed outlier: 5.497A pdb=" N MET A 837 " --> pdb=" O ARG A 833 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N SER A 838 " --> pdb=" O ASN A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 856 removed outlier: 3.689A pdb=" N LEU A 856 " --> pdb=" O ILE A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 861 Processing helix chain 'A' and resid 863 through 876 removed outlier: 3.675A pdb=" N GLU A 876 " --> pdb=" O GLU A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 889 Processing helix chain 'A' and resid 891 through 895 Processing helix chain 'A' and resid 904 through 913 removed outlier: 3.562A pdb=" N VAL A 913 " --> pdb=" O VAL A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 920 Processing helix chain 'A' and resid 922 through 937 Processing helix chain 'A' and resid 938 through 940 No H-bonds generated for 'chain 'A' and resid 938 through 940' Processing helix chain 'A' and resid 950 through 964 removed outlier: 3.612A pdb=" N ASP A 958 " --> pdb=" O ALA A 954 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL A 962 " --> pdb=" O ASP A 958 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR A 963 " --> pdb=" O GLN A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1017 Processing helix chain 'A' and resid 1020 through 1038 removed outlier: 3.518A pdb=" N THR A1024 " --> pdb=" O THR A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1077 Processing helix chain 'A' and resid 1080 through 1083 Processing helix chain 'A' and resid 1084 through 1101 Processing helix chain 'A' and resid 1133 through 1135 No H-bonds generated for 'chain 'A' and resid 1133 through 1135' Processing helix chain 'A' and resid 1136 through 1159 Processing helix chain 'A' and resid 1235 through 1254 removed outlier: 3.856A pdb=" N VAL A1254 " --> pdb=" O ALA A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1280 Processing helix chain 'A' and resid 1281 through 1283 No H-bonds generated for 'chain 'A' and resid 1281 through 1283' Processing helix chain 'A' and resid 1284 through 1289 Processing helix chain 'A' and resid 1291 through 1303 removed outlier: 3.520A pdb=" N SER A1301 " --> pdb=" O GLY A1297 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1322 Processing helix chain 'A' and resid 1325 through 1330 Processing helix chain 'A' and resid 1355 through 1361 Processing helix chain 'A' and resid 1361 through 1375 removed outlier: 3.508A pdb=" N ALA A1373 " --> pdb=" O THR A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1421 through 1426 Processing helix chain 'A' and resid 1427 through 1439 Processing helix chain 'A' and resid 1443 through 1460 Processing helix chain 'A' and resid 1463 through 1468 Processing helix chain 'A' and resid 1471 through 1486 removed outlier: 4.010A pdb=" N PHE A1481 " --> pdb=" O VAL A1477 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU A1482 " --> pdb=" O LEU A1478 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR A1483 " --> pdb=" O LYS A1479 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL A1486 " --> pdb=" O GLU A1482 " (cutoff:3.500A) Processing helix chain 'A' and resid 1491 through 1494 Processing helix chain 'A' and resid 1495 through 1509 removed outlier: 3.949A pdb=" N TYR A1508 " --> pdb=" O VAL A1504 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU A1509 " --> pdb=" O LEU A1505 " (cutoff:3.500A) Processing helix chain 'A' and resid 1518 through 1532 Processing helix chain 'A' and resid 1539 through 1554 Proline residue: A1546 - end of helix Processing helix chain 'A' and resid 1564 through 1579 removed outlier: 4.125A pdb=" N THR A1568 " --> pdb=" O LYS A1564 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG A1579 " --> pdb=" O SER A1575 " (cutoff:3.500A) Processing helix chain 'A' and resid 1583 through 1599 removed outlier: 3.532A pdb=" N MET A1589 " --> pdb=" O GLN A1585 " (cutoff:3.500A) Processing helix chain 'A' and resid 1601 through 1622 removed outlier: 3.616A pdb=" N ILE A1615 " --> pdb=" O GLN A1611 " (cutoff:3.500A) Proline residue: A1618 - end of helix Processing helix chain 'A' and resid 1629 through 1643 removed outlier: 3.721A pdb=" N GLU A1641 " --> pdb=" O ASN A1637 " (cutoff:3.500A) Processing helix chain 'A' and resid 1644 through 1649 Processing helix chain 'A' and resid 1651 through 1658 Processing helix chain 'A' and resid 1667 through 1689 removed outlier: 3.708A pdb=" N VAL A1684 " --> pdb=" O ALA A1680 " (cutoff:3.500A) Processing helix chain 'A' and resid 1690 through 1702 Processing helix chain 'A' and resid 1704 through 1708 removed outlier: 3.718A pdb=" N ILE A1708 " --> pdb=" O PRO A1705 " (cutoff:3.500A) Processing helix chain 'A' and resid 1709 through 1719 Processing helix chain 'A' and resid 1737 through 1759 Processing helix chain 'A' and resid 1767 through 1791 Processing helix chain 'A' and resid 1794 through 1805 Processing helix chain 'A' and resid 1816 through 1827 Processing helix chain 'A' and resid 1831 through 1845 Processing helix chain 'A' and resid 1849 through 1857 removed outlier: 4.653A pdb=" N GLU A1855 " --> pdb=" O ARG A1851 " (cutoff:3.500A) Processing helix chain 'A' and resid 1890 through 1911 Processing helix chain 'A' and resid 1915 through 1932 removed outlier: 7.463A pdb=" N GLN A1927 " --> pdb=" O VAL A1923 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASP A1928 " --> pdb=" O ASN A1924 " (cutoff:3.500A) Processing helix chain 'A' and resid 1935 through 1946 Processing helix chain 'A' and resid 1948 through 1961 Processing helix chain 'A' and resid 1962 through 1967 Processing helix chain 'A' and resid 1968 through 1978 Processing helix chain 'A' and resid 1983 through 1985 No H-bonds generated for 'chain 'A' and resid 1983 through 1985' Processing helix chain 'A' and resid 1986 through 1998 Processing helix chain 'A' and resid 2003 through 2024 Processing helix chain 'A' and resid 2036 through 2048 Processing helix chain 'A' and resid 2049 through 2054 Processing helix chain 'A' and resid 2054 through 2066 Processing helix chain 'A' and resid 2098 through 2111 removed outlier: 4.044A pdb=" N HIS A2104 " --> pdb=" O ASP A2100 " (cutoff:3.500A) Processing helix chain 'A' and resid 2117 through 2127 removed outlier: 3.685A pdb=" N ARG A2127 " --> pdb=" O GLU A2123 " (cutoff:3.500A) Processing helix chain 'A' and resid 2129 through 2139 removed outlier: 3.581A pdb=" N MET A2133 " --> pdb=" O PRO A2129 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ASN A2134 " --> pdb=" O ALA A2130 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ALA A2135 " --> pdb=" O GLU A2131 " (cutoff:3.500A) Processing helix chain 'A' and resid 2143 through 2145 No H-bonds generated for 'chain 'A' and resid 2143 through 2145' Processing helix chain 'A' and