Starting phenix.real_space_refine on Mon Jun 23 03:00:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d4x_27201/06_2025/8d4x_27201.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d4x_27201/06_2025/8d4x_27201.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d4x_27201/06_2025/8d4x_27201.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d4x_27201/06_2025/8d4x_27201.map" model { file = "/net/cci-nas-00/data/ceres_data/8d4x_27201/06_2025/8d4x_27201.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d4x_27201/06_2025/8d4x_27201.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.024 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 Zn 6 6.06 5 S 199 5.16 5 C 16679 2.51 5 N 4621 2.21 5 O 4904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26409 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 13260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1684, 13260 Classifications: {'peptide': 1684} Link IDs: {'PTRANS': 97, 'TRANS': 1586} Chain breaks: 12 Chain: "B" Number of atoms: 13143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1669, 13143 Classifications: {'peptide': 1669} Link IDs: {'PTRANS': 96, 'TRANS': 1572} Chain breaks: 12 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4816 SG CYS A1179 48.615 97.605 76.420 1.00 59.11 S ATOM 5041 SG CYS A1208 49.414 94.891 79.001 1.00 69.92 S ATOM 5063 SG CYS A1211 49.710 94.086 75.305 1.00 76.05 S ATOM 5226 SG CYS A1232 52.124 96.544 76.970 1.00 86.19 S ATOM 5063 SG CYS A1211 49.710 94.086 75.305 1.00 76.05 S ATOM 5092 SG CYS A1215 48.670 92.206 72.193 1.00 72.88 S ATOM 5240 SG CYS A1234 52.170 93.890 72.380 1.00103.60 S ATOM 5293 SG CYS A1240 49.013 95.932 72.050 1.00 58.11 S ATOM 4956 SG CYS A1196 56.824 86.856 73.073 1.00 78.80 S ATOM 4980 SG CYS A1199 55.680 89.032 69.995 1.00 75.97 S ATOM 18076 SG CYS B1179 79.259 44.370 168.939 1.00 64.61 S ATOM 18301 SG CYS B1208 77.004 46.217 166.361 1.00 68.88 S ATOM 18323 SG CYS B1211 76.867 47.133 170.044 1.00 75.92 S ATOM 18486 SG CYS B1232 80.017 47.823 168.069 1.00 96.73 S ATOM 18323 SG CYS B1211 76.867 47.133 170.044 1.00 75.92 S ATOM 18352 SG CYS B1215 74.672 47.374 173.131 1.00 72.68 S ATOM 18500 SG CYS B1234 78.170 49.188 172.966 1.00100.82 S ATOM 18553 SG CYS B1240 77.764 45.460 173.350 1.00 77.71 S ATOM 18216 SG CYS B1196 74.986 57.188 172.228 1.00 97.94 S ATOM 18240 SG CYS B1199 76.159 55.437 175.566 1.00 81.49 S Time building chain proxies: 17.87, per 1000 atoms: 0.68 Number of scatterers: 26409 At special positions: 0 Unit cell: (116.748, 141.588, 245.916, 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) Zn 6 29.99 S 199 16.00 O 4904 8.00 N 4621 7.00 C 16679 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.42 Conformation dependent library (CDL) restraints added in 3.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2801 " pdb="ZN ZN A2801 " - pdb=" SG CYS A1232 " pdb="ZN ZN A2801 " - pdb=" SG CYS A1179 " pdb="ZN ZN A2801 " - pdb=" SG CYS A1208 " pdb="ZN ZN A2801 " - pdb=" SG CYS A1211 " pdb=" ZN A2802 " pdb="ZN ZN A2802 " - pdb=" SG CYS A1240 " pdb="ZN ZN A2802 " - pdb=" SG CYS A1215 " pdb="ZN ZN A2802 " - pdb=" SG CYS A1211 " pdb="ZN ZN A2802 " - pdb=" SG CYS A1234 " pdb=" ZN A2803 " pdb="ZN ZN A2803 " - pdb=" ND1 HIS A1216 " pdb="ZN ZN A2803 " - pdb=" ND1 HIS A1219 " pdb="ZN ZN A2803 " - pdb=" SG CYS A1196 " pdb="ZN ZN A2803 " - pdb=" SG CYS A1199 " pdb=" ZN B2801 " pdb="ZN ZN B2801 " - pdb=" SG CYS B1232 " pdb="ZN ZN B2801 " - pdb=" SG CYS B1211 " pdb="ZN ZN B2801 " - pdb=" SG CYS B1179 " pdb="ZN ZN B2801 " - pdb=" SG CYS B1208 " pdb=" ZN B2802 " pdb="ZN ZN B2802 " - pdb=" SG CYS B1240 " pdb="ZN ZN B2802 " - pdb=" SG CYS B1215 " pdb="ZN ZN B2802 " - pdb=" SG CYS B1211 " pdb="ZN ZN B2802 " - pdb=" SG CYS B1234 " pdb=" ZN B2803 " pdb="ZN ZN B2803 " - pdb=" ND1 HIS B1216 " pdb="ZN ZN B2803 " - pdb=" ND1 HIS B1219 " pdb="ZN ZN B2803 " - pdb=" SG CYS B1199 " pdb="ZN ZN B2803 " - pdb=" SG CYS B1196 " Number of angles added : 28 6602 Ramachandran restraints generated. 3301 Oldfield, 0 Emsley, 3301 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6386 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 26 sheets defined 49.6% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.67 Creating SS restraints... Processing helix chain 'A' and resid 14 through 31 removed outlier: 3.585A pdb=" N LEU A 18 " --> pdb=" O THR A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 40 through 46 removed outlier: 3.864A pdb=" N ALA A 46 " --> pdb=" O VAL A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 418 removed outlier: 3.931A pdb=" N THR A 415 " --> pdb=" O HIS A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 422 Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 498 through 514 Processing helix chain 'A' and resid 551 through 555 Processing helix chain 'A' and resid 578 through 583 Processing helix chain 'A' and resid 652 through 656 removed outlier: 3.902A pdb=" N GLU A 655 " --> pdb=" O SER A 652 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL A 656 " --> pdb=" O LEU A 653 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 652 through 656' Processing helix chain 'A' and resid 787 through 793 Processing helix chain 'A' and resid 795 through 799 removed outlier: 3.893A pdb=" N ASN A 798 " --> pdb=" O ASN A 795 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL A 799 " --> pdb=" O GLU A 796 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 795 through 799' Processing helix chain 'A' and resid 874 through 882 Processing helix chain 'A' and resid 884 through 902 Processing helix chain 'A' and resid 904 through 913 Processing helix chain 'A' and resid 921 through 930 Processing helix chain 'A' and resid 1077 through 1095 Processing helix chain 'A' and resid 1098 through 1108 removed outlier: 4.620A pdb=" N ARG A1103 " --> pdb=" O GLN A1099 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N GLU A1104 " --> pdb=" O PRO A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1115 through 1123 Processing helix chain 'A' and resid 1125 through 1143 Processing helix chain 'A' and resid 1149 through 1159 removed outlier: 3.777A pdb=" N VAL A1153 " --> pdb=" O LYS A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1167 Processing helix chain 'A' and resid 1168 through 1175 Processing helix chain 'A' and resid 1180 through 1185 Processing helix chain 'A' and resid 1208 through 1214 Processing helix chain 'A' and resid 1247 through 1262 Processing helix chain 'A' and resid 1263 through 1267 removed outlier: 3.566A pdb=" N THR A1266 " --> pdb=" O ASN A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1274 through 1291 removed outlier: 4.073A pdb=" N CYS A1291 " --> pdb=" O THR A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1335 removed outlier: 3.508A pdb=" N ASP A1335 " --> pdb=" O ARG A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1335 through 1344 Processing helix chain 'A' and resid 1364 through 1374 removed outlier: 4.254A pdb=" N GLN A1374 " --> pdb=" O TYR A1370 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1389 Processing helix chain 'A' and resid 1395 through 1410 Processing helix chain 'A' and resid 1416 through 1443 removed outlier: 4.101A pdb=" N GLU A1420 " --> pdb=" O GLY A1416 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1451 removed outlier: 4.145A pdb=" N ASN A1451 " --> pdb=" O LYS A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1454 through 1467 Processing helix chain 'A' and resid 1467 through 1488 removed outlier: 3.733A pdb=" N GLU A1473 " --> pdb=" O PRO A1469 " (cutoff:3.500A) Proline residue: A1485 - end of helix Processing helix chain 'A' and resid 1503 through 1515 Processing helix chain 'A' and resid 1706 through 1710 Processing helix chain 'A' and resid 1714 through 1718 Processing helix chain 'A' and resid 1776 through 1802 removed outlier: 3.678A pdb=" N SER A1780 " --> pdb=" O SER A1776 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A1802 " --> pdb=" O LEU A1798 " (cutoff:3.500A) Processing helix chain 'A' and resid 1804 through 1809 Processing helix chain 'A' and resid 1820 through 1863 removed outlier: 3.751A pdb=" N ALA A1824 " --> pdb=" O THR A1820 " (cutoff:3.500A) Proline residue: A1837 - end of helix Processing helix chain 'A' and resid 1873 through 1877 Processing helix chain 'A' and resid 1912 through 1929 removed outlier: 4.210A pdb=" N ASN A1929 " --> pdb=" O MET A1925 " (cutoff:3.500A) Processing helix chain 'A' and resid 1940 through 1943 Processing helix chain 'A' and resid 1944 through 1966 Processing helix chain 'A' and resid 2043 through 2048 Processing helix chain 'A' and resid 2048 through 2053 removed outlier: 3.768A pdb=" N ASP A2052 " --> pdb=" O ILE A2048 " (cutoff:3.500A) Processing helix chain 'A' and resid 2054 through 2057 removed outlier: 3.617A pdb=" N LEU A2057 " --> pdb=" O PRO A2054 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2054 through 2057' Processing helix chain 'A' and resid 2062 through 2068 removed outlier: 3.552A pdb=" N LEU A2066 " --> pdb=" O ARG A2062 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2102 Proline residue: A2099 - end of helix removed outlier: 3.994A pdb=" N MET A2102 " --> pdb=" O LEU A2098 " (cutoff:3.500A) Processing helix chain 'A' and resid 2165 through 2169 removed outlier: 3.593A pdb=" N PHE A2169 " --> pdb=" O LEU A2166 " (cutoff:3.500A) Processing helix chain 'A' and resid 2181 through 2189 Processing helix chain 'A' and resid 2189 through 2200 Processing helix chain 'A' and resid 2210 through 2215 Processing helix chain 'A' and resid 2217 through 2234 removed outlier: 3.688A pdb=" N LYS A2221 " --> pdb=" O GLY A2217 " (cutoff:3.500A) Processing helix chain 'A' and resid 2247 through 2264 Processing helix chain 'A' and resid 2288 through 2304 removed outlier: 3.625A pdb=" N ALA A2292 " --> pdb=" O GLY A2288 " (cutoff:3.500A) Processing helix chain 'A' and resid 2522 through 2542 Processing helix chain 'A' and resid 2551 through 2560 Processing helix chain 'A' and resid 2564 through 2571 Processing helix chain 'A' and resid 2572 through 2587 removed outlier: 3.567A pdb=" N GLN A2587 " --> pdb=" O ILE A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2590 through 2599 Processing helix chain 'A' and resid 2627 through 2629 No H-bonds generated for 'chain 'A' and resid 2627 through 2629' Processing helix chain 'A' and resid 2630 through 2642 Processing helix chain 'A' and resid 2647 through 2660 removed outlier: 3.696A pdb=" N LYS A2656 " --> pdb=" O HIS A2652 " (cutoff:3.500A) Processing helix chain 'A' and resid 2671 through 2680 Processing helix chain 'A' and resid 2686 through 2693 removed outlier: 3.667A pdb=" N PHE A2693 " --> pdb=" O MET A2689 " (cutoff:3.500A) Processing helix chain 'A' and resid 2703 through 2720 Processing helix chain 'A' and resid 2722 through 2735 Processing helix chain 'A' and resid 2779 through 2793 Processing helix chain 'B' and resid 14 through 31 removed outlier: 3.769A pdb=" N LEU B 18 " --> pdb=" O THR B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 412 through 418 Processing helix chain 'B' and resid 419 through 422 Processing helix chain 'B' and resid 449 through 455 removed outlier: 5.008A pdb=" N SER B 453 " --> pdb=" O THR B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 513 Processing helix chain 'B' and resid 552 through 555 removed outlier: 3.527A pdb=" N ILE B 555 " --> pdb=" O SER B 552 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 552 through 555' Processing helix chain 'B' and resid 578 through 583 removed outlier: 3.929A pdb=" N LYS B 583 " --> pdb=" O GLU B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 793 Processing helix chain 'B' and resid 874 through 883 Processing helix chain 'B' and resid 884 through 901 Processing helix chain 'B' and resid 906 through 913 Processing helix chain 'B' and resid 921 through 931 Processing helix chain 'B' and resid 1077 through 1095 Processing helix chain 'B' and resid 1101 through 1106 Processing helix chain 'B' and resid 1115 through 1123 Processing helix chain 'B' and resid 1125 through 1142 Processing helix chain 'B' and resid 1149 through 1159 removed outlier: 3.693A pdb=" N GLY B1156 " --> pdb=" O ASP B1152 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N MET B1157 " --> pdb=" O VAL B1153 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1167 Processing helix chain 'B' and resid 1168 through 1175 Processing helix chain 'B' and resid 1179 through 1185 removed outlier: 4.096A pdb=" N TRP B1183 " --> pdb=" O CYS B1179 " (cutoff:3.500A) Processing helix chain 'B' and resid 1208 through 1215 Processing helix chain 'B' and resid 1233 through 1238 removed outlier: 3.887A pdb=" N LYS B1237 " --> pdb=" O ASP B1233 " (cutoff:3.500A) Processing helix chain 'B' and resid 1247 through 1262 Processing helix chain 'B' and resid 1263 through 1267 