Starting phenix.real_space_refine on Wed Mar 20 05:11:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d4x_27201/03_2024/8d4x_27201.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d4x_27201/03_2024/8d4x_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d4x_27201/03_2024/8d4x_27201.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d4x_27201/03_2024/8d4x_27201.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d4x_27201/03_2024/8d4x_27201.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d4x_27201/03_2024/8d4x_27201.pdb" } 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 Residue "A GLU 397": "OE1" <-> "OE2" Residue "A GLU 745": "OE1" <-> "OE2" Residue "A GLU 1104": "OE1" <-> "OE2" Residue "A GLU 1320": "OE1" <-> "OE2" Residue "A GLU 1512": "OE1" <-> "OE2" Residue "A GLU 2207": "OE1" <-> "OE2" Residue "B GLU 872": "OE1" <-> "OE2" Residue "B GLU 896": "OE1" <-> "OE2" Residue "B GLU 1330": "OE1" <-> "OE2" Residue "B GLU 1474": "OE1" <-> "OE2" Residue "B GLU 1832": "OE1" <-> "OE2" Residue "B GLU 2046": "OE1" <-> "OE2" Residue "B GLU 2219": "OE1" <-> "OE2" Residue "B GLU 2222": "OE1" <-> "OE2" Residue "B GLU 2673": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 12.79, per 1000 atoms: 0.48 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 - 3.50 Amino acid : False - 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: 9.38 Conformation dependent library (CDL) restraints added in 5.2 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: 3.52 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: 12.29 Time building geometry restraints manager: 10.23 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: 97.44 - 104.76: 566 104.76 - 112.09: 13407 112.09 - 119.41: 9197 119.41 - 126.73: 12930 126.73 - 134.06: 416 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 2.520 nonbonded pdb=" O ASN B1962 " pdb=" OG1 THR B1965 " model vdw 2.200 2.440 nonbonded pdb=" O ASN A1962 " pdb=" OG1 THR A1965 " model vdw 2.205 2.440 nonbonded pdb=" O LEU A2690 " pdb=" OG1 THR A2694 " model vdw 2.207 2.440 nonbonded pdb=" OD2 ASP A2500 " pdb=" OG1 THR A2522 " model vdw 2.210 2.440 ... (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 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: 5.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.260 Check model and map are aligned: 0.380 Set scattering table: 0.220 Process input model: 74.140 Find NCS groups from input model: 1.930 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.750 ------------------------------------------------------------------------------- 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 26953 Z= 0.232 Angle : 0.691 11.173 36516 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 *********************** 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 fitting. rotamer outliers: 78 poor density : 495 time to evaluate : 2.870 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: 1.2430 time to fit residues: 815.5154 Evaluate side-chains 552 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 483 time to evaluate : 2.817 ------------------------------------------------------------------------------- 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: 0.5980 chunk 140 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 170 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 159 optimal weight: 20.0000 chunk 194 optimal weight: 8.9990 chunk 303 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.0633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 26953 Z= 0.245 Angle : 0.589 10.098 36516 Z= 0.292 Chirality : 0.041 0.185 4111 Planarity : 0.005 0.088 4726 Dihedral : 6.230 59.981 3719 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.37 % Allowed : 27.05 % Favored : 68.58 % 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: 1.50 (0.14), residues: 1436 sheet: -0.18 (0.27), residues: 389 loop : -0.40 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 765 HIS 0.007 0.001 HIS A2553 PHE 0.028 0.002 PHE A 72 TYR 0.018 0.002 TYR B1949 ARG 0.008 0.000 ARG A 889 *********************** 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 644 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 515 time to evaluate : 2.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 751 VAL cc_start: 0.8777 (t) cc_final: 0.8523 (p) REVERT: A 884 ASP cc_start: 0.7689 (t0) cc_final: 0.7464 (t0) REVERT: A 1090 LYS cc_start: 0.8676 (tppp) cc_final: 0.8458 (tppp) REVERT: A 1195 GLU cc_start: 0.7155 (pm20) cc_final: 0.6784 (pm20) REVERT: A 1709 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7430 (mp10) REVERT: A 2246 ARG cc_start: 0.8040 (tmm160) cc_final: 0.7832 (tmm160) REVERT: A 2563 VAL cc_start: 0.7948 (OUTLIER) cc_final: 0.7479 (m) REVERT: A 2721 MET cc_start: 0.8178 (tmm) cc_final: 0.7873 (tmm) REVERT: B 732 GLN cc_start: 0.7248 (OUTLIER) cc_final: 0.6468 (tm-30) REVERT: B 827 MET cc_start: 0.6634 (tmm) cc_final: 0.6332 (tmm) REVERT: B 891 TYR cc_start: 0.7957 (t80) cc_final: 0.7616 (t80) REVERT: B 1195 GLU cc_start: 0.7344 (pp20) cc_final: 0.7122 (pp20) REVERT: B 1511 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7297 (tm-30) REVERT: B 2032 LEU cc_start: 0.8682 (tp) cc_final: 0.8475 (tt) REVERT: B 2044 LEU cc_start: 0.8281 (tm) cc_final: 0.8077 (tt) REVERT: B 2087 GLU cc_start: 0.6908 (pm20) cc_final: 0.6171 (pm20) REVERT: B 2225 PHE cc_start: 0.8241 (t80) cc_final: 0.7893 (t80) REVERT: B 2579 LEU cc_start: 0.8572 (mt) cc_final: 0.8366 (mt) outliers start: 129 outliers final: 58 residues processed: 591 average time/residue: 1.2057 time to fit residues: 842.6370 Evaluate side-chains 550 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 489 time to evaluate : 2.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR 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 478 CYS Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 883 CYS 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 1164 ASN Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1231 TYR 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 2027 ASP Chi-restraints excluded: chain A residue 2085 LEU Chi-restraints excluded: chain A residue 2178 MET 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 47 THR 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 814 ASP 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 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 1350 ASN 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 1811 SER 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 168 optimal weight: 6.9990 chunk 94 optimal weight: 0.8980 chunk 252 optimal weight: 1.9990 chunk 206 optimal weight: 0.9980 chunk 83 optimal weight: 0.0670 chunk 303 optimal weight: 2.9990 chunk 328 optimal weight: 2.9990 chunk 270 optimal weight: 0.7980 chunk 301 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 243 optimal weight: 0.7980 overall