resid 2146 through 2159 removed outlier: 3.627A pdb=" N SER A2156 " --> pdb=" O SER A2152 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU A2157 " --> pdb=" O LEU A2153 " (cutoff:3.500A) Processing helix chain 'A' and resid 2164 through 2183 removed outlier: 3.525A pdb=" N GLN A2183 " --> pdb=" O SER A2179 " (cutoff:3.500A) Processing helix chain 'A' and resid 2200 through 2212 removed outlier: 4.274A pdb=" N LYS A2206 " --> pdb=" O ALA A2202 " (cutoff:3.500A) Processing helix chain 'A' and resid 2213 through 2218 Processing helix chain 'A' and resid 2218 through 2232 removed outlier: 3.535A pdb=" N THR A2222 " --> pdb=" O GLN A2218 " (cutoff:3.500A) Processing helix chain 'A' and resid 2238 through 2242 Processing helix chain 'A' and resid 2244 through 2246 No H-bonds generated for 'chain 'A' and resid 2244 through 2246' Processing helix chain 'A' and resid 2247 through 2269 Processing helix chain 'A' and resid 2273 through 2290 Processing helix chain 'A' and resid 2290 through 2298 Processing helix chain 'A' and resid 2299 through 2301 No H-bonds generated for 'chain 'A' and resid 2299 through 2301' Processing helix chain 'A' and resid 2302 through 2322 Processing helix chain 'A' and resid 2355 through 2372 removed outlier: 3.749A pdb=" N THR A2359 " --> pdb=" O PRO A2355 " (cutoff:3.500A) Processing helix chain 'A' and resid 2380 through 2384 Processing helix chain 'A' and resid 2390 through 2402 Processing helix chain 'A' and resid 2407 through 2413 removed outlier: 3.825A pdb=" N VAL A2413 " --> pdb=" O SER A2409 " (cutoff:3.500A) Processing helix chain 'A' and resid 2414 through 2420 removed outlier: 3.794A pdb=" N TRP A2418 " --> pdb=" O PRO A2414 " (cutoff:3.500A) Processing helix chain 'A' and resid 2440 through 2444 Processing helix chain 'A' and resid 2447 through 2459 Processing helix chain 'A' and resid 2462 through 2478 Processing helix chain 'A' and resid 2497 through 2515 removed outlier: 3.863A pdb=" N ALA A2515 " --> pdb=" O LEU A2511 " (cutoff:3.500A) Processing helix chain 'A' and resid 2538 through 2542 removed outlier: 3.621A pdb=" N LEU A2541 " --> pdb=" O LEU A2538 " (cutoff:3.500A) Processing helix chain 'A' and resid 2543 through 2565 removed outlier: 3.576A pdb=" N LYS A2548 " --> pdb=" O ARG A2544 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A2549 " --> pdb=" O PHE A2545 " (cutoff:3.500A) Processing helix chain 'A' and resid 2595 through 2599 Processing helix chain 'A' and resid 2620 through 2628 removed outlier: 3.538A pdb=" N ASN A2628 " --> pdb=" O VAL A2624 " (cutoff:3.500A) Processing helix chain 'A' and resid 2669 through 2686 removed outlier: 4.342A pdb=" N LEU A2677 " --> pdb=" O CYS A2673 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU A2678 " --> pdb=" O SER A2674 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N LEU A2680 " --> pdb=" O PHE A2676 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A2682 " --> pdb=" O LEU A2678 " (cutoff:3.500A) Processing helix chain 'A' and resid 2697 through 2710 Processing helix chain 'A' and resid 2711 through 2713 No H-bonds generated for 'chain 'A' and resid 2711 through 2713' Processing helix chain 'A' and resid 2719 through 2725 removed outlier: 3.987A pdb=" N TYR A2723 " --> pdb=" O PHE A2719 " (cutoff:3.500A) Processing helix chain 'A' and resid 2784 through 2792 removed outlier: 6.254A pdb=" N TYR A2790 " --> pdb=" O HIS A2786 " (cutoff:3.500A) Processing helix chain 'A' and resid 2829 through 2845 Processing helix chain 'A' and resid 2856 through 2865 removed outlier: 3.763A pdb=" N GLY A2862 " --> pdb=" O ILE A2858 " (cutoff:3.500A) Processing helix chain 'A' and resid 2873 through 2889 removed outlier: 3.616A pdb=" N LEU A2889 " --> pdb=" O GLU A2885 " (cutoff:3.500A) Processing helix chain 'A' and resid 2890 through 2892 No H-bonds generated for 'chain 'A' and resid 2890 through 2892' Processing helix chain 'A' and resid 2914 through 2930 Processing helix chain 'A' and resid 2956 through 2970 removed outlier: 4.420A pdb=" N LEU A2963 " --> pdb=" O ARG A2959 " (cutoff:3.500A) Processing helix chain 'A' and resid 2971 through 2990 Proline residue: A2983 - end of helix Processing helix chain 'A' and resid 2991 through 3005 removed outlier: 4.662A pdb=" N ASN A2997 " --> pdb=" O GLN A2993 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LYS A2998 " --> pdb=" O ASP A2994 " (cutoff:3.500A) Processing helix chain 'A' and resid 3010 through 3029 removed outlier: 4.222A pdb=" N THR A3016 " --> pdb=" O GLN A3012 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL A3017 " --> pdb=" O PHE A3013 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR A3019 " --> pdb=" O ALA A3015 " (cutoff:3.500A) Processing helix chain 'A' and resid 3032 through 3048 removed outlier: 5.239A pdb=" N VAL A3038 " --> pdb=" O VAL A3034 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N SER A3043 " --> pdb=" O MET A3039 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ASN A3044 " --> pdb=" O LEU A3040 " (cutoff:3.500A) Processing helix chain 'A' and resid 3050 through 3066 Processing helix chain 'A' and resid 3074 through 3081 Processing helix chain 'A' and resid 3086 through 3104 Processing helix chain 'A' and resid 3108 through 3123 removed outlier: 3.626A pdb=" N VAL A3121 " --> pdb=" O VAL A3117 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A3123 " --> pdb=" O GLU A3119 " (cutoff:3.500A) Processing helix chain 'A' and resid 3127 through 3134 removed outlier: 3.713A pdb=" N ARG A3130 " --> pdb=" O PRO A3127 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 106 removed outlier: 3.994A pdb=" N LEU B 88 " --> pdb=" O PRO B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 135 Processing helix chain 'B' and resid 137 through 155 Processing helix chain 'B' and resid 157 through 173 removed outlier: 3.959A pdb=" N GLY B 163 " --> pdb=" O ALA B 159 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS B 164 " --> pdb=" O ALA B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 194 Processing helix chain 'B' and resid 196 through 216 removed outlier: 3.519A pdb=" N SER B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 281 removed outlier: 3.642A pdb=" N VAL B 265 " --> pdb=" O ALA B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 298 removed outlier: 3.770A pdb=" N LYS B 297 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR B 298 " --> pdb=" O THR B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 331 removed outlier: 3.668A pdb=" N HIS B 330 " --> pdb=" O VAL B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 345 Processing helix chain 'B' and resid 349 through 365 Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 6 removed outlier: 5.760A pdb=" N ILE C 12 " --> pdb=" O TRP C 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 2 through 5 1302 hydrogen bonds defined for protein. 