Starting phenix.real_space_refine on Thu Dec 26 03:26:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z1l_14447/12_2024/7z1l_14447.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z1l_14447/12_2024/7z1l_14447.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z1l_14447/12_2024/7z1l_14447.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z1l_14447/12_2024/7z1l_14447.map" model { file = "/net/cci-nas-00/data/ceres_data/7z1l_14447/12_2024/7z1l_14447.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z1l_14447/12_2024/7z1l_14447.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 7 Type Number sf(0) Gaussians Zn 7 6.06 5 P 63 5.49 5 Mg 1 5.21 5 S 217 5.16 5 C 26638 2.51 5 N 7293 2.21 5 O 8111 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 42330 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 11228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1436, 11228 Classifications: {'peptide': 1436} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 66, 'TRANS': 1369} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 8693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1101, 8693 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 41, 'TRANS': 1059} Chain breaks: 1 Chain: "C" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2647 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 20, 'TRANS': 313} Chain: "D" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1185 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 3, 'TRANS': 141} Chain breaks: 1 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 671 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1594 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 186} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1084 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain breaks: 1 Chain: "I" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 873 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain breaks: 1 Chain: "K" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 801 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "L" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 358 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 10, 'TRANS': 185} Chain breaks: 1 Chain: "N" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1196 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain breaks: 2 Chain: "O" Number of atoms: 4577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4577 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 20, 'TRANS': 549} Chain breaks: 1 Chain: "P" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1159 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Q" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 981 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 8, 'TRANS': 114} Chain breaks: 1 Chain: "R" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 195 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna3p': 8} Chain: "S" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 507 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "T" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 597 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 1, ' ZN': 2, '4QM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'4QM': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 500 SG CYS A 67 112.986 78.487 107.960 1.00 64.89 S ATOM 518 SG CYS A 70 111.704 75.007 107.000 1.00 64.68 S ATOM 565 SG CYS A 77 110.345 78.145 105.219 1.00 58.96 S ATOM 803 SG CYS A 107 81.459 100.327 137.919 1.00 57.33 S ATOM 826 SG CYS A 110 82.502 97.228 139.918 1.00 59.33 S ATOM 1192 SG CYS A 154 78.799 98.158 139.604 1.00 68.88 S ATOM 1216 SG CYS A 157 81.215 100.181 141.732 1.00 69.42 S ATOM 19494 SG CYS B1095 98.225 69.942 117.054 1.00 56.67 S ATOM 19517 SG CYS B1098 97.720 73.702 117.560 1.00 56.41 S ATOM 19583 SG CYS B1107 101.159 72.310 116.959 1.00 61.02 S ATOM 19603 SG CYS B1110 99.427 71.622 120.263 1.00 62.41 S ATOM 29397 SG CYS I 69 14.357 125.238 101.740 1.00184.32 S ATOM 29647 SG CYS I 100 14.496 124.588 97.349 1.00172.72 S ATOM 29668 SG CYS I 103 16.652 126.696 98.993 1.00175.25 S ATOM 28900 SG CYS I 5 63.049 153.575 108.651 1.00 83.47 S ATOM 28919 SG CYS I 8 66.757 152.775 107.910 1.00 83.37 S ATOM 29047 SG CYS I 26 65.111 150.979 110.772 1.00 86.92 S ATOM 29070 SG CYS I 29 65.583 154.768 110.934 1.00 90.21 S ATOM 29788 SG CYS J 7 92.747 91.347 38.719 1.00 41.91 S ATOM 29811 SG CYS J 10 92.181 88.474 36.191 1.00 43.42 S ATOM 30091 SG CYS J 45 89.337 90.847 37.384 1.00 43.96 S ATOM 30097 SG CYS J 46 92.070 91.863 34.922 1.00 44.15 S ATOM 31154 SG CYS L 31 126.234 110.568 59.006 1.00 77.34 S ATOM 31174 SG CYS L 34 128.057 111.576 55.892 1.00 79.39 S ATOM 31278 SG CYS L 48 130.050 110.991 59.076 1.00 84.50 S ATOM 31301 SG CYS L 51 127.865 114.028 58.831 1.00 84.76 S Time building chain proxies: 21.66, per 1000 atoms: 0.51 Number of scatterers: 42330 At special positions: 0 Unit cell: (147.822, 194.667, 197.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 S 217 16.00 P 63 15.00 Mg 1 11.99 O 8111 8.00 N 7293 7.00 C 26638 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.03 Conformation dependent library (CDL) restraints added in 5.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2000 " pdb="ZN ZN A2000 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 67 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 70 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 77 " pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 157 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 110 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 154 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 107 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1107 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1095 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1098 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1110 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 100 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 69 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 8 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 5 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 26 " pdb=" ZN J 100 " pdb="ZN ZN J 100 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 100 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 100 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 100 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " Number of angles added : 33 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9724 Finding SS restraints... Secondary structure from input PDB file: 199 helices and 49 sheets defined 42.1% alpha, 14.5% beta 14 base pairs and 54 stacking pairs defined. Time for finding SS restraints: 15.67 Creating SS restraints... Processing helix chain 'A' and resid 22 through 29 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 95 through 105 Processing helix chain 'A' and resid 116 through 128 Processing helix chain 'A' and resid 133 through 150 Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 191 through 206 Processing helix chain 'A' and resid 208 through 215 removed outlier: 3.582A pdb=" N LEU A 211 " --> pdb=" O ASN A 208 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ARG A 213 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 233 removed outlier: 4.091A pdb=" N GLN A 233 " --> pdb=" O ASN A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 252 through 255 Processing helix chain 'A' and resid 283 through 306 Processing helix chain 'A' and resid 308 through 328 Processing helix chain 'A' and resid 329 through 332 removed outlier: 3.819A pdb=" N VAL A 332 " --> pdb=" O SER A 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 329 through 332' Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 412 through 423 Processing helix chain 'A' and resid 450 through 455 Processing helix chain 'A' and resid 481 through 483 No H-bonds generated for 'chain 'A' and resid 481 through 483' Processing helix chain 'A' and resid 504 through 509 removed outlier: 3.917A pdb=" N TYR A 508 " --> pdb=" O VAL A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 Processing helix chain 'A' and resid 537 through 541 removed outlier: 4.000A pdb=" N LEU A 541 " --> pdb=" O LYS A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 565 Processing helix chain 'A' and resid 572 through 583 Processing helix chain 'A' and resid 606 through 615 Processing helix chain 'A' and resid 642 through 649 removed outlier: 6.144A pdb=" N GLN A 647 " --> pdb=" O GLU A 644 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ASN A 648 " --> pdb=" O MET A 645 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASP A 649 " --> pdb=" O SER A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 686 Processing helix chain 'A' and resid 686 through 708 removed outlier: 3.722A pdb=" N ALA A 690 " --> pdb=" O GLY A 686 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG A 703 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU A 705 " --> pdb=" O CYS A 701 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N GLY A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN A 707 " --> pdb=" O ARG A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 748 removed outlier: 3.770A pdb=" N GLU A 728 " --> pdb=" O LYS A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 783 Processing helix chain 'A' and resid 789 through 798 Processing helix chain 'A' and resid 802 through 811 Processing helix chain 'A' and resid 841 through 845 Processing helix chain 'A' and resid 857 through 894 removed outlier: 4.372A pdb=" N THR A 879 " --> pdb=" O THR A 875 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ALA A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU A 881 " --> pdb=" O VAL A 877 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR A 884 " --> pdb=" O ALA A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 919 removed outlier: 3.512A pdb=" N ASP A 919 " --> pdb=" O TYR A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 926 removed outlier: 3.855A pdb=" N MET A 926 " --> pdb=" O PRO A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 946 Processing helix chain 'A' and resid 955 through 973 Proline residue: A 969 - end of helix Processing helix chain 'A' and resid 985 through 989 removed outlier: 3.783A pdb=" N LEU A 989 " --> pdb=" O ARG A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 995 removed outlier: 3.541A pdb=" N TYR A 994 " --> pdb=" O LYS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1026 Processing helix chain 'A' and resid 1052 through 1060 Processing helix chain 'A' and resid 1063 through 1080 Processing helix chain 'A' and resid 1088 through 1104 Proline residue: A1100 - end of helix Processing helix chain 'A' and resid 1122 through 1131 removed outlier: 3.610A pdb=" N ASN A1131 " --> pdb=" O LYS A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1162 removed outlier: 3.572A pdb=" N ARG A1160 " --> pdb=" O VAL A1156 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A1161 " --> pdb=" O VAL A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1190 through 1197 Processing helix chain 'A' and resid 1201 through 1212 removed outlier: 3.510A pdb=" N ALA A1212 " --> pdb=" O ALA A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1216 Processing helix chain 'A' and resid 1254 through 1267 removed outlier: 3.795A pdb=" N TYR A1258 " --> pdb=" O ASN A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1305 Processing helix chain 'A' and resid 1318 through 1327 removed outlier: 3.862A pdb=" N VAL A1322 " --> pdb=" O HIS A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1327 through 1346 removed outlier: 3.569A pdb=" N TYR A1333 " --> pdb=" O GLU A1329 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS A1346 " --> pdb=" O THR A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1351 through 1363 removed outlier: 4.110A pdb=" N ILE A1355 " --> pdb=" O ASP A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1372 through 1380 removed outlier: 3.562A pdb=" N LYS A1378 " --> pdb=" O PHE A1374 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1388 Processing helix chain 'A' and resid 1391 through 1403 Processing helix chain 'A' and resid 1410 through 1418 Processing helix chain 'A' and resid 1423 through 1426 removed outlier: 3.673A pdb=" N GLY A1426 " --> pdb=" O ILE A1423 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1423 through 1426' Processing helix chain 'A' and resid 1438 through 1442 removed outlier: 3.607A pdb=" N VAL A1442 " --> pdb=" O LYS A1439 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1452 removed outlier: 3.631A pdb=" N SER A1450 " --> pdb=" O CYS A1446 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 45 No H-bonds generated for 'chain 'B' and resid 43 through 45' Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.789A pdb=" N ALA B 50 " --> pdb=" O HIS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 71 removed outlier: 3.944A pdb=" N LEU B 62 " --> pdb=" O VAL B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 80 removed outlier: 3.522A pdb=" N LYS B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN B 80 " --> pdb=" O ILE B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 122 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 253 through 260 removed outlier: 3.613A pdb=" N CYS B 260 " --> pdb=" O VAL B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'B' and resid 276 through 293 removed outlier: 4.920A pdb=" N VAL B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ASN B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU B 287 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU B 289 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER B 290 " --> pdb=" O ASN B 286 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 307 Processing helix chain 'B' and resid 318 through 330 Processing helix chain 'B' and resid 342 through 362 removed outlier: 3.506A pdb=" N ASN B 362 " --> pdb=" O MET B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 379 through 408 removed outlier: 3.885A pdb=" N ASP B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 422 through 439 removed outlier: 5.676A pdb=" N ASN B 428 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE B 429 " --> pdb=" O HIS B 425 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B 430 " --> pdb=" O SER B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 470 Processing helix chain 'B' and resid 490 through 494 Processing helix chain 'B' and resid 526 through 537 removed outlier: 3.536A pdb=" N GLY B 537 " --> pdb=" O CYS B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 552 removed outlier: 3.578A pdb=" N LEU B 551 " --> pdb=" O SER B 548 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASN B 552 " --> pdb=" O LEU B 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 548 through 552' Processing helix chain 'B' and resid 567 through 582 Processing helix chain 'B' and resid 623 through 633 Processing helix chain 'B' and resid 636 through 643 Processing helix chain 'B' and resid 651 through 656 removed outlier: 3.668A pdb=" N ASP B 656 " --> pdb=" O ASN B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 666 Processing helix chain 'B' and resid 676 through 681 removed outlier: 3.725A pdb=" N THR B 679 " --> pdb=" O GLU B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 688 Processing helix chain 'B' and resid 690 through 694 Processing helix chain 'B' and resid 695 through 706 Processing helix chain 'B' and resid 707 through 709 No H-bonds generated for 'chain 'B' and resid 707 through 709' Processing helix chain 'B' and resid 738 through 744 Processing helix chain 'B' and resid 763 through 767 removed outlier: 4.015A pdb=" N ASP B 766 " --> pdb=" O SER B 763 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE B 767 " --> pdb=" O GLY B 764 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 763 through 767' Processing helix chain 'B' and resid 775 through 780 Processing helix chain 'B' and resid 818 through 822 Processing helix chain 'B' and resid 927 through 931 Processing helix chain 'B' and resid 945 through 949 removed outlier: 3.584A pdb=" N GLY B 948 " --> pdb=" O ASN B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 971 removed outlier: 3.857A pdb=" N MET B 958 " --> pdb=" O THR B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 994 removed outlier: 3.558A pdb=" N MET B 987 " --> pdb=" O LYS B 983 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1034 Processing helix chain 'B' and resid 1053 through 1057 Processing helix chain 'B' and resid 1063 through 1073 Processing helix chain 'B' and resid 1075 through 1084 Processing helix chain 'B' and resid 1123 through 1135 Processing helix chain 'C' and resid 32 through 40 Processing helix chain 'C' and resid 60 through 74 Processing helix chain 'C' and resid 93 through 103 Processing helix chain 'C' and resid 109 through 113 removed outlier: 3.553A pdb=" N LEU C 113 " --> pdb=" O PRO C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 126 removed outlier: 4.678A pdb=" N PHE C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 157 Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 174 through 179 Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 241 through 249 removed outlier: 3.523A pdb=" N ARG C 245 " --> pdb=" O GLY C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 removed outlier: 3.610A pdb=" N LYS C 272 " --> pdb=" O ASP C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 286 removed outlier: 3.532A pdb=" N TYR C 282 " --> pdb=" O VAL C 279 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLU C 283 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU C 284 " --> pdb=" O ARG C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 331 Processing helix chain 'D' and resid 12 through 27 Processing helix chain 'D' and resid 30 through 37 Processing helix chain 'D' and resid 52 through 68 Processing helix chain 'D' and resid 99 through 112 removed outlier: 3.675A pdb=" N SER D 112 " --> pdb=" O THR D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 127 Processing helix chain 'D' and resid 130 through 138 removed outlier: 3.720A pdb=" N VAL D 138 " --> pdb=" O LEU D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 146 through 159 Processing helix chain 'E' and resid 5 through 26 Processing helix chain 'E' and resid 31 through 35 Processing helix chain 'E' and resid 38 through 47 removed outlier: 3.602A pdb=" N CYS E 47 " --> pdb=" O LYS E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 90 through 104 Processing helix chain 'E' and resid 117 through 122 removed outlier: 3.693A pdb=" N LYS E 122 " --> pdb=" O PRO E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 141 removed outlier: 3.529A pdb=" N VAL E 141 " --> pdb=" O ALA E 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 138 through 141' Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.637A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 removed outlier: 3.774A pdb=" N GLU F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 162 through 175 Processing helix chain 'H' and resid 88 through 93 removed outlier: 3.953A pdb=" N ASP H 92 " --> pdb=" O LEU H 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 removed outlier: 3.679A pdb=" N LEU J 36 " --> pdb=" O GLU J 32 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER J 37 " --> pdb=" O GLY J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.733A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'J' and resid 62 through 64 No H-bonds generated for 'chain 'J' and resid 62 through 64' Processing helix chain 'K' and resid 69 through 82 removed outlier: 4.419A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS K 82 " --> pdb=" O TYR K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 142 removed outlier: 3.675A pdb=" N LYS K 140 " --> pdb=" O THR K 136 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET K 142 " --> pdb=" O LYS K 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 140 removed outlier: 3.632A pdb=" N ALA M 136 " --> pdb=" O ASN M 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 199 Processing helix chain 'M' and resid 229 through 240 Processing helix chain 'M' and resid 251 through 263 Processing helix chain 'M' and resid 273 through 280 removed outlier: 3.737A pdb=" N ASN M 280 " --> pdb=" O ASP M 276 " (cutoff:3.500A) Processing helix chain 'N' and resid 195 through 200 removed outlier: 3.562A pdb=" N GLN N 198 " --> pdb=" O ARG N 195 " (cutoff:3.500A) Processing helix chain 'N' and resid 208 through 212 removed outlier: 3.595A pdb=" N VAL N 212 " --> pdb=" O HIS N 209 " (cutoff:3.500A) Processing