Processing helix chain 'B' and resid 1274 through 1290 Processing helix chain 'B' and resid 1291 through 1293 No H-bonds generated for 'chain 'B' and resid 1291 through 1293' Processing helix chain 'B' and resid 1323 through 1335 removed outlier: 4.050A pdb=" N LEU B1327 " --> pdb=" O ARG B1323 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN B1334 " --> pdb=" O GLU B1330 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP B1335 " --> pdb=" O ARG B1331 " (cutoff:3.500A) Processing helix chain 'B' and resid 1335 through 1344 Processing helix chain 'B' and resid 1364 through 1374 removed outlier: 3.833A pdb=" N TYR B1370 " --> pdb=" O GLU B1366 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN B1374 " --> pdb=" O TYR B1370 " (cutoff:3.500A) Processing helix chain 'B' and resid 1377 through 1389 Processing helix chain 'B' and resid 1395 through 1410 Processing helix chain 'B' and resid 1416 through 1443 removed outlier: 3.647A pdb=" N GLU B1420 " --> pdb=" O GLY B1416 " (cutoff:3.500A) Processing helix chain 'B' and resid 1447 through 1451 removed outlier: 4.177A pdb=" N ASN B1451 " --> pdb=" O LYS B1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 1454 through 1467 Processing helix chain 'B' and resid 1467 through 1489 removed outlier: 4.434A pdb=" N GLU B1473 " --> pdb=" O PRO B1469 " (cutoff:3.500A) Proline residue: B1485 - end of helix Processing helix chain 'B' and resid 1502 through 1515 removed outlier: 4.575A pdb=" N GLN B1508 " --> pdb=" O ILE B1504 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N GLY B1509 " --> pdb=" O ASP B1505 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER B1510 " --> pdb=" O ALA B1506 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLU B1512 " --> pdb=" O GLN B1508 " (cutoff:3.500A) Processing helix chain 'B' and resid 1706 through 1710 Processing helix chain 'B' and resid 1711 through 1718 removed outlier: 4.921A pdb=" N TRP B1716 " --> pdb=" O SER B1713 " (cutoff:3.500A) Processing helix chain 'B' and resid 1776 through 1801 removed outlier: 3.627A pdb=" N SER B1780 " --> pdb=" O SER B1776 " (cutoff:3.500A) Processing helix chain 'B' and resid 1804 through 1809 Processing helix chain 'B' and resid 1820 through 1862 Proline residue: B1837 - end of helix Processing helix chain 'B' and resid 1873 through 1878 removed outlier: 4.461A pdb=" N SER B1878 " --> pdb=" O SER B1875 " (cutoff:3.500A) Processing helix chain 'B' and resid 1912 through 1929 Processing helix chain 'B' and resid 1940 through 1943 Processing helix chain 'B' and resid 1944 through 1966 Processing helix chain 'B' and resid 2043 through 2048 Processing helix chain 'B' and resid 2048 through 2053 removed outlier: 3.921A pdb=" N ASP B2052 " --> pdb=" O ILE B2048 " (cutoff:3.500A) Processing helix chain 'B' and resid 2054 through 2057 removed outlier: 4.061A pdb=" N LEU B2057 " --> pdb=" O PRO B2054 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2054 through 2057' Processing helix chain 'B' and resid 2062 through 2068 Processing helix chain 'B' and resid 2093 through 2098 Processing helix chain 'B' and resid 2165 through 2169 removed outlier: 3.907A pdb=" N PHE B2169 " --> pdb=" O LEU B2166 " (cutoff:3.500A) Processing helix chain 'B' and resid 2181 through 2189 removed outlier: 3.587A pdb=" N LEU B2185 " --> pdb=" O SER B2181 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2200 Processing helix chain 'B' and resid 2203 through 2207 removed outlier: 3.548A pdb=" N GLU B2207 " --> pdb=" O VAL B2204 " (cutoff:3.500A) Processing helix chain 'B' and resid 2210 through 2215 Processing helix chain 'B' and resid 2217 through 2235 removed outlier: 3.868A pdb=" N LYS B2221 " --> pdb=" O GLY B2217 " (cutoff:3.500A) Processing helix chain 'B' and resid 2247 through 2264 removed outlier: 4.216A pdb=" N ARG B2257 " --> pdb=" O GLN B2253 " (cutoff:3.500A) Processing helix chain 'B' and resid 2288 through 2305 removed outlier: 3.686A pdb=" N ALA B2292 " --> pdb=" O GLY B2288 " (cutoff:3.500A) Processing helix chain 'B' and resid 2522 through 2542 Processing helix chain 'B' and resid 2551 through 2560 Processing helix chain 'B' and resid 2566 through 2572 removed outlier: 3.823A pdb=" N PHE B2570 " --> pdb=" O HIS B2566 " (cutoff:3.500A) Processing helix chain 'B' and resid 2572 through 2587 removed outlier: 3.545A pdb=" N GLN B2587 " --> pdb=" O ILE B2583 " (cutoff:3.500A) Processing helix chain 'B' and resid 2590 through 2599 Processing helix chain 'B' and resid 2627 through 2629 No H-bonds generated for 'chain 'B' and resid 2627 through 2629' Processing helix chain 'B' and resid 2630 through 2644 Processing helix chain 'B' and resid 2647 through 2660 Processing helix chain 'B' and resid 2664 through 2668 Processing helix chain 'B' and resid 2671 through 2680 Processing helix chain 'B' and resid 2686 through 2693 removed outlier: 3.764A pdb=" N PHE B2693 " --> pdb=" O MET B2689 " (cutoff:3.500A) Processing helix chain 'B' and resid 2703 through 2720 removed outlier: 3.679A pdb=" N GLN B2709 " --> pdb=" O GLU B2705 " (cutoff:3.500A) Processing helix chain 'B' and resid 2722 through 2735 Processing helix chain 'B' and resid 2780 through 2793 removed outlier: 3.633A pdb=" N THR B2793 " --> pdb=" O LEU B2789 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 10 removed outlier: 6.860A pdb=" N ALA A 864 " --> pdb=" O VAL A 848 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL A 848 " --> pdb=" O ALA A 864 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL A 866 " --> pdb=" O MET A 846 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET A 846 " --> pdb=" O VAL A 866 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE A 868 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU A 844 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA A 870 " --> pdb=" O SER A 842 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 53 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 53 Processing sheet with id=AA4, first strand: chain 'A' and resid 371 through 375 removed outlier: 3.926A pdb=" N CYS A 373 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 424 through 429 Processing sheet with id=AA6, first strand: chain 'A' and resid 475 through 477 removed outlier: 4.589A pdb=" N LEU A 491 " --> pdb=" O LEU A 738 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLY A 495 " --> pdb=" O THR A 734 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N THR A 734 " --> pdb=" O GLY A 495 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 648 through 651 Processing sheet with id=AA8, first strand: chain 'A' and resid 745 through 752 removed outlier: 6.678A pdb=" N VAL A 759 " --> pdb=" O LEU A 747 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL A 749 " --> pdb=" O HIS A 757 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N HIS A 757 " --> pdb=" O VAL A 749 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N VAL A 751 " --> pdb=" O GLY A 755 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLY A 755 " --> pdb=" O VAL A 751 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 800 through 802 removed outlier: 4.228A pdb=" N LEU A 812 " --> pdb=" O TYR A 820 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1194 through 1196 Processing sheet with id=AB2, first strand: chain 'A' and resid 2505 through 2506 Processing sheet with id=AB3, first strand: chain 'A' and resid 2603 through 2605 Processing sheet with id=AB4, first strand: chain 'A' and resid 2695 through 2696 removed outlier: 6.575A pdb=" N SER A2695 " --> pdb=" O ILE A2752 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N ILE A2754 " --> pdb=" O SER A2695 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N SER A2751 " --> pdb=" O LEU A2772 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N VAL A2774 " --> pdb=" O SER A2751 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N THR A2753 " --> pdb=" O VAL A2774 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 2 through 10 removed outlier: 5.386A pdb=" N GLU B 872 " --> pdb=" O ILE B 841 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE B 841 " --> pdb=" O GLU B 872 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 51 through 53 removed outlier: 3.574A pdb=" N ALA B 58 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 51 through 53 removed outlier: 3.574A pdb=" N ALA B 58 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG B 69 " --> pdb=" O GLN B 361 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN B 361 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 371 through 375 removed outlier: 6.700A pdb=" N VAL B 384 " --> pdb=" O ILE B 372 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE B 374 " --> pdb=" O LEU B 382 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU B 382 " --> pdb=" O ILE B 374 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 424 through 429 removed outlier: 5.026A pdb=" N LYS B 442 " --> pdb=" O THR B 438 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL B 443 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA B 462 " --> pdb=" O VAL B 443 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 475 through 478 Processing sheet with id=AC2, first strand: chain 'B' and resid 648 through 652 Processing sheet with id=AC3, first strand: chain 'B' and resid 745 through 751 removed outlier: 5.392A pdb=" N ILE B 746 " --> pdb=" O LYS B 761 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS B 761 " --> pdb=" O ILE B 746 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA B 748 " --> pdb=" O VAL B 759 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 800 through 802 removed outlier: 4.360A pdb=" N LEU B 812 " --> pdb=" O TYR B 820 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 1194 through 1196 Processing sheet with id=AC6, first strand: chain 'B' and resid 2505 through 2506 Processing sheet with id=AC7, first strand: chain 'B' and resid 2603 through 2606 Processing sheet with id=AC8, first strand: chain 'B' and resid 2695 through 2696 removed outlier: 7.089A pdb=" N SER B2695 " --> pdb=" O ILE B2752 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N ILE B2754 " --> pdb=" O SER B2695 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N SER B2751 " --> pdb=" O LEU B2772 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N VAL B2774 " --> pdb=" O SER B2751 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N THR B2753 " --> pdb=" O VAL B2774 " (cutoff:3.500A) 1220 hydrogen bonds defined for protein. 3435 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.54 Time building geometry restraints manager: 7.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4396 1.31 - 1.44: 6854 1.44 - 1.56: 15407 1.56 - 1.69: 2 1.69 - 1.81: 294 Bond restraints: 26953 Sorted by residual: bond pdb=" C PRO A2547 " pdb=" O PRO A2547 " ideal model delta sigma weight residual 1.235 1.190 0.045 1.30e-02 5.92e+03 1.22e+01 bond pdb=" C GLN A1508 " pdb=" O GLN A1508 " ideal model delta sigma weight residual 1.236 1.276 -0.039 1.15e-02 7.56e+03 1.16e+01 bond pdb=" CA SER A1510 " pdb=" CB SER A1510 " ideal model delta sigma weight residual 1.528 1.477 0.052 1.56e-02 4.11e+03 1.09e+01 bond pdb=" C SER A1510 " pdb=" O SER A1510 " ideal model delta sigma weight residual 1.237 1.201 0.036 1.17e-02 7.31e+03 9.30e+00 bond pdb=" C GLU A1511 " pdb=" O GLU A1511 " ideal model delta sigma weight residual 1.237 1.203 0.034 1.17e-02 7.31e+03 8.35e+00 ... (remaining 26948 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 35834 2.23 - 4.47: 545 4.47 - 6.70: 102 6.70 - 8.94: 28 8.94 - 11.17: 7 Bond angle restraints: 36516 Sorted by residual: angle pdb=" C GLU B1203 " pdb=" CA GLU B1203 " pdb=" CB GLU B1203 " ideal model delta sigma weight residual 116.54 110.16 6.38 1.15e+00 7.56e-01 3.08e+01 angle pdb=" CA PRO B2547 " pdb=" N PRO B2547 " pdb=" CD PRO B2547 " ideal model delta sigma weight residual 112.00 105.71 6.29 1.40e+00 5.10e-01 2.02e+01 angle pdb=" C LEU A2545 " pdb=" N CYS A2546 " pdb=" CA CYS A2546 " ideal model delta sigma weight residual 120.49 114.43 6.06 1.42e+00 4.96e-01 1.82e+01 angle pdb=" CA GLU A1511 " pdb=" C GLU A1511 " pdb=" O GLU A1511 " ideal model delta sigma weight residual 120.55 116.29 4.26 1.06e+00 8.90e-01 1.62e+01 angle pdb=" CA CYS A2546 " pdb=" C CYS A2546 " pdb=" N PRO A2547 " ideal model delta sigma weight residual 118.23 121.71 -3.48 9.20e-01 1.18e+00 1.43e+01 ... (remaining 36511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 14134 17.93 - 35.86: 1797 35.86 - 53.79: 465 53.79 - 71.72: 81 71.72 - 89.65: 31 Dihedral angle restraints: 16508 sinusoidal: 6711 harmonic: 9797 Sorted by residual: dihedral pdb=" CA PHE B2218 " pdb=" C PHE B2218 " pdb=" N GLU B2219 " pdb=" CA GLU B2219 " ideal model delta harmonic sigma weight residual 180.00 -156.93 -23.07 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA MET A2721 " pdb=" C MET