Starting phenix.real_space_refine on Mon Sep 14 16:01:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7aoz_11848/09_2026/7aoz_11848_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7aoz_11848/09_2026/7aoz_11848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7aoz_11848/09_2026/7aoz_11848_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7aoz_11848/09_2026/7aoz_11848_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7aoz_11848/09_2026/7aoz_11848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7aoz_11848/09_2026/7aoz_11848.map" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 4 6.06 5 P 41 5.49 5 Mg 1 5.21 5 S 142 5.16 5 C 20102 2.51 5 N 5254 2.21 5 O 5968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31512 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 10188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1268, 10188 Classifications: {'peptide': 1268} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 1223} Chain: "B" Number of atoms: 9091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 9091 Classifications: {'peptide': 1129} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1076} Chain breaks: 2 Chain: "C" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2484 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 9, 'TRANS': 294} Chain: "E" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1495 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 8, 'TRANS': 175} Chain: "F" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 849 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "G" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1192 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 3, 'TRANS': 149} Chain breaks: 1 Chain: "I" Number of atoms: 3903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3903 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 443} Chain breaks: 3 Chain: "J" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 490 Classifications: {'peptide': 61} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 58} Chain: "N" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 327 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "P" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 108 Classifications: {'RNA': 5} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4} Chain: "S" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 952 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 114} 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: "T" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 428 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain breaks: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "I" 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 360 SG CYS A 49 88.906 103.054 62.445 1.00 93.69 S ATOM 382 SG CYS A 52 92.632 103.229 61.685 1.00 87.66 S ATOM 434 SG CYS A 59 91.146 99.994 63.072 1.00 85.61 S ATOM 694 SG CYS A 90 75.431 100.324 109.399 1.00113.59 S ATOM 718 SG CYS A 93 76.899 103.755 110.294 1.00116.72 S ATOM 1016 SG CYS A 130 76.654 101.059 112.924 1.00119.32 S ATOM 1059 SG CYS A 135 73.507 102.695 111.733 1.00122.90 S ATOM 18688 SG CYS B1087 99.163 104.548 76.572 1.00 74.24 S ATOM 18711 SG CYS B1090 95.648 103.339 77.448 1.00 75.71 S ATOM 18800 SG CYS B1103 96.039 105.895 74.870 1.00 76.68 S ATOM 18825 SG CYS B1106 96.715 106.919 78.411 1.00 78.28 S ATOM 27059 SG CYS I 326 101.623 96.083 38.599 1.00153.19 S ATOM 27372 SG CYS I 363 99.580 92.819 39.498 1.00135.23 S ATOM 27396 SG CYS I 366 102.989 93.435 41.068 1.00134.35 S Time building chain proxies: 6.01, per 1000 atoms: 0.19 Number of scatterers: 31512 At special positions: 0 Unit cell: (162.716, 152.081, 154.208, 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 4 29.99 S 142 16.00 P 41 15.00 Mg 1 11.99 O 5968 8.00 N 5254 7.00 C 20102 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS J 7 " - pdb=" SG CYS J 39 " distance=2.04 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: 2.86 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1302 " pdb="ZN ZN A1302 " - pdb=" NE2 HIS A 62 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 52 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 59 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 49 " pdb=" ZN A1303 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 135 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 93 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 90 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1103 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1090 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1106 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1087 " pdb=" ZN I 801 " pdb="ZN ZN I 801 " - pdb=" ND1 HIS I 328 " pdb="ZN ZN I 801 " - pdb=" SG CYS I 366 " pdb="ZN ZN I 801 " - pdb=" SG CYS I 363 " pdb="ZN ZN I 801 " - pdb=" SG CYS I 326 " Number of angles added : 18 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7228 Finding SS