helix chain 'N' and resid 214 through 225 removed outlier: 4.602A pdb=" N GLU N 218 " --> pdb=" O THR N 214 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER N 224 " --> pdb=" O GLN N 220 " (cutoff:3.500A) Processing helix chain 'N' and resid 274 through 297 Processing helix chain 'N' and resid 352 through 356 removed outlier: 3.853A pdb=" N LEU N 356 " --> pdb=" O THR N 353 " (cutoff:3.500A) Processing helix chain 'O' and resid 27 through 35 Processing helix chain 'O' and resid 43 through 57 Processing helix chain 'O' and resid 58 through 72 Processing helix chain 'O' and resid 75 through 83 Processing helix chain 'O' and resid 87 through 101 removed outlier: 3.567A pdb=" N LEU O 101 " --> pdb=" O SER O 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 123 through 132 removed outlier: 3.973A pdb=" N ILE O 127 " --> pdb=" O ASN O 123 " (cutoff:3.500A) Processing helix chain 'O' and resid 132 through 144 removed outlier: 3.795A pdb=" N MET O 144 " --> pdb=" O ILE O 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 149 through 167 Processing helix chain 'O' and resid 171 through 176 Processing helix chain 'O' and resid 180 through 197 Processing helix chain 'O' and resid 210 through 225 Processing helix chain 'O' and resid 233 through 254 Processing helix chain 'O' and resid 255 through 259 removed outlier: 4.305A pdb=" N LEU O 259 " --> pdb=" O PRO O 256 " (cutoff:3.500A) Processing helix chain 'O' and resid 283 through 301 removed outlier: 3.613A pdb=" N PHE O 287 " --> pdb=" O ASN O 283 " (cutoff:3.500A) Processing helix chain 'O' and resid 306 through 319 Processing helix chain 'O' and resid 328 through 333 Processing helix chain 'O' and resid 334 through 337 removed outlier: 3.877A pdb=" N GLN O 337 " --> pdb=" O GLY O 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 334 through 337' Processing helix chain 'O' and resid 338 through 356 removed outlier: 3.817A pdb=" N GLU O 354 " --> pdb=" O GLU O 350 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR O 356 " --> pdb=" O VAL O 352 " (cutoff:3.500A) Processing helix chain 'O' and resid 363 through 368 removed outlier: 3.727A pdb=" N ARG O 368 " --> pdb=" O ILE O 364 " (cutoff:3.500A) Processing helix chain 'O' and resid 449 through 462 Processing helix chain 'O' and resid 479 through 501 Proline residue: O 485 - end of helix Processing helix chain 'O' and resid 501 through 514 removed outlier: 3.512A pdb=" N MET O 505 " --> pdb=" O GLY O 501 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN O 514 " --> pdb=" O CYS O 510 " (cutoff:3.500A) Processing helix chain 'O' and resid 518 through 526 Processing helix chain 'O' and resid 529 through 542 removed outlier: 3.866A pdb=" N ARG O 542 " --> pdb=" O ALA O 538 " (cutoff:3.500A) Processing helix chain 'O' and resid 569 through 599 removed outlier: 3.538A pdb=" N SER O 573 " --> pdb=" O LYS O 569 " (cutoff:3.500A) Processing helix chain 'O' and resid 599 through 607 Processing helix chain 'O' and resid 614 through 619 removed outlier: 3.606A pdb=" N LEU O 619 " --> pdb=" O GLU O 615 " (cutoff:3.500A) Processing helix chain 'O' and resid 620 through 649 Processing helix chain 'O' and resid 650 through 653 Processing helix chain 'P' and resid 171 through 191 removed outlier: 3.529A pdb=" N PHE P 191 " --> pdb=" O SER P 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 194 through 200 removed outlier: 3.690A pdb=" N PHE P 198 " --> pdb=" O GLY P 194 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN P 200 " --> pdb=" O LYS P 196 " (cutoff:3.500A) Processing helix chain 'P' and resid 218 through 229 removed outlier: 3.526A pdb=" N GLN P 229 " --> pdb=" O ILE P 225 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 250 Processing helix chain 'P' and resid 264 through 272 removed outlier: 3.655A pdb=" N ILE P 268 " --> pdb=" O THR P 264 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET P 271 " --> pdb=" O SER P 267 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN P 272 " --> pdb=" O ILE P 268 " (cutoff:3.500A) Processing helix chain 'P' and resid 295 through 299 Processing helix chain 'Q' and resid 48 through 67 Processing helix chain 'Q' and resid 107 through 111 Processing helix chain 'Q' and resid 128 through 132 removed outlier: 3.628A pdb=" N PHE Q 132 " --> pdb=" O LEU Q 129 " (cutoff:3.500A) Processing helix chain 'Q' and resid 133 through 140 removed outlier: 4.677A pdb=" N ASN Q 138 " --> pdb=" O GLU Q 135 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL Q 139 " --> pdb=" O LEU Q 136 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1405 through 1407 removed outlier: 6.716A pdb=" N ARG B1142 " --> pdb=" O LYS A 14 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU A 16 " --> pdb=" O ARG B1140 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ARG B1140 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE A 18 " --> pdb=" O ALA B1138 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA B1138 " --> pdb=" O PHE A 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 33 removed outlier: 7.344A pdb=" N HIS A 83 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLU A 33 " --> pdb=" O HIS A 83 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N LYS A 85 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ARG A 259 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 10.551A pdb=" N LEU A 88 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 10.432A pdb=" N ILE A 257 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 163 through 166 removed outlier: 4.320A pdb=" N ILE A 178 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 371 through 372 Processing sheet with id=AA5, first strand: chain 'B' and resid 1036 through 1037 removed outlier: 3.736A pdb=" N LEU A 500 " --> pdb=" O SER A 382 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 403 through 407 removed outlier: 3.925A pdb=" N TYR A 432 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N HIS A 465 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ALA A 430 " --> pdb=" O HIS A 465 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 570 through 571 Processing sheet with id=AA8, first strand: chain 'A' and resid 626 through 629 removed outlier: 6.191A pdb=" N ILE A 653 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 814 through 815 Processing sheet with id=AB1, first strand: chain 'A' and resid 897 through 898 removed outlier: 7.049A pdb=" N VAL A 904 " --> pdb=" O VAL A 912 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1280 through 1285 removed outlier: 3.616A pdb=" N ARG A1280 " --> pdb=" O GLU A1296 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ARG A1291 " --> pdb=" O LEU A1145 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU A1145 " --> pdb=" O ARG A1291 " (cutoff:3.500A) removed outlier: 11.316A pdb=" N ILE A1140 " --> pdb=" O THR A1314 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N THR A1314 " --> pdb=" O ILE A1140 " (cutoff:3.500A) removed outlier: 11.326A pdb=" N ASN A1142 " --> pdb=" O SER A1312 " (cutoff:3.500A) removed outlier: 8.974A pdb=" N SER A1312 " --> pdb=" O ASN A1142 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N VAL A1144 " --> pdb=" O ILE A1310 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 3.754A pdb=" N LYS A1273 " --> pdb=" O THR A1164 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1222 through 1225 removed outlier: 4.459A pdb=" N SER A1182 " --> pdb=" O VAL A1234 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N PHE A1183 " --> pdb=" O ASP A1175 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ASP A1175 " --> pdb=" O PHE A1183 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLN A1185 " --> pdb=" O VAL A1173 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL A1173 " --> pdb=" O GLN A1185 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG A1187 " --> pdb=" O PHE A1171 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A1173 " --> pdb=" O LYS I 44 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP A1175 " --> pdb=" O ASP I 42 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP I 42 " --> pdb=" O ASP A1175 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE I 40 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1365 through 1366 removed outlier: 3.817A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1428 through 1432 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1428 through 1432 current: chain 'F' and resid 143 through 147 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 143 through 147 current: chain 'G' and resid 43 through 54 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 43 through 54 current: chain 'G' and resid 66 through 77 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 82 through 84 removed outlier: 7.655A pdb=" N LEU B 93 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N THR B 136 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N TYR B 95 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLU B 134 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP B 97 " --> pdb=" O ASP B 132 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ALA B 127 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLY B 150 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE B 129 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU B 148 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N VAL B 131 " --> pdb=" O ASP B 146 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP B 146 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG B 137 " --> pdb=" O ASN B 140 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASN B 140 " --> pdb=" O ARG B 137 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AB9, first strand: chain 'B' and resid 375 through 378 removed outlier: 6.824A pdb=" N VAL B 196 " --> pdb=" O SER B 474 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 205 through 210 removed outlier: 4.577A pdb=" N VAL B 216 " --> pdb=" O THR B 235 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 442 through 444 Processing sheet with id=AC3, first strand: chain 'B' and resid 519 through 520 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 619 through 620 current: chain 'B' and resid 672 through 673 Processing sheet with id=AC4, first strand: chain 'B' and resid 539 through 540 removed outlier: 5.272A pdb=" N LEU