3783 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: 10.55 Time building geometry restraints manager: 4.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.88: 10 0.88 - 1.13: 20720 1.13 - 1.37: 6908 1.37 - 1.61: 13775 1.61 - 1.85: 187 Bond restraints: 41600 Sorted by residual: bond pdb=" CZ ARG B 273 " pdb=" NH2 ARG B 273 " ideal model delta sigma weight residual 1.330 1.166 0.164 1.30e-02 5.92e+03 1.60e+02 bond pdb=" CZ ARG A2544 " pdb=" NH2 ARG A2544 " ideal model delta sigma weight residual 1.330 1.167 0.163 1.30e-02 5.92e+03 1.57e+02 bond pdb=" CZ ARG A2127 " pdb=" NH1 ARG A2127 " ideal model delta sigma weight residual 1.323 1.156 0.167 1.40e-02 5.10e+03 1.43e+02 bond pdb=" C ACE D 1 " pdb=" N DTY D 2 " ideal model delta sigma weight residual 1.329 1.548 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" CE LYS A3020 " pdb=" NZ LYS A3020 " ideal model delta sigma weight residual 1.489 1.176 0.313 3.00e-02 1.11e+03 1.09e+02 ... (remaining 41595 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.48: 72774 5.48 - 10.96: 2512 10.96 - 16.44: 89 16.44 - 21.93: 4 21.93 - 27.41: 7 Bond angle restraints: 75386 Sorted by residual: angle pdb=" O VAL A3018 " pdb=" C VAL A3018 " pdb=" N TYR A3019 " ideal model delta sigma weight residual 122.31 94.90 27.41 1.36e+00 5.41e-01 4.06e+02 angle pdb=" C SER A3066 " pdb=" N THR A3067 " pdb=" CA THR A3067 " ideal model delta sigma weight residual 120.79 144.63 -23.84 1.39e+00 5.18e-01 2.94e+02 angle pdb=" CD ARG A2127 " pdb=" NE ARG A2127 " pdb=" CZ ARG A2127 " ideal model delta sigma weight residual 124.40 147.11 -22.71 1.40e+00 5.10e-01 2.63e+02 angle pdb=" O SER A3066 " pdb=" C SER A3066 " pdb=" N THR A3067 " ideal model delta sigma weight residual 122.81 106.90 15.91 1.23e+00 6.61e-01 1.67e+02 angle pdb=" CA SER A3066 " pdb=" C SER A3066 " pdb=" N THR A3067 " ideal model delta sigma weight residual 115.56 131.75 -16.19 1.30e+00 5.92e-01 1.55e+02 ... (remaining 75381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 17715 17.71 - 35.42: 1019 35.42 - 53.13: 354 53.13 - 70.84: 369 70.84 - 88.55: 33 Dihedral angle restraints: 19490 sinusoidal: 10709 harmonic: 8781 Sorted by residual: dihedral pdb=" CH3 ACE C 1 " pdb=" C ACE C 1 " pdb=" N DTY C 2 " pdb=" CA DTY C 2 " ideal model delta sinusoidal sigma weight residual -180.00 -94.48 -85.52 1 5.00e+00 4.00e-02 3.54e+02 dihedral pdb=" CH3 ACE E 1 " pdb=" C ACE E 1 " pdb=" N TYR E 2 " pdb=" CA TYR E 2 " ideal model delta sinusoidal sigma weight residual -180.00 -96.03 -83.97 1 5.00e+00 4.00e-02 3.44e+02 dihedral pdb=" C VAL A2518 " pdb=" N VAL A2518 " pdb=" CA VAL A2518 " pdb=" CB VAL A2518 " ideal model delta harmonic sigma weight residual -122.00 -139.62 17.62 0 2.50e+00 1.60e-01 4.97e+01 ... (remaining 19487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 2803 0.123 - 0.246: 486 0.246 - 0.369: 50 0.369 - 0.492: 10 0.492 - 0.615: 2 Chirality restraints: 3351 Sorted by residual: chirality pdb=" CA DTY C 2 " pdb=" N DTY C 2 " pdb=" C DTY C 2 " pdb=" CB DTY C 2 " both_signs ideal model delta sigma weight residual False -2.51 -1.90 -0.61 2.00e-01 2.50e+01 9.45e+00 chirality pdb=" CA VAL A2518 " pdb=" N VAL A2518 " pdb=" C VAL A2518 " pdb=" CB VAL A2518 " both_signs ideal model delta sigma weight residual False 2.44 1.84 0.60 2.00e-01 2.50e+01 9.10e+00 chirality pdb=" CA LEU A 327 " pdb=" N LEU A 327 " pdb=" C LEU A 327 " pdb=" CB LEU A 327 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.02e+00 ... (remaining 3348 not shown) Planarity restraints: 6001 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ACE E 1 " 0.075 2.00e-02 2.50e+03 5.02e-01 3.78e+03 pdb=" O ACE E 1 " 0.596 2.00e-02 2.50e+03 pdb=" CH3 ACE E 1 " -0.332 2.00e-02 2.50e+03 pdb=" N TYR E 2 " -0.412 2.00e-02 2.50e+03 pdb=" CA TYR E 2 " 0.695 2.00e-02 2.50e+03 pdb=" H TYR E 2 " -0.623 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE C 1 " -0.108 2.00e-02 2.50e+03 4.08e-01 2.08e+03 pdb=" O ACE C 1 " 0.161 2.00e-02 2.50e+03 pdb=" CH3 ACE C 1 " 0.157 2.00e-02 2.50e+03 pdb=" N DTY C 2 " -0.717 2.00e-02 2.50e+03 pdb=" CA DTY C 2 " 0.507 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A3018 " -0.100 2.00e-02 2.50e+03 1.66e-01 2.75e+02 pdb=" C VAL A3018 " 0.287 2.00e-02 2.50e+03 pdb=" O VAL A3018 " -0.094 2.00e-02 2.50e+03 pdb=" N TYR A3019 " -0.093 2.00e-02 2.50e+03 ... (remaining 5998 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 1408 2.12 - 2.74: 64687 2.74 - 3.36: 124414 3.36 - 3.98: 163749 3.98 - 4.60: 238434 Nonbonded interactions: 592692 Sorted by model distance: nonbonded pdb=" O ACE C 1 " pdb=" OE1 GLN A2055 " model vdw 1.499 2.800 nonbonded pdb=" O CYS C 18 " pdb=" O LEU A3085 " model vdw 1.545 2.800 nonbonded pdb=" HH TYR A1508 " pdb=" OD1 ASP A1550 " model vdw 1.584 2.450 nonbonded pdb=" HG SER A2152 " pdb=" OXT VAL B 371 " model vdw 1.587 2.450 nonbonded pdb=" OE2 GLU A 175 " pdb=" HG SER A 184 " model vdw 1.592 2.450 ... (remaining 592687 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 9.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.250 Extract box with map and model: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 39.120 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 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 : 0.014 0.313 20808 Z= 0.866 Angle : 1.892 27.406 28248 Z= 1.286 Chirality : 0.097 0.615 3351 Planarity : 0.020 0.408 3555 Dihedral : 14.058 88.546 7621 Min Nonbonded Distance : 1.499 Molprobity Statistics. All-atom Clashscore : 0.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.93 % Allowed : 4.73 % Favored : 94.35 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.16), residues: 2531 helix: -0.54 (0.11), residues: 1798 sheet: None (None), residues: 0 loop : -0.05 (0.25), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A2716 TYR 0.133 0.023 TYR A1464 PHE 0.122 0.014 PHE C 17 TRP 0.107 0.020 TRP A1128 HIS 0.021 0.003 HIS C 15 Details of bonding type rmsd covalent geometry : bond 0.01373 (20802) covalent geometry : angle 1.89170 (28248) hydrogen bonds : bond 0.19046 ( 1302) hydrogen bonds : angle 6.64104 ( 3783) Misc. bond : bond 0.08858 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 610 time to evaluate : 1.149 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: 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: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.6436 (m-40) cc_final: 0.6170 (m-40) REVERT: A 131 MET cc_start: 0.6085 (mmm) cc_final: 0.5866 (mmm) REVERT: A 745 GLU cc_start: 0.6999 (tt0) cc_final: 0.6424 (tt0) REVERT: A 1465 CYS cc_start: 0.7328 (t) cc_final: 0.7074 (t) REVERT: A 1929 LEU cc_start: 0.7960 (mt) cc_final: 0.7725 (mt) REVERT: A 1935 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6970 (mm-30) REVERT: A 2423 SER cc_start: 0.7607 (p) cc_final: 0.7312 (t) REVERT: A 2704 ARG cc_start: 0.7352 (ttt90) cc_final: 0.5985 (tpp-160) REVERT: A 2723 TYR cc_start: 0.4448 (m-10) cc_final: 0.3518 (m-10) REVERT: A 2918 MET cc_start: 0.8092 (tpp) cc_final: 0.7658 (tpp) REVERT: A 3064 SER cc_start: 0.7446 (m) cc_final: 0.7228 (t) outliers start: 21 outliers final: 7 residues processed: 624 average time/residue: 1.2862 time to fit residues: 921.8700 Evaluate side-chains 549 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 542 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain E residue 17 CYS Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1564 LYS Chi-restraints excluded: chain A residue 2469 THR Chi-restraints excluded: chain A residue 3107 GLU Chi-restraints excluded: chain B residue 191 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 9 ASN A 164 ASN A 802 ASN A 959 GLN A 990 ASN A1445 GLN A1637 ASN A1858 GLN A1892 ASN A1965 ASN A1977 GLN A2139 ASN A2183 GLN A2265 HIS A2289 GLN A2383 ASN A2561 GLN A2573 HIS A2602 GLN ** A2628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2844 ASN B 182 GLN B 313 GLN B 323 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.155719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.137635 restraints weight = 69662.873| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 1.44 r_work: 0.3733 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 20808 Z= 0.203 Angle : 0.708 10.313 28248 Z= 0.382 Chirality : 0.041 0.242 3351 Planarity : 0.006 0.073 3555 Dihedral : 7.028 165.695 2792 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.65 % Favored : 97.31 % Rotamer: Outliers : 2.39 % Allowed : 10.29 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.16), residues: 2531 helix: 0.64 (0.12), residues: 1813 sheet: None (None), residues: 0 loop : 0.11 (0.25), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A2063 TYR 0.023 0.002 TYR B 298 PHE 0.020 0.002 PHE A3061 TRP 0.019 0.002 TRP A2418 HIS 0.007 0.002 HIS A1847 Details of bonding type rmsd covalent geometry : bond 0.00447 (20802) covalent geometry : angle 0.70834 (28248) hydrogen bonds : bond 0.06815 ( 1302) hydrogen bonds : angle 4.85414 ( 3783) Misc. bond : bond 0.00300 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 565 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.6759 (m-40) cc_final: 0.6510 (m-40) REVERT: A 131 MET cc_start: 0.6267 (mmm) cc_final: 0.6066 (mmm) REVERT: A 241 PHE cc_start: 0.8092 (m-80) cc_final: 0.7878 (m-80) REVERT: A 254 LEU cc_start: 0.8605 (mt) cc_final: 0.8403 (mt) REVERT: A 745 GLU cc_start: 0.7230 (tt0) cc_final: 0.6798 (tt0) REVERT: A 746 TYR cc_start: 0.8758 (m-80) cc_final: 0.8143 (m-80) REVERT: A 826 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7324 (tttt) REVERT: A 1756 ASP cc_start: 0.7448 (m-30) cc_final: 0.7079 (m-30) REVERT: A 1935 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7536 (mm-30) REVERT: A 2011 ASP cc_start: 0.7053 (t0) cc_final: 0.6757 (t0) REVERT: A 2016 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7062 (mtp85) REVERT: A 2035 MET cc_start: 0.6478 (mpt) cc_final: 0.6211 (mpt) REVERT: A 2704 ARG cc_start: 0.7627 (ttt90) cc_final: 0.6094 (tpp-160) REVERT: A 2723 TYR cc_start: 0.5265 (m-10) cc_final: 0.4033 (m-80) REVERT: A 2918 MET cc_start: 0.8169 (tpp) cc_final: 0.7929 (tpp) REVERT: A 2928 MET cc_start: 0.7996 (mmm) cc_final: 0.7693 (mmm) REVERT: A 2989 PHE cc_start: 0.8168 (m-80) cc_final: 0.7961 (m-80) outliers start: 54 outliers final: 18 residues processed: 588 average time/residue: 1.4058 time to fit residues: 943.4145 Evaluate side-chains 559 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 539 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 826 LYS Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1151 ILE Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1279 ILE Chi-restraints excluded: chain A residue 1521 LYS Chi-restraints excluded: chain A residue 1564 LYS Chi-restraints excluded: chain A residue 1652 ASP Chi-restraints excluded: chain A residue 1670 THR Chi-restraints excluded: chain A residue 1690 THR Chi-restraints excluded: chain A residue 1711 THR Chi-restraints excluded: chain A residue 1822 LEU Chi-restraints excluded: chain A residue 1825 ARG Chi-restraints excluded: chain A residue 2016 ARG Chi-restraints excluded: chain A residue 2219 SER Chi-restraints excluded: chain A residue 2670 ILE Chi-restraints excluded: chain A residue 3107 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 214 optimal weight: 1.9990 chunk 254 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 236 optimal weight: 0.6980 chunk 74 optimal weight: 0.0050 chunk 18 optimal weight: 0.9990 chunk 166 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 chunk 195 optimal weight: 0.6980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 GLN A 373 ASN A1545 GLN A1934 HIS A1977 GLN A2506 GLN A2628 ASN B 191 GLN B 293 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.155421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.137697 restraints weight = 70076.470| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 1.43 r_work: 0.3743 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20808 Z= 0.163 Angle : 0.606 10.273 28248 Z= 0.320 Chirality : 0.038 0.140 3351 Planarity : 0.005 0.049 3555 Dihedral : 6.350 170.054 2785 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.03 % Allowed : 12.59 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.17), residues: 2531 helix: 1.09 (0.12), residues: 1801 sheet: None (None), residues: 0 loop : 0.11 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1510 TYR 0.020 0.002 TYR B 298 PHE 0.015 0.002 PHE A1955 TRP 0.011 0.002 TRP A 190 HIS 0.006 0.001 HIS A2311 Details of bonding type rmsd covalent geometry : bond 0.00359 (20802) covalent geometry : angle 0.60623 (28248) hydrogen bonds : bond 0.05600 ( 1302) hydrogen bonds : angle 4.49908 ( 3783) Misc. bond : bond 0.00160 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 547 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.6804 (m-40) cc_final: 0.6551 (m-40) REVERT: A 241 PHE cc_start: 0.8079 (m-80) cc_final: 0.7856 (m-80) REVERT: A 745 GLU cc_start: 0.7267 (tt0) cc_final: 0.6845 (tt0) REVERT: A 746 TYR cc_start: 0.8747 (m-80) cc_final: 0.8185 (m-80) REVERT: A 826 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.7268 (tttt) REVERT: A 2016 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7012 (mtp85) REVERT: A 2035 MET cc_start: 0.6521 (mpt) cc_final: 0.6249 (mpt) REVERT: A 2704 ARG cc_start: 0.7602 (ttt90) cc_final: 0.6124 (tpp-160) REVERT: A 2723 TYR cc_start: 0.5254 (m-10) cc_final: 