restraints... Secondary structure from input PDB file: 151 helices and 46 sheets defined 41.6% alpha, 15.3% beta 16 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 3.25 Creating SS restraints... Processing helix chain 'A' and resid 13 through 19 Processing helix chain 'A' and resid 78 through 87 Processing helix chain 'A' and resid 113 through 126 Processing helix chain 'A' and resid 161 through 171 removed outlier: 3.691A pdb=" N ILE A 165 " --> pdb=" O PRO A 161 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER A 171 " --> pdb=" O GLN A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 176 through 181 Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 218 through 233 Processing helix chain 'A' and resid 236 through 249 removed outlier: 3.874A pdb=" N ILE A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 253 Processing helix chain 'A' and resid 261 through 267 removed outlier: 3.853A pdb=" N ILE A 265 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 304 through 311 Processing helix chain 'A' and resid 321 through 331 Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 428 through 438 Processing helix chain 'A' and resid 460 through 471 Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'A' and resid 485 through 488 removed outlier: 4.053A pdb=" N ARG A 488 " --> pdb=" O LYS A 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 485 through 488' Processing helix chain 'A' and resid 499 through 508 removed outlier: 3.574A pdb=" N ILE A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.884A pdb=" N VAL A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 549 Processing helix chain 'A' and resid 550 through 573 Processing helix chain 'A' and resid 577 through 582 removed outlier: 3.715A pdb=" N LEU A 581 " --> pdb=" O THR A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 615 Processing helix chain 'A' and resid 622 through 656 Processing helix chain 'A' and resid 659 through 668 Processing helix chain 'A' and resid 672 through 681 Processing helix chain 'A' and resid 711 through 715 Processing helix chain 'A' and resid 727 through 764 Processing helix chain 'A' and resid 809 through 821 Processing helix chain 'A' and resid 841 through 846 removed outlier: 3.806A pdb=" N VAL A 844 " --> pdb=" O ASN A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 877 Processing helix chain 'A' and resid 882 through 893 removed outlier: 3.588A pdb=" N GLU A 886 " --> pdb=" O ILE A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 919 removed outlier: 3.620A pdb=" N THR A 919 " --> pdb=" O LYS A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 943 Processing helix chain 'A' and resid 944 through 946 No H-bonds generated for 'chain 'A' and resid 944 through 946' Processing helix chain 'A' and resid 960 through 970 Processing helix chain 'A' and resid 984 through 996 removed outlier: 4.071A pdb=" N LEU A 988 " --> pdb=" O ASP A 984 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 991 " --> pdb=" O LYS A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1004 Processing helix chain 'A' and resid 1024 through 1030 Processing helix chain 'A' and resid 1033 through 1048 removed outlier: 3.660A pdb=" N PHE A1047 " --> pdb=" O ARG A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1093 removed outlier: 3.555A pdb=" N ASN A1081 " --> pdb=" O PRO A1077 " (cutoff:3.500A) Proline residue: A1090 - end of helix Processing helix chain 'A' and resid 1131 through 1136 removed outlier: 4.089A pdb=" N SER A1135 " --> pdb=" O GLU A1132 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE A1136 " --> pdb=" O LEU A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1155 Processing helix chain 'A' and resid 1155 through 1170 Processing helix chain 'A' and resid 1175 through 1177 No H-bonds generated for 'chain 'A' and resid 1175 through 1177' Processing helix chain 'A' and resid 1178 through 1190 Processing helix chain 'A' and resid 1207 through 1215 Processing helix chain 'A' and resid 1218 through 1227 Processing helix chain 'A' and resid 1234 through 1241 Processing helix chain 'A' and resid 1247 through 1252 removed outlier: 3.705A pdb=" N TYR A1252 " --> pdb=" O THR A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1258 through 1263 Processing helix chain 'B' and resid 9 through 17 Processing helix chain 'B' and resid 28 through 43 removed outlier: 4.603A pdb=" N PHE B 33 " --> pdb=" O ARG B 29 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLN B 34 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 51 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 233 through 241 Processing helix chain 'B' and resid 244 through 253 removed outlier: 3.712A pdb=" N ILE B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 278 removed outlier: 3.861A pdb=" N LEU B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 298 Processing helix chain 'B' and resid 307 through 314 removed outlier: 3.763A pdb=" N ASN