best weight: 0.7118 ------------------------------------------------------------------------------- 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** A1852 GLN A1952 GLN B1411 ASN B2507 GLN B2543 ASN B2551 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.0768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26953 Z= 0.210 Angle : 0.565 8.872 36516 Z= 0.280 Chirality : 0.040 0.144 4111 Planarity : 0.005 0.061 4726 Dihedral : 5.097 59.759 3637 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.81 % Allowed : 26.75 % Favored : 68.44 % 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: 0.71 (0.15), residues: 3301 helix: 1.56 (0.14), residues: 1434 sheet: -0.10 (0.27), residues: 379 loop : -0.40 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 765 HIS 0.007 0.001 HIS A2553 PHE 0.017 0.001 PHE A1917 TYR 0.017 0.001 TYR A1370 ARG 0.008 0.000 ARG A 889 *********************** 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 657 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 515 time to evaluate : 3.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 VAL cc_start: 0.9026 (OUTLIER) cc_final: 0.8800 (t) REVERT: A 380 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.3232 (tm-30) REVERT: A 488 GLU cc_start: 0.6848 (tp30) cc_final: 0.6255 (tp30) REVERT: A 568 MET cc_start: 0.7562 (pmm) cc_final: 0.7345 (tmm) REVERT: A 822 MET cc_start: 0.8254 (mmm) cc_final: 0.7850 (tpt) REVERT: A 884 ASP cc_start: 0.7660 (t0) cc_final: 0.7402 (t0) REVERT: A 894 ASN cc_start: 0.7924 (m-40) cc_final: 0.7709 (m-40) REVERT: A 1090 LYS cc_start: 0.8687 (tppp) cc_final: 0.8404 (tppp) REVERT: A 1149 LYS cc_start: 0.7948 (mppt) cc_final: 0.7683 (mppt) REVERT: A 1195 GLU cc_start: 0.7143 (pm20) cc_final: 0.6759 (pm20) REVERT: A 1222 LYS cc_start: 0.7755 (mtmm) cc_final: 0.7381 (mtmm) REVERT: A 1507 MET cc_start: 0.7371 (OUTLIER) cc_final: 0.7060 (mpt) REVERT: A 2018 GLN cc_start: 0.8579 (tm-30) cc_final: 0.7944 (tm-30) REVERT: A 2029 MET cc_start: 0.6841 (mmp) cc_final: 0.5221 (mmp) REVERT: A 2102 MET cc_start: 0.4145 (ppp) cc_final: 0.3716 (pp-130) REVERT: A 2545 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6744 (pp) REVERT: A 2563 VAL cc_start: 0.7987 (OUTLIER) cc_final: 0.7495 (m) REVERT: B 732 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.6391 (tm-30) REVERT: B 827 MET cc_start: 0.6583 (tmm) cc_final: 0.6316 (tmm) REVERT: B 891 TYR cc_start: 0.7956 (t80) cc_final: 0.7624 (t80) REVERT: B 1195 GLU cc_start: 0.7387 (pp20) cc_final: 0.7085 (pp20) REVERT: B 1330 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7649 (tm-30) REVERT: B 1511 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7341 (tm-30) REVERT: B 2032 LEU cc_start: 0.8676 (tp) cc_final: 0.8473 (tt) REVERT: B 2044 LEU cc_start: 0.8290 (tm) cc_final: 0.8063 (tt) REVERT: B 2083 LYS cc_start: 0.8358 (mttp) cc_final: 0.8137 (mttp) REVERT: B 2225 PHE cc_start: 0.8243 (t80) cc_final: 0.7860 (t80) REVERT: B 2510 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8691 (mttp) outliers start: 142 outliers final: 67 residues processed: 601 average time/residue: 1.2171 time to fit residues: 860.8861 Evaluate side-chains 573 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 499 time to evaluate : 2.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 40 LEU 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 478 CYS Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 883 CYS Chi-restraints excluded: chain A residue 911 PHE Chi-restraints excluded: chain A residue 930 CYS Chi-restraints excluded: chain A residue 1155 MET 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 1241 LYS 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 1507 MET Chi-restraints excluded: chain A residue 1935 VAL Chi-restraints excluded: chain A residue 2178 MET Chi-restraints excluded: chain A residue 2184 MET Chi-restraints excluded: chain A residue 2255 THR 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 47 THR 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 562 MET 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 813 ARG Chi-restraints excluded: chain B residue 814 ASP Chi-restraints excluded: chain B residue 911 PHE Chi-restraints excluded: chain B residue 1153 VAL Chi-restraints excluded: chain B residue 1164 ASN 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 1350 ASN 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 1819 LEU Chi-restraints excluded: chain B residue 1935 VAL Chi-restraints excluded: chain B residue 1957 TRP Chi-restraints excluded: chain B residue 2092 ARG Chi-restraints excluded: chain B residue 2220 VAL Chi-restraints excluded: chain B residue 2230 GLU Chi-restraints excluded: chain B residue 2251 LEU Chi-restraints excluded: chain B residue 2510 LYS Chi-restraints excluded: chain B residue 2549 THR 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 2685 VAL Chi-restraints excluded: chain B residue 2690 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 300 optimal weight: 20.0000 chunk 228 optimal weight: 0.5980 chunk 157 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 204 optimal weight: 0.5980 chunk 304 optimal weight: 0.4980 chunk 322 optimal weight: 2.9990 chunk 159 optimal weight: 0.5980 chunk 289 optimal weight: 0.0070 chunk 87 optimal weight: 10.0000 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 HIS A 501 GLN A 849 HIS ** A 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1086 HIS A1952 GLN ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1411 ASN B2543 ASN B2551 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26953 Z= 0.174 Angle : 0.569 9.657 36516 Z= 0.280 Chirality : 0.040 0.212 4111 Planarity : 0.004 0.061 4726 Dihedral : 4.997 59.930 3634 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.68 % Allowed : 27.02 % Favored : 68.31 % 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: 0.79 (0.15), residues: 3301 helix: 1.64 (0.14), residues: 1433 sheet: -0.04 (0.27), residues: 370 loop : -0.38 (0.17), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 765 HIS 0.006 0.001 HIS A 849 PHE 0.029 0.001 PHE A 72 TYR 0.016 0.001 TYR A1256 ARG 0.008 0.000 ARG A 889 *********************** 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 654 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 516 time to evaluate : 2.713 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: 0.8006 (tp) cc_final: 0.7389 (tp) REVERT: A 488 GLU cc_start: 0.6869 (tp30) cc_final: 0.6271 (tp30) REVERT: A 884 ASP cc_start: 0.7679 (t0) cc_final: 0.7416 (t0) REVERT: A 1090 LYS cc_start: 0.8695 (tppp) cc_final: 0.8349 (tppp) REVERT: A 1149 LYS cc_start: 0.7909 (mppt) cc_final: 0.7598 (mppt) REVERT: A 1195 GLU cc_start: 0.7122 (pm20) cc_final: 0.6777 (pm20) REVERT: A 1222 LYS cc_start: 0.7774 (mtmm) cc_final: 0.7333 (mtmm) REVERT: A 1507 MET cc_start: 0.7330 (OUTLIER) cc_final: 0.7076 (mpt) REVERT: A 1842 MET cc_start: 0.8711 (tmm) cc_final: 0.8504 (ttp) REVERT: A 2018 GLN cc_start: 0.8564 (tm-30) cc_final: 0.7926 (tm-30) REVERT: A 2029 MET cc_start: 0.6721 (mmp) cc_final: 0.5046 (mmp) REVERT: A 2067 PHE cc_start: 0.7674 (m-80) cc_final: 0.7474 (m-80) REVERT: A 2102 MET cc_start: 0.4143 (ppp) cc_final: 0.3631 (pp-130) REVERT: A 2545 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6771 (pp) REVERT: A 2563 VAL cc_start: 0.7949 (OUTLIER) cc_final: 0.7543 (m) REVERT: A 2731 TYR cc_start: 0.7235 (t80) cc_final: 0.6927 (t80) REVERT: B 827 MET cc_start: 0.6567 (tmm) cc_final: 0.6272 (tmm) REVERT: B 891 TYR cc_start: 0.7924 (t80) cc_final: 0.7342 (t80) REVERT: B 893 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7659 (mtt) REVERT: B 895 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7730 (mm) REVERT: B 1195 GLU cc_start: 0.7394 (pp20) cc_final: 0.7041 (pp20) REVERT: B 1443 MET cc_start: 0.7824 (mpp) cc_final: 0.7604 (mmp) REVERT: B 1468 LEU cc_start: 0.8422 (tt) cc_final: 0.8113 (tp) REVERT: B 1511 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7273 (tm-30) REVERT: B 2044 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8051 (tt) REVERT: B 2225 PHE cc_start: 0.8231 (t80) cc_final: 0.7839 (t80) outliers start: 138 outliers final: 71 residues processed: 597 average time/residue: 1.2148 time to fit residues: 855.2548 Evaluate side-chains 579 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 502 time to evaluate : 3.134 ------------------------------------------------------------------------------- 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 416 PHE Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 551 ILE 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 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 1238 CYS Chi-restraints excluded: chain A residue 1241 LYS 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 2085 LEU Chi-restraints excluded: chain A residue 2178 MET Chi-restraints excluded: chain A residue 2255 THR 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 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 47 THR 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 491 LEU Chi-restraints excluded: chain B residue 732 GLN Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 814 ASP Chi-restraints excluded: chain B residue 893 MET Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain B residue 911 PHE Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 1118 MET Chi-restraints excluded: chain B residue 1153 VAL 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 1341 SER Chi-restraints excluded: chain B residue 1350 ASN 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 1801 LEU Chi-restraints excluded: chain B residue 1804 LYS 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 2044 LEU Chi-restraints excluded: chain B residue 2220 VAL Chi-restraints excluded: chain B residue 2251 LEU Chi-restraints excluded: chain B residue 2574 VAL Chi-restraints excluded: chain B residue 2633 GLU 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 2776 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 268 optimal weight: 2.9990 chunk 183 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 240 optimal weight: 2.9990 chunk 133 optimal weight: 8.9990 chunk 275 optimal weight: 0.0770 chunk 223 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 164 optimal weight: 0.0050 chunk 289 optimal weight: 0.0040 chunk 81 optimal weight: 0.9980 overall best weight: 0.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** A 430 ASN ** 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 B1411 ASN B2543 ASN B2551 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26953 Z= 0.196 Angle : 0.577 9.773 36516 Z= 0.283 Chirality : 0.040 0.143 4111 Planarity : 0.004 0.061 4726 Dihedral : 4.884 58.991 3628 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.75 % Allowed : 27.66 % Favored : 67.59 % 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: 0.78 (0.15), residues: 3301 helix: 1.65 (0.14), residues: 1434 sheet: -0.12 (0.27), residues: 365 loop : -0.38 (0.17), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP A 765 HIS 0.006 0.001 HIS A 849 PHE 0.017 0.001 PHE A1917 TYR 0.019 0.001 TYR A1370 ARG 0.009 0.000 ARG A 889 *********************** 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 650 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 510 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: A 380 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.3384 (tp30) REVERT: A 390 LEU cc_start: 0.8067 (tp) cc_final: 0.7838 (tp) REVERT: A 488 GLU cc_start: 0.6871 (tp30) cc_final: 0.6261 (tp30) REVERT: A 503 LYS cc_start: 0.7834 (tppp) cc_final: 0.7380 (tppt) REVERT: A 884 ASP cc_start: 0.7698 (t0) cc_final: 0.7388 (t0) REVERT: A 1090 LYS cc_start: 0.8690 (tppp) cc_final: 0.8341 (tppp) REVERT: A 1149 LYS cc_start: 0.7918 (mppt) cc_final: 0.7611 (mppt) REVERT: A 1195 GLU cc_start: 0.7124 (pm20) cc_final: 0.6760 (pm20) REVERT: A 1222 LYS cc_start: 0.7802 (mtmm) cc_final: 0.7348 (mtmm) REVERT: A 2018 GLN cc_start: 0.8589 (tm-30) cc_final: 0.7926 (tm-30) REVERT: A 2029 MET cc_start: 0.6699 (mmp) cc_final: 0.5030 (mmp) REVERT: A 2102 MET cc_start: 0.4214 (ppp) cc_final: 0.3699 (pp-130) REVERT: A 2215 LEU cc_start: 0.8205 (mt) cc_final: 0.7622 (pp) REVERT: A 2563 VAL cc_start: 0.7948 (OUTLIER) cc_final: 0.7516 (m) REVERT: A 2721 MET cc_start: 0.8524 (ppp) cc_final: 0.7354 (ppp) REVERT: A 2726 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7717 (mtt90) REVERT: A 2731 TYR cc_start: 0.7203 (t80) cc_final: 0.6914 (t80) REVERT: B 61 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8124 (tp) REVERT: B 745 GLU cc_start: 0.7276 (tm-30) cc_final: 0.6933 (tm-30) REVERT: B 827 MET cc_start: 0.6654 (tmm) cc_final: 0.6359 (tmm) REVERT: B 891 TYR cc_start: 0.7931 (t80) cc_final: 0.7345 (t80) REVERT: B 895 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7725 (mm) REVERT: B 1082 LYS cc_start: 0.8075 (mtpt) cc_final: 0.7831 (ttpt) REVERT: B 1195 GLU cc_start: 0.7403 (pp20) cc_final: 0.7012 (pp20) REVERT: B 1263 ASN cc_start: 0.7362 (p0) cc_final: 0.7150 (p0) REVERT: B 1326 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7698 (mp-120) REVERT: B 1443 MET cc_start: 0.7893 (mpp) cc_final: 0.7513 (mmm) REVERT: B 1511 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7228 (tm-30) REVERT: B 2028 SER cc_start: 0.7915 (OUTLIER) cc_final: 0.5295 (m) REVERT: B 2044 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8052 (tt) REVERT: B 2175 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.7600 (t80) REVERT: B 2219 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7212 (mm-30) REVERT: B 2225 PHE cc_start: 0.8220 (t80) cc_final: 0.7845 (t80) outliers start: 140 outliers final: 80 residues processed: 593 average time/residue: 1.2609 time to fit residues: 880.0998 Evaluate side-chains 587 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 498 time to evaluate : 2.