B 561 " --> pdb=" O LEU B 557 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU B 557 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY B 563 " --> pdb=" O VAL B 555 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR B 553 " --> pdb=" O ILE B 565 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 724 through 728 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 785 through 795 current: chain 'B' and resid 879 through 888 removed outlier: 6.559A pdb=" N LEU B 899 " --> pdb=" O ASP B 882 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL B 884 " --> pdb=" O LYS B 897 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS B 897 " --> pdb=" O VAL B 884 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N MET B 886 " --> pdb=" O LEU B 895 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU B 895 " --> pdb=" O MET B 886 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 894 through 904 current: chain 'L' and resid 37 through 38 Processing sheet with id=AC6, first strand: chain 'B' and resid 736 through 737 Processing sheet with id=AC7, first strand: chain 'B' and resid 1001 through 1002 removed outlier: 7.209A pdb=" N LEU B 771 " --> pdb=" O GLY B 923 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE B 925 " --> pdb=" O LEU B 771 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU B 773 " --> pdb=" O ILE B 925 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ILE B 942 " --> pdb=" O ASN B 754 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N THR B 756 " --> pdb=" O ILE B 942 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N MET B 944 " --> pdb=" O THR B 756 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA B 758 " --> pdb=" O MET B 944 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE B1018 " --> pdb=" O VAL B 759 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 841 through 843 removed outlier: 3.827A pdb=" N ILE B 843 " --> pdb=" O VAL B 871 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 846 through 848 Processing sheet with id=AD1, first strand: chain 'B' and resid 1101 through 1102 removed outlier: 4.458A pdb=" N ASP B1093 " --> pdb=" O GLY B1102 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 4 through 7 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 12 through 13 current: chain 'C' and resid 51 through 57 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 51 through 57 current: chain 'C' and resid 289 through 304 Processing sheet with id=AD3, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.368A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL L 65 " --> pdb=" O PHE C 85 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 161 through 163 Processing sheet with id=AD5, first strand: chain 'C' and resid 256 through 258 Processing sheet with id=AD6, first strand: chain 'E' and resid 60 through 62 Processing sheet with id=AD7, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AD8, first strand: chain 'G' and resid 152 through 155 removed outlier: 3.752A pdb=" N ARG G 152 " --> pdb=" O LEU G 197 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE G 108 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLY G 96 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N CYS G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LYS G 98 " --> pdb=" O SER G 90 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.501A pdb=" N ALA G 127 " --> pdb=" O THR G 122 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.685A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU H 121 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LEU H 111 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 13 through 15 removed outlier: 3.597A pdb=" N THR I 15 " --> pdb=" O THR I 23 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR I 23 " --> pdb=" O THR I 15 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 64 through 66 removed outlier: 3.785A pdb=" N TRP I 107 " --> pdb=" O TYR I 98 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N CYS I 100 " --> pdb=" O HIS I 105 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N HIS I 105 " --> pdb=" O CYS I 100 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 47 through 49 Processing sheet with id=AE5, first strand: chain 'M' and resid 70 through 78 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 70 through 78 current: chain 'M' and resid 118 through 124 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 145 through 154 current: chain 'M' and resid 168 through 182 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 168 through 182 current: chain 'N' and resid 371 through 375 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 378 through 380 current: chain 'N' and resid 405 through 417 Processing sheet with id=AE6, first strand: chain 'M' and resid 96 through 97 Processing sheet with id=AE7, first strand: chain 'O' and resid 106 through 110 Processing sheet with id=AE8, first strand: chain 'O' and resid 168 through 170 Processing sheet with id=AE9, first strand: chain 'O' and resid 361 through 362 removed outlier: 7.413A pdb=" N VAL O 475 " --> pdb=" O THR O 471 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR O 471 " --> pdb=" O VAL O 475 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 380 through 381 Processing sheet with id=AF2, first strand: chain 'O' and resid 516 through 517 Processing sheet with id=AF3, first strand: chain 'P' and resid 165 through 166 Processing sheet with id=AF4, first strand: chain 'P' and resid 216 through 217 removed outlier: 7.237A pdb=" N CYS P 260 " --> pdb=" O VAL P 256 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL P 256 " --> pdb=" O CYS P 260 " (cutoff:3.500A) 1670 hydrogen bonds defined for protein. 4632 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 54 stacking parallelities Total time for adding SS restraints: 23.44 Time building geometry restraints manager: 12.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13562 1.34 - 1.46: 9000 1.46 - 1.58: 20182 1.58 - 1.70: 130 1.70 - 1.83: 352 Bond restraints: 43226 Sorted by residual: bond pdb=" C15 4QM C 401 " pdb=" C16 4QM C 401 " ideal model delta sigma weight residual 1.529 1.594 -0.065 2.00e-02 2.50e+03 1.04e+01 bond pdb=" C15 4QM A2003 " pdb=" C16 4QM A2003 " ideal model delta sigma weight residual 1.529 1.593 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C16 4QM A2003 " pdb=" C17 4QM A2003 " ideal model delta sigma weight residual 1.527 1.589 -0.062 2.00e-02 2.50e+03 9.62e+00 bond pdb=" C16 4QM C 401 " pdb=" C17 4QM C 401 " ideal model delta sigma weight residual 1.527 1.589 -0.062 2.00e-02 2.50e+03 9.56e+00 bond pdb=" C19 4QM C 401 " pdb=" C2 4QM C 401 " ideal model delta sigma weight residual 1.551 1.612 -0.061 2.00e-02 2.50e+03 9.16e+00 ... (remaining 43221 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 57872 2.34 - 4.67: 656 4.67 - 7.01: 87 7.01 - 9.35: 32 9.35 - 11.69: 3 Bond angle restraints: 58650 Sorted by residual: angle pdb=" N ILE A 550 " pdb=" CA ILE A 550 " pdb=" C ILE A 550 " ideal model delta sigma weight residual 113.53 108.46 5.07 9.80e-01 1.04e+00 2.68e+01 angle pdb=" C LEU B 293 " pdb=" N ASP B 294 " pdb=" CA ASP B 294 " ideal model delta sigma weight residual 121.54 130.09 -8.55 1.91e+00 2.74e-01 2.01e+01 angle pdb=" C TYR B 164 " pdb=" N ASP B 165 " pdb=" CA ASP B 165 " ideal model delta sigma weight residual 121.54 129.74 -8.20 1.91e+00 2.74e-01 1.84e+01 angle pdb=" C GLN A 555 " pdb=" N ASP A 556 " pdb=" CA ASP A 556 " ideal model delta sigma weight residual 121.54 129.31 -7.77 1.91e+00 2.74e-01 1.65e+01 angle pdb=" C10 4QM C 401 " pdb=" C5 4QM C 401 " pdb=" C6 4QM C 401 " ideal model delta sigma weight residual 112.56 100.87 11.69 3.00e+00 1.11e-01 1.52e+01 ... (remaining 58645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.91: 25505 27.91 - 55.83: 902 55.83 - 83.74: 73 83.74 - 111.66: 4 111.66 - 139.57: 1 Dihedral angle restraints: 26485 sinusoidal: 11456 harmonic: 15029 Sorted by residual: dihedral pdb=" CA ASN O 514 " pdb=" C ASN O 514 " pdb=" N LYS O 515 " pdb=" CA LYS O 515 " ideal model delta harmonic sigma weight residual -180.00 -151.39 -28.61 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA GLN E 179 " pdb=" C GLN E 179 " pdb=" N ARG E 180 " pdb=" CA ARG E 180 " ideal model delta harmonic sigma weight residual 180.00 159.69 20.31 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA PHE B1018 " pdb=" C PHE B1018 " pdb=" N PHE B1019 " pdb=" CA PHE B1019 " ideal model delta harmonic sigma weight residual 180.00 -160.04 -19.96 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 26482 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 5786 0.069 - 0.137: 804 0.137 - 0.206: 22 0.206 - 0.275: 6 0.275 - 0.344: 6 Chirality restraints: 6624 Sorted by residual: chirality pdb=" C9 4QM C 401 " pdb=" C20 4QM C 401 " pdb=" C5 4QM C 401 " pdb=" C8 4QM C 401 " both_signs ideal model delta sigma weight residual False 2.61 2.95 -0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" C9 4QM A2003 " pdb=" C20 4QM A2003 " pdb=" C5 4QM A2003 " pdb=" C8 4QM A2003 " both_signs ideal model delta sigma weight residual False 2.61 2.95 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" C17 4QM C 401 " pdb=" C16 4QM C 401 " pdb=" C18 4QM C 401 " pdb=" O3 4QM C 401 " both_signs ideal model delta sigma weight residual False 2.39 2.71 -0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 6621 not shown) Planarity restraints: 7322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP P 251 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.97e+00 pdb=" C ASP P 251 " 0.042 2.00e-02 2.50e+03 pdb=" O ASP P 251 " -0.016 2.00e-02 2.50e+03 pdb=" N LYS P 252 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 676 " 0.039 5.00e-02 4.00e+02 5.94e-02 5.65e+00 pdb=" N PRO B 677 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 677 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 677 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 433 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.40e+00 pdb=" C LEU B 433 " -0.040 2.00e-02 2.50e+03 pdb=" O LEU B 433 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN B 434 " 0.013 2.00e-02 2.50e+03 ... (remaining 7319 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 407 2.64 - 3.21: 36693 3.21 - 3.77: 64893 3.77 - 4.34: 91242 4.34 - 4.90: 151113 Nonbonded interactions: 344348 Sorted by model distance: nonbonded pdb=" O3' G R 19 " pdb="MG MG A2002 " model vdw 2.079 2.170 nonbonded pdb=" OD1 ASP A 511 " pdb="MG MG A2002 " model vdw 2.092 2.170 nonbonded pdb=" OD1 ASP A 513 " pdb="MG MG A2002 " model vdw 2.132 2.170 nonbonded pdb=" OE2 GLU B 676 " pdb=" OG1 THR B 679 " model vdw 2.169 3.040 nonbonded pdb=" O PHE C 86 " pdb=" OG SER C 203 " model vdw 2.218 3.040 ... (remaining 344343 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 1.790 Check model and map are aligned: 0.310 Set scattering table: 0.400 Process input model: 115.480 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:16.