B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 344 removed outlier: 3.509A pdb=" N LYS B 327 " --> pdb=" O PRO B 323 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 348 removed outlier: 3.524A pdb=" N TYR B 348 " --> pdb=" O THR B 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 345 through 348' Processing helix chain 'B' and resid 353 through 357 removed outlier: 3.545A pdb=" N CYS B 356 " --> pdb=" O SER B 353 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS B 357 " --> pdb=" O MET B 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 353 through 357' Processing helix chain 'B' and resid 361 through 391 removed outlier: 3.570A pdb=" N TYR B 365 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 416 Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 463 through 467 Processing helix chain 'B' and resid 498 through 515 Processing helix chain 'B' and resid 518 through 522 Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 544 through 558 removed outlier: 3.657A pdb=" N ASP B 551 " --> pdb=" O ASP B 547 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET B 558 " --> pdb=" O ARG B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 611 removed outlier: 4.150A pdb=" N SER B 609 " --> pdb=" O PRO B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 614 No H-bonds generated for 'chain 'B' and resid 612 through 614' Processing helix chain 'B' and resid 615 through 623 Processing helix chain 'B' and resid 632 through 637 removed outlier: 3.653A pdb=" N PHE B 637 " --> pdb=" O GLU B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 649 removed outlier: 3.660A pdb=" N MET B 649 " --> pdb=" O GLN B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 656 removed outlier: 3.666A pdb=" N LYS B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 669 removed outlier: 3.890A pdb=" N ASP B 669 " --> pdb=" O GLU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 676 Processing helix chain 'B' and resid 678 through 682 Processing helix chain 'B' and resid 683 through 695 removed outlier: 3.946A pdb=" N LYS B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 731 Processing helix chain 'B' and resid 762 through 767 Processing helix chain 'B' and resid 795 through 799 Processing helix chain 'B' and resid 898 through 902 removed outlier: 3.822A pdb=" N LEU B 902 " --> pdb=" O GLU B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 923 removed outlier: 3.728A pdb=" N PHE B 921 " --> pdb=" O SER B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 941 removed outlier: 4.043A pdb=" N LEU B 929 " --> pdb=" O THR B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 977 removed outlier: 3.565A pdb=" N TYR B 965 " --> pdb=" O SER B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 990 Processing helix chain 'B' and resid 1054 through 1065 removed outlier: 3.521A pdb=" N GLY B1065 " --> pdb=" O LEU B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1074 Processing helix chain 'B' and resid 1077 through 1081 removed outlier: 3.660A pdb=" N TYR B1081 " --> pdb=" O GLU B1078 " (cutoff:3.500A) Processing helix chain 'B' and resid 1103 through 1109 Processing helix chain 'B' and resid 1121 through 1134 Processing helix chain 'C' and resid 15 through 30 Processing helix chain 'C' and resid 48 through 58 removed outlier: 4.152A pdb=" N HIS C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 64 removed outlier: 5.353A pdb=" N MET C 62 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS C 63 " --> pdb=" O PRO C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 68 through 74 Processing helix chain 'C' and resid 95 through 99 Processing helix chain 'C' and resid 117 through 123 Processing helix chain 'C' and resid 152 through 157 removed outlier: 3.641A pdb=" N SER C 156 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS C 157 " --> pdb=" O ASP C 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 152 through 157' Processing helix chain 'C' and resid 162 through 177 Processing helix chain 'C' and resid 191 through 193 No H-bonds generated for 'chain 'C' and resid 191 through 193' Processing helix chain 'C' and resid 207 through 229 removed outlier: 3.909A pdb=" N CYS C 211 " --> pdb=" O ASP C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 265 Processing helix chain 'C' and resid 278 through 282 Processing helix chain 'C' and resid 283 through 304 Processing helix chain 'E' and resid 4 through 22 removed outlier: 3.963A pdb=" N TYR E 8 " --> pdb=" O TYR E 4 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU E 15 " --> pdb=" O LYS E 11 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR E 17 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 33 removed outlier: 3.625A pdb=" N LEU E 32 " --> pdb=" O ASN E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 101 removed outlier: 4.039A pdb=" N TYR E 101 " --> pdb=" O ASN E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 98 through 101' Processing helix