A2721 " pdb=" N SER A2722 " pdb=" CA SER A2722 " ideal model delta harmonic sigma weight residual 180.00 -158.46 -21.54 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA ASN B 440 " pdb=" C ASN B 440 " pdb=" N ASN B 441 " pdb=" CA ASN B 441 " ideal model delta harmonic sigma weight residual 180.00 160.22 19.78 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 16505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3540 0.059 - 0.119: 515 0.119 - 0.178: 47 0.178 - 0.238: 8 0.238 - 0.297: 1 Chirality restraints: 4111 Sorted by residual: chirality pdb=" CA LEU B 382 " pdb=" N LEU B 382 " pdb=" C LEU B 382 " pdb=" CB LEU B 382 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CA CYS A2546 " pdb=" N CYS A2546 " pdb=" C CYS A2546 " pdb=" CB CYS A2546 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA PRO A2547 " pdb=" N PRO A2547 " pdb=" C PRO A2547 " pdb=" CB PRO A2547 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 4108 not shown) Planarity restraints: 4726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 9 " -0.070 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO A 10 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO A 10 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 10 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 765 " 0.030 2.00e-02 2.50e+03 2.31e-02 1.33e+01 pdb=" CG TRP A 765 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP A 765 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 765 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 765 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 765 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 765 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 765 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 765 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 765 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A2053 " -0.059 5.00e-02 4.00e+02 8.98e-02 1.29e+01 pdb=" N PRO A2054 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO A2054 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A2054 " -0.049 5.00e-02 4.00e+02 ... (remaining 4723 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1713 2.73 - 3.27: 26800 3.27 - 3.82: 43987 3.82 - 4.36: 50883 4.36 - 4.90: 86943 Nonbonded interactions: 210326 Sorted by model distance: nonbonded pdb=" N GLU A2087 " pdb=" OE1 GLU A2087 " model vdw 2.189 3.120 nonbonded pdb=" O ASN B1962 " pdb=" OG1 THR B1965 " model vdw 2.200 3.040 nonbonded pdb=" O ASN A1962 " pdb=" OG1 THR A1965 " model vdw 2.205 3.040 nonbonded pdb=" O LEU A2690 " pdb=" OG1 THR A2694 " model vdw 2.207 3.040 nonbonded pdb=" OD2 ASP A2500 " pdb=" OG1 THR A2522 " model vdw 2.210 3.040 ... (remaining 210321 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 1525 or resid 1705 through 2794 or resid 2801 th \ rough 2803)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.030 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: 0.030 Extract box with map and model: 1.130 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 72.250 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.120 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: 0.020 Load rotamer database and sin/cos tables:15.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 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 : 0.004 0.105 26977 Z= 0.163 Angle : 0.695 11.173 36544 Z= 0.355 Chirality : 0.043 0.297 4111 Planarity : 0.005 0.104 4726 Dihedral : 17.093 89.650 10122 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.64 % Allowed : 30.20 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.15), residues: 3301 helix: 1.44 (0.14), residues: 1418 sheet: -0.22 (0.27), residues: 403 loop : -0.36 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP A 765 HIS 0.007 0.001 HIS A 849 PHE 0.049 0.002 PHE B2218 TYR 0.017 0.001 TYR A1370 ARG 0.014 0.000 ARG A 889 Details of bonding type rmsd hydrogen bonds : bond 0.13388 ( 1207) hydrogen bonds : angle 5.30581 ( 3435) metal coordination : bond 0.00739 ( 24) metal coordination : angle 2.58811 ( 28) covalent geometry : bond 0.00351 (26953) covalent geometry : angle 0.69143 (36516) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6602 Ramachandran restraints generated. 3301 Oldfield, 0 Emsley, 3301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6602 Ramachandran restraints generated. 3301 Oldfield, 0 Emsley, 3301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 495 time to evaluate : 2.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.7770 (ptm160) cc_final: 0.7565 (ptm160) REVERT: A 2029 MET cc_start: 0.6538 (mmp) cc_final: 0.5076 (mmp) REVERT: A 2563 VAL cc_start: 0.7967 (p) cc_final: 0.7563 (m) REVERT: A 2644 LEU cc_start: 0.8019 (tt) cc_final: 0.7809 (tm) REVERT: B 732 GLN cc_start: 0.7359 (OUTLIER) cc_final: 0.7008 (tm-30) REVERT: B 891 TYR cc_start: 0.7978 (t80) cc_final: 0.7651 (t80) REVERT: B 2044 LEU cc_start: 0.8443 (tm) cc_final: 0.8210 (tt) REVERT: B 2219 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7249 (mm-30) REVERT: B 2225 PHE cc_start: 0.8169 (t80) cc_final: 0.7828 (t80) REVERT: B 2640 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6985 (mt-10) outliers start: 78 outliers final: 67 residues processed: 556 average time/residue: 1.2723 time to fit residues: 830.3002 Evaluate side-chains 552 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 483 time to evaluate : 2.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1164 ASN Chi-restraints excluded: chain A residue 1238 CYS Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1382 CYS Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1507 MET Chi-restraints excluded: chain A residue 1801 LEU Chi-restraints excluded: chain A residue 1836 ILE Chi-restraints excluded: chain A residue 1844 SER Chi-restraints excluded: chain A residue 1939 LEU Chi-restraints excluded: chain A residue 2074 LEU Chi-restraints excluded: chain A residue 2255 THR Chi-restraints excluded: chain A residue 2515 THR Chi-restraints excluded: chain A residue 2545 LEU Chi-restraints excluded: chain A residue 2546 CYS Chi-restraints excluded: chain A residue 2661 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 732 GLN Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 799 VAL Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 860 ILE Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain B residue 1153 VAL Chi-restraints excluded: chain B residue 1182 THR Chi-restraints excluded: chain B residue 1193 ILE Chi-restraints excluded: chain B residue 1244 ILE Chi-restraints excluded: chain B residue 1298 ILE Chi-restraints excluded: chain B residue 1341 SER Chi-restraints excluded: chain B residue 1350 ASN Chi-restraints excluded: chain B residue 1377 THR Chi-restraints excluded: chain B residue 1389 VAL Chi-restraints excluded: chain B residue 1411 ASN Chi-restraints excluded: chain B residue 1719 ARG Chi-restraints excluded: chain B residue 1775 SER Chi-restraints excluded: chain B residue 1801 LEU Chi-restraints excluded: chain B residue 1811 SER Chi-restraints excluded: chain B residue 1935 VAL Chi-restraints excluded: chain B residue 1955 ILE Chi-restraints excluded: chain B residue 1957 TRP Chi-restraints excluded: chain B residue 2057 LEU Chi-restraints excluded: chain B residue 2101 LYS Chi-restraints excluded: chain B residue 2167 THR Chi-restraints excluded: chain B residue 2183 ASP Chi-restraints excluded: chain B residue 2219 GLU Chi-restraints excluded: chain B residue 2220 VAL Chi-restraints excluded: chain B residue 2244 VAL Chi-restraints excluded: chain B residue 2667 LEU Chi-restraints excluded: chain B residue 2742 SER Chi-restraints excluded: chain B residue 2776 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 282 optimal weight: 3.9990 chunk 253 optimal weight: 0.6980 chunk 140 optimal weight: 0.5980 chunk 86 optimal weight: 0.5980 chunk 170 optimal weight: 0.9990 chunk 135 optimal weight: 7.9990 chunk 261 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 159 optimal weight: 20.0000 chunk 194 optimal weight: 7.9990 chunk 303 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 849 HIS ** A 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1508 GLN A1952 GLN A2652 HIS B1411 ASN B2543 ASN B2551 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.183545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.145742 restraints weight = 41644.260| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.58 r_work: 0.3762 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.0728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26977 Z= 0.151 Angle : 0.609 9.932 36544 Z= 0.301 Chirality : 0.041 0.183 4111 Planarity : 0.005 0.087 4726 Dihedral : 6.224 59.474 3719 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.41 % Allowed : 26.07 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.15), residues: 3301 helix: 1.45 (0.14), residues: 1440 sheet: -0.13 (0.27), residues: 390 loop : -0.41 (0.17), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 765 HIS 0.009 0.001 HIS A2553 PHE 0.027 0.002 PHE A 72 TYR 0.017 0.002 TYR B1949 ARG 0.009 0.000 ARG B1331 Details of bonding type rmsd hydrogen bonds : bond 0.04086 ( 1207) hydrogen bonds : angle 4.45309 ( 3435) metal coordination : bond 0.01011 ( 24) metal coordination : angle 2.83186 ( 28) covalent geometry : bond 0.00346 (26953) covalent geometry : angle 0.60408 (36516) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6602 Ramachandran restraints generated. 3301 Oldfield, 0 Emsley, 3301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6602 Ramachandran restraints generated. 3301 Oldfield, 0 Emsley, 3301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 521 time to evaluate : 2.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 751 VAL cc_start: 0.8788 (t) cc_final: 0.8533 (p) REVERT: A 762 THR cc_start: 0.8197 (t) cc_final: 0.7868 (t) REVERT: A 890 GLN cc_start: 0.7641 (mm-40) cc_final: 0.7347 (mm-40) REVERT: A 1090 LYS cc_start: 0.8692 (tppp) cc_final: 0.8384 (tppp) REVERT: A 1195 GLU cc_start: 0.7032 (pm20) cc_final: 0.6660 (pm20) REVERT: A 1709 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7488 (mp10) REVERT: A 2563 VAL cc_start: 0.7890 (OUTLIER) cc_final: 0.7386 (m) REVERT: A 2721 MET cc_start: 0.8187 (tmm) cc_final: 0.7847 (tmm) REVERT: A 2749 MET cc_start: 0.6993 (ttm) cc_final: 0.6791 (ttm) REVERT: B 891 TYR cc_start: 0.7929 (t80) cc_final: 0.7599 (t80) REVERT: B 1195 GLU cc_start: 0.7339 (pp20) cc_final: 0.7115 (pp20) REVERT: B 1511 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7302 (tm-30) REVERT: B 2044 LEU cc_start: 0.8197 (tm) cc_final: 0.7996 (tt) REVERT: B 2225 PHE cc_start: 0.8222 (t80) cc_final: 0.7852 (t80) REVERT: B 2248 ARG cc_start: 0.7202 (ttm110) cc_final: 0.6890 (ttm-80) REVERT: B 2579 LEU cc_start: 0.8536 (mt) cc_final: 0.8325 (mt) REVERT: B 2684 GLU cc_start: 0.7447 (pm20) cc_final: 0.7119 (pp20) outliers start: 130 outliers final: 55 residues processed: 603 average time/residue: 1.2889 time to fit residues: 916.2814 Evaluate side-chains 553 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 496 time to evaluate : 2.