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 43226 Z= 0.220 Angle : 0.652 11.687 58650 Z= 0.341 Chirality : 0.047 0.344 6624 Planarity : 0.005 0.059 7322 Dihedral : 13.554 139.573 16761 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.02 % Allowed : 0.20 % Favored : 99.78 % 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: -0.22 (0.11), residues: 5094 helix: 0.47 (0.12), residues: 1874 sheet: 0.03 (0.21), residues: 656 loop : -0.58 (0.12), residues: 2564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 211 HIS 0.006 0.001 HIS A 427 PHE 0.029 0.001 PHE A 474 TYR 0.026 0.001 TYR O 121 ARG 0.007 0.000 ARG A1152 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 4559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 556 time to evaluate : 4.977 Fit side-chains REVERT: A 583 MET cc_start: 0.8817 (ptp) cc_final: 0.8440 (ptp) REVERT: A 829 ASP cc_start: 0.7588 (m-30) cc_final: 0.7280 (m-30) REVERT: A 988 ASP cc_start: 0.7663 (p0) cc_final: 0.7229 (p0) REVERT: A 1147 ASN cc_start: 0.7970 (t0) cc_final: 0.7569 (t0) REVERT: A 1255 ASP cc_start: 0.6992 (m-30) cc_final: 0.6708 (t0) REVERT: B 797 ARG cc_start: 0.7454 (mtm180) cc_final: 0.7205 (mtm180) REVERT: B 892 ASP cc_start: 0.7640 (m-30) cc_final: 0.7415 (m-30) REVERT: D 130 ASN cc_start: 0.6196 (t0) cc_final: 0.5977 (t0) REVERT: D 133 HIS cc_start: 0.6865 (t-170) cc_final: 0.6638 (t-170) REVERT: L 47 ARG cc_start: 0.8573 (ptm-80) cc_final: 0.8334 (ptm-80) REVERT: O 158 GLU cc_start: 0.7317 (pt0) cc_final: 0.6995 (pt0) REVERT: O 368 ARG cc_start: 0.7564 (mtm110) cc_final: 0.7298 (mtm110) REVERT: O 381 LEU cc_start: 0.7589 (tp) cc_final: 0.7208 (tp) outliers start: 1 outliers final: 0 residues processed: 557 average time/residue: 1.6700 time to fit residues: 1134.9656 Evaluate side-chains 452 residues out of total 4559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 452 time to evaluate : 5.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 433 optimal weight: 3.9990 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 262 optimal weight: 2.9990 chunk 207 optimal weight: 0.5980 chunk 402 optimal weight: 7.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 299 optimal weight: 4.9990 chunk 465 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1262 GLN ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN D 69 ASN E 101 GLN G 32 ASN G 69 ASN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 597 GLN P 189 ASN Q 44 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 43226 Z= 0.362 Angle : 0.579 7.601 58650 Z= 0.303 Chirality : 0.045 0.193 6624 Planarity : 0.004 0.054 7322 Dihedral : 10.459 142.828 6455 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.14 % Allowed : 8.19 % Favored : 90.66 % 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: 0.27 (0.12), residues: 5094 helix: 1.11 (0.12), residues: 1894 sheet: -0.00 (0.20), residues: 672 loop : -0.41 (0.12), residues: 2528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 201 HIS 0.012 0.001 HIS A 427 PHE 0.023 0.002 PHE B1018 TYR 0.017 0.002 TYR O 121 ARG 0.006 0.000 ARG B 874 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 4559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 495 time to evaluate : 5.343 Fit side-chains REVERT: A 65 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8009 (mm) REVERT: A 145 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7957 (tp) REVERT: A 572 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7406 (p0) REVERT: A 829 ASP cc_start: 0.7638 (m-30) cc_final: 0.7314 (m-30) REVERT: A 1147 ASN cc_start: 0.7754 (t0) cc_final: 0.7506 (t0) REVERT: A 1199 GLU cc_start: 0.7377 (pt0) cc_final: 0.7117 (pt0) REVERT: A 1255 ASP cc_start: 0.7107 (m-30) cc_final: 0.6808 (t0) REVERT: B 102 LYS cc_start: 0.8287 (tptt) cc_final: 0.8032 (tmtm) REVERT: B 369 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7684 (mtm110) REVERT: B 445 LYS cc_start: 0.8628 (mmmm) cc_final: 0.8301 (mmmt) REVERT: B 882 ASP cc_start: 0.7796 (t70) cc_final: 0.7468 (t0) REVERT: D 107 MET cc_start: 0.7217 (ttt) cc_final: 0.6897 (ttt) REVERT: D 130 ASN cc_start: 0.5744 (t0) cc_final: 0.5414 (t0) REVERT: D 133 HIS cc_start: 0.6888 (t-170) cc_final: 0.6618 (t-170) REVERT: E 1 MET cc_start: 0.6780 (ppp) cc_final: 0.6215 (ppp) REVERT: K 137 GLU cc_start: 0.7791 (pp20) cc_final: 0.7441 (tm-30) REVERT: L 47 ARG cc_start: 0.8596 (ptm-80) cc_final: 0.8381 (ptm-80) REVERT: N 217 ARG cc_start: 0.7318 (mmp-170) cc_final: 0.7116 (mmm160) REVERT: N 377 ASN cc_start: 0.7931 (m-40) cc_final: 0.7654 (m-40) REVERT: N 390 PHE cc_start: 0.8665 (p90) cc_final: 0.8348 (p90) REVERT: O 158 GLU cc_start: 0.7325 (pt0) cc_final: 0.7066 (pt0) REVERT: O 368 ARG cc_start: 0.7595 (mtm110) cc_final: 0.7322 (mtm110) REVERT: O 381 LEU cc_start: 0.7505 (tp) cc_final: 0.7108 (tt) outliers start: 52 outliers final: 20 residues processed: 514 average time/residue: 1.5873 time to fit residues: 1011.0042 Evaluate side-chains 486 residues out of total 4559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 462 time to evaluate : 4.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1189 ASP Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 369 ARG Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain G residue 24 SER Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 81 MET Chi-restraints excluded: chain K residue 136 THR Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain P residue 250 ASP Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain Q residue 139 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 258 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 387 optimal weight: 0.7980 chunk 317 optimal weight: 0.6980 chunk 128 optimal weight: 0.5980 chunk 466 optimal weight: 0.9980 chunk 504 optimal weight: 6.9990 chunk 415 optimal weight: 5.9990 chunk 462 optimal weight: 20.0000 chunk 159 optimal weight: 2.9990 chunk 374 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN A 540 ASN A1262 GLN A1284 ASN B 60 GLN ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN D 64 ASN E 101 GLN J 64 ASN O 456 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 43226 Z= 0.191 Angle : 0.503 6.846 58650 Z= 0.265 Chirality : 0.042 0.169 6624 Planarity : 0.004 0.046 7322 Dihedral : 10.403 142.757 6455 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.10 % Allowed : 10.79 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.12), residues: 5094 helix: 1.46 (0.12), residues: 1890 sheet: 0.12 (0.20), residues: 668 loop : -0.33 (0.12), residues: 2536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 201 HIS 0.006 0.001 HIS A 427 PHE 0.019 0.001 PHE B 678 TYR 0.019 0.001 TYR O 494 ARG 0.006 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 4559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 488 time to evaluate : 5.065 Fit side-chains REVERT: A 65 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8035 (mm) REVERT: A 273 MET cc_start: 0.6774 (tpt) cc_final: 0.5750 (mtm) REVERT: A 829 ASP cc_start: 0.7660 (m-30) cc_final: 0.7342 (m-30) REVERT: A 1147 ASN cc_start: 0.7756 (t0) cc_final: 0.7510 (t0) REVERT: A 1199 GLU cc_start: 0.7310 (pt0) cc_final: 0.6848 (pt0) REVERT: A 1255 ASP cc_start: 0.6978 (m-30) cc_final: 0.6693 (t0) REVERT: B 102 LYS cc_start: 0.8271 (tptt) cc_final: 0.8012 (tmtm) REVERT: B 414 MET cc_start: 0.5907 (tpt) cc_final: 0.4717 (ptm) REVERT: B 445 LYS cc_start: 0.8550 (mmmm) cc_final: 0.8188 (mmmt) REVERT: B 882 ASP cc_start: 0.7772 (t70) cc_final: 0.7383 (t0) REVERT: D 69 ASN cc_start: 0.7285 (p0) cc_final: 0.7036 (p0) REVERT: D 105 GLU cc_start: 0.7176 (pp20) cc_final: 0.6921 (pp20) REVERT: D 107 MET cc_start: 0.7283 (ttt) cc_final: 0.7065 (ttt) REVERT: D 111 ASN cc_start: 0.7342 (m110) cc_final: 0.7045 (p0) REVERT: E 1 MET cc_start: 0.6710 (ppp) cc_final: 0.6199 (ppp) REVERT: E 103 LYS cc_start: 0.8146 (mmpt) cc_final: 0.7489 (ttmm) REVERT: G 1 MET cc_start: 0.7231 (tpp) cc_final: 0.6906 (tpt) REVERT: K 137 GLU cc_start: 0.7766 (pp20) cc_final: 0.7417 (tm-30) REVERT: L 47 ARG cc_start: 0.8578 (ptm-80) cc_final: 0.8338 (ptm-80) REVERT: N 208 ARG cc_start: 0.7099 (mtm110) cc_final: 0.6896 (mtp-110) REVERT: N 377 ASN cc_start: 0.7877 (m-40) cc_final: 0.7387 (m-40) REVERT: O 158 GLU cc_start: 0.7296 (pt0) cc_final: 0.7020 (pt0) REVERT: O 368 ARG cc_start: 0.7572 (mtm110) cc_final: 0.7308 (mtm110) REVERT: O 381 LEU cc_start: 0.7499 (tp) cc_final: 0.7153 (tt) REVERT: O 458 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7561 (tppp) REVERT: P 205 ASN cc_start: 0.8979 (p0) cc_final: 0.8766 (p0) outliers start: 50 outliers final: 15 residues processed: 503 average time/residue: 1.6023 time to fit residues: 992.0134 Evaluate side-chains 487 residues out of total 4559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 470 time to evaluate : 5.