chain 'E' and resid 117 through 129 Processing helix chain 'E' and resid 146 through 153 Processing helix chain 'F' and resid 63 through 75 removed outlier: 3.778A pdb=" N ARG F 75 " --> pdb=" O ARG F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 95 removed outlier: 3.543A pdb=" N ILE F 82 " --> pdb=" O SER F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 123 Processing helix chain 'F' and resid 140 through 142 No H-bonds generated for 'chain 'F' and resid 140 through 142' Processing helix chain 'F' and resid 143 through 161 Processing helix chain 'G' and resid 15 through 19 Processing helix chain 'G' and resid 22 through 36 Processing helix chain 'G' and resid 109 through 113 removed outlier: 3.529A pdb=" N SER G 112 " --> pdb=" O SER G 109 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY G 113 " --> pdb=" O ARG G 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 109 through 113' Processing helix chain 'I' and resid 105 through 119 Processing helix chain 'I' and resid 170 through 186 removed outlier: 6.075A pdb=" N ASP I 180 " --> pdb=" O GLU I 176 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N GLN I 181 " --> pdb=" O LYS I 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 254 through 264 removed outlier: 3.711A pdb=" N ASP I 258 " --> pdb=" O ASN I 254 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LYS I 261 " --> pdb=" O SER I 257 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL I 262 " --> pdb=" O ASP I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 267 No H-bonds generated for 'chain 'I' and resid 265 through 267' Processing helix chain 'I' and resid 269 through 272 Processing helix chain 'I' and resid 273 through 279 Processing helix chain 'I' and resid 283 through 285 No H-bonds generated for 'chain 'I' and resid 283 through 285' Processing helix chain 'I' and resid 286 through 291 Processing helix chain 'I' and resid 326 through 336 removed outlier: 3.887A pdb=" N ILE I 330 " --> pdb=" O CYS I 326 " (cutoff:3.500A) Processing helix chain 'I' and resid 341 through 353 Processing helix chain 'I' and resid 638 through 649 Processing helix chain 'I' and resid 688 through 694 removed outlier: 4.159A pdb=" N TYR I 692 " --> pdb=" O LEU I 688 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE I 693 " --> pdb=" O LYS I 689 " (cutoff:3.500A) Processing helix chain 'I' and resid 705 through 710 Processing helix chain 'I' and resid 723 through 742 Processing helix chain 'I' and resid 756 through 770 removed outlier: 3.571A pdb=" N LYS I 770 " --> pdb=" O ILE I 766 " (cutoff:3.500A) Processing helix chain 'I' and resid 773 through 793 removed outlier: 5.524A pdb=" N THR I 783 " --> pdb=" O ASP I 779 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ARG I 784 " --> pdb=" O GLU I 780 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 20 removed outlier: 3.631A pdb=" N LYS J 20 " --> pdb=" O HIS J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 36 removed outlier: 3.791A pdb=" N SER J 34 " --> pdb=" O ASP J 30 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS J 36 " --> pdb=" O LEU J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 47 Processing helix chain 'S' and resid 37 through 51 Processing helix chain 'S' and resid 59 through 63 Processing helix chain 'S' and resid 72 through 81 Processing helix chain 'S' and resid 82 through 85 Processing helix chain 'S' and resid 102 through 109 Processing helix chain 'S' and resid 112 through 131 removed outlier: 3.542A pdb=" N GLU S 116 " --> pdb=" O GLY S 112 " (cutoff:3.500A) Processing helix chain 'S' and resid 144 through 149 removed outlier: 3.562A pdb=" N PHE S 148 " --> pdb=" O TYR S 144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1229 through 1231 Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 24 removed outlier: 4.397A pdb=" N SER A 67 " --> pdb=" O ILE A 24 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 74 Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 144 removed outlier: 4.295A pdb=" N PHE A 151 " --> pdb=" O VAL A 160 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1027 through 1029 removed outlier: 7.351A pdb=" N ILE A 402 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL A 289 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ILE A 404 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N GLY A 291 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 312 through 316 removed outlier: 7.341A pdb=" N ALA A 369 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N VAL A 334 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 518 through 519 Processing sheet with id=AA8, first strand: chain 'A' and resid 684 through 685 Processing sheet with id=AA9, first strand: chain 'A' and resid 767 through 768 removed outlier: 6.456A pdb=" N VAL A 774 " --> pdb=" O ILE A 781 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 796 through 799 Processing sheet with id=AB2, first strand: chain 