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 416 PHE Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 911 PHE Chi-restraints excluded: chain A residue 912 ILE Chi-restraints excluded: chain A residue 930 CYS Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1137 GLN Chi-restraints excluded: chain A residue 1155 MET Chi-restraints excluded: chain A residue 1238 CYS Chi-restraints excluded: chain A residue 1382 CYS Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1709 GLN Chi-restraints excluded: chain A residue 1935 VAL Chi-restraints excluded: chain A residue 2095 LEU Chi-restraints excluded: chain A residue 2178 MET Chi-restraints excluded: chain A residue 2545 LEU Chi-restraints excluded: chain A residue 2556 LYS Chi-restraints excluded: chain A residue 2563 VAL Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2661 VAL Chi-restraints excluded: chain A residue 2667 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 732 GLN Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 799 VAL Chi-restraints excluded: chain B residue 911 PHE Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain B residue 1193 ILE Chi-restraints excluded: chain B residue 1231 TYR Chi-restraints excluded: chain B residue 1244 ILE Chi-restraints excluded: chain B residue 1287 THR Chi-restraints excluded: chain B residue 1377 THR Chi-restraints excluded: chain B residue 1389 VAL Chi-restraints excluded: chain B residue 1719 ARG Chi-restraints excluded: chain B residue 1801 LEU Chi-restraints excluded: chain B residue 1819 LEU Chi-restraints excluded: chain B residue 1820 THR Chi-restraints excluded: chain B residue 1935 VAL Chi-restraints excluded: chain B residue 1957 TRP Chi-restraints excluded: chain B residue 2230 GLU Chi-restraints excluded: chain B residue 2555 ILE Chi-restraints excluded: chain B residue 2661 VAL Chi-restraints excluded: chain B residue 2685 VAL Chi-restraints excluded: chain B residue 2690 LEU Chi-restraints excluded: chain B residue 2694 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 224 optimal weight: 1.9990 chunk 161 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 290 optimal weight: 2.9990 chunk 196 optimal weight: 40.0000 chunk 83 optimal weight: 0.6980 chunk 228 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 162 optimal weight: 0.6980 chunk 306 optimal weight: 0.7980 chunk 194 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 849 HIS ** A 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1086 HIS A1852 GLN A1952 GLN ** A2680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1411 ASN B2543 ASN B2551 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.182840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.144844 restraints weight = 41589.172| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.59 r_work: 0.3751 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26977 Z= 0.167 Angle : 0.601 9.181 36544 Z= 0.297 Chirality : 0.041 0.160 4111 Planarity : 0.005 0.069 4726 Dihedral : 5.181 59.611 3640 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.47 % Allowed : 26.71 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.15), residues: 3301 helix: 1.43 (0.14), residues: 1440 sheet: -0.15 (0.27), residues: 372 loop : -0.44 (0.17), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 765 HIS 0.007 0.001 HIS A2553 PHE 0.040 0.001 PHE B2218 TYR 0.017 0.002 TYR A1370 ARG 0.008 0.000 ARG A1197 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 1207) hydrogen bonds : angle 4.37025 ( 3435) metal coordination : bond 0.01235 ( 24) metal coordination : angle 2.80164 ( 28) covalent geometry : bond 0.00389 (26953) covalent geometry : angle 0.59590 (36516) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6602 Ramachandran restraints generated. 3301 Oldfield, 0 Emsley, 3301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6602 Ramachandran restraints generated. 3301 Oldfield, 0 Emsley, 3301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 519 time to evaluate : 3.015 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: A 390 LEU cc_start: 0.8160 (tp) cc_final: 0.7912 (tp) REVERT: A 488 GLU cc_start: 0.6995 (tp30) cc_final: 0.6388 (tp30) REVERT: A 890 GLN cc_start: 0.7656 (mm-40) cc_final: 0.7110 (mm-40) REVERT: A 894 ASN cc_start: 0.8007 (m-40) cc_final: 0.7766 (m-40) REVERT: A 1090 LYS cc_start: 0.8705 (tppp) cc_final: 0.8412 (tppp) REVERT: A 1195 GLU cc_start: 0.7039 (pm20) cc_final: 0.6688 (pm20) REVERT: A 1222 LYS cc_start: 0.7797 (mtmm) cc_final: 0.7446 (mtmm) REVERT: A 2545 LEU cc_start: 0.7138 (OUTLIER) cc_final: 0.6619 (pp) REVERT: A 2563 VAL cc_start: 0.7906 (OUTLIER) cc_final: 0.7413 (m) REVERT: A 2749 MET cc_start: 0.7026 (ttm) cc_final: 0.6813 (ttm) REVERT: B 891 TYR cc_start: 0.7927 (t80) cc_final: 0.7602 (t80) REVERT: B 1149 LYS cc_start: 0.7757 (mtmm) cc_final: 0.7298 (mtmm) REVERT: B 1195 GLU cc_start: 0.7380 (pp20) cc_final: 0.7076 (pp20) REVERT: B 1443 MET cc_start: 0.8107 (tpp) cc_final: 0.7901 (mpp) REVERT: B 1468 LEU cc_start: 0.8388 (tt) cc_final: 0.8108 (tp) REVERT: B 1511 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7302 (tm-30) REVERT: B 2044 LEU cc_start: 0.8229 (tm) cc_final: 0.8011 (tt) REVERT: B 2083 LYS cc_start: 0.8271 (mttp) cc_final: 0.7851 (mttp) REVERT: B 2176 MET cc_start: 0.5519 (ttm) cc_final: 0.5188 (ttm) REVERT: B 2225 PHE cc_start: 0.8243 (t80) cc_final: 0.7841 (t80) outliers start: 132 outliers final: 63 residues processed: 604 average time/residue: 1.3516 time to fit residues: 966.0652 Evaluate side-chains 563 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 498 time to evaluate : 3.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 416 PHE Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 911 PHE Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 930 CYS Chi-restraints excluded: chain A residue 1155 MET Chi-restraints excluded: chain A residue 1231 TYR Chi-restraints excluded: chain A residue 1238 CYS Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1382 CYS Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1443 MET Chi-restraints excluded: chain A residue 1935 VAL Chi-restraints excluded: chain A residue 2095 LEU Chi-restraints excluded: chain A residue 2178 MET Chi-restraints excluded: chain A residue 2184 MET Chi-restraints excluded: chain A residue 2545 LEU Chi-restraints excluded: chain A residue 2556 LYS Chi-restraints excluded: chain A residue 2563 VAL Chi-restraints excluded: chain A residue 2661 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 732 GLN Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 911 PHE Chi-restraints excluded: chain B residue 1153 VAL Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1193 ILE Chi-restraints excluded: chain B residue 1231 TYR Chi-restraints excluded: chain B residue 1241 LYS Chi-restraints excluded: chain B residue 1244 ILE Chi-restraints excluded: chain B residue 1287 THR Chi-restraints excluded: chain B residue 1298 ILE Chi-restraints excluded: chain B residue 1377 THR Chi-restraints excluded: chain B residue 1389 VAL Chi-restraints excluded: chain B residue 1507 MET Chi-restraints excluded: chain B residue 1719 ARG Chi-restraints excluded: chain B residue 1801 LEU Chi-restraints excluded: chain B residue 1804 LYS Chi-restraints excluded: chain B residue 1811 SER Chi-restraints excluded: chain B residue 1819 LEU Chi-restraints excluded: chain B residue 1820 THR Chi-restraints excluded: chain B residue 1935 VAL Chi-restraints excluded: chain B residue 1957 TRP Chi-restraints excluded: chain B residue 2020 HIS Chi-restraints excluded: chain B residue 2220 VAL Chi-restraints excluded: chain B residue 2251 LEU Chi-restraints excluded: chain B residue 2555 ILE Chi-restraints excluded: chain B residue 2627 THR Chi-restraints excluded: chain B residue 2633 GLU Chi-restraints excluded: chain B residue 2685 VAL Chi-restraints excluded: chain B residue 2690 LEU Chi-restraints excluded: chain B residue 2742 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 54 optimal weight: 0.6980 chunk 306 optimal weight: 1.9990 chunk 178 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 159 optimal weight: 8.9990 chunk 88 optimal weight: 0.0050 chunk 33 optimal weight: 0.6980 chunk 191 optimal weight: 5.9990 chunk 284 optimal weight: 0.7980 chunk 206 optimal weight: 6.9990 chunk 197 optimal weight: 20.0000 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN A 849 HIS ** A 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1952 GLN ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1176 ASN B1411 ASN B2543 ASN B2551 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.183388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.145566 restraints weight = 41949.984| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.60 r_work: 0.3758 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26977 Z= 0.135 Angle : 0.600 9.349 36544 Z= 0.295 Chirality : 0.041 0.204 4111 Planarity : 0.005 0.068 4726 Dihedral : 5.117 59.688 3635 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.81 % Allowed : 25.83 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.15), residues: 3301 helix: 1.49 (0.14), residues: 1440 sheet: -0.13 (0.27), residues: 363 loop : -0.46 (0.17), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP A 765 HIS 0.008 0.001 HIS A 411 PHE 0.041 0.002 PHE B2218 TYR 0.017 0.001 TYR A1370 ARG 0.009 0.000 ARG A 889 Details of bonding type rmsd hydrogen bonds : bond 0.03806 ( 1207) hydrogen bonds : angle 4.27795 ( 3435) metal coordination : bond 0.00880 ( 24) metal coordination : angle 2.78371 ( 28) covalent geometry : bond 0.00310 (26953) covalent geometry : angle 0.59569 (36516) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6602 Ramachandran restraints generated. 3301 Oldfield, 0 Emsley, 3301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6602 Ramachandran restraints generated. 3301 Oldfield, 0 Emsley, 3301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 518 time to evaluate : 2.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.3444 (tp30) REVERT: A 390 LEU cc_start: 0.8294 (tp) cc_final: 0.7799 (tp) REVERT: A 488 GLU cc_start: 0.7006 (tp30) cc_final: 0.6393 (tp30) REVERT: A 890 GLN cc_start: 0.7675 (mm-40) cc_final: 0.7134 (mm-40) REVERT: A 1090 LYS cc_start: 0.8707 (tppp) cc_final: 0.8365 (tppp) REVERT: A 1149 LYS cc_start: 0.7916 (mppt) cc_final: 0.7712 (mppt) REVERT: A 1195 GLU cc_start: 0.7014 (pm20) cc_final: 0.6671 (pm20) REVERT: A 1222 LYS cc_start: 0.7826 (mtmm) cc_final: 0.7325 (mtmm) REVERT: A 1507 MET cc_start: 0.7184 (OUTLIER) cc_final: 0.6944 (mpt) REVERT: A 2018 GLN cc_start: 0.8529 (tm-30) cc_final: 0.7828 (tm-30) REVERT: A 2563 VAL cc_start: 0.7907 (OUTLIER) cc_final: 0.7417 (m) REVERT: A 2749 MET cc_start: 0.6979 (ttm) cc_final: 0.6748 (ttm) REVERT: B 795 ASN cc_start: 0.7995 (t0) cc_final: 0.7690 (t0) REVERT: B 891 TYR cc_start: 0.7911 (t80) cc_final: 0.7342 (t80) REVERT: B 895 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7718 (mm) REVERT: B 1149 LYS cc_start: 0.7747 (mtmm) cc_final: 0.7291 (mtmm) REVERT: B 1195 GLU cc_start: 0.7365 (pp20) cc_final: 0.6996 (pp20) REVERT: B 1326 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7516 (mp-120) REVERT: B 1443 MET cc_start: 0.8138 (tpp) cc_final: 0.7874 (mpp) REVERT: B 1468 LEU cc_start: 0.8361 (tt) cc_final: 0.8079 (tp) REVERT: B 1511 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7253 (tm-30) REVERT: B 2044 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7975 (tt) REVERT: B 2083 LYS cc_start: 0.8306 (mttp) cc_final: 0.7927 (mttp) REVERT: B 2176 MET cc_start: 0.5581 (ttm) cc_final: 0.5281 (ttm) REVERT: B 2225 PHE cc_start: 0.8231 (t80) cc_final: 0.7854 (t80) REVERT: B 2248 ARG cc_start: 0.7430 (ttm110) cc_final: 0.7225 (ttm-80) outliers start: 142 outliers final: 68 residues processed: 603 average time/residue: 1.8615 time to fit residues: 1365.5691 Evaluate side-chains 571 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 497 time to evaluate : 3.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 416 PHE Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 911 PHE Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 930 CYS Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1137 GLN Chi-restraints excluded: chain A residue 1231 TYR Chi-restraints excluded: chain A residue 1238 CYS Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1382 CYS Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1441 VAL Chi-restraints excluded: chain A residue 1507 MET Chi-restraints excluded: chain A residue 1935 VAL Chi-restraints excluded: chain A residue 2027 ASP Chi-restraints excluded: chain A residue 2065 ASP Chi-restraints excluded: chain A residue 2178 MET Chi-restraints excluded: chain A residue 2251 LEU Chi-restraints excluded: chain A residue 2556 LYS Chi-restraints excluded: chain A residue 2563 VAL Chi-restraints excluded: chain A residue 2661 VAL Chi-restraints excluded: chain A residue 2667 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 732 GLN Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain B residue 911 PHE Chi-restraints excluded: chain B residue 913 SER Chi-restraints excluded: chain B residue 1118 MET Chi-restraints excluded: chain B residue 1153 VAL Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1193 ILE Chi-restraints excluded: chain B residue 1231 TYR Chi-restraints excluded: chain B residue 1287 THR Chi-restraints excluded: chain B residue 1298 ILE Chi-restraints excluded: chain B residue 1326 GLN Chi-restraints excluded: chain B residue 1367 GLU Chi-restraints excluded: chain B residue 1389 VAL Chi-restraints excluded: chain B residue 1507 MET Chi-restraints excluded: chain B residue 1719 ARG Chi-restraints excluded: chain B residue 1801 LEU Chi-restraints excluded: chain B residue 1811 SER Chi-restraints excluded: chain B residue 1819 LEU Chi-restraints excluded: chain B residue 1820 THR Chi-restraints excluded: chain B residue 1935 VAL Chi-restraints excluded: chain B residue 1957 TRP Chi-restraints excluded: chain B residue 2020 HIS Chi-restraints excluded: chain B residue 2044 LEU Chi-restraints excluded: chain B residue 2090 VAL Chi-restraints excluded: chain B residue 2220 VAL Chi-restraints excluded: chain B residue 2251 LEU Chi-restraints excluded: chain B residue 2633 GLU Chi-restraints excluded: chain B residue 2661 VAL Chi-restraints excluded: chain B residue 2685 VAL Chi-restraints excluded: chain B residue 2690 LEU Chi-restraints excluded: chain B residue 2742 SER Chi-restraints excluded: chain B residue 2776 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 134 optimal weight: 0.8980 chunk 302 optimal weight: 0.0040 chunk 268 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 284 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 194 optimal weight: 20.0000 chunk 207 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 849 HIS ** A 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1952 GLN ** A2680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 798 ASN ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1411 ASN B2543 ASN B2551 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.182850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.144386 restraints weight = 41847.502| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.87 r_work: 0.3731 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26977 Z= 0.148 Angle : 0.606 9.848 36544 Z= 0.298 Chirality : 0.041 0.176 4111 Planarity : 0.005 0.068 4726 Dihedral : 5.030 58.727 3627 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.75 % Allowed : 26.37 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.15), residues: 3301 helix: 1.48 (0.14), residues: 1441 sheet: -0.15 (0.27), residues: 362 loop : -0.49 (0.17), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 765 HIS 0.009 0.001 HIS A 411 PHE 0.043 0.001 PHE B2218 TYR 0.018 0.001 TYR A1370 ARG 0.009 0.000 ARG A1197 Details of bonding type rmsd hydrogen bonds : bond 0.03847 ( 1207) hydrogen bonds : angle 4.25720 ( 3435) metal coordination : bond 0.01067 ( 24) metal coordination : angle 2.73540 ( 28) covalent geometry : bond 0.00346 (26953) covalent geometry : angle 0.60160 (36516) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6602 Ramachandran restraints generated. 