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1221 ASP Chi-restraints excluded: chain A residue 1269 ASP Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain O residue 458 LYS Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain Q residue 139 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 461 optimal weight: 2.9990 chunk 350 optimal weight: 4.9990 chunk 242 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 222 optimal weight: 4.9990 chunk 313 optimal weight: 0.9980 chunk 468 optimal weight: 1.9990 chunk 495 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 443 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1262 GLN A1284 ASN ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN C 234 ASN D 64 ASN D 130 ASN E 32 GLN E 101 GLN P 205 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 43226 Z= 0.298 Angle : 0.531 8.686 58650 Z= 0.277 Chirality : 0.043 0.180 6624 Planarity : 0.004 0.045 7322 Dihedral : 10.462 143.100 6455 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.49 % Allowed : 12.04 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.12), residues: 5094 helix: 1.45 (0.12), residues: 1903 sheet: 0.10 (0.21), residues: 665 loop : -0.33 (0.12), residues: 2526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 211 HIS 0.010 0.001 HIS A 427 PHE 0.019 0.001 PHE B 678 TYR 0.016 0.001 TYR J 44 ARG 0.008 0.000 ARG B 376 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 4559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 479 time to evaluate : 4.933 Fit side-chains REVERT: A 65 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8035 (mm) REVERT: A 273 MET cc_start: 0.6892 (tpt) cc_final: 0.5830 (mtm) REVERT: A 829 ASP cc_start: 0.7665 (m-30) cc_final: 0.7352 (m-30) REVERT: A 1147 ASN cc_start: 0.7875 (t0) cc_final: 0.7619 (t0) REVERT: A 1199 GLU cc_start: 0.7435 (pt0) cc_final: 0.7042 (pt0) REVERT: A 1255 ASP cc_start: 0.7043 (m-30) cc_final: 0.6767 (t0) REVERT: A 1269 ASP cc_start: 0.7612 (t70) cc_final: 0.7322 (t0) REVERT: B 102 LYS cc_start: 0.8331 (tptt) cc_final: 0.8051 (tmtm) REVERT: B 143 MET cc_start: 0.6982 (pp-130) cc_final: 0.6730 (ppp) REVERT: B 269 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7207 (tmm) REVERT: B 414 MET cc_start: 0.5941 (tpt) cc_final: 0.4833 (ptm) REVERT: B 445 LYS cc_start: 0.8537 (mmmm) cc_final: 0.8179 (mmmt) REVERT: B 545 ASP cc_start: 0.7262 (t0) cc_final: 0.7041 (t0) REVERT: B 882 ASP cc_start: 0.7773 (t70) cc_final: 0.7410 (t0) REVERT: C 258 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8589 (pp) REVERT: D 107 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6938 (ttt) REVERT: E 1 MET cc_start: 0.6665 (ppp) cc_final: 0.6183 (ppp) REVERT: E 31 THR cc_start: 0.8775 (t) cc_final: 0.8482 (p) REVERT: E 103 LYS cc_start: 0.8196 (mmpt) cc_final: 0.7461 (tppp) REVERT: G 1 MET cc_start: 0.7353 (tpp) cc_final: 0.7135 (tpt) REVERT: G 9 ASP cc_start: 0.7911 (t0) cc_final: 0.7665 (t0) REVERT: G 205 MET cc_start: 0.6850 (mmm) cc_final: 0.6497 (mmm) REVERT: H 55 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7830 (pp) REVERT: J 64 ASN cc_start: 0.8385 (t0) cc_final: 0.8145 (t0) REVERT: K 137 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7396 (tm-30) REVERT: L 47 ARG cc_start: 0.8614 (ptm-80) cc_final: 0.8380 (ptm-80) REVERT: N 208 ARG cc_start: 0.7114 (mtm110) cc_final: 0.6912 (mtp-110) REVERT: N 377 ASN cc_start: 0.7863 (m-40) cc_final: 0.7581 (m-40) REVERT: O 158 GLU cc_start: 0.7298 (pt0) cc_final: 0.7017 (pt0) REVERT: O 368 ARG cc_start: 0.7586 (mtm110) cc_final: 0.7329 (mtm110) REVERT: O 458 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7582 (tppp) REVERT: P 205 ASN cc_start: 0.9043 (OUTLIER) cc_final: 0.8814 (p0) REVERT: P 251 ASP cc_start: 0.8461 (t0) cc_final: 0.8014 (t0) outliers start: 68 outliers final: 31 residues processed: 504 average time/residue: 1.6154 time to fit residues: 1004.4893 Evaluate side-chains 502 residues out of total 4559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 463 time to evaluate : 5.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1189 ASP Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain G residue 24 SER Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 81 MET Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 356 LEU Chi-restraints excluded: chain O residue 458 LYS Chi-restraints excluded: chain P residue 205 ASN Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain Q residue 139 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 412 optimal weight: 0.0060 chunk 281 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 369 optimal weight: 6.9990 chunk 204 optimal weight: 3.9990 chunk 423 optimal weight: 1.9990 chunk 342 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 253 optimal weight: 2.9990 chunk 445 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 618 HIS A 648 ASN A1262 GLN A1284 ASN B 693 HIS D 64 ASN D 69 ASN D 130 ASN E 32 GLN E 101 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 43226 Z= 0.466 Angle : 0.604 9.437 58650 Z= 0.314 Chirality : 0.047 0.201 6624 Planarity : 0.004 0.050 7322 Dihedral : 10.624 143.327 6455 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.07 % Allowed : 13.05 % Favored : 84.89 % 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: 0.39 (0.12), residues: 5094 helix: 1.30 (0.12), residues: 1888 sheet: -0.04 (0.20), residues: 689 loop : -0.40 (0.12), residues: 2517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 201 HIS 0.012 0.002 HIS A 427 PHE 0.030 0.002 PHE A 610 TYR 0.019 0.002 TYR J 44 ARG 0.006 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 4559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 476 time to evaluate : 5.140 Fit side-chains REVERT: A 65 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8013 (mm) REVERT: A 572 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7450 (p0) REVERT: A 829 ASP cc_start: 0.7649 (m-30) cc_final: 0.7344 (m-30) REVERT: A 1147 ASN cc_start: 0.7780 (t0) cc_final: 0.7518 (t0) REVERT: A 1199 GLU cc_start: 0.7486 (pt0) cc_final: 0.7086 (pt0) REVERT: A 1255 ASP cc_start: 0.7178 (m-30) cc_final: 0.6864 (t0) REVERT: B 102 LYS cc_start: 0.8331 (tptt) cc_final: 0.8031 (tmtm) REVERT: B 267 GLU cc_start: 0.7470 (tt0) cc_final: 0.7233 (tt0) REVERT: B 269 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7144 (tmm) REVERT: B 445 LYS cc_start: 0.8539 (mmmm) cc_final: 0.8199 (mmmt) REVERT: B 882 ASP cc_start: 0.7808 (t70) cc_final: 0.7459 (t0) REVERT: C 258 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8569 (pp) REVERT: D 107 MET cc_start: 0.7429 (OUTLIER) cc_final: 0.7067 (ttt) REVERT: D 111 ASN cc_start: 0.7517 (m110) cc_final: 0.7185 (m110) REVERT: D 130 ASN cc_start: 0.5247 (t0) cc_final: 0.4881 (t0) REVERT: D 133 HIS cc_start: 0.6924 (t-170) cc_final: 0.6677 (t-170) REVERT: E 1 MET cc_start: 0.6752 (OUTLIER) cc_final: 0.6259 (ppp) REVERT: G 1 MET cc_start: 0.7439 (tpp) cc_final: 0.7189 (tpp) REVERT: G 205 MET cc_start: 0.6981 (mmm) cc_final: 0.6773 (mmm) REVERT: H 34 ASP cc_start: 0.7125 (t70) cc_final: 0.6847 (t0) REVERT: J 64 ASN cc_start: 0.8520 (t0) cc_final: 0.8284 (t0) REVERT: K 85 ASP cc_start: 0.7090 (t0) cc_final: 0.6723 (t0) REVERT: K 137 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7412 (tm-30) REVERT: M 273 LYS cc_start: 0.7337 (tppt) cc_final: 0.6754 (tttp) REVERT: N 208 ARG cc_start: 0.7128 (mtm110) cc_final: 0.6918 (mtp-110) REVERT: O 158 GLU cc_start: 0.7305 (pt0) cc_final: 0.7023 (pt0) REVERT: O 232 LEU cc_start: 0.5132 (OUTLIER) cc_final: 0.4526 (pp) REVERT: O 314 ILE cc_start: 0.8335 (mm) cc_final: 0.8097 (mp) REVERT: O 368 ARG cc_start: 0.7640 (mtm110) cc_final: 0.7293 (mtm110) REVERT: O 458 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7614 (tppp) REVERT: O 621 PRO cc_start: 0.6232 (Cg_exo) cc_final: 0.5998 (Cg_endo) REVERT: P 251 ASP cc_start: 0.8367 (t0) cc_final: 0.7920 (t0) REVERT: Q 35 GLU cc_start: 0.8525 (tp30) cc_final: 0.8183 (mm-30) outliers start: 94 outliers final: 52 residues processed: 521 average time/residue: 1.5826 time to fit residues: 1019.4470 Evaluate side-chains 529 residues out of total 4559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 468 time to evaluate : 5.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 857 SER Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1189 ASP Chi-restraints excluded: chain A residue 1221 ASP Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain G residue 24 SER Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 81 MET Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 136 THR Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain M residue 115 LYS Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 356 LEU Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain O residue 232 LEU Chi-restraints excluded: chain O residue 458 LYS Chi-restraints excluded: chain P residue 205 ASN Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain Q residue 139 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 166 optimal weight: 3.9990 chunk 446 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 291 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 496 optimal weight: 0.6980 chunk 412 optimal weight: 0.7980 chunk 229 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 260 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1262 GLN A1284 ASN D 51 ASN D 64 ASN E 101 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 43226 Z= 0.197 Angle : 0.515 10.335 58650 Z= 0.270 Chirality : 0.042 0.234 6624 Planarity : 0.004 0.045 7322 Dihedral : 10.489 143.032 6455 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.78 % Allowed : 14.19 % Favored : 84.03 % 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 (0.12), residues: 5094 helix: 1.54 (0.12), residues: 1900 sheet: -0.00 (0.21), residues: 672 loop : -0.30 (0.12), residues: 2522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 201 HIS 0.010 0.001 HIS A 618 PHE 0.019 0.001 PHE B 678 TYR 0.016 0.001 TYR O 494 ARG 0.007 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 4559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 480 time to evaluate : 4.974 Fit side-chains REVERT: A 65 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8010 (mm) REVERT: A 184 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7121 (ttp80) REVERT: A 273 MET cc_start: 0.6897 (tpt) cc_final: 0.5982 (mtm) REVERT: A 829 ASP cc_start: 0.7662 (m-30) cc_final: 0.7361 (m-30) REVERT: A 1127 LYS cc_start: 0.7586 (tttt) cc_final: 0.7244 (ttpp) REVERT: A 1147 ASN cc_start: 0.7813 (t0) cc_final: 0.7547 (t0) REVERT: A 1152 ARG cc_start: 0.8197 (mtm180) cc_final: 0.7969 (mtt90) REVERT: A 1199 GLU cc_start: 0.7421 (pt0) cc_final: 0.6988 (pt0) REVERT: A 1255 ASP cc_start: 0.7020 (m-30) cc_final: 0.6740 (t0) REVERT: B 102 LYS cc_start: 0.8325 (tptt) cc_final: 0.8023 (tmtm) REVERT: B 143 MET cc_start: 0.6970 (pp-130) cc_final: 0.6766 (ppp) REVERT: B 414 MET cc_start: 0.6158 (tpt) cc_final: 0.4947 (ptm) REVERT: B 444 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8085 (mt) REVERT: B 882 ASP cc_start: 0.7753 (t70) cc_final: 0.7416 (t0) REVERT: C 258 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8598 (pp) REVERT: D 107 MET cc_start: 0.7372 (OUTLIER) cc_final: 0.7159 (ttt) REVERT: D 111 ASN cc_start: 0.7519 (m110) cc_final: 0.7222 (p0) REVERT: E 1 MET cc_start: 0.6720 (OUTLIER) cc_final: 0.6302 (ppp) REVERT: E 31 THR cc_start: 0.8676 (t) cc_final: 0.8413 (p) REVERT: E 103 LYS cc_start: 0.8133 (mmpt) cc_final: 0.7484 (ttpp) REVERT: G 1 MET cc_start: 0.7424 (tpp) cc_final: 0.7153 (tpt) REVERT: G 9 ASP cc_start: 0.7897 (t0) cc_final: 0.7637 (t0) REVERT: G 205 MET cc_start: 0.6939 (mmm) cc_final: 0.6699 (mmm) REVERT: H 34 ASP cc_start: 0.7110 (t70) cc_final: 0.6840 (t0) REVERT: H 55 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7772 (pp) REVERT: H 77 ARG cc_start: 0.7828 (mtp180) cc_final: 0.7623 (mtm180) REVERT: J 64 ASN cc_start: 0.8413 (t0) cc_final: 0.8195 (t0) REVERT: K 85 ASP cc_start: 0.7063 (t0) cc_final: 0.6698 (t0) REVERT: K 137 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7383 (tm-30) REVERT: N 208 ARG cc_start: 0.7100 (mtm110) cc_final: 0.6879 (mtp-110) REVERT: O 158 GLU cc_start: 0.7267 (pt0) cc_final: 0.6964 (pt0) REVERT: O 232 LEU cc_start: 0.5064 (OUTLIER) cc_final: 0.4475 (pp) REVERT: O 314 ILE cc_start: 0.8316 (mm) cc_final: 0.8063 (mp) REVERT: O 368 ARG cc_start: 0.7612 (mtm110) cc_final: 0.7296 (mtm110) REVERT: O 458 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7602 (tppp) REVERT: O 621 PRO cc_start: 0.6194 (Cg_exo) cc_final: 0.5964 (Cg_endo) REVERT: Q 35 GLU cc_start: 0.8428 (tp30) cc_final: 0.8099 (mm-30) outliers start: 81 outliers final: 43 residues processed: 519 average time/residue: 1.5759 time to fit residues: 1012.3955 Evaluate side-chains 517 residues out of total 4559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 464 time to evaluate : 5.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 857 SER Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1221 ASP Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain G residue 24 SER Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 81 MET Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain O residue 232 LEU Chi-restraints excluded: chain O residue 458 LYS Chi-restraints excluded: chain P residue 205 ASN Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain P residue 247 LEU Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain Q residue 139 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 478 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 282 optimal weight: 2.9990 chunk 362 optimal weight: 10.0000 chunk 280 optimal weight: 0.9980 chunk 417 optimal weight: 5.9990 chunk 277 optimal weight: 3.9990 chunk 494 optimal weight: 4.9990 chunk 309 optimal weight: 2.9990 chunk 301 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 HIS A1262 GLN A1284 ASN D 51 ASN D 64 ASN D 69 ASN E 101 GLN O 448 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 43226 Z= 0.375 Angle : 0.572 11.388 58650 Z= 0.297 Chirality : 0.045 0.249 6624 Planarity : 0.004 0.047 7322 Dihedral : 10.585 143.301 6455 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.04 % Allowed : 14.72 % Favored : 83.24 % 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 (0.12), residues: 5094 helix: 1.45 (0.12), residues: 1891 sheet: -0.01 (0.21), residues: 680 loop : -0.35 (0.12), residues: 2523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 201 HIS 0.011 0.001 HIS A 427 PHE 0.025 0.002 PHE A 610 TYR 0.018 0.002 TYR J 44 ARG 0.005 0.000 ARG O 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 4559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 470 time to evaluate : 5.825 Fit side-chains REVERT: A 65 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8006 (mm) REVERT: A 273 MET cc_start: 0.6933 (tpt) cc_final: 0.5934 (mtm) REVERT: A 829 ASP cc_start: 0.7648 (m-30) cc_final: 0.7347 (m-30) REVERT: A 1127 LYS cc_start: 0.7678 (tttt) cc_final: 0.7395 (ttpp) REVERT: A 1147 ASN cc_start: 0.7839 (t0) cc_final: 0.7589 (t0) REVERT: A 1199 GLU cc_start: 0.7488 (pt0) cc_final: 0.7090 (pt0) REVERT: A 1255 ASP cc_start: 0.7083 (m-30) cc_final: 0.6785 (t0) REVERT: B 102 LYS cc_start: 0.8344 (tptt) cc_final: 0.8037 (tmtm) REVERT: B 143 MET cc_start: 0.6997 (pp-130) cc_final: 0.6780 (ppp) REVERT: B 414 MET cc_start: 0.6068 (tpt) cc_final: 0.4878 (ptm) REVERT: B 444 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8106 (mt) REVERT: B 445 LYS cc_start: 0.8567 (mmmm) cc_final: 0.8214 (mmmt) REVERT: C 258 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8599 (pp) REVERT: D 107 MET cc_start: 0.7347 (OUTLIER) cc_final: 0.7023 (ttt) REVERT: E 1 MET cc_start: 0.6665 (OUTLIER) cc_final: 0.6141 (ppp) REVERT: E 31 THR cc_start: 0.8660 (t) cc_final: 0.8395 (p) REVERT: E 103 LYS cc_start: 0.8298 (mmpt) cc_final: 0.7616 (tppp) REVERT: G 1 MET cc_start: 0.7443 (tpp) cc_final: 0.7167 (tpt) REVERT: H 34 ASP cc_start: 0.7190 (t70) cc_final: 0.6825 (t0) REVERT: J 64 ASN cc_start: 0.8506 (t0) cc_final: 0.8284 (t0) REVERT: K 85 ASP cc_start: 0.7063 (t0) cc_final: 0.6698 (t0) REVERT: K 137 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7331 (tm-30) REVERT: L 63 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.7594 (mtm180) REVERT: N 208 ARG cc_start: 0.7146 (mtm110) cc_final: 0.6922 (mtp-110) REVERT: O 158 GLU cc_start: 0.7285 (pt0) cc_final: 0.6975 (pt0) REVERT: O 314 ILE cc_start: 0.8328 (mm) cc_final: 0.8085 (mp) REVERT: O 368 ARG cc_start: 0.7660 (mtm110) cc_final: 0.7284 (mtm110) REVERT: O 458 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7621 (tppp) REVERT: O 621 PRO cc_start: 0.6226 (Cg_exo) cc_final: 0.5991 (Cg_endo) REVERT: Q 35 GLU cc_start: 0.8474 (tp30) cc_final: 0.8123 (mm-30) outliers start: 93 outliers final: 59 residues processed: 521 average time/residue: 1.6402 time to fit residues: 1059.1289 Evaluate side-chains 538 residues out of total 4559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 471 time to evaluate : 6.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 857 SER Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1189 ASP Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1393 THR Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain G residue 24 SER Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 190 LYS Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain I residue 10 ASN Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 81 MET Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 136 THR Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 356 LEU Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain O residue 232 LEU Chi-restraints excluded: chain O residue 458 LYS Chi-restraints excluded: chain P residue 205 ASN Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain Q residue 139 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 305 optimal weight: 0.0970 chunk 197 optimal weight: 0.6980 chunk 295 optimal weight: 7.9990 chunk 148 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 314 optimal weight: 2.9990 chunk 336 optimal weight: 0.8980 chunk 244 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 388 optimal weight: 5.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1262 GLN A1284 ASN B 702 GLN D 51 ASN E 101 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 43226 Z= 0.174 Angle : 0.513 11.594 58650 Z= 0.267 Chirality : 0.042 0.229 6624 Planarity : 0.003 0.046 7322 Dihedral : 10.465 142.919 6455 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.65 % Allowed : 15.64 % Favored : 82.71 % 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: 0.75 (0.12), residues: 5094 helix: 1.69 (0.12), residues: 1889 sheet: 0.03 (0.21), residues: 667 loop : -0.24 (0.12), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 107 HIS 0.011 0.001 HIS D 133 PHE 0.020 0.001 PHE B 678 TYR 0.014 0.001 TYR O 106 ARG 0.006 0.000 ARG B 874 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 4559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 473 time to evaluate : 5.087 Fit side-chains REVERT: A 65 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.7965 (mm) REVERT: A 184 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7122 (ttp80) REVERT: A 273 MET cc_start: 0.6830 (tpt) cc_final: 0.5829 (mtm) REVERT: A 274 MET cc_start: 0.4824 (ttp) cc_final: 0.4402 (tmm) REVERT: A 829 ASP cc_start: 0.7653 (m-30) cc_final: 0.7357 (m-30) REVERT: A 1010 GLU cc_start: 0.7393 (tt0) cc_final: 0.7052 (tt0) REVERT: A 1127 LYS cc_start: 0.7594 (tttt) cc_final: 0.7326 (ttpp) REVERT: A 1147 ASN cc_start: 0.7788 (t0) cc_final: 0.7552 (t0) REVERT: A 1199 GLU cc_start: 0.7406 (pt0) cc_final: 0.6978 (pt0) REVERT: A 1255 ASP cc_start: 0.6943 (m-30) cc_final: 0.6679 (t0) REVERT: B 102 LYS cc_start: 0.8336 (tptt) cc_final: 0.8036 (tmtm) REVERT: B 143 MET cc_start: 0.6992 (pp-130) cc_final: 0.6763 (ppp) REVERT: B 414 MET cc_start: 0.6111 (tpt) cc_final: 0.4967 (ptm) REVERT: B 444 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8066 (mt) REVERT: B 445 LYS cc_start: 0.8509 (mmmm) cc_final: 0.8129 (mmmt) REVERT: D 107 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.7079 (ttt) REVERT: D 111 ASN cc_start: 0.7467 (m110) cc_final: 0.7208 (p0) REVERT: E 1 MET cc_start: 0.6579 (OUTLIER) cc_final: 0.6075 (ppp) REVERT: E 31 THR cc_start: 0.8645 (t) cc_final: 0.8386 (p) REVERT: E 103 LYS cc_start: 0.8112 (mmpt) cc_final: 0.7422 (tppp) REVERT: E 114 ASN cc_start: 0.8398 (OUTLIER) cc_final: 0.8036 (t0) REVERT: G 1 MET cc_start: 0.7388 (tpp) cc_final: 0.7175 (tpt) REVERT: G 9 ASP cc_start: 0.7881 (t0) cc_final: 0.7657 (t0) REVERT: H 34 ASP cc_start: 0.7142 (t70) cc_final: 0.6780 (t0) REVERT: H 55 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7840 (pp) REVERT: J 64 ASN cc_start: 0.8404 (t0) cc_final: 0.8201 (t0) REVERT: K 85 ASP cc_start: 0.7029 (t0) cc_final: 0.6678 (t0) REVERT: K 137 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7392 (tm-30) REVERT: O 158 GLU cc_start: 0.7275 (pt0) cc_final: 0.6958 (pt0) REVERT: O 368 ARG cc_start: 0.7559 (mtm110) cc_final: 0.7187 (mtm110) REVERT: O 458 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7600 (tppp) REVERT: O 621 PRO cc_start: 0.6191 (Cg_exo) cc_final: 0.5966 (Cg_endo) REVERT: Q 35 GLU cc_start: 0.8430 (tp30) cc_final: 0.8106 (mm-30) outliers start: 75 outliers final: 45 residues processed: 509 average time/residue: 1.6402 time to fit residues: 1040.8441 Evaluate side-chains 511 residues out of total 4559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 457 time to evaluate : 5.