'A' and resid 825 through 826 Processing sheet with id=AB3, first strand: chain 'A' and resid 1106 through 1107 Processing sheet with id=AB4, first strand: chain 'A' and resid 998 through 999 Processing sheet with id=AB5, first strand: chain 'A' and resid 1008 through 1012 Processing sheet with id=AB6, first strand: chain 'F' and resid 137 through 138 removed outlier: 3.685A pdb=" N LYS A1253 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N TYR A1254 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 137 through 138 removed outlier: 3.685A pdb=" N LYS A1253 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N TYR A1254 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS G 47 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ALA G 77 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ALA G 45 " --> pdb=" O ALA G 77 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1264 through 1265 Processing sheet with id=AB9, first strand: chain 'B' and resid 54 through 59 removed outlier: 5.602A pdb=" N ILE B 68 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 57 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LYS B 104 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LYS B 116 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL B 106 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ILE B 114 " --> pdb=" O VAL B 106 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 74 through 76 Processing sheet with id=AC2, first strand: chain 'B' and resid 157 through 158 Processing sheet with id=AC3, first strand: chain 'B' and resid 359 through 360 removed outlier: 6.553A pdb=" N ASN B 169 " --> pdb=" O GLY B 445 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 179 through 184 removed outlier: 6.479A pdb=" N SER B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 493 through 494 Processing sheet with id=AC6, first strand: chain 'B' and resid 598 through 599 Processing sheet with id=AC7, first strand: chain 'B' and resid 535 through 540 removed outlier: 6.783A pdb=" N ILE B 530 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SER B 539 " --> pdb=" O PHE B 528 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N PHE B 528 " --> pdb=" O SER B 539 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE B 580 " --> pdb=" O PRO B 529 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N THR B 531 " --> pdb=" O ILE B 580 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.771A pdb=" N ILE B 772 " --> pdb=" O ARG B 875 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LYS B 864 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LEU B 861 " --> pdb=" O LYS B 864 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYS B 866 " --> pdb=" O VAL B 859 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL B 859 " --> pdb=" O LYS B 866 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARG B 868 " --> pdb=" O VAL B 857 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL B 857 " --> pdb=" O ARG B 868 " (cutoff:3.500A) removed outlier: 9.183A pdb=" N ASP J 61 " --> pdb=" O GLU B 855 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL B 857 " --> pdb=" O ASP J 61 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 723 through 724 Processing sheet with id=AD1, first strand: chain 'B' and resid 992 through 993 removed outlier: 6.528A pdb=" N ILE B 758 " --> pdb=" O ALA B 894 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N VAL B 896 " --> pdb=" O ILE B 758 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE B 760 " --> pdb=" O VAL B 896 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE B1009 " --> pdb=" O LEU B 746 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1086 through 1087 Processing sheet with id=AD3, first strand: chain 'B' and resid 1095 through 1097 Processing sheet with id=AD4, first strand: chain 'C' and resid 5 through 13 Processing sheet with id=AD5, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AD6, first strand: chain 'C' and resid 37 through 43 removed outlier: 5.418A pdb=" N GLY C 38 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N PHE C 144 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N VAL C 40 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE C 142 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 93 through 94 Processing sheet with id=AD8, first strand: chain 'C' and resid 251 through 253 Processing sheet with id=AD9, first strand: chain 'E' and resid 35 through 38 Processing sheet with id=AE1, first strand: chain 'E' and resid 63 through 65 removed outlier: 6.439A pdb=" N ILE E 83 " --> pdb=" O PHE E 95 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 113 through 115 removed outlier: 6.319A pdb=" N MET E 142 " --> pdb=" O ILE E 181 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 84 through 91 removed outlier: 4.411A pdb=" N VAL G 97 " --> pdb=" O LEU G 108 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL G 153 