0.3807 (m-80) outliers start: 46 outliers final: 19 residues processed: 564 average time/residue: 1.2602 time to fit residues: 815.1110 Evaluate side-chains 553 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 532 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 17 CYS Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 826 LYS Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 995 ILE Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1279 ILE Chi-restraints excluded: chain A residue 1313 CYS Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1564 LYS Chi-restraints excluded: chain A residue 1670 THR Chi-restraints excluded: chain A residue 1711 THR Chi-restraints excluded: chain A residue 1825 ARG Chi-restraints excluded: chain A residue 2016 ARG Chi-restraints excluded: chain A residue 2564 VAL Chi-restraints excluded: chain A residue 2670 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 211 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 252 optimal weight: 1.9990 chunk 47 optimal weight: 0.0270 chunk 173 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 154 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1545 GLN A1965 ASN A2270 GLN A2465 GLN A3077 HIS B 100 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.154636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.136675 restraints weight = 69639.393| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 1.43 r_work: 0.3728 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20808 Z= 0.190 Angle : 0.592 8.993 28248 Z= 0.313 Chirality : 0.038 0.139 3351 Planarity : 0.005 0.045 3555 Dihedral : 6.128 175.456 2782 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.03 % Allowed : 13.69 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.17), residues: 2531 helix: 1.17 (0.12), residues: 1807 sheet: None (None), residues: 0 loop : -0.05 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 833 TYR 0.020 0.002 TYR A1508 PHE 0.019 0.002 PHE A2985 TRP 0.011 0.002 TRP A2204 HIS 0.006 0.001 HIS A2311 Details of bonding type rmsd covalent geometry : bond 0.00434 (20802) covalent geometry : angle 0.59183 (28248) hydrogen bonds : bond 0.05537 ( 1302) hydrogen bonds : angle 4.41838 ( 3783) Misc. bond : bond 0.00332 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 538 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.6790 (m-40) cc_final: 0.6542 (m-40) REVERT: A 223 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6958 (mp0) REVERT: A 241 PHE cc_start: 0.8091 (m-80) cc_final: 0.7831 (m-80) REVERT: A 745 GLU cc_start: 0.7202 (tt0) cc_final: 0.6869 (tt0) REVERT: A 746 TYR cc_start: 0.8749 (m-80) cc_final: 0.8181 (m-80) REVERT: A 798 THR cc_start: 0.7966 (m) cc_final: 0.7572 (p) REVERT: A 826 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7273 (tttt) REVERT: A 2016 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7120 (mtp85) REVERT: A 2035 MET cc_start: 0.6479 (mpt) cc_final: 0.6212 (mpt) REVERT: A 2704 ARG cc_start: 0.7621 (ttt90) cc_final: 0.6150 (tpp-160) REVERT: A 2723 TYR cc_start: 0.5267 (m-10) cc_final: 0.3757 (m-80) REVERT: A 3081 ARG cc_start: 0.7070 (mtp85) cc_final: 0.6622 (mmp80) outliers start: 46 outliers final: 25 residues processed: 558 average time/residue: 1.2689 time to fit residues: 811.4937 Evaluate side-chains 554 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 526 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 17 CYS Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 826 LYS Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 995 ILE Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1279 ILE Chi-restraints excluded: chain A residue 1313 CYS Chi-restraints excluded: chain A residue 1564 LYS Chi-restraints excluded: chain A residue 1670 THR Chi-restraints excluded: chain A residue 1711 THR Chi-restraints excluded: chain A residue 1825 ARG Chi-restraints excluded: chain A residue 2016 ARG Chi-restraints excluded: chain A residue 2030 MET Chi-restraints excluded: chain A residue 2128 ILE Chi-restraints excluded: chain A residue 2219 SER Chi-restraints excluded: chain A residue 2564 VAL Chi-restraints excluded: chain A residue 2670 ILE Chi-restraints excluded: chain A residue 2834 MET Chi-restraints excluded: chain B residue 337 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 209 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 238 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 182 optimal weight: 0.9990 chunk 230 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 196 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1515 GLN A1545 GLN A1847 HIS A1927 GLN A1977 GLN A2162 GLN A2373 GLN A2465 GLN A2506 GLN A3077 HIS B 100 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.153252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.135269 restraints weight = 69474.818| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 1.43 r_work: 0.3711 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3571 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 20808 Z= 0.254 Angle : 0.629 8.343 28248 Z= 0.333 Chirality : 0.041 0.148 3351 Planarity : 0.005 0.051 3555 Dihedral : 6.158 174.271 2782 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.03 % Allowed : 14.49 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.17), residues: 2531 helix: 1.01 (0.12), residues: 1800 sheet: None (None), residues: 0 loop : -0.23 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1683 TYR 0.023 0.002 TYR A1464 PHE 0.021 0.002 PHE A2985 TRP 0.015 0.002 TRP A2204 HIS 0.008 0.001 HIS A1626 Details of bonding type rmsd covalent geometry : bond 0.00591 (20802) covalent geometry : angle 0.62875 (28248) hydrogen bonds : bond 0.06027 ( 1302) hydrogen bonds : angle 4.48218 ( 3783) Misc. bond : bond 0.00069 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 543 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.6736 (m-40) cc_final: 0.6487 (m-40) REVERT: A 223 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7106 (pm20) REVERT: A 241 PHE cc_start: 0.8121 (m-80) cc_final: 0.7855 (m-80) REVERT: A 798 THR cc_start: 0.8056 (m) cc_final: 0.7648 (p) REVERT: A 826 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7287 (tttt) REVERT: A 1606 LYS cc_start: 0.8162 (mttt) cc_final: 0.7951 (mttm) REVERT: A 2016 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7283 (mtp180) REVERT: A 2035 MET cc_start: 0.6517 (mpt) cc_final: 0.6208 (mpt) REVERT: A 2704 ARG cc_start: 0.7640 (ttt90) cc_final: 0.6167 (tpp-160) REVERT: A 2723 TYR cc_start: 0.5211 (m-10) cc_final: 0.3804 (m-80) REVERT: A 3081 ARG cc_start: 0.7129 (mtp85) cc_final: 0.6617 (mmp80) outliers start: 46 outliers final: 25 residues processed: 561 average time/residue: 1.3501 time to fit residues: 866.3116 