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 857 SER Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain I residue 10 ASN Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 81 MET Chi-restraints excluded: chain K residue 136 THR Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain O residue 232 LEU Chi-restraints excluded: chain O residue 458 LYS Chi-restraints excluded: chain P residue 205 ASN Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain P residue 247 LEU Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain Q residue 139 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 449 optimal weight: 6.9990 chunk 473 optimal weight: 5.9990 chunk 432 optimal weight: 0.8980 chunk 460 optimal weight: 4.9990 chunk 277 optimal weight: 3.9990 chunk 200 optimal weight: 0.9980 chunk 361 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 416 optimal weight: 7.9990 chunk 435 optimal weight: 0.9990 chunk 459 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1262 GLN A1284 ASN B 702 GLN D 64 ASN D 69 ASN E 101 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 43226 Z= 0.306 Angle : 0.554 11.898 58650 Z= 0.286 Chirality : 0.044 0.237 6624 Planarity : 0.004 0.046 7322 Dihedral : 10.526 143.117 6455 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.56 % Allowed : 15.84 % Favored : 82.60 % 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: 0.66 (0.12), residues: 5094 helix: 1.59 (0.12), residues: 1893 sheet: -0.02 (0.20), residues: 690 loop : -0.27 (0.12), residues: 2511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 201 HIS 0.009 0.001 HIS A 427 PHE 0.021 0.001 PHE A 610 TYR 0.016 0.001 TYR J 44 ARG 0.008 0.000 ARG B 874 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 4559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 464 time to evaluate : 5.066 Fit side-chains REVERT: A 65 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7971 (mm) REVERT: A 184 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7135 (ttp80) REVERT: A 273 MET cc_start: 0.6835 (tpt) cc_final: 0.5825 (mtm) REVERT: A 274 MET cc_start: 0.4770 (ttp) cc_final: 0.3877 (tmt) REVERT: A 829 ASP cc_start: 0.7664 (m-30) cc_final: 0.7367 (m-30) REVERT: A 1127 LYS cc_start: 0.7674 (tttt) cc_final: 0.7395 (ttpp) REVERT: A 1147 ASN cc_start: 0.7788 (t0) cc_final: 0.7569 (t0) REVERT: A 1199 GLU cc_start: 0.7431 (pt0) cc_final: 0.7024 (pt0) REVERT: A 1255 ASP cc_start: 0.6989 (m-30) cc_final: 0.6728 (t0) REVERT: B 102 LYS cc_start: 0.8341 (tptt) cc_final: 0.8031 (tmtm) REVERT: B 143 MET cc_start: 0.7011 (pp-130) cc_final: 0.6783 (ppp) REVERT: B 414 MET cc_start: 0.6047 (tpt) cc_final: 0.4963 (ptm) REVERT: B 444 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8077 (mt) REVERT: B 445 LYS cc_start: 0.8530 (mmmm) cc_final: 0.8141 (mmmt) REVERT: D 107 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.7015 (ttt) REVERT: D 111 ASN cc_start: 0.7498 (m110) cc_final: 0.7222 (m110) REVERT: E 1 MET cc_start: 0.6534 (OUTLIER) cc_final: 0.5950 (ppp) REVERT: E 31 THR cc_start: 0.8648 (t) cc_final: 0.8389 (p) REVERT: E 103 LYS cc_start: 0.8198 (mmpt) cc_final: 0.7525 (tppp) REVERT: E 114 ASN cc_start: 0.8440 (OUTLIER) cc_final: 0.8058 (t0) REVERT: G 1 MET cc_start: 0.7410 (tpp) cc_final: 0.7160 (tpt) REVERT: H 34 ASP cc_start: 0.7154 (t70) cc_final: 0.6775 (t0) REVERT: H 55 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7928 (pp) REVERT: J 64 ASN cc_start: 0.8476 (t0) cc_final: 0.8263 (t0) REVERT: K 85 ASP cc_start: 0.7056 (t0) cc_final: 0.6700 (t0) REVERT: K 137 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7400 (tm-30) REVERT: O 158 GLU cc_start: 0.7291 (pt0) cc_final: 0.6973 (pt0) REVERT: O 314 ILE cc_start: 0.8309 (mm) cc_final: 0.8062 (mp) REVERT: O 368 ARG cc_start: 0.7641 (mtm110) cc_final: 0.7267 (mtm110) REVERT: O 458 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7617 (tppp) REVERT: Q 35 GLU cc_start: 0.8468 (tp30) cc_final: 0.8119 (mm-30) outliers start: 71 outliers final: 52 residues processed: 505 average time/residue: 1.6270 time to fit residues: 1019.6609 Evaluate side-chains 526 residues out of total 4559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 465 time to evaluate : 5.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 857 SER Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain G residue 24 SER Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain I residue 10 ASN Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 81 MET Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 136 THR Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain O residue 232 LEU Chi-restraints excluded: chain O residue 458 LYS Chi-restraints excluded: chain P residue 172 ILE Chi-restraints excluded: chain P residue 175 ILE Chi-restraints excluded: chain P residue 205 ASN Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain Q residue 139 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 302 optimal weight: 2.9990 chunk 487 optimal weight: 0.0670 chunk 297 optimal weight: 0.9980 chunk 231 optimal weight: 0.6980 chunk 338 optimal weight: 5.9990 chunk 511 optimal weight: 5.9990 chunk 470 optimal weight: 0.9980 chunk 406 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 314 optimal weight: 0.1980 chunk 249 optimal weight: 4.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1262 GLN A1284 ASN ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 GLN E 101 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 43226 Z= 0.174 Angle : 0.519 12.295 58650 Z= 0.269 Chirality : 0.041 0.220 6624 Planarity : 0.003 0.046 7322 Dihedral : 10.468 142.914 6455 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.38 % Allowed : 16.06 % Favored : 82.56 % 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 (0.12), residues: 5094 helix: 1.74 (0.12), residues: 1898 sheet: 0.00 (0.21), residues: 674 loop : -0.23 (0.12), residues: 2522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 197 HIS 0.008 0.001 HIS A 618 PHE 0.017 0.001 PHE B 678 TYR 0.014 0.001 TYR O 494 ARG 0.009 0.000 ARG B 874 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 4559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 463 time to evaluate : 4.975 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.7951 (mm) REVERT: A 184 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7127 (ttp80) REVERT: A 273 MET cc_start: 0.6777 (tpt) cc_final: 0.5800 (mtm) REVERT: A 274 MET cc_start: 0.4801 (ttp) cc_final: 0.4553 (tmm) REVERT: A 829 ASP cc_start: 0.7653 (m-30) cc_final: 0.7358 (m-30) REVERT: A 1010 GLU cc_start: 0.7395 (tt0) cc_final: 0.7054 (tt0) REVERT: A 1127 LYS cc_start: 0.7595 (tttt) cc_final: 0.7325 (ttpp) REVERT: A 1147 ASN cc_start: 0.7774 (t0) cc_final: 0.7522 (t0) REVERT: A 1199 GLU cc_start: 0.7395 (pt0) cc_final: 0.7000 (pt0) REVERT: A 1255 ASP cc_start: 0.6919 (m-30) cc_final: 0.6653 (t0) REVERT: B 102 LYS cc_start: 0.8345 (tptt) cc_final: 0.8041 (tmtm) REVERT: B 143 MET cc_start: 0.6995 (pp-130) cc_final: 0.6762 (ppp) REVERT: B 414 MET cc_start: 0.6023 (tpt) cc_final: 0.4956 (ptm) REVERT: B 445 LYS cc_start: 0.8511 (mmmm) cc_final: 0.8119 (mmmt) REVERT: D 107 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.6991 (ttt) REVERT: E 1 MET cc_start: 0.6487 (OUTLIER) cc_final: 0.5944 (ppp) REVERT: E 31 THR cc_start: 0.8641 (t) cc_final: 0.8385 (p) REVERT: E 103 LYS cc_start: 0.8062 (mmpt) cc_final: 0.7363 (tppp) REVERT: E 114 ASN cc_start: 0.8406 (OUTLIER) cc_final: 0.8044 (t0) REVERT: G 9 ASP cc_start: 0.7732 (t0) cc_final: 0.7506 (t0) REVERT: H 34 ASP cc_start: 0.7133 (t70) cc_final: 0.6766 (t0) REVERT: H 55 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7854 (pp) REVERT: K 85 ASP cc_start: 0.7023 (t0) cc_final: 0.6676 (t0) REVERT: K 137 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7384 (tm-30) REVERT: O 158 GLU cc_start: 0.7283 (pt0) cc_final: 0.6961 (pt0) REVERT: O 368 ARG cc_start: 0.7548 (mtm110) cc_final: 0.7180 (mtm110) REVERT: O 458 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7594 (tppp) REVERT: O 528 MET cc_start: 0.8062 (ptt) cc_final: 0.7759 (ptm) REVERT: Q 35 GLU cc_start: 0.8431 (tp30) cc_final: 0.8088 (mm-30) outliers start: 63 outliers final: 49 residues processed: 501 average time/residue: 1.5722 time to fit residues: 975.8283 Evaluate side-chains 512 residues out of total 4559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 455 time to evaluate : 5.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 857 SER Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain I residue 10 ASN Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 81 MET Chi-restraints excluded: chain K residue 136 THR Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain O residue 232 LEU Chi-restraints excluded: chain O residue 458 LYS Chi-restraints excluded: chain P residue 205 ASN Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain P residue 247 LEU Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain Q residue 139 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 323 optimal weight: 2.9990 chunk 433 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 375 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 407 optimal weight: 10.0000 chunk 170 optimal weight: 5.9990 chunk 418 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1262 GLN A1284 ASN B 702 GLN ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 ASN D 64 ASN D 69 ASN D 133 HIS E 101 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.105873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.077743 restraints weight = 68424.569| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.06 r_work: 0.3024 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 43226 Z= 0.429 Angle : 0.602 12.062 58650 Z= 0.311 Chirality : 0.046 0.240 6624 Planarity : 0.004 0.046 7322 Dihedral : 10.663 143.174 6455 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.54 % Allowed : 15.99 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.12), residues: 5094 helix: 1.47 (0.12), residues: 1894 sheet: -0.05 (0.20), residues: 695 loop : -0.36 (0.12), residues: 2505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 201 HIS 0.011 0.001 HIS A 427 PHE 0.027 0.002 PHE A 610 TYR 0.019 0.002 TYR J 44 ARG 0.008 0.000 ARG B 874 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15364.70 seconds wall clock time: 276 minutes 46.67 seconds (16606.67 seconds total)