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 8 VAL 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 478 CYS 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 893 MET Chi-restraints excluded: chain A residue 895 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 1241 LYS 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 1836 ILE Chi-restraints excluded: chain A residue 1935 VAL Chi-restraints excluded: chain A residue 2027 ASP Chi-restraints excluded: chain A residue 2085 LEU Chi-restraints excluded: chain A residue 2178 MET Chi-restraints excluded: chain A residue 2251 LEU Chi-restraints excluded: chain A residue 2255 THR 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 2722 SER Chi-restraints excluded: chain A residue 2726 ARG Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 47 THR 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 814 ASP 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 1193 ILE Chi-restraints excluded: chain B residue 1231 TYR 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 1314 MET Chi-restraints excluded: chain B residue 1323 ARG Chi-restraints excluded: chain B residue 1326 GLN Chi-restraints excluded: chain B residue 1341 SER 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 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 2175 PHE Chi-restraints excluded: chain B residue 2220 VAL Chi-restraints excluded: chain B residue 2251 LEU Chi-restraints excluded: chain B residue 2549 THR 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 2776 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 108 optimal weight: 0.7980 chunk 290 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 323 optimal weight: 0.9990 chunk 268 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 169 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 ASN ** 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 B1411 ASN B2507 GLN B2543 ASN B2551 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 26953 Z= 0.325 Angle : 0.628 10.009 36516 Z= 0.310 Chirality : 0.043 0.216 4111 Planarity : 0.005 0.062 4726 Dihedral : 4.961 57.120 3624 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 5.19 % Allowed : 27.36 % Favored : 67.46 % 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: 1.50 (0.14), residues: 1430 sheet: -0.17 (0.28), residues: 347 loop : -0.52 (0.17), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 765 HIS 0.008 0.001 HIS A1946 PHE 0.029 0.002 PHE A2675 TYR 0.029 0.002 TYR A1370 ARG 0.011 0.000 ARG A 889 *********************** 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 690 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 537 time to evaluate : 2.829 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 380 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.3572 (tp30) REVERT: A 390 LEU cc_start: 0.8252 (tp) cc_final: 0.7665 (tp) REVERT: A 488 GLU cc_start: 0.6954 (tp30) cc_final: 0.6325 (tp30) REVERT: A 503 LYS cc_start: 0.7857 (tppp) cc_final: 0.7401 (tppt) REVERT: A 884 ASP cc_start: 0.7734 (t0) cc_final: 0.7433 (t0) REVERT: A 1090 LYS cc_start: 0.8699 (tppp) cc_final: 0.8344 (tppp) REVERT: A 1149 LYS cc_start: 0.8034 (mppt) cc_final: 0.7729 (mppt) REVERT: A 1195 GLU cc_start: 0.7129 (pm20) cc_final: 0.6768 (pm20) REVERT: A 1222 LYS cc_start: 0.7811 (mtmm) cc_final: 0.7363 (mtmm) REVERT: A 1377 THR cc_start: 0.8385 (OUTLIER) cc_final: 0.8009 (m) REVERT: A 2018 GLN cc_start: 0.8557 (tm-30) cc_final: 0.7846 (tm-30) REVERT: A 2102 MET cc_start: 0.4559 (ppp) cc_final: 0.4007 (pp-130) REVERT: A 2215 LEU cc_start: 0.8197 (mt) cc_final: 0.7611 (pp) REVERT: A 2501 ASN cc_start: 0.6486 (t0) cc_final: 0.6142 (t0) REVERT: A 2563 VAL cc_start: 0.8151 (OUTLIER) cc_final: 0.7649 (m) REVERT: A 2648 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7180 (mm-30) REVERT: B 61 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8153 (tp) REVERT: B 745 GLU cc_start: 0.7301 (tm-30) cc_final: 0.7098 (tp30) REVERT: B 746 ILE cc_start: 0.8574 (mp) cc_final: 0.7852 (tt) REVERT: B 827 MET cc_start: 0.6756 (tmm) cc_final: 0.6324 (tmm) REVERT: B 891 TYR cc_start: 0.8043 (t80) cc_final: 0.7468 (t80) REVERT: B 895 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7792 (mm) REVERT: B 1195 GLU cc_start: 0.7412 (pp20) cc_final: 0.6999 (pp20) REVERT: B 1263 ASN cc_start: 0.7493 (p0) cc_final: 0.7270 (p0) REVERT: B 1326 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7760 (mp-120) REVERT: B 1331 ARG cc_start: 0.8058 (mmm160) cc_final: 0.7853 (tmt170) REVERT: B 1511 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7235 (tm-30) REVERT: B 2028 SER cc_start: 0.7948 (OUTLIER) cc_final: 0.4772 (t) REVERT: B 2032 LEU cc_start: 0.8723 (tp) cc_final: 0.8522 (tt) REVERT: B 2038 ASN cc_start: 0.7651 (t0) cc_final: 0.7274 (t0) REVERT: B 2044 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8074 (tt) REVERT: B 2046 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7573 (mm-30) REVERT: B 2087 GLU cc_start: 0.6970 (pm20) cc_final: 0.6370 (pm20) REVERT: B 2225 PHE cc_start: 0.8294 (t80) cc_final: 0.7916 (t80) REVERT: B 2633 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7402 (tp30) outliers start: 153 outliers final: 81 residues processed: 620 average time/residue: 1.2212 time to fit residues: 891.2166 Evaluate side-chains 613 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 523 time to evaluate : 3.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 47 THR 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 478 CYS Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 789 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 1102 LEU Chi-restraints excluded: chain A residue 1189 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 1377 THR 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 1443 MET Chi-restraints excluded: chain A residue 1934 ASP Chi-restraints excluded: chain A residue 1935 VAL Chi-restraints excluded: chain A residue 2027 ASP Chi-restraints excluded: chain A residue 2035 ILE Chi-restraints excluded: chain A residue 2085 LEU Chi-restraints excluded: chain A residue 2178 MET Chi-restraints excluded: chain A residue 2251 LEU Chi-restraints excluded: chain A residue 2255 THR Chi-restraints excluded: chain A residue 2515 THR 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 2722 SER Chi-restraints excluded: chain A residue 2779 SER Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 47 THR 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 814 ASP Chi-restraints excluded: chain B residue 895 LEU 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 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 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 1507 MET Chi-restraints excluded: chain B residue 1801 