3301 Oldfield, 0 Emsley, 3301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6602 Ramachandran restraints generated. 3301 Oldfield, 0 Emsley, 3301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 519 time to evaluate : 3.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.3514 (tp30) REVERT: A 390 LEU cc_start: 0.8334 (tp) cc_final: 0.8006 (tp) REVERT: A 430 ASN cc_start: 0.7110 (OUTLIER) cc_final: 0.6866 (m110) REVERT: A 488 GLU cc_start: 0.7126 (tp30) cc_final: 0.6450 (tp30) REVERT: A 890 GLN cc_start: 0.7782 (mm-40) cc_final: 0.7382 (mm-40) REVERT: A 1090 LYS cc_start: 0.8739 (tppp) cc_final: 0.8358 (tppp) REVERT: A 1149 LYS cc_start: 0.7965 (mppt) cc_final: 0.7705 (mppt) REVERT: A 1195 GLU cc_start: 0.7061 (pm20) cc_final: 0.6679 (pm20) REVERT: A 1222 LYS cc_start: 0.7853 (mtmm) cc_final: 0.7330 (mtmm) REVERT: A 2018 GLN cc_start: 0.8506 (tm-30) cc_final: 0.7774 (tm-30) REVERT: A 2102 MET cc_start: 0.4006 (ppp) cc_final: 0.3653 (pp-130) REVERT: A 2563 VAL cc_start: 0.7943 (OUTLIER) cc_final: 0.7465 (m) REVERT: A 2644 LEU cc_start: 0.7873 (tt) cc_final: 0.7458 (tp) REVERT: A 2648 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7356 (mm-30) REVERT: A 2749 MET cc_start: 0.7016 (ttm) cc_final: 0.6769 (ttm) REVERT: B 61 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8190 (tp) REVERT: B 795 ASN cc_start: 0.7920 (t0) cc_final: 0.7595 (t0) REVERT: B 891 TYR cc_start: 0.7982 (t80) cc_final: 0.7379 (t80) REVERT: B 895 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7735 (mm) REVERT: B 1149 LYS cc_start: 0.7758 (mtmm) cc_final: 0.7284 (mtmm) REVERT: B 1195 GLU cc_start: 0.7415 (pp20) cc_final: 0.6998 (pp20) REVERT: B 1222 LYS cc_start: 0.8301 (mmmm) cc_final: 0.8008 (mmmm) REVERT: B 1326 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7512 (mp-120) REVERT: B 1331 ARG cc_start: 0.8009 (mmm160) cc_final: 0.7805 (tpt90) REVERT: B 1443 MET cc_start: 0.8142 (tpp) cc_final: 0.7824 (mpp) REVERT: B 1468 LEU cc_start: 0.8362 (tt) cc_final: 0.8158 (tt) REVERT: B 1511 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7249 (tm-30) REVERT: B 2044 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7968 (tt) REVERT: B 2083 LYS cc_start: 0.8290 (mttp) cc_final: 0.7892 (mttp) REVERT: B 2176 MET cc_start: 0.5716 (ttm) cc_final: 0.5409 (ttm) REVERT: B 2225 PHE cc_start: 0.8226 (t80) cc_final: 0.7831 (t80) REVERT: B 2662 LEU cc_start: 0.8323 (mt) cc_final: 0.8122 (mp) outliers start: 140 outliers final: 78 residues processed: 603 average time/residue: 1.2290 time to fit residues: 874.1769 Evaluate side-chains 589 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 504 time to evaluate : 2.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 416 PHE Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 875 THR Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 911 PHE Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 930 CYS Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1164 ASN Chi-restraints excluded: chain A residue 1231 TYR Chi-restraints excluded: chain A residue 1238 CYS Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1382 CYS Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1399 ASP Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1441 VAL Chi-restraints excluded: chain A residue 1836 ILE Chi-restraints excluded: chain A residue 1933 SER Chi-restraints excluded: chain A residue 1935 VAL Chi-restraints excluded: chain A residue 2027 ASP Chi-restraints excluded: chain A residue 2178 MET Chi-restraints excluded: chain A residue 2251 LEU Chi-restraints excluded: chain A residue 2556 LYS Chi-restraints excluded: chain A residue 2563 VAL Chi-restraints excluded: chain A residue 2661 VAL Chi-restraints excluded: chain A residue 2667 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 732 GLN Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain B residue 911 PHE Chi-restraints excluded: chain B residue 913 SER Chi-restraints excluded: chain B residue 1118 MET Chi-restraints excluded: chain B residue 1153 VAL Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1193 ILE Chi-restraints excluded: chain B residue 1231 TYR Chi-restraints excluded: chain B residue 1287 THR Chi-restraints excluded: chain B residue 1298 ILE Chi-restraints excluded: chain B residue 1323 ARG Chi-restraints excluded: chain B residue 1326 GLN Chi-restraints excluded: chain B residue 1367 GLU Chi-restraints excluded: chain B residue 1377 THR Chi-restraints excluded: chain B residue 1389 VAL Chi-restraints excluded: chain B residue 1507 MET Chi-restraints excluded: chain B residue 1801 LEU Chi-restraints excluded: chain B residue 1804 LYS Chi-restraints excluded: chain B residue 1811 SER Chi-restraints excluded: chain B residue 1819 LEU Chi-restraints excluded: chain B residue 1820 THR Chi-restraints excluded: chain B residue 1935 VAL Chi-restraints excluded: chain B residue 1957 TRP Chi-restraints excluded: chain B residue 2044 LEU Chi-restraints excluded: chain B residue 2090 VAL Chi-restraints excluded: chain B residue 2220 VAL Chi-restraints excluded: chain B residue 2251 LEU Chi-restraints excluded: chain B residue 2510 LYS Chi-restraints excluded: chain B residue 2526 LEU Chi-restraints excluded: chain B residue 2627 THR Chi-restraints excluded: chain B residue 2633 GLU Chi-restraints excluded: chain B residue 2661 VAL Chi-restraints excluded: chain B residue 2667 LEU Chi-restraints excluded: chain B residue 2685 VAL Chi-restraints excluded: chain B residue 2690 LEU Chi-restraints excluded: chain B residue 2742 SER Chi-restraints excluded: chain B residue 2776 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 116 optimal weight: 7.9990 chunk 91 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 143 optimal weight: 3.9990 chunk 105 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 208 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 123 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 849 HIS ** A 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1952 GLN ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1176 ASN B1411 ASN B2234 ASN B2543 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.183010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.146390 restraints weight = 41465.094| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.66 r_work: 0.3757 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26977 Z= 0.132 Angle : 0.614 10.168 36544 Z= 0.300 Chirality : 0.041 0.226 4111 Planarity : 0.005 0.070 4726 Dihedral : 4.907 58.730 3623 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.34 % Allowed : 27.19 % Favored : 68.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.15), residues: 3301 helix: 1.54 (0.14), residues: 1435 sheet: -0.06 (0.28), residues: 349 loop : -0.49 (0.17), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP A 765 HIS 0.006 0.001 HIS A 849 PHE 0.041 0.001 PHE B2218 TYR 0.018 0.001 TYR A1370 ARG 0.011 0.000 ARG A 889 Details of bonding type rmsd hydrogen bonds : bond 0.03682 ( 1207) hydrogen bonds : angle 4.21520 ( 3435) metal coordination : bond 0.00923 ( 24) metal coordination : angle 3.07722 ( 28) covalent geometry : bond 0.00307 (26953) covalent geometry : angle 0.60843 (36516) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6602 Ramachandran restraints generated. 3301 Oldfield, 0 Emsley, 3301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6602 Ramachandran restraints generated. 3301 Oldfield, 0 Emsley, 3301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 522 time to evaluate : 2.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.3371 (tp30) REVERT: A 390 LEU cc_start: 0.8293 (tp) cc_final: 0.7847 (tp) REVERT: A 488 GLU cc_start: 0.7085 (tp30) cc_final: 0.6410 (tp30) REVERT: A 751 VAL cc_start: 0.8831 (t) cc_final: 0.8574 (p) REVERT: A 890 GLN cc_start: 0.7769 (mm-40) cc_final: 0.7344 (mm-40) REVERT: A 1090 LYS cc_start: 0.8715 (tppp) cc_final: 0.7862 (tppp) REVERT: A 1149 LYS cc_start: 0.7935 (mppt) cc_final: 0.7637 (mppt) REVERT: A 1195 GLU cc_start: 0.7048 (pm20) cc_final: 0.6666 (pm20) REVERT: A 1222 LYS cc_start: 0.7838 (mtmm) cc_final: 0.7292 (mtmm) REVERT: A 2018 GLN cc_start: 0.8517 (tm-30) cc_final: 0.7767 (tm-30) REVERT: A 2102 MET cc_start: 0.3999 (ppp) cc_final: 0.3583 (pp-130) REVERT: A 2215 LEU cc_start: 0.8208 (mt) cc_final: 0.7637 (pp) REVERT: A 2248 ARG cc_start: 0.7997 (ptt180) cc_final: 0.7699 (ppt170) REVERT: A 2563 VAL cc_start: 0.7949 (OUTLIER) cc_final: 0.7480 (m) REVERT: A 2731 TYR cc_start: 0.7314 (t80) cc_final: 0.6998 (t80) REVERT: A 2749 MET cc_start: 0.7004 (ttm) cc_final: 0.6750 (ttm) REVERT: B 61 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8187 (tp) REVERT: B 795 ASN cc_start: 0.7675 (t0) cc_final: 0.7318 (t0) REVERT: B 891 TYR cc_start: 0.7988 (t80) cc_final: 0.7409 (t80) REVERT: B 895 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7744 (mm) REVERT: B 1195 GLU cc_start: 0.7407 (pp20) cc_final: 0.6944 (pp20) REVERT: B 1222 LYS cc_start: 0.8271 (mmmm) cc_final: 0.7995 (mmmm) REVERT: B 1511 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7182 (tm-30) REVERT: B 1512 GLU cc_start: 0.7449 (pp20) cc_final: 0.6965 (pp20) REVERT: B 2028 SER cc_start: 0.7538 (OUTLIER) cc_final: 0.5164 (m) REVERT: B 2032 LEU cc_start: 0.8677 (tp) cc_final: 0.8471 (tt) REVERT: B 2044 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7987 (tt) REVERT: B 2083 LYS cc_start: 0.8275 (mttp) cc_final: 0.7867 (mttp) REVERT: B 2176 MET cc_start: 0.5665 (ttm) cc_final: 0.5360 (ttm) REVERT: B 2219 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7521 (mm-30) REVERT: B 2225 PHE cc_start: 0.8215 (t80) cc_final: 0.7830 (t80) REVERT: B 2293 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7421 (mtm180) REVERT: B 2564 ASN cc_start: 0.8050 (p0) cc_final: 0.7749 (p0) outliers start: 128 outliers final: 75 residues processed: 594 average time/residue: 1.2798 time to fit residues: 895.7685 Evaluate side-chains 584 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 502 time to evaluate : 2.