Evaluate side-chains 563 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 535 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 17 CYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 826 LYS Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 995 ILE Chi-restraints excluded: chain A residue 1001 GLU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1279 ILE Chi-restraints excluded: chain A residue 1313 CYS Chi-restraints excluded: chain A residue 1564 LYS Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1670 THR Chi-restraints excluded: chain A residue 1711 THR Chi-restraints excluded: chain A residue 1822 LEU Chi-restraints excluded: chain A residue 1825 ARG Chi-restraints excluded: chain A residue 2016 ARG Chi-restraints excluded: chain A residue 2030 MET Chi-restraints excluded: chain A residue 2219 SER Chi-restraints excluded: chain A residue 2243 LEU Chi-restraints excluded: chain A residue 2370 GLU Chi-restraints excluded: chain A residue 2834 MET Chi-restraints excluded: chain B residue 296 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 57 optimal weight: 0.9990 chunk 234 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 247 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 203 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 30 optimal weight: 0.1980 chunk 26 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1463 ASN A1545 GLN A1858 GLN A1965 ASN A1977 GLN A2465 GLN A3077 HIS B 100 GLN ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.154141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.136252 restraints weight = 69404.075| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 1.43 r_work: 0.3720 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 20808 Z= 0.195 Angle : 0.586 8.047 28248 Z= 0.309 Chirality : 0.038 0.184 3351 Planarity : 0.005 0.053 3555 Dihedral : 6.058 175.636 2782 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.86 % Allowed : 15.72 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.17), residues: 2531 helix: 1.19 (0.12), residues: 1800 sheet: None (None), residues: 0 loop : -0.19 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2553 TYR 0.026 0.002 TYR A1464 PHE 0.018 0.002 PHE A1500 TRP 0.014 0.002 TRP A2470 HIS 0.009 0.001 HIS A2311 Details of bonding type rmsd covalent geometry : bond 0.00449 (20802) covalent geometry : angle 0.58606 (28248) hydrogen bonds : bond 0.05467 ( 1302) hydrogen bonds : angle 4.36819 ( 3783) Misc. bond : bond 0.00119 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 537 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.6674 (m-40) cc_final: 0.6454 (m-40) REVERT: A 223 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.7057 (pm20) REVERT: A 241 PHE cc_start: 0.8092 (m-80) cc_final: 0.7847 (m-80) REVERT: A 798 THR cc_start: 0.8047 (m) cc_final: 0.7692 (p) REVERT: A 826 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7287 (tttt) REVERT: A 894 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.7104 (mtt90) REVERT: A 1606 LYS cc_start: 0.8151 (mttt) cc_final: 0.7943 (mttm) REVERT: A 1610 ARG cc_start: 0.7805 (tpp-160) cc_final: 0.7580 (tpp-160) REVERT: A 2016 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7200 (mtp180) REVERT: A 2035 MET cc_start: 0.6438 (mpt) cc_final: 0.6115 (mpt) REVERT: A 2538 LEU cc_start: 0.7910 (mt) cc_final: 0.7707 (mt) REVERT: A 2704 ARG cc_start: 0.7605 (ttt90) cc_final: 0.6165 (tpp-160) REVERT: A 2723 TYR cc_start: 0.5117 (m-10) cc_final: 0.3701 (m-80) REVERT: A 2860 MET cc_start: 0.5434 (tpt) cc_final: 0.5138 (tpp) REVERT: A 3081 ARG cc_start: 0.7151 (mtp85) cc_final: 0.6609 (mmp80) outliers start: 42 outliers final: 25 residues processed: 553 average time/residue: 1.3300 time to fit residues: 842.4657 Evaluate side-chains 557 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 528 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 17 CYS Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 826 LYS Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 894 ARG Chi-restraints excluded: chain A residue 995 ILE Chi-restraints excluded: chain A residue 1001 GLU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1270 ARG Chi-restraints excluded: chain A residue 1279 ILE Chi-restraints excluded: chain A residue 1313 CYS Chi-restraints excluded: chain A residue 1564 LYS Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1670 THR Chi-restraints excluded: chain A residue 1711 THR Chi-restraints excluded: chain A residue 1822 LEU Chi-restraints excluded: chain A residue 1825 ARG Chi-restraints excluded: chain A residue 2016 ARG Chi-restraints excluded: chain A residue 2030 MET Chi-restraints excluded: chain A residue 2243 LEU Chi-restraints excluded: chain A residue 2564 VAL Chi-restraints excluded: chain A residue 2918 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 139 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 217 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 247 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN A1545 GLN A1858 GLN A1977 GLN A2465 GLN A2506 GLN A2997 ASN A3077 HIS B 100 GLN ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.154388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.136754 restraints weight = 69970.875| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 1.42 r_work: 0.3726 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20808 Z= 0.173 Angle : 0.571 7.622 28248 Z= 0.300 Chirality : 0.037 0.164 3351 Planarity : 0.005 0.079 3555 Dihedral : 5.979 176.500 2782 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.86 % Allowed : 16.03 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.17), residues: 2531 helix: 1.33 (0.12), residues: 1800 sheet: None (None), residues: 0 loop : -0.14 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A2607 TYR 0.025 0.002 TYR A1464 PHE 0.020 0.002 PHE A1805 TRP 0.014 0.002 TRP A2204 HIS 0.011 0.001 HIS A2830 Details of bonding type rmsd covalent geometry : bond 0.00395 (20802) covalent geometry : angle 0.57059 (28248) hydrogen bonds : bond 0.05202 ( 1302) hydrogen bonds : angle 4.30600 ( 3783) Misc. bond : bond 0.00104 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 537 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.6668 (m-40) cc_final: 0.6443 (m-40) REVERT: A 223 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.7009 (mp0) REVERT: A 241 PHE cc_start: 0.8079 (m-80) cc_final: 0.7840 (m-80) REVERT: A 798 THR cc_start: 0.8044 (m) cc_final: 0.7681 (p) REVERT: A 894 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.7105 (mtt90) REVERT: A 1610 ARG cc_start: 0.7772 (tpp-160) cc_final: 0.7406 (tpp-160) REVERT: A 2016 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7627 (mtm-85) REVERT: A 2035 MET cc_start: 0.6466 (mpt) cc_final: 0.6109 (mpt) REVERT: A 2146 LEU cc_start: 0.8358 (mt) cc_final: 0.8150 (mt) REVERT: A 2538 LEU cc_start: 0.7910 (mt) cc_final: 0.7699 (mt) REVERT: A 2704 ARG cc_start: 0.7605 (ttt90) cc_final: 0.6143 (tpp-160) REVERT: A 2723 TYR cc_start: 0.5113 (m-10) cc_final: 0.3705 (m-80) outliers start: 42 outliers final: 26 residues processed: 555 average time/residue: 1.3054 time to fit residues: 830.4024 Evaluate side-chains 557 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 528 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 17 CYS Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 894 ARG Chi-restraints excluded: chain A residue 995 ILE Chi-restraints excluded: chain A residue 1001 GLU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1270 ARG Chi-restraints excluded: chain A residue 1279 ILE Chi-restraints excluded: chain A residue 1313 CYS Chi-restraints excluded: chain A residue 1564 LYS Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1670 THR Chi-restraints excluded: chain A residue 1711 THR Chi-restraints excluded: chain A residue 1755 GLU Chi-restraints excluded: chain A residue 1825 ARG Chi-restraints excluded: chain A residue 2016 ARG Chi-restraints excluded: chain A residue 2030 MET Chi-restraints excluded: chain A residue 2243 LEU Chi-restraints excluded: chain A residue 2270 GLN Chi-restraints excluded: chain A residue 2727 THR Chi-restraints excluded: chain B residue 296 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 11 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 253 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1545 GLN A1858 GLN A1977 GLN A2465 GLN A3077 HIS B 100 GLN ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.152629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.134895 restraints weight = 69275.778| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 1.42 r_work: 0.3705 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 20808 Z= 0.264 Angle : 0.618 7.206 28248 Z= 0.328 Chirality : 0.041 0.149 3351 Planarity : 0.005 0.059 3555 Dihedral : 6.079 175.177 2782 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.08 % Allowed : 16.48 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.17), residues: 2531 helix: 1.06 (0.12), residues: 1803 sheet: None (None), residues: 0 loop : -0.29 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1607 TYR 0.029 0.002 TYR A1464 PHE 0.024 0.002 PHE A1500 TRP 0.019 0.002 TRP A2204 HIS 0.009 0.001 HIS A2830 Details of bonding type rmsd covalent geometry : bond 0.00616 (20802) covalent geometry : angle 0.61782 (28248) hydrogen bonds : bond 0.05888 ( 1302) hydrogen bonds : angle 4.42059 ( 3783) Misc. bond : bond 0.00118 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 536 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.6664 (m-40) cc_final: 0.6424 (m-40) REVERT: A 223 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7054 (mp0) REVERT: A 241 PHE cc_start: 0.8099 (m-80) cc_final: 0.7848 (m-80) REVERT: A 793 MET cc_start: 0.8308 (mmm) cc_final: 0.8051 (mmp) REVERT: A 798 THR cc_start: 0.8036 (m) cc_final: 0.7709 (p) REVERT: A 826 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7292 (tttt) REVERT: A 894 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.7115 (mtt180) REVERT: A 2035 MET cc_start: 0.6547 (mpt) cc_final: 0.6150 (mpt) REVERT: A 2146 LEU cc_start: 0.8351 (mt) cc_final: 0.8145 (mt) REVERT: A 2538 LEU cc_start: 0.7983 (mt) cc_final: 0.7777 (mt) REVERT: A 2704 ARG cc_start: 0.7630 (ttt90) cc_final: 0.6186 (tpp-160) REVERT: A 2723 TYR cc_start: 0.5145 (m-10) cc_final: 0.3828 (m-10) outliers start: 47 outliers final: 27 residues processed: 556 average time/residue: 1.4038 time to fit residues: 893.2688 Evaluate side-chains 558 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 528 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain E residue 17 CYS Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 826 LYS Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 894 ARG Chi-restraints excluded: chain A residue 995 ILE Chi-restraints excluded: chain A residue 1001 GLU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1279 ILE Chi-restraints excluded: chain A residue 1313 CYS Chi-restraints excluded: chain A residue 1485 GLU Chi-restraints excluded: chain A residue 1564 LYS Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1661 THR Chi-restraints excluded: chain A residue 1670 THR Chi-restraints excluded: chain A residue 1711 THR Chi-restraints excluded: chain A residue 1755 GLU Chi-restraints excluded: chain A residue 1822 LEU Chi-restraints excluded: chain A residue 1825 ARG Chi-restraints excluded: chain A residue 2030 MET Chi-restraints excluded: chain A residue 2243 LEU Chi-restraints excluded: chain A residue 2727 THR Chi-restraints excluded: chain B residue 296 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 32 optimal weight: 0.6980 chunk 115 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 208 optimal weight: 1.9990 chunk 217 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 221 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 244 optimal weight: 0.9990 chunk 97 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1545 GLN A1858 GLN A1977 GLN A2270 GLN A2465 GLN A3077 HIS B 100 GLN ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.153550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.135806 restraints weight = 69402.130| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 1.43 r_work: 0.3717 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20808 Z= 0.186 Angle : 0.580 7.003 28248 Z= 0.306 Chirality : 0.037 0.143 3351 Planarity : 0.005 0.066 3555 Dihedral : 5.998 177.011 2782 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.63 % Allowed : 17.14 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.17), residues: 2531 helix: 1.27 (0.12), residues: 1801 sheet: None (None), residues: 0 loop : -0.23 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1607 TYR 0.028 0.002 TYR A1464 PHE 0.020 0.002 PHE A1500 TRP 0.019 0.002 TRP A2204 HIS 0.008 0.001 HIS A2830 Details of bonding type rmsd covalent geometry : bond 0.00425 (20802) covalent geometry : angle 0.58019 (28248) hydrogen bonds : bond 0.05318 ( 1302) hydrogen bonds : angle 4.33343 ( 3783) Misc. bond : bond 0.00104 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 536 time to evaluate : 1.067 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: A 111 ASN cc_start: 0.6669 (m-40) cc_final: 0.6439 (m-40) REVERT: A 241 PHE cc_start: 0.8084 (m-80) cc_final: 0.7799 (m-80) REVERT: A 793 MET cc_start: 0.8301 (mmm) cc_final: 0.8035 (mmp) REVERT: A 798 THR cc_start: 0.8025 (m) cc_final: 0.7698 (p) REVERT: A 894 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.7100 (mtt90) REVERT: A 2035 MET cc_start: 0.6491 (mpt) cc_final: 0.6115 (mpt) REVERT: A 2538 LEU cc_start: 0.7980 (mt) cc_final: 0.7766 (mt) REVERT: A 2704 ARG cc_start: 0.7593 (ttt90) cc_final: 0.6152 (tpp-160) REVERT: A 2723 TYR cc_start: 0.5154 (m-10) cc_final: 0.3829 (m-10) outliers start: 37 outliers final: 26 residues processed: 550 average time/residue: 1.1183 time to fit residues: 707.7334 Evaluate side-chains 558 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 531 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain E residue 17 CYS Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 894 ARG Chi-restraints excluded: chain A residue 995 ILE Chi-restraints excluded: chain A residue 1001 GLU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1279 ILE Chi-restraints excluded: chain A residue 1313 CYS Chi-restraints excluded: chain A residue 1564 LYS Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1661 THR Chi-restraints excluded: chain A residue 1670 THR Chi-restraints excluded: chain A residue 1711 THR Chi-restraints excluded: chain A residue 1755 GLU Chi-restraints excluded: chain A residue 1822 LEU Chi-restraints excluded: chain A residue 1825 ARG Chi-restraints excluded: chain A residue 2030 MET Chi-restraints excluded: chain A residue 2243 LEU Chi-restraints excluded: chain A residue 2727 THR Chi-restraints excluded: chain B residue 296 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 63 optimal weight: 0.0770 chunk 249 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 chunk 209 optimal weight: 0.9980 chunk 254 optimal weight: 0.9990 chunk 243 optimal weight: 0.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1545 GLN A1858 GLN A1977 GLN A3077 HIS B 100 GLN ** B 323 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 = 0.4038 r_free = 0.4038 target = 0.153857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.136128 restraints weight = 69182.561| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 1.42 r_work: 0.3720 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3587 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 20808 Z= 0.193 Angle : 0.583 7.138 28248 Z= 0.307 Chirality : 0.038 0.138 3351 Planarity : 0.005 0.082 3555 Dihedral : 5.969 176.804 2782 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.63 % Allowed : 17.49 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.17), residues: 2531 helix: 1.30 (0.12), residues: 1795 sheet: None (None), residues: 0 loop : -0.24 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1461 TYR 0.028 0.002 TYR A1464 PHE 0.023 0.002 PHE A1500 TRP 0.021 0.002 TRP A2204 HIS 0.006 0.001 HIS A2830 Details of bonding type rmsd covalent geometry : bond 0.00446 (20802) covalent geometry : angle 0.58315 (28248) hydrogen bonds : bond 0.05307 ( 1302) hydrogen bonds : angle 4.32198 ( 3783) Misc. bond : bond 0.00103 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 536 time to evaluate : 1.181 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: symmetry clash REVERT: A 111 ASN cc_start: 0.6653 (m-40) cc_final: 0.6436 (m-40) REVERT: A 241 PHE cc_start: 0.8066 (m-80) cc_final: 0.7784 (m-80) REVERT: A 793 MET cc_start: 0.8304 (mmm) cc_final: 0.8023 (mmp) REVERT: A 798 THR cc_start: 0.8046 (m) cc_final: 0.7700 (p) REVERT: A 826 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7275 (tttt) REVERT: A 894 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.7106 (mtt90) REVERT: A 2016 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7255 (mtm180) REVERT: A 2035 MET cc_start: 0.6457 (mpt) cc_final: 0.6132 (mpt) REVERT: A 2538 LEU cc_start: 0.7995 (mt) cc_final: 0.7778 (mt) REVERT: A 2704 ARG cc_start: 0.7596 (ttt90) cc_final: 0.6158 (tpp-160) REVERT: A 2723 TYR cc_start: 0.5152 (m-10) cc_final: 0.3850 (m-10) outliers start: 37 outliers final: 29 residues processed: 551 average time/residue: 1.2551 time to fit residues: 795.5988 Evaluate side-chains 562 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 530 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain E residue 17 CYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 750 GLN Chi-restraints excluded: chain A residue 826 LYS Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 894 ARG Chi-restraints excluded: chain A residue 995 ILE Chi-restraints excluded: chain A residue 1001 GLU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1270 ARG Chi-restraints excluded: chain A residue 1279 ILE Chi-restraints excluded: chain A residue 1313 CYS Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1564 LYS Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1616 ILE Chi-restraints excluded: chain A residue 1661 THR Chi-restraints excluded: chain A residue 1670 THR Chi-restraints excluded: chain A residue 1711 THR Chi-restraints excluded: chain A residue 1755 GLU Chi-restraints excluded: chain A residue 1822 LEU Chi-restraints excluded: chain A residue 1825 ARG Chi-restraints excluded: chain A residue 2016 ARG Chi-restraints excluded: chain A residue 2030 MET Chi-restraints excluded: chain A residue 2243 LEU Chi-restraints excluded: chain A residue 2727 THR Chi-restraints excluded: chain B residue 296 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 150 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 179 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 250 optimal weight: 2.9990 chunk 239 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 180 optimal weight: 0.5980 chunk 173 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN A 959 GLN A1545 GLN A1858 GLN A1892 ASN A2465 GLN A3077 HIS ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.153641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.135937 restraints weight = 69178.888| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 1.42 r_work: 0.3717 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 20808 Z= 0.206 Angle : 0.591 6.478 28248 Z= 0.311 Chirality : 0.038 0.165 3351 Planarity : 0.006 0.068 3555 Dihedral : 5.987 176.766 2782 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.59 % Allowed : 17.62 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.17), residues: 2531 helix: 1.27 (0.12), residues: 1793 sheet: None (None), residues: 0 loop : -0.28 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1607 TYR 0.023 0.002 TYR A1464 PHE 0.024 0.002 PHE A1500 TRP 0.022 0.002 TRP A2204 HIS 0.006 0.001 HIS A2915 Details of bonding type rmsd covalent geometry : bond 0.00476 (20802) covalent geometry : angle 0.59100 (28248) hydrogen bonds : bond 0.05409 ( 1302) hydrogen bonds : angle 4.34017 ( 3783) Misc. bond : bond 0.00101 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19521.26 seconds wall clock time: 329 minutes 37.70 seconds (19777.70 seconds total)