LEU Chi-restraints excluded: chain B residue 1804 LYS 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 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 2272 MET Chi-restraints excluded: chain B residue 2555 ILE Chi-restraints excluded: chain B residue 2633 GLU Chi-restraints excluded: chain B residue 2644 LEU 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 2776 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 311 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 184 optimal weight: 0.9980 chunk 235 optimal weight: 0.9980 chunk 182 optimal weight: 9.9990 chunk 272 optimal weight: 0.7980 chunk 180 optimal weight: 0.0980 chunk 321 optimal weight: 5.9990 chunk 201 optimal weight: 4.9990 chunk 196 optimal weight: 30.0000 chunk 148 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 430 ASN ** 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 ** A2543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1411 ASN B2234 ASN B2543 ASN B2551 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26953 Z= 0.228 Angle : 0.620 10.605 36516 Z= 0.304 Chirality : 0.041 0.243 4111 Planarity : 0.005 0.065 4726 Dihedral : 4.818 58.264 3619 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.41 % Allowed : 28.64 % Favored : 66.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.49 (0.14), residues: 1438 sheet: -0.12 (0.27), residues: 352 loop : -0.50 (0.17), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A 765 HIS 0.007 0.001 HIS A 849 PHE 0.034 0.001 PHE A2571 TYR 0.023 0.001 TYR A1370 ARG 0.013 0.000 ARG A 889 *********************** 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 660 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 530 time to evaluate : 3.177 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 380 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.3507 (tp30) REVERT: A 390 LEU cc_start: 0.8208 (tp) cc_final: 0.7829 (tp) REVERT: A 488 GLU cc_start: 0.6910 (tp30) cc_final: 0.6268 (tp30) REVERT: A 503 LYS cc_start: 0.7788 (tppp) cc_final: 0.7368 (tppt) REVERT: A 872 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7408 (tp30) REVERT: A 884 ASP cc_start: 0.7754 (t0) cc_final: 0.7484 (t0) REVERT: A 1090 LYS cc_start: 0.8690 (tppp) cc_final: 0.7907 (tppp) REVERT: A 1149 LYS cc_start: 0.8012 (mppt) cc_final: 0.7689 (mppt) REVERT: A 1195 GLU cc_start: 0.7131 (pm20) cc_final: 0.6756 (pm20) REVERT: A 1222 LYS cc_start: 0.7820 (mtmm) cc_final: 0.7360 (mtmm) REVERT: A 1377 THR cc_start: 0.8357 (OUTLIER) cc_final: 0.8000 (m) REVERT: A 2018 GLN cc_start: 0.8567 (tm-30) cc_final: 0.7880 (tm-30) REVERT: A 2023 PHE cc_start: 0.8168 (m-80) cc_final: 0.7949 (m-80) REVERT: A 2029 MET cc_start: 0.7004 (mmp) cc_final: 0.5798 (mmp) REVERT: A 2102 MET cc_start: 0.4534 (ppp) cc_final: 0.3792 (ppp) REVERT: A 2215 LEU cc_start: 0.8180 (mt) cc_final: 0.7650 (pp) REVERT: A 2501 ASN cc_start: 0.6684 (t0) cc_final: 0.6305 (t0) REVERT: A 2563 VAL cc_start: 0.8101 (p) cc_final: 0.7662 (m) REVERT: A 2726 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7775 (mtt90) REVERT: A 2731 TYR cc_start: 0.7253 (t80) cc_final: 0.6972 (t80) REVERT: B 61 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8140 (tp) REVERT: B 745 GLU cc_start: 0.7286 (tm-30) cc_final: 0.7076 (tp30) REVERT: B 746 ILE cc_start: 0.8561 (mp) cc_final: 0.7810 (tt) REVERT: B 795 ASN cc_start: 0.8103 (t0) cc_final: 0.7839 (t0) REVERT: B 827 MET cc_start: 0.6741 (tmm) cc_final: 0.6463 (tmm) REVERT: B 891 TYR cc_start: 0.8010 (t80) cc_final: 0.7448 (t80) REVERT: B 893 MET cc_start: 0.7717 (mtt) cc_final: 0.7381 (mtt) REVERT: B 895 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7797 (mm) REVERT: B 1195 GLU cc_start: 0.7399 (pp20) cc_final: 0.6964 (pp20) REVERT: B 1263 ASN cc_start: 0.7440 (p0) cc_final: 0.7188 (p0) REVERT: B 1331 ARG cc_start: 0.8021 (mmm160) cc_final: 0.7820 (tmt170) REVERT: B 1468 LEU cc_start: 0.8475 (tt) cc_final: 0.8233 (tt) REVERT: B 1511 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7193 (tm-30) REVERT: B 2028 SER cc_start: 0.7923 (OUTLIER) cc_final: 0.5289 (m) REVERT: B 2038 ASN cc_start: 0.7651 (t0) cc_final: 0.7272 (t0) REVERT: B 2044 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8081 (tt) REVERT: B 2087 GLU cc_start: 0.6920 (pm20) cc_final: 0.6353 (pm20) REVERT: B 2222 GLU cc_start: 0.7558 (pp20) cc_final: 0.7352 (pp20) REVERT: B 2225 PHE cc_start: 0.8263 (t80) cc_final: 0.7862 (t80) REVERT: B 2633 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7411 (tp30) outliers start: 130 outliers final: 73 residues processed: 602 average time/residue: 1.2528 time to fit residues: 885.4276 Evaluate side-chains 601 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 520 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 20 ASP 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 478 CYS Chi-restraints excluded: chain A residue 551 ILE 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 1164 ASN Chi-restraints excluded: chain A residue 1189 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 1377 THR 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 1934 ASP Chi-restraints excluded: chain A residue 2027 ASP Chi-restraints excluded: chain A residue 2085 LEU Chi-restraints excluded: chain A residue 2178 MET Chi-restraints excluded: chain A residue 2251 LEU Chi-restraints excluded: chain A residue 2255 THR 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 2726 ARG Chi-restraints excluded: chain A residue 2779 SER Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 47 THR 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 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 814 ASP 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 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 1341 SER Chi-restraints excluded: chain B residue 1350 ASN 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 1819 LEU Chi-restraints excluded: chain B residue 1935 VAL 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 2272 MET Chi-restraints excluded: chain B residue 2526 LEU Chi-restraints excluded: chain B residue 2555 ILE Chi-restraints excluded: chain B residue 2574 VAL Chi-restraints excluded: chain B residue 2579 LEU Chi-restraints excluded: chain B residue 2633 GLU Chi-restraints excluded: chain B residue 2644 LEU Chi-restraints excluded: chain B residue 2667 LEU 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 199 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 192 optimal weight: 1.9990 chunk 96 optimal weight: 30.0000 chunk 63 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 204 optimal weight: 0.8980 chunk 219 optimal weight: 0.0370 chunk 159 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 overall best weight: 0.9460 ------------------------------------------------------------------------------- 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 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 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** B1411 ASN B1715 GLN B2234 ASN B2507 GLN B2543 ASN B2551 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 26953 Z= 0.261 Angle : 0.651 10.629 36516 Z= 0.316 Chirality : 0.042 0.227 4111 Planarity : 0.005 0.065 4726 Dihedral : 4.834 58.045 3619 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.07 % Allowed : 29.25 % Favored : 66.68 % 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: 0.55 (0.15), residues: 3301 helix: 1.43 (0.14), residues: 1438 sheet: -0.16 (0.28), residues: 340 loop : -0.50 (0.17), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 765 HIS 0.007 0.001 HIS A 849 PHE 0.031 0.002 PHE B2295 TYR 0.023 0.002 TYR A1370 ARG 0.013 0.000 ARG A 889 *********************** 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 646 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 526 time to evaluate : 2.