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 416 PHE Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 875 THR Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 911 PHE Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 930 CYS Chi-restraints excluded: chain A residue 1137 GLN Chi-restraints excluded: chain A residue 1164 ASN Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1231 TYR Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1382 CYS Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1441 VAL Chi-restraints excluded: chain A residue 1933 SER Chi-restraints excluded: chain A residue 2027 ASP Chi-restraints excluded: chain A residue 2178 MET Chi-restraints excluded: chain A residue 2251 LEU Chi-restraints excluded: chain A residue 2556 LYS Chi-restraints excluded: chain A residue 2563 VAL Chi-restraints excluded: chain A residue 2661 VAL Chi-restraints excluded: chain A residue 2667 LEU Chi-restraints excluded: chain A residue 2690 LEU Chi-restraints excluded: chain A residue 2779 SER Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 732 GLN Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain B residue 911 PHE Chi-restraints excluded: chain B residue 1118 MET Chi-restraints excluded: chain B residue 1153 VAL Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1193 ILE Chi-restraints excluded: chain B residue 1287 THR Chi-restraints excluded: chain B residue 1298 ILE Chi-restraints excluded: chain B residue 1323 ARG Chi-restraints excluded: chain B residue 1367 GLU Chi-restraints excluded: chain B residue 1377 THR Chi-restraints excluded: chain B residue 1389 VAL Chi-restraints excluded: chain B residue 1801 LEU Chi-restraints excluded: chain B residue 1804 LYS Chi-restraints excluded: chain B residue 1811 SER Chi-restraints excluded: chain B residue 1819 LEU Chi-restraints excluded: chain B residue 1935 VAL Chi-restraints excluded: chain B residue 1957 TRP Chi-restraints excluded: chain B residue 2020 HIS Chi-restraints excluded: chain B residue 2028 SER Chi-restraints excluded: chain B residue 2044 LEU Chi-restraints excluded: chain B residue 2090 VAL Chi-restraints excluded: chain B residue 2220 VAL Chi-restraints excluded: chain B residue 2251 LEU Chi-restraints excluded: chain B residue 2272 MET Chi-restraints excluded: chain B residue 2293 ARG Chi-restraints excluded: chain B residue 2510 LYS Chi-restraints excluded: chain B residue 2574 VAL Chi-restraints excluded: chain B residue 2633 GLU Chi-restraints excluded: chain B residue 2661 VAL Chi-restraints excluded: chain B residue 2667 LEU Chi-restraints excluded: chain B residue 2685 VAL Chi-restraints excluded: chain B residue 2690 LEU Chi-restraints excluded: chain B residue 2742 SER Chi-restraints excluded: chain B residue 2776 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 327 optimal weight: 9.9990 chunk 249 optimal weight: 1.9990 chunk 237 optimal weight: 2.9990 chunk 279 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 270 optimal weight: 0.5980 chunk 95 optimal weight: 0.0670 chunk 318 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 288 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 501 GLN A 849 HIS ** A 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1952 GLN ** A2680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1411 ASN B2234 ASN B2543 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.183126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.145244 restraints weight = 41687.203| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.59 r_work: 0.3761 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26977 Z= 0.141 Angle : 0.625 10.428 36544 Z= 0.305 Chirality : 0.041 0.192 4111 Planarity : 0.005 0.068 4726 Dihedral : 4.788 58.919 3620 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.44 % Allowed : 27.80 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.15), residues: 3301 helix: 1.53 (0.14), residues: 1436 sheet: -0.13 (0.28), residues: 339 loop : -0.48 (0.17), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP A 765 HIS 0.007 0.001 HIS A 757 PHE 0.032 0.001 PHE A 72 TYR 0.021 0.001 TYR A1370 ARG 0.013 0.000 ARG A 889 Details of bonding type rmsd hydrogen bonds : bond 0.03725 ( 1207) hydrogen bonds : angle 4.20935 ( 3435) metal coordination : bond 0.00985 ( 24) metal coordination : angle 3.14398 ( 28) covalent geometry : bond 0.00330 (26953) covalent geometry : angle 0.61888 (36516) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6602 Ramachandran restraints generated. 3301 Oldfield, 0 Emsley, 3301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6602 Ramachandran restraints generated. 3301 Oldfield, 0 Emsley, 3301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 519 time to evaluate : 2.919 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 380 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.3358 (tp30) REVERT: A 390 LEU cc_start: 0.8270 (tp) cc_final: 0.7850 (tp) REVERT: A 488 GLU cc_start: 0.7043 (tp30) cc_final: 0.6385 (tp30) REVERT: A 890 GLN cc_start: 0.7713 (mm-40) cc_final: 0.7326 (mm-40) REVERT: A 912 ILE cc_start: 0.8202 (mm) cc_final: 0.7880 (tp) REVERT: A 1090 LYS cc_start: 0.8547 (tppp) cc_final: 0.8270 (tppp) REVERT: A 1149 LYS cc_start: 0.7942 (mppt) cc_final: 0.7684 (mppt) REVERT: A 1195 GLU cc_start: 0.7025 (pm20) cc_final: 0.6658 (pm20) REVERT: A 1222 LYS cc_start: 0.7844 (mtmm) cc_final: 0.7292 (mtmm) REVERT: A 1318 ASP cc_start: 0.7412 (p0) cc_final: 0.7199 (p0) REVERT: A 1507 MET cc_start: 0.7146 (OUTLIER) cc_final: 0.6718 (mpt) REVERT: A 2018 GLN cc_start: 0.8513 (tm-30) cc_final: 0.7765 (tm-30) REVERT: A 2027 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7961 (p0) REVERT: A 2102 MET cc_start: 0.4042 (ppp) cc_final: 0.3642 (pp-130) REVERT: A 2215 LEU cc_start: 0.8178 (mt) cc_final: 0.7637 (pp) REVERT: A 2248 ARG cc_start: 0.7946 (ptt180) cc_final: 0.7683 (ppt170) REVERT: A 2563 VAL cc_start: 0.7976 (OUTLIER) cc_final: 0.7540 (m) REVERT: A 2644 LEU cc_start: 0.7867 (tp) cc_final: 0.7343 (tt) REVERT: A 2648 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7235 (mm-30) REVERT: A 2731 TYR cc_start: 0.7171 (t80) cc_final: 0.6909 (t80) REVERT: A 2749 MET cc_start: 0.6919 (ttm) cc_final: 0.6673 (ttm) REVERT: B 61 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8175 (tp) REVERT: B 746 ILE cc_start: 0.8419 (mp) cc_final: 0.7751 (tt) REVERT: B 891 TYR cc_start: 0.7952 (t80) cc_final: 0.7424 (t80) REVERT: B 895 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7737 (mm) REVERT: B 1150 GLU cc_start: 0.6945 (tp30) cc_final: 0.6712 (tp30) REVERT: B 1195 GLU cc_start: 0.7390 (pp20) cc_final: 0.6948 (pp20) REVERT: B 1222 LYS cc_start: 0.8285 (mmmm) cc_final: 0.8048 (mmmm) REVERT: B 1511 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7250 (tm-30) REVERT: B 1512 GLU cc_start: 0.7430 (pp20) cc_final: 0.6915 (pp20) REVERT: B 2028 SER cc_start: 0.7598 (OUTLIER) cc_final: 0.5236 (m) REVERT: B 2044 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.8019 (tt) REVERT: B 2083 LYS cc_start: 0.8294 (mttp) cc_final: 0.7901 (mttp) REVERT: B 2176 MET cc_start: 0.5587 (ttm) cc_final: 0.5300 (ttm) REVERT: B 2219 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7398 (mm-30) REVERT: B 2225 PHE cc_start: 0.8198 (t80) cc_final: 0.7825 (t80) REVERT: B 2293 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7453 (mtm180) REVERT: B 2504 LEU cc_start: 0.6489 (OUTLIER) cc_final: 0.6235 (mp) REVERT: B 2564 ASN cc_start: 0.8009 (p0) cc_final: 0.7713 (p0) REVERT: B 2633 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7543 (tp30) outliers start: 131 outliers final: 76 residues processed: 593 average time/residue: 1.2631 time to fit residues: 881.8491 Evaluate side-chains 599 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 512 time to evaluate : 3.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 416 PHE Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 875 THR Chi-restraints excluded: chain A residue 883 CYS Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 911 PHE Chi-restraints excluded: chain A residue 930 CYS Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1164 ASN Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1193 ILE Chi-restraints excluded: chain A residue 1231 TYR Chi-restraints excluded: chain A residue 1238 CYS Chi-restraints excluded: chain A residue 1241 LYS Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1441 VAL Chi-restraints excluded: chain A residue 1507 MET Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1802 ILE Chi-restraints excluded: chain A residue 1933 SER Chi-restraints excluded: chain A residue 2027 ASP Chi-restraints excluded: chain A residue 2178 MET Chi-restraints excluded: chain A residue 2251 LEU Chi-restraints excluded: chain A residue 2556 LYS Chi-restraints excluded: chain A residue 2563 VAL Chi-restraints excluded: chain A residue 2661 VAL Chi-restraints excluded: chain A residue 2667 LEU Chi-restraints excluded: chain A residue 2690 LEU Chi-restraints excluded: chain A residue 2779 SER Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 732 GLN Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain B residue 911 PHE Chi-restraints excluded: chain B residue 913 SER Chi-restraints excluded: chain B residue 1118 MET Chi-restraints excluded: chain B residue 1153 VAL Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1193 ILE Chi-restraints excluded: chain B residue 1241 LYS Chi-restraints excluded: chain B residue 1287 THR Chi-restraints excluded: chain B residue 1298 ILE Chi-restraints excluded: chain B residue 1323 ARG Chi-restraints excluded: chain B residue 1367 GLU Chi-restraints excluded: chain B residue 1377 THR Chi-restraints excluded: chain B residue 1389 VAL Chi-restraints excluded: chain B residue 1719 ARG Chi-restraints excluded: chain B residue 1801 LEU Chi-restraints excluded: chain B residue 1811 SER Chi-restraints excluded: chain B residue 1819 LEU Chi-restraints excluded: chain B residue 1935 VAL Chi-restraints excluded: chain B residue 1957 TRP Chi-restraints excluded: chain B residue 2028 SER Chi-restraints excluded: chain B residue 2044 LEU Chi-restraints excluded: chain B residue 2090 VAL Chi-restraints excluded: chain B residue 2220 VAL Chi-restraints excluded: chain B residue 2251 LEU Chi-restraints excluded: chain B residue 2272 MET Chi-restraints excluded: chain B residue 2293 ARG Chi-restraints excluded: chain B residue 2504 LEU Chi-restraints excluded: chain B residue 2510 LYS Chi-restraints excluded: chain B residue 2526 LEU Chi-restraints excluded: chain B residue 2551 ASN Chi-restraints excluded: chain B residue 2555 ILE Chi-restraints excluded: chain B residue 2574 VAL Chi-restraints excluded: chain B residue 2633 GLU Chi-restraints excluded: chain B residue 2661 VAL Chi-restraints excluded: chain B residue 2667 LEU Chi-restraints excluded: chain B residue 2685 VAL Chi-restraints excluded: chain B residue 2690 LEU Chi-restraints excluded: chain B residue 2742 SER Chi-restraints excluded: chain B residue 2776 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 264 optimal weight: 3.9990 chunk 258 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 chunk 165 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 34 optimal weight: 0.0470 chunk 307 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 180 optimal weight: 7.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 410 HIS ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 849 HIS ** A 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1952 GLN ** A2543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1411 ASN B2234 ASN B2543 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.183259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.145287 restraints weight = 41866.878| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 2.60 r_work: 0.3764 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26977 Z= 0.140 Angle : 0.653 10.892 36544 Z= 0.315 Chirality : 0.042 0.199 4111 Planarity : 0.005 0.070 4726 Dihedral : 4.744 59.635 3619 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.10 % Allowed : 28.27 % Favored : 67.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.15), residues: 3301 helix: 1.52 (0.14), residues: 1435 sheet: -0.13 (0.28), residues: 339 loop : -0.49 (0.17), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP A 765 HIS 0.006 0.001 HIS A 849 PHE 0.029 0.002 PHE B2295 TYR 0.022 0.001 TYR B1777 ARG 0.013 0.000 ARG A 889 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 1207) hydrogen bonds : angle 4.21730 ( 3435) metal coordination : bond 0.00932 ( 24) metal coordination : angle 3.11396 ( 28) covalent geometry : bond 0.00329 (26953) covalent geometry : angle 0.64741 (36516) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6602 Ramachandran restraints generated. 3301 Oldfield, 0 Emsley, 3301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6602 Ramachandran restraints generated. 