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.3506 (tp30) REVERT: A 390 LEU cc_start: 0.8211 (tp) cc_final: 0.7827 (tp) REVERT: A 488 GLU cc_start: 0.6928 (tp30) cc_final: 0.6274 (tp30) REVERT: A 503 LYS cc_start: 0.7754 (tppp) cc_final: 0.7358 (tppt) REVERT: A 884 ASP cc_start: 0.7754 (t0) cc_final: 0.7429 (t0) REVERT: A 1090 LYS cc_start: 0.8574 (tppp) cc_final: 0.8298 (tppp) REVERT: A 1149 LYS cc_start: 0.8018 (mppt) cc_final: 0.7702 (mppt) REVERT: A 1195 GLU cc_start: 0.7140 (pm20) cc_final: 0.6770 (pm20) REVERT: A 1222 LYS cc_start: 0.7821 (mtmm) cc_final: 0.7337 (mtmm) REVERT: A 1377 THR cc_start: 0.8362 (OUTLIER) cc_final: 0.8010 (m) REVERT: A 2018 GLN cc_start: 0.8574 (tm-30) cc_final: 0.7870 (tm-30) REVERT: A 2023 PHE cc_start: 0.8200 (m-80) cc_final: 0.7918 (m-80) REVERT: A 2029 MET cc_start: 0.7012 (mmp) cc_final: 0.5820 (mmp) REVERT: A 2102 MET cc_start: 0.4662 (ppp) cc_final: 0.3916 (ppp) REVERT: A 2215 LEU cc_start: 0.8178 (mt) cc_final: 0.7637 (pp) REVERT: A 2218 PHE cc_start: 0.7952 (t80) cc_final: 0.7716 (t80) REVERT: A 2501 ASN cc_start: 0.6731 (t0) cc_final: 0.6352 (t0) REVERT: A 2563 VAL cc_start: 0.8131 (p) cc_final: 0.7672 (m) REVERT: A 2643 MET cc_start: 0.5378 (OUTLIER) cc_final: 0.5069 (tmt) REVERT: A 2726 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7851 (mtt90) REVERT: B 61 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8110 (tp) REVERT: B 69 ARG cc_start: 0.6753 (OUTLIER) cc_final: 0.5995 (ptt180) REVERT: B 489 ASN cc_start: 0.7926 (m-40) cc_final: 0.7634 (m-40) REVERT: B 745 GLU cc_start: 0.7256 (tm-30) cc_final: 0.7035 (tp30) REVERT: B 746 ILE cc_start: 0.8564 (mp) cc_final: 0.7790 (tt) REVERT: B 795 ASN cc_start: 0.7964 (t0) cc_final: 0.7638 (t0) REVERT: B 827 MET cc_start: 0.6775 (tmm) cc_final: 0.6477 (tmm) REVERT: B 891 TYR cc_start: 0.8011 (t80) cc_final: 0.7442 (t80) REVERT: B 895 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7810 (mm) REVERT: B 1195 GLU cc_start: 0.7399 (pp20) cc_final: 0.6948 (pp20) REVERT: B 1222 LYS cc_start: 0.8370 (mmmm) cc_final: 0.8144 (mmmm) REVERT: B 1263 ASN cc_start: 0.7454 (p0) cc_final: 0.7193 (p0) REVERT: B 1326 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7724 (mp-120) REVERT: B 1331 ARG cc_start: 0.8035 (mmm160) cc_final: 0.7830 (tmt170) REVERT: B 1468 LEU cc_start: 0.8542 (tt) cc_final: 0.8313 (tt) REVERT: B 1511 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7194 (tm-30) REVERT: B 2028 SER cc_start: 0.7933 (OUTLIER) cc_final: 0.5278 (m) REVERT: B 2038 ASN cc_start: 0.7654 (t0) cc_final: 0.7279 (t0) REVERT: B 2044 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8085 (tt) REVERT: B 2087 GLU cc_start: 0.6873 (pm20) cc_final: 0.6481 (pm20) REVERT: B 2095 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7754 (mm) REVERT: B 2225 PHE cc_start: 0.8263 (t80) cc_final: 0.7901 (t80) REVERT: B 2633 GLU cc_start: 0.7824 (tp30) cc_final: 0.7430 (tp30) REVERT: B 2721 MET cc_start: 0.7442 (pmm) cc_final: 0.7138 (mpp) outliers start: 120 outliers final: 78 residues processed: 592 average time/residue: 1.2671 time to fit residues: 881.0943 Evaluate side-chains 607 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 518 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 20 ASP 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 47 THR 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 478 CYS 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 1097 VAL 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 1231 TYR Chi-restraints excluded: chain A residue 1238 CYS Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1377 THR 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 1443 MET Chi-restraints excluded: chain A residue 1934 ASP Chi-restraints excluded: chain A residue 2027 ASP Chi-restraints excluded: chain A residue 2085 LEU Chi-restraints excluded: chain A residue 2178 MET Chi-restraints excluded: chain A residue 2251 LEU Chi-restraints excluded: chain A residue 2255 THR Chi-restraints excluded: chain A residue 2556 LYS Chi-restraints excluded: chain A residue 2643 MET Chi-restraints excluded: chain A residue 2661 VAL Chi-restraints excluded: chain A residue 2667 LEU Chi-restraints excluded: chain A residue 2726 ARG Chi-restraints excluded: chain A residue 2779 SER Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 47 THR 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 69 ARG 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 814 ASP Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain B residue 911 PHE Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 1118 MET Chi-restraints excluded: chain B residue 1153 VAL 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 1350 ASN 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 1819 LEU Chi-restraints excluded: chain B residue 1935 VAL 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 2095 LEU Chi-restraints excluded: chain B residue 2183 ASP 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 2526 LEU Chi-restraints excluded: chain B residue 2555 ILE Chi-restraints excluded: chain B residue 2574 VAL Chi-restraints excluded: chain B residue 2644 LEU Chi-restraints excluded: chain B residue 2667 LEU 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 292 optimal weight: 0.7980 chunk 308 optimal weight: 0.9980 chunk 281 optimal weight: 0.6980 chunk 299 optimal weight: 3.9990 chunk 180 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 235 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 271 optimal weight: 0.3980 chunk 283 optimal weight: 0.7980 chunk 298 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 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 B1411 ASN B2234 ASN B2543 ASN B2551 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26953 Z= 0.218 Angle : 0.651 11.653 36516 Z= 0.315 Chirality : 0.042 0.230 4111 Planarity : 0.005 0.064 4726 Dihedral : 4.796 58.494 3619 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.46 % Allowed : 30.10 % Favored : 66.44 % 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: 1.47 (0.14), residues: 1445 sheet: -0.19 (0.27), residues: 354 loop : -0.49 (0.17), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP A 765 HIS 0.006 0.001 HIS B2262 PHE 0.029 0.001 PHE A 72 TYR 0.021 0.001 TYR A1370 ARG 0.014 0.000 ARG A 889 *********************** 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 626 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 524 time to evaluate : 2.872 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 380 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.3532 (tm-30) REVERT: A 488 GLU cc_start: 0.6903 (tp30) cc_final: 0.6260 (tp30) REVERT: A 489 ASN cc_start: 0.8012 (m110) cc_final: 0.6686 (m-40) REVERT: A 503 LYS cc_start: 0.7769 (tppp) cc_final: 0.7382 (tppt) REVERT: A 762 THR cc_start: 0.8163 (t) cc_final: 0.7846 (t) REVERT: A 884 ASP cc_start: 0.7763 (t0) cc_final: 0.7428 (t0) REVERT: A 912 ILE cc_start: 0.8273 (mm) cc_final: 0.7943 (tp) REVERT: A 1090 LYS cc_start: 0.8692 (tppp) cc_final: 0.8312 (tppp) REVERT: A 1149 LYS cc_start: 0.7997 (mppt) cc_final: 0.7683 (mppt) REVERT: A 1195 GLU cc_start: 0.7139 (pm20) cc_final: 0.6774 (pm20) REVERT: A 1222 LYS cc_start: 0.7826 (mtmm) cc_final: 0.7319 (mtmm) REVERT: A 1377 THR cc_start: 0.8356 (OUTLIER) cc_final: 0.8009 (m) REVERT: A 1842 MET cc_start: 0.8668 (tmm) cc_final: 0.8451 (ttp) REVERT: A 2018 GLN cc_start: 0.8579 (tm-30) cc_final: 0.7883 (tm-30) REVERT: A 2023 PHE cc_start: 0.8192 (m-80) cc_final: 0.7908 (m-80) REVERT: A 2029 MET cc_start: 0.6963 (mmp) cc_final: 0.5792 (mmp) REVERT: A 2102 MET cc_start: 0.4600 (ppp) cc_final: 0.3870 (ppp) REVERT: A 2215 LEU cc_start: 0.8162 (mt) cc_final: 0.7644 (pp) REVERT: A 2218 PHE cc_start: 0.7954 (t80) cc_final: 0.7686 (t80) REVERT: A 2501 ASN cc_start: 0.6597 (t0) cc_final: 0.6214 (t0) REVERT: A 2563 VAL cc_start: 0.8137 (p) cc_final: 0.7703 (m) REVERT: A 2721 MET cc_start: 0.8630 (ppp) cc_final: 0.7355 (pp-130) REVERT: A 2726 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7782 (mtt90) REVERT: A 2731 TYR cc_start: 0.7260 (t80) cc_final: 0.6975 (t80) REVERT: B 61 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8086 (tp) REVERT: B 69 ARG cc_start: 0.6761 (ptt180) cc_final: 0.5923 (ptm160) REVERT: B 489 ASN cc_start: 0.7914 (m-40) cc_final: 0.7602 (m-40) REVERT: B 746 ILE cc_start: 0.8554 (mp) cc_final: 0.7763 (tt) REVERT: B 767 ARG cc_start: 0.8300 (mtm110) cc_final: 0.8081 (mtm180) REVERT: B 795 ASN cc_start: 0.7853 (t0) cc_final: 0.7512 (t0) REVERT: B 797 ARG cc_start: 0.7235 (mtt90) cc_final: 0.6999 (mtt90) REVERT: B 827 MET cc_start: 0.6779 (tmm) cc_final: 0.6466 (tmm) REVERT: B 891 TYR cc_start: 0.7999 (t80) cc_final: 0.7441 (t80) REVERT: B 895 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7776 (mm) REVERT: B 1195 GLU cc_start: 0.7400 (pp20) cc_final: 0.6939 (pp20) REVERT: B 1222 LYS cc_start: 0.8377 (mmmm) cc_final: 0.8141 (mmmm) REVERT: B 1263 ASN cc_start: 0.7397 (p0) cc_final: 0.7130 (p0) REVERT: B 1326 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7717 (mp-120) REVERT: B 1331 ARG cc_start: 0.8018 (mmm160) cc_final: 0.7817 (tmt170) REVERT: B 1468 LEU cc_start: 0.8485 (tt) cc_final: 0.8260 (tt) REVERT: B 1511 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7161 (tm-30) REVERT: B 2028 SER cc_start: 0.7922 (OUTLIER) cc_final: 0.5289 (m) REVERT: B 2032 LEU cc_start: 0.8698 (tp) cc_final: 0.8491 (tt) REVERT: B 2038 ASN cc_start: 0.7654 (t0) cc_final: 0.7277 (t0) REVERT: B 2044 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8098 (tt) REVERT: B 2074 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7784 (mt) REVERT: B 2087 GLU cc_start: 0.6875 (pm20) cc_final: 0.6436 (pm20) REVERT: B 2225 PHE cc_start: 0.8228 (t80) cc_final: 0.7839 (t80) REVERT: B 2564 ASN cc_start: 0.8155 (p0) cc_final: 0.7924 (p0) REVERT: B 2633 GLU cc_start: 0.7803 (tp30) cc_final: 0.7457 (tp30) REVERT: B 2721 MET cc_start: 0.7461 (pmm) cc_final: 0.7175 (mpp) outliers start: 102 outliers final: 69 residues processed: 579 average time/residue: 1.2700 time to fit residues: 860.8685 Evaluate side-chains 593 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 515 time to evaluate : 2.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR 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 50 GLN 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 478 CYS Chi-restraints excluded: chain A residue 875 THR 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 1097 VAL 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 1298 ILE Chi-restraints excluded: chain A residue 1377 THR 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 1934 ASP Chi-restraints excluded: chain A residue 2085 LEU Chi-restraints excluded: chain A residue 2178 MET Chi-restraints excluded: chain A residue 2251 LEU Chi-restraints excluded: chain A residue 2255 THR 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 2726 ARG Chi-restraints excluded: chain A residue 2779 SER Chi-restraints excluded: chain B residue 2 THR 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 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 814 ASP 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 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 1350 ASN 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 1935 VAL Chi-restraints excluded: chain B residue 2028 SER Chi-restraints excluded: chain B residue 2044 LEU Chi-restraints excluded: chain B residue 2074 LEU Chi-restraints excluded: chain B residue 2090 VAL Chi-restraints excluded: chain B residue 2183 ASP 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 2526 LEU Chi-restraints excluded: chain B residue 2644 LEU Chi-restraints excluded: chain B residue 2667 LEU Chi-restraints excluded: chain B residue 2671 THR 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 196 optimal weight: 10.0000 chunk 317 optimal weight: 4.9990 chunk 193 optimal weight: 7.9990 chunk 150 optimal weight: 0.5980 chunk 220 optimal weight: 3.9990 chunk 332 optimal weight: 10.0000 chunk 306 optimal weight: 0.6980 chunk 264 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 204 optimal weight: 0.5980 chunk 162 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 HIS ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 849 HIS ** A 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1952 GLN B 19 ASN B1411 ASN B2234 ASN B2507 GLN B2543 ASN B2551 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 26953 Z= 0.307 Angle : 0.687 11.709 36516 Z= 0.333 Chirality : 0.043 0.244 4111 Planarity : 0.005 0.065 4726 Dihedral : 4.876 57.319 3618 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.25 % Allowed : 30.41 % Favored : 66.34 % 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: 1.35 (0.14), residues: 1446 sheet: -0.25 (0.27), residues: 352 