3301 Oldfield, 0 Emsley, 3301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 514 time to evaluate : 2.830 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 380 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.3465 (tm-30) REVERT: A 390 LEU cc_start: 0.8261 (tp) cc_final: 0.7756 (tp) REVERT: A 488 GLU cc_start: 0.7051 (tp30) cc_final: 0.6384 (tp30) REVERT: A 890 GLN cc_start: 0.7711 (mm-40) cc_final: 0.7381 (mm-40) REVERT: A 897 GLN cc_start: 0.7684 (mm-40) cc_final: 0.7356 (mm-40) REVERT: A 912 ILE cc_start: 0.8208 (mm) cc_final: 0.7887 (tp) REVERT: A 1090 LYS cc_start: 0.8681 (tppp) cc_final: 0.8282 (tppp) REVERT: A 1149 LYS cc_start: 0.7955 (mppt) cc_final: 0.7692 (mppt) REVERT: A 1195 GLU cc_start: 0.7036 (pm20) cc_final: 0.6677 (pm20) REVERT: A 1222 LYS cc_start: 0.7855 (mtmm) cc_final: 0.7299 (mtmm) REVERT: A 1507 MET cc_start: 0.7124 (OUTLIER) cc_final: 0.6663 (mpt) REVERT: A 2018 GLN cc_start: 0.8520 (tm-30) cc_final: 0.7770 (tm-30) REVERT: A 2027 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7994 (p0) REVERT: A 2029 MET cc_start: 0.6830 (mmp) cc_final: 0.5966 (mmp) REVERT: A 2102 MET cc_start: 0.4032 (ppp) cc_final: 0.3506 (pp-130) REVERT: A 2215 LEU cc_start: 0.8168 (mt) cc_final: 0.7636 (pp) REVERT: A 2218 PHE cc_start: 0.7973 (t80) cc_final: 0.7696 (t80) REVERT: A 2248 ARG cc_start: 0.7946 (ptt180) cc_final: 0.7661 (ppt170) REVERT: A 2563 VAL cc_start: 0.7993 (OUTLIER) cc_final: 0.7565 (m) REVERT: A 2731 TYR cc_start: 0.7176 (t80) cc_final: 0.6902 (t80) REVERT: A 2749 MET cc_start: 0.6896 (ttm) cc_final: 0.6647 (ttm) REVERT: B 61 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8186 (tp) REVERT: B 746 ILE cc_start: 0.8418 (mp) cc_final: 0.7750 (tt) REVERT: B 795 ASN cc_start: 0.7550 (t0) cc_final: 0.7321 (t0) REVERT: B 891 TYR cc_start: 0.7928 (t80) cc_final: 0.7388 (t80) REVERT: B 895 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7755 (mm) REVERT: B 1195 GLU cc_start: 0.7405 (pp20) cc_final: 0.6952 (pp20) REVERT: B 1222 LYS cc_start: 0.8292 (mmmm) cc_final: 0.8050 (mmmm) REVERT: B 1326 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7530 (mp-120) REVERT: B 1511 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7242 (tm-30) REVERT: B 1512 GLU cc_start: 0.7418 (pp20) cc_final: 0.6911 (pp20) REVERT: B 2028 SER cc_start: 0.7628 (OUTLIER) cc_final: 0.5217 (m) REVERT: B 2038 ASN cc_start: 0.7588 (t0) cc_final: 0.7221 (t0) REVERT: B 2044 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.8026 (tt) REVERT: B 2083 LYS cc_start: 0.8299 (mttp) cc_final: 0.7905 (mttp) REVERT: B 2095 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7586 (mm) REVERT: B 2176 MET cc_start: 0.5566 (ttm) cc_final: 0.5281 (ttm) REVERT: B 2225 PHE cc_start: 0.8208 (t80) cc_final: 0.7816 (t80) REVERT: B 2293 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7453 (mtm180) REVERT: B 2504 LEU cc_start: 0.6451 (OUTLIER) cc_final: 0.6186 (mp) REVERT: B 2534 ARG cc_start: 0.7600 (mtt180) cc_final: 0.7136 (mtp180) REVERT: B 2564 ASN cc_start: 0.8012 (p0) cc_final: 0.7709 (p0) REVERT: B 2575 MET cc_start: 0.7561 (tpt) cc_final: 0.7332 (tpt) REVERT: B 2633 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7434 (tp30) REVERT: B 2636 ARG cc_start: 0.8182 (tmm160) cc_final: 0.7811 (tmm160) REVERT: B 2684 GLU cc_start: 0.7448 (pm20) cc_final: 0.7212 (pp20) REVERT: B 2784 LYS cc_start: 0.8483 (mptp) cc_final: 0.8190 (mtmt) outliers start: 121 outliers final: 77 residues processed: 589 average time/residue: 1.2900 time to fit residues: 891.5096 Evaluate side-chains 597 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 507 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 416 PHE Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 875 THR Chi-restraints excluded: chain A residue 883 CYS Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 911 PHE Chi-restraints excluded: chain A residue 930 CYS Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1137 GLN Chi-restraints excluded: chain A residue 1164 ASN Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1193 ILE Chi-restraints excluded: chain A residue 1231 TYR Chi-restraints excluded: chain A residue 1238 CYS Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1441 VAL Chi-restraints excluded: chain A residue 1507 MET Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1802 ILE Chi-restraints excluded: chain A residue 1933 SER Chi-restraints excluded: chain A residue 2027 ASP Chi-restraints excluded: chain A residue 2178 MET Chi-restraints excluded: chain A residue 2251 LEU Chi-restraints excluded: chain A residue 2556 LYS Chi-restraints excluded: chain A residue 2563 VAL Chi-restraints excluded: chain A residue 2661 VAL Chi-restraints excluded: chain A residue 2667 LEU Chi-restraints excluded: chain A residue 2690 LEU Chi-restraints excluded: chain A residue 2779 SER Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 732 GLN Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 762 THR Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain B residue 911 PHE Chi-restraints excluded: chain B residue 913 SER Chi-restraints excluded: chain B residue 1118 MET Chi-restraints excluded: chain B residue 1153 VAL Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1193 ILE Chi-restraints excluded: chain B residue 1241 LYS Chi-restraints excluded: chain B residue 1287 THR Chi-restraints excluded: chain B residue 1298 ILE Chi-restraints excluded: chain B residue 1323 ARG Chi-restraints excluded: chain B residue 1326 GLN Chi-restraints excluded: chain B residue 1367 GLU Chi-restraints excluded: chain B residue 1389 VAL Chi-restraints excluded: chain B residue 1719 ARG Chi-restraints excluded: chain B residue 1801 LEU Chi-restraints excluded: chain B residue 1811 SER Chi-restraints excluded: chain B residue 1819 LEU Chi-restraints excluded: chain B residue 1935 VAL Chi-restraints excluded: chain B residue 1957 TRP Chi-restraints excluded: chain B residue 2020 HIS Chi-restraints excluded: chain B residue 2028 SER Chi-restraints excluded: chain B residue 2044 LEU Chi-restraints excluded: chain B residue 2057 LEU Chi-restraints excluded: chain B residue 2090 VAL Chi-restraints excluded: chain B residue 2095 LEU Chi-restraints excluded: chain B residue 2220 VAL Chi-restraints excluded: chain B residue 2251 LEU Chi-restraints excluded: chain B residue 2272 MET Chi-restraints excluded: chain B residue 2293 ARG Chi-restraints excluded: chain B residue 2504 LEU Chi-restraints excluded: chain B residue 2526 LEU Chi-restraints excluded: chain B residue 2574 VAL Chi-restraints excluded: chain B residue 2627 THR Chi-restraints excluded: chain B residue 2633 GLU Chi-restraints excluded: chain B residue 2685 VAL Chi-restraints excluded: chain B residue 2690 LEU Chi-restraints excluded: chain B residue 2742 SER Chi-restraints excluded: chain B residue 2776 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 228 optimal weight: 0.7980 chunk 300 optimal weight: 8.9990 chunk 80 optimal weight: 0.4980 chunk 225 optimal weight: 0.9980 chunk 234 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 306 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 92 optimal weight: 0.0010 chunk 66 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 410 HIS ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 849 HIS ** A 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1952 GLN A2543 ASN ** A2680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1176 ASN B1411 ASN B2234 ASN B2543 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.183264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.145608 restraints weight = 41827.725| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.59 r_work: 0.3766 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26977 Z= 0.139 Angle : 0.671 11.441 36544 Z= 0.324 Chirality : 0.042 0.231 4111 Planarity : 0.005 0.069 4726 Dihedral : 4.757 59.669 3619 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.53 % Allowed : 29.36 % Favored : 67.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.15), residues: 3301 helix: 1.51 (0.14), residues: 1436 sheet: -0.16 (0.28), residues: 341 loop : -0.46 (0.17), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 765 HIS 0.007 0.001 HIS A 757 PHE 0.032 0.001 PHE B2218 TYR 0.020 0.001 TYR B1777 ARG 0.014 0.000 ARG A 889 Details of bonding type rmsd hydrogen bonds : bond 0.03696 ( 1207) hydrogen bonds : angle 4.21838 ( 3435) metal coordination : bond 0.00864 ( 24) metal coordination : angle 3.00049 ( 28) covalent geometry : bond 0.00328 (26953) covalent geometry : angle 0.66632 (36516) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6602 Ramachandran restraints generated. 3301 Oldfield, 0 Emsley, 3301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6602 Ramachandran restraints generated. 3301 Oldfield, 0 Emsley, 3301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 514 time to evaluate : 2.799 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 380 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.3466 (tm-30) REVERT: A 390 LEU cc_start: 0.8259 (tp) cc_final: 0.7812 (tp) REVERT: A 488 GLU cc_start: 0.7053 (tp30) cc_final: 0.6366 (tp30) REVERT: A 503 LYS cc_start: 0.7810 (tppp) cc_final: 0.7420 (tppt) REVERT: A 762 THR cc_start: 0.8031 (t) cc_final: 0.7715 (t) REVERT: A 890 GLN cc_start: 0.7708 (mm-40) cc_final: 0.7374 (mm-40) REVERT: A 897 GLN cc_start: 0.7710 (mm-40) cc_final: 0.7386 (mm-40) REVERT: A 912 ILE cc_start: 0.8194 (mm) cc_final: 0.7876 (tp) REVERT: A 1090 LYS cc_start: 0.8672 (tppp) cc_final: 0.7947 (tppp) REVERT: A 1149 LYS cc_start: 0.7950 (mppt) cc_final: 0.7693 (mppt) REVERT: A 1195 GLU cc_start: 0.7035 (pm20) cc_final: 0.6683 (pm20) REVERT: A 1222 LYS cc_start: 0.7851 (mtmm) cc_final: 0.7289 (mtmm) REVERT: A 1507 MET cc_start: 0.7134 (OUTLIER) cc_final: 0.6669 (mpt) REVERT: A 2018 GLN cc_start: 0.8526 (tm-30) cc_final: 0.7782 (tm-30) REVERT: A 2027 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7980 (p0) REVERT: A 2029 MET cc_start: 0.6812 (mmp) cc_final: 0.5773 (mmp) REVERT: A 2102 MET cc_start: 0.4026 (ppp) cc_final: 0.3600 (pp-130) REVERT: A 2215 LEU cc_start: 0.8160 (mt) cc_final: 0.7646 (pp) REVERT: A 2218 PHE cc_start: 0.7996 (t80) cc_final: 0.7730 (t80) REVERT: A 2248 ARG cc_start: 0.7968 (ptt180) cc_final: 0.7711 (ppt170) REVERT: A 2563 VAL cc_start: 0.7988 (p) cc_final: 0.7545 (m) REVERT: A 2644 LEU cc_start: 0.7651 (tt) cc_final: 0.7228 (tp) REVERT: A 2721 MET cc_start: 0.8528 (pp-130) cc_final: 0.8223 (ppp) REVERT: A 2731 TYR cc_start: 0.7136 (t80) cc_final: 0.6861 (t80) REVERT: A 2749 MET cc_start: 0.6835 (ttm) cc_final: 0.6600 (ttm) REVERT: B 61 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8156 (tp) REVERT: B 69 ARG cc_start: 0.6843 (ptt180) cc_final: 0.6034 (ptt180) REVERT: B 488 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7510 (tp30) REVERT: B 746 ILE cc_start: 0.8437 (mp) cc_final: 0.7799 (tt) REVERT: B 795 ASN cc_start: 0.7573 (t0) cc_final: 0.7333 (t0) REVERT: B 891 TYR cc_start: 0.7948 (t80) cc_final: 0.7407 (t80) REVERT: B 893 MET cc_start: 0.7712 (mtt) cc_final: 0.7480 (mtt) REVERT: B 895 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7750 (mm) REVERT: B 1195 GLU cc_start: 0.7416 (pp20) cc_final: 0.6968 (pp20) REVERT: B 1326 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7538 (mp-120) REVERT: B 1511 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7223 (tm-30) REVERT: B 1512 GLU cc_start: 0.7439 (pp20) cc_final: 0.6936 (pp20) REVERT: B 2028 SER cc_start: 0.7604 (OUTLIER) cc_final: 0.5205 (m) REVERT: B 2032 LEU cc_start: 0.8680 (tp) cc_final: 0.8465 (tt) REVERT: B 2038 ASN cc_start: 0.7577 (t0) cc_final: 0.7198 (t0) REVERT: B 2044 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.8016 (tt) REVERT: B 2083 LYS cc_start: 0.8314 (mttp) cc_final: 0.7896 (mttp) REVERT: B 2176 MET cc_start: 0.5555 (ttm) cc_final: 0.5253 (ttm) REVERT: B 2225 PHE cc_start: 0.8180 (t80) cc_final: 0.7913 (t80) REVERT: B 2248 ARG cc_start: 0.7474 (ttm110) cc_final: 0.7264 (ttm110) REVERT: B 2293 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7374 (mtm180) REVERT: B 2504 LEU cc_start: 0.6393 (OUTLIER) cc_final: 0.6141 (mp) REVERT: B 2534 ARG cc_start: 0.7582 (mtt180) cc_final: 0.7138 (mtp180) REVERT: B 2564 ASN cc_start: 0.7998 (p0) cc_final: 0.7693 (p0) REVERT: B 2633 GLU cc_start: 0.7964 (tp30) cc_final: 0.7407 (tp30) REVERT: B 2636 ARG cc_start: 0.8177 (tmm160) cc_final: 0.7810 (tmm160) REVERT: B 2664 LYS cc_start: 0.8089 (tmmt) cc_final: 0.7774 (tmmt) REVERT: B 2684 GLU cc_start: 0.7437 (pm20) cc_final: 0.7179 (pp20) outliers start: 104 outliers final: 74 residues processed: 578 average time/residue: 1.4277 time to fit residues: 970.6741 Evaluate side-chains 591 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 507 time to evaluate : 3.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 416 PHE Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 875 THR Chi-restraints excluded: chain A residue 883 CYS Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 911 PHE Chi-restraints excluded: chain A residue 930 CYS Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1137 GLN Chi-restraints excluded: chain A residue 1164 ASN Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1193 ILE Chi-restraints excluded: chain A residue 1231 TYR Chi-restraints excluded: chain A residue 1238 CYS Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1441 VAL Chi-restraints excluded: chain A residue 1507 MET Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1933 SER Chi-restraints excluded: chain A residue 2027 ASP Chi-restraints excluded: chain A residue 2178 MET Chi-restraints excluded: chain A residue 2251 LEU Chi-restraints excluded: chain A residue 2556 LYS Chi-restraints excluded: chain A residue 2661 VAL Chi-restraints excluded: chain A residue 2667 LEU Chi-restraints excluded: chain A residue 2690 LEU Chi-restraints excluded: chain A residue 2779 SER Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 732 GLN Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain B residue 911 PHE Chi-restraints excluded: chain B residue 913 SER Chi-restraints excluded: chain B residue 1118 MET Chi-restraints excluded: chain B residue 1153 VAL Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1193 ILE Chi-restraints excluded: chain B residue 1231 TYR Chi-restraints excluded: chain B residue 1287 THR Chi-restraints excluded: chain B residue 1298 ILE Chi-restraints excluded: chain B residue 1323 ARG Chi-restraints excluded: chain B residue 1326 GLN Chi-restraints excluded: chain B residue 1367 GLU Chi-restraints excluded: chain B residue 1377 THR Chi-restraints excluded: chain B residue 1389 VAL Chi-restraints excluded: chain B residue 1719 ARG Chi-restraints excluded: chain B residue 1801 LEU Chi-restraints excluded: chain B residue 1811 SER Chi-restraints excluded: chain B residue 1819 LEU Chi-restraints excluded: chain B residue 1935 VAL Chi-restraints excluded: chain B residue 1957 TRP Chi-restraints excluded: chain B residue 2020 HIS Chi-restraints excluded: chain B residue 2028 SER Chi-restraints excluded: chain B residue 2044 LEU Chi-restraints excluded: chain B residue 2090 VAL Chi-restraints excluded: chain B residue 2220 VAL Chi-restraints excluded: chain B residue 2251 LEU Chi-restraints excluded: chain B residue 2272 MET Chi-restraints excluded: chain B residue 2293 ARG Chi-restraints excluded: chain B residue 2504 LEU Chi-restraints excluded: chain B residue 2526 LEU Chi-restraints excluded: chain B residue 2551 ASN Chi-restraints excluded: chain B residue 2574 VAL Chi-restraints excluded: chain B residue 2627 THR Chi-restraints excluded: chain B residue 2685 VAL Chi-restraints excluded: chain B residue 2690 LEU Chi-restraints excluded: chain B residue 2742 SER Chi-restraints excluded: chain B residue 2776 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 229 optimal weight: 0.9980 chunk 173 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 208 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 8 optimal weight: 8.9990 chunk 209 optimal weight: 0.7980 chunk 26 optimal weight: 30.0000 chunk 333 optimal weight: 8.9990 chunk 73 optimal weight: 0.5980 chunk 112 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 410 HIS ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 849 HIS ** A 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1099 GLN A1952 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1411 ASN B2234 ASN B2543 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.183125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.145288 restraints weight = 41408.538| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.59 r_work: 0.3760 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26977 Z= 0.151 Angle : 0.691 12.067 36544 Z= 0.333 Chirality : 0.042 0.236 4111 Planarity : 0.005 0.069 4726 Dihedral : 4.785 59.152 3619 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.19 % Allowed : 29.73 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.15), residues: 3301 helix: 1.46 (0.14), residues: 1436 sheet: -0.18 (0.28), residues: 340 loop : -0.47 (0.17), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP A 765 HIS 0.007 0.001 HIS A 757 PHE 0.035 0.002 PHE B2218 TYR 0.022 0.001 TYR A1370 ARG 0.016 0.000 ARG A 889 Details of bonding type rmsd hydrogen bonds : bond 0.03781 ( 1207) hydrogen bonds : angle 4.24053 ( 3435) metal coordination : bond 0.01011 ( 24) metal coordination : angle 3.05052 ( 28) covalent geometry : bond 0.00358 (26953) covalent geometry : angle 0.68613 (36516) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6602 Ramachandran restraints generated. 3301 Oldfield, 0 Emsley, 3301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6602 Ramachandran restraints generated. 3301 Oldfield, 0 Emsley, 3301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 519 time to evaluate : 2.934 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 380 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.3495 (tm-30) REVERT: A 390 LEU cc_start: 0.8236 (tp) cc_final: 0.7787 (tp) REVERT: A 488 GLU cc_start: 0.7062 (tp30) cc_final: 0.6400 (tp30) REVERT: A 503 LYS cc_start: 0.7774 (tppp) cc_final: 0.7402 (tppt) REVERT: A 751 VAL cc_start: 0.8812 (t) cc_final: 0.8581 (p) REVERT: A 890 GLN cc_start: 0.7713 (mm-40) cc_final: 0.7289 (mm-40) REVERT: A 897 GLN cc_start: 0.7731 (mm-40) cc_final: 0.7447 (mm-40) REVERT: A 912 ILE cc_start: 0.8206 (mm) cc_final: 0.7894 (tp) REVERT: A 1090 LYS cc_start: 0.8547 (tppp) cc_final: 0.8248 (tppp) REVERT: A 1149 LYS cc_start: 0.7968 (mppt) cc_final: 0.7709 (mppt) REVERT: A 1195 GLU cc_start: 0.7041 (pm20) cc_final: 0.6687 (pm20) REVERT: A 1222 LYS cc_start: 0.7855 (mtmm) cc_final: 0.7290 (mtmm) REVERT: A 1418 ARG cc_start: 0.8299 (mtp85) cc_final: 0.8085 (ttt-90) REVERT: A 1507 MET cc_start: 0.7123 (OUTLIER) cc_final: 0.6664 (mpt) REVERT: A 1842 MET cc_start: 0.8468 (tmm) cc_final: 0.8246 (ttp) REVERT: A 2018 GLN cc_start: 0.8534 (tm-30) cc_final: 0.7791 (tm-30) REVERT: A 2027 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7982 (p0) REVERT: A 2029 MET cc_start: 0.6833 (mmp) cc_final: 0.5980 (mmp) REVERT: A 2102 MET cc_start: 0.4150 (ppp) cc_final: 0.3718 (pp-130) REVERT: A 2215 LEU cc_start: 0.8158 (mt) cc_final: 0.7659 (pp) REVERT: A 2218 PHE cc_start: 0.8036 (t80) cc_final: 0.7741 (t80) REVERT: A 2248 ARG cc_start: 0.7985 (ptt180) cc_final: 0.7721 (ppt170) REVERT: A 2501 ASN cc_start: 0.6594 (t0) cc_final: 0.6186 (t0) REVERT: A 2553 HIS cc_start: 0.6842 (t-170) cc_final: 0.6525 (t-170) REVERT: A 2563 VAL cc_start: 0.8031 (p) cc_final: 0.7808 (m) REVERT: A 2642 ARG cc_start: 0.8162 (mmm-85) cc_final: 0.7944 (mmm-85) REVERT: A 2721 MET cc_start: 0.8571 (pp-130) cc_final: 0.8266 (ppp) REVERT: A 2731 TYR cc_start: 0.7156 (t80) cc_final: 0.6863 (t80) REVERT: A 2749 MET cc_start: 0.6828 (ttm) cc_final: 0.6581 (ttm) REVERT: B 61 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8096 (tp) REVERT: B 69 ARG cc_start: 0.6840 (ptt180) cc_final: 0.6022 (ptt180) REVERT: B 488 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7488 (tp30) REVERT: B 746 ILE cc_start: 0.8441 (mp) cc_final: 0.7807 (tt) REVERT: B 795 ASN cc_start: 0.7604 (t0) cc_final: 0.7371 (t0) REVERT: B 891 TYR cc_start: 0.7949 (t80) cc_final: 0.7415 (t80) REVERT: B 893 MET cc_start: 0.7675 (mtt) cc_final: 0.7416 (mtt) REVERT: B 895 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7790 (mm) REVERT: B 1195 GLU cc_start: 0.7431 (pp20) cc_final: 0.6986 (pp20) REVERT: B 1326 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7549 (mp-120) REVERT: B 1511 GLU cc_start: 0.7625 (tm-30) cc_final: 0.7207 (tm-30) REVERT: B 2028 SER cc_start: 0.7626 (OUTLIER) cc_final: 0.5217 (m) REVERT: B 2038 ASN cc_start: 0.7580 (t0) cc_final: 0.7205 (t0) REVERT: B 2044 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.8010 (tt) REVERT: B 2083 LYS cc_start: 0.8316 (mttp) cc_final: 0.7871 (mttp) REVERT: B 2176 MET cc_start: 0.5573 (ttm) cc_final: 0.5259 (ttm) REVERT: B 2225 PHE cc_start: 0.8182 (t80) cc_final: 0.7908 (t80) REVERT: B 2248 ARG cc_start: 0.7487 (ttm110) cc_final: 0.7260 (ttm110) REVERT: B 2293 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7376 (mtm180) REVERT: B 2504 LEU cc_start: 0.6419 (OUTLIER) cc_final: 0.6155 (mp) REVERT: B 2534 ARG cc_start: 0.7577 (mtt180) cc_final: 0.7149 (mtp180) REVERT: B 2564 ASN cc_start: 0.7995 (p0) cc_final: 0.7686 (p0) REVERT: B 2633 GLU cc_start: 0.7950 (tp30) cc_final: 0.7389 (tp30) REVERT: B 2636 ARG cc_start: 0.8180 (tmm160) cc_final: 0.7748 (tmm160) REVERT: B 2664 LYS cc_start: 0.8099 (tmmt) cc_final: 0.7793 (tmmt) outliers start: 94 outliers final: 76 residues processed: 577 average time/residue: 1.4347 time to fit residues: 972.3087 Evaluate side-chains 599 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 513 time to evaluate : 2.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 416 PHE Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 875 THR Chi-restraints excluded: chain A residue 883 CYS Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 911 PHE Chi-restraints excluded: chain A residue 930 CYS Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1137 GLN Chi-restraints excluded: chain A residue 1164 ASN Chi-restraints excluded: chain A residue 1193 ILE Chi-restraints excluded: chain A residue 1231 TYR Chi-restraints excluded: chain A residue 1238 CYS Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1441 VAL Chi-restraints excluded: chain A residue 1507 MET Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1933 SER Chi-restraints excluded: chain A residue 2027 ASP Chi-restraints excluded: chain A residue 2178 MET Chi-restraints excluded: chain A residue 2243 GLU Chi-restraints excluded: chain A residue 2251 LEU Chi-restraints excluded: chain A residue 2556 LYS Chi-restraints excluded: chain A residue 2661 VAL Chi-restraints excluded: chain A residue 2667 LEU Chi-restraints excluded: chain A residue 2690 LEU Chi-restraints excluded: chain A residue 2779 SER Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 732 GLN Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 810 ILE Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain B residue 911 PHE Chi-restraints excluded: chain B residue 913 SER Chi-restraints excluded: chain B residue 1118 MET Chi-restraints excluded: chain B residue 1153 VAL Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1193 ILE Chi-restraints excluded: chain B residue 1259 LEU Chi-restraints excluded: chain B residue 1287 THR Chi-restraints excluded: chain B residue 1298 ILE Chi-restraints excluded: chain B residue 1323 ARG Chi-restraints excluded: chain B residue 1326 GLN Chi-restraints excluded: chain B residue 1377 THR Chi-restraints excluded: chain B residue 1389 VAL Chi-restraints excluded: chain B residue 1719 ARG Chi-restraints excluded: chain B residue 1801 LEU Chi-restraints excluded: chain B residue 1811 SER Chi-restraints excluded: chain B residue 1813 ILE Chi-restraints excluded: chain B residue 1819 LEU Chi-restraints excluded: chain B residue 1935 VAL Chi-restraints excluded: chain B residue 1957 TRP Chi-restraints excluded: chain B residue 2020 HIS Chi-restraints excluded: chain B residue 2028 SER Chi-restraints excluded: chain B residue 2044 LEU Chi-restraints excluded: chain B residue 2090 VAL Chi-restraints excluded: chain B residue 2220 VAL Chi-restraints excluded: chain B residue 2251 LEU Chi-restraints excluded: chain B residue 2272 MET Chi-restraints excluded: chain B residue 2293 ARG Chi-restraints excluded: chain B residue 2504 LEU Chi-restraints excluded: chain B residue 2526 LEU Chi-restraints excluded: chain B residue 2551 ASN Chi-restraints excluded: chain B residue 2574 VAL Chi-restraints excluded: chain B residue 2627 THR Chi-restraints excluded: chain B residue 2685 VAL Chi-restraints excluded: chain B residue 2690 LEU Chi-restraints excluded: chain B residue 2742 SER Chi-restraints excluded: chain B residue 2776 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 327 optimal weight: 9.9990 chunk 240 optimal weight: 0.6980 chunk 324 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 182 optimal weight: 10.0000 chunk 117 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 171 optimal weight: 7.9990 chunk 95 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 410 HIS ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 849 HIS A 924 HIS A1952 GLN ** A2680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1411 ASN B2234 ASN B2543 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.181400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.143350 restraints weight = 41597.364| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.76 r_work: 0.3723 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 26977 Z= 0.211 Angle : 0.723 13.580 36544 Z= 0.351 Chirality : 0.045 0.242 4111 Planarity : 0.005 0.069 4726 Dihedral : 4.894 58.822 3619 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.19 % Allowed : 29.83 % Favored : 66.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.15), residues: 3301 helix: 1.36 (0.14), residues: 1442 sheet: -0.26 (0.28), residues: 336 loop : -0.55 (0.17), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.002 TRP A 765 HIS 0.008 0.001 HIS A 757 PHE 0.049 0.002 PHE B2218 TYR 0.028 0.002 TYR A1370 ARG 0.017 0.000 ARG A 889 Details of bonding type rmsd hydrogen bonds : bond 0.04253 ( 1207) hydrogen bonds : angle 4.32948 ( 3435) metal coordination : bond 0.01738 ( 24) metal coordination : angle 3.47161 ( 28) covalent geometry : bond 0.00492 (26953) covalent geometry : angle 0.71641 (36516) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26285.33 seconds wall clock time: 458 minutes 25.61 seconds (27505.61 seconds total)