loop : -0.54 (0.17), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP A 765 HIS 0.007 0.001 HIS A1946 PHE 0.037 0.002 PHE B2295 TYR 0.030 0.002 TYR A1370 ARG 0.014 0.000 ARG A 889 ********************** 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 620 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 524 time to evaluate : 3.031 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 380 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.3546 (tp30) REVERT: A 488 GLU cc_start: 0.6947 (tp30) cc_final: 0.6186 (tp30) REVERT: A 489 ASN cc_start: 0.8046 (m110) cc_final: 0.6559 (m-40) REVERT: A 503 LYS cc_start: 0.7761 (tppp) cc_final: 0.7374 (tppt) REVERT: A 884 ASP cc_start: 0.7769 (t0) cc_final: 0.7474 (t0) REVERT: A 1090 LYS cc_start: 0.8698 (tppp) cc_final: 0.8024 (tppp) REVERT: A 1149 LYS cc_start: 0.8045 (mppt) cc_final: 0.7731 (mppt) REVERT: A 1195 GLU cc_start: 0.7142 (pm20) cc_final: 0.6756 (pm20) REVERT: A 1222 LYS cc_start: 0.7839 (mtmm) cc_final: 0.7362 (mtmm) REVERT: A 1377 THR cc_start: 0.8370 (OUTLIER) cc_final: 0.8022 (m) REVERT: A 1842 MET cc_start: 0.8738 (tmm) cc_final: 0.8479 (ttp) REVERT: A 2018 GLN cc_start: 0.8584 (tm-30) cc_final: 0.7852 (tm-30) REVERT: A 2023 PHE cc_start: 0.8236 (m-80) cc_final: 0.7909 (m-80) REVERT: A 2029 MET cc_start: 0.7109 (mmp) cc_final: 0.5899 (mmp) REVERT: A 2102 MET cc_start: 0.4888 (ppp) cc_final: 0.4124 (ppp) REVERT: A 2215 LEU cc_start: 0.8179 (mt) cc_final: 0.7673 (pp) REVERT: A 2218 PHE cc_start: 0.8000 (t80) cc_final: 0.7700 (t80) REVERT: A 2501 ASN cc_start: 0.6597 (t0) cc_final: 0.6248 (t0) REVERT: A 2563 VAL cc_start: 0.8174 (p) cc_final: 0.7726 (m) REVERT: A 2721 MET cc_start: 0.8640 (ppp) cc_final: 0.7301 (pp-130) REVERT: A 2726 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7750 (mtt90) REVERT: A 2731 TYR cc_start: 0.7270 (t80) cc_final: 0.7004 (t80) REVERT: B 61 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8087 (tp) REVERT: B 69 ARG cc_start: 0.6794 (ptt180) cc_final: 0.5951 (ptm160) REVERT: B 489 ASN cc_start: 0.7941 (m-40) cc_final: 0.7579 (m-40) REVERT: B 745 GLU cc_start: 0.7301 (tm-30) cc_final: 0.7070 (tm-30) REVERT: B 746 ILE cc_start: 0.8520 (mp) cc_final: 0.7897 (tt) REVERT: B 827 MET cc_start: 0.6780 (tmm) cc_final: 0.6522 (tmm) REVERT: B 891 TYR cc_start: 0.8022 (t80) cc_final: 0.7465 (t80) REVERT: B 895 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7823 (mm) REVERT: B 1195 GLU cc_start: 0.7408 (pp20) cc_final: 0.6940 (pp20) REVERT: B 1222 LYS cc_start: 0.8397 (mmmm) cc_final: 0.8166 (mmmm) REVERT: B 1263 ASN cc_start: 0.7475 (p0) cc_final: 0.7212 (p0) REVERT: B 1331 ARG cc_start: 0.8055 (mmm160) cc_final: 0.7825 (tmt170) REVERT: B 1511 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7173 (tm-30) REVERT: B 2028 SER cc_start: 0.7953 (OUTLIER) cc_final: 0.4815 (t) REVERT: B 2038 ASN cc_start: 0.7677 (t0) cc_final: 0.7297 (t0) REVERT: B 2044 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8102 (tt) REVERT: B 2074 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7862 (mt) REVERT: B 2087 GLU cc_start: 0.6908 (pm20) cc_final: 0.6432 (pm20) REVERT: B 2225 PHE cc_start: 0.8218 (t80) cc_final: 0.7905 (t80) REVERT: B 2579 LEU cc_start: 0.8621 (mp) cc_final: 0.8356 (mp) REVERT: B 2633 GLU cc_start: 0.7822 (tp30) cc_final: 0.6969 (tp30) REVERT: B 2636 ARG cc_start: 0.8135 (tmm160) cc_final: 0.7517 (tmm160) REVERT: B 2721 MET cc_start: 0.7478 (pmm) cc_final: 0.7212 (mpp) outliers start: 96 outliers final: 69 residues processed: 577 average time/residue: 1.3236 time to fit residues: 897.2211 Evaluate side-chains 590 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 513 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 20 ASP 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 47 THR 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 789 ILE Chi-restraints excluded: chain A residue 875 THR 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 1097 VAL 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 1224 LYS 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 1377 THR 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 1443 MET Chi-restraints excluded: chain A residue 1802 ILE Chi-restraints excluded: chain A residue 1934 ASP Chi-restraints excluded: chain A residue 2085 LEU Chi-restraints excluded: chain A residue 2178 MET Chi-restraints excluded: chain A residue 2251 LEU Chi-restraints excluded: chain A residue 2255 THR 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 2726 ARG Chi-restraints excluded: chain A residue 2779 SER Chi-restraints excluded: chain B residue 2 THR 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 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 814 ASP Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain B residue 911 PHE Chi-restraints excluded: chain B residue 1153 VAL 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 1350 ASN 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 1935 VAL Chi-restraints excluded: chain B residue 2028 SER Chi-restraints excluded: chain B residue 2044 LEU Chi-restraints excluded: chain B residue 2074 LEU Chi-restraints excluded: chain B residue 2183 ASP 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 2555 ILE Chi-restraints excluded: chain B residue 2644 LEU Chi-restraints excluded: chain B residue 2667 LEU 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 210 optimal weight: 8.9990 chunk 282 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 244 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 265 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 chunk 272 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 56 ASN ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 HIS ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 849 HIS ** A 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1952 GLN B1411 ASN B2234 ASN B2543 ASN B2551 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.182566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.144891 restraints weight = 41602.865| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.58 r_work: 0.3755 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26953 Z= 0.228 Angle : 0.672 11.334 36516 Z= 0.326 Chirality : 0.042 0.251 4111 Planarity : 0.005 0.066 4726 Dihedral : 4.858 58.865 3618 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.98 % Allowed : 30.88 % Favored : 66.14 % 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: 0.52 (0.15), residues: 3301 helix: 1.40 (0.14), residues: 1445 sheet: -0.19 (0.27), residues: 353 loop : -0.51 (0.17), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP A 765 HIS 0.006 0.001 HIS A 849 PHE 0.023 0.001 PHE A2571 TYR 0.025 0.001 TYR A1370 ARG 0.013 0.000 ARG A 889 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12318.91 seconds wall clock time: 216 minutes 46.33 seconds (13006.33 seconds total)