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ALA G 144 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU G 155 " --> pdb=" O MET G 142 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 114 through 116 Processing sheet with id=AE5, first strand: chain 'I' and resid 121 through 124 removed outlier: 4.447A pdb=" N TYR I 234 " --> pdb=" O ARG I 124 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 161 through 166 removed outlier: 6.400A pdb=" N ILE I 128 " --> pdb=" O LYS I 162 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE I 164 " --> pdb=" O ILE I 128 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ILE I 130 " --> pdb=" O ILE I 164 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N PHE I 166 " --> pdb=" O ILE I 130 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N VAL I 132 " --> pdb=" O PHE I 166 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 209 through 217 Processing sheet with id=AE8, first strand: chain 'I' and resid 355 through 357 Processing sheet with id=AE9, first strand: chain 'I' and resid 657 through 659 Processing sheet with id=AF1, first strand: chain 'I' and resid 667 through 670 removed outlier: 4.209A pdb=" N LYS I 667 " --> pdb=" O GLU I 678 " (cutoff:3.500A) 1295 hydrogen bonds defined for protein. 3558 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 6.68 Time building geometry restraints manager: 3.61 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: 9880 1.34 - 1.46: 7559 1.46 - 1.59: 14494 1.59 - 1.71: 79 1.71 - 1.83: 223 Bond restraints: 32235 Sorted by residual: bond pdb=" C3' DT N 56 " pdb=" C2' DT N 56 " ideal model delta sigma weight residual 1.516 1.570 -0.054 8.00e-03 1.56e+04 4.59e+01 bond pdb=" C3' DA N 53 " pdb=" C2' DA N 53 " ideal model delta sigma weight residual 1.516 1.569 -0.053 8.00e-03 1.56e+04 4.34e+01 bond pdb=" C3' DT N 55 " pdb=" C2' DT N 55 " ideal model delta sigma weight residual 1.516 1.568 -0.052 8.00e-03 1.56e+04 4.20e+01 bond pdb=" C3' DC N 52 " pdb=" C2' DC N 52 " ideal model delta sigma weight residual 1.516 1.567 -0.051 8.00e-03 1.56e+04 4.01e+01 bond pdb=" C3' DC N 51 " pdb=" C2' DC N 51 " ideal model delta sigma weight residual 1.516 1.566 -0.050 8.00e-03 1.56e+04 3.87e+01 ... (remaining 32230 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 42662 1.77 - 3.54: 879 3.54 - 5.31: 175 5.31 - 7.08: 29 7.08 - 8.84: 2 Bond angle restraints: 43747 Sorted by residual: angle pdb=" O4' DG N 60 " pdb=" C1' DG N 60 " pdb=" N9 DG N 60 " ideal model delta sigma weight residual 108.00 104.38 3.62 7.00e-01 2.04e+00 2.67e+01 angle pdb=" O5' DA T 14 " pdb=" C5' DA T 14 " pdb=" C4' DA T 14 " ideal model delta sigma weight residual 109.40 113.27 -3.87 8.00e-01 1.56e+00 2.34e+01 angle pdb=" N3 DT T 13 " pdb=" C4 DT T 13 " pdb=" O4 DT T 13 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.64e+01 angle pdb=" N3 DT N 47 " pdb=" C4 DT N 47 " pdb=" O4 DT N 47 " ideal model delta sigma weight residual 119.90 122.30 -2.40 6.00e-01 2.78e+00 1.60e+01 angle pdb=" N3 DT N 56 " pdb=" C4 DT N 56 " pdb=" O4 DT N 56 " ideal model delta sigma weight residual 119.90 122.27 -2.37 6.00e-01 2.78e+00 1.56e+01 ... (remaining 43742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 18159 17.98 - 35.96: 949 35.96 - 53.93: 273 53.93 - 71.91: 77 71.91 - 89.89: 8 Dihedral angle restraints: 19466 sinusoidal: 8272 harmonic: 11194 Sorted by residual: dihedral pdb=" CB CYS J 7 " pdb=" SG CYS J 7 " pdb=" SG CYS J 39 " pdb=" CB CYS J 39 " ideal model delta sinusoidal sigma weight residual -86.00 -159.60 73.60 1 1.00e+01 1.00e-02 6.89e+01 dihedral pdb=" CA VAL I 660 " pdb=" C VAL I 660 " pdb=" N HIS I 661 " pdb=" CA HIS I 661 " ideal model delta harmonic sigma weight residual 180.00 -143.67 -36.33 0 5.00e+00 4.00e-02 5.28e+01 dihedral pdb=" CA ILE A 458 " pdb=" C ILE A 458 " pdb=" N GLN A 459 " pdb=" CA GLN A 459 " ideal model delta harmonic sigma weight residual 180.00 147.71 32.29 0 5.00e+00 4.00e-02 4.17e+01 ... (remaining 19463 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2956 0.034 - 0.068: 1338 0.068 - 0.102: 366 0.102 - 0.136: 245 0.136 - 0.170: 47 Chirality restraints: 4952 Sorted by residual: chirality pdb=" CA ILE I 200 " pdb=" N ILE I 200 " pdb=" C ILE I 200 " pdb=" CB ILE I 200 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.25e-01 chirality pdb=" CA PHE A 938 " pdb=" N PHE A 938 " pdb=" C PHE A 938 " pdb=" CB PHE A 938 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.71e-01 chirality pdb=" CA ILE C 59 " pdb=" N ILE C 59 " pdb=" C ILE C 59 " pdb=" CB ILE C 59 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.68e-01 ... (remaining 4949 not shown) Planarity restraints: 5392 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 856 " 0.012 2.00e-02 2.50e+03 2.52e-02 6.35e+00 pdb=" C ARG B 856 " -0.044 2.00e-02 2.50e+03 pdb=" O ARG B 856 " 0.017 2.00e-02 2.50e+03 pdb=" N VAL B 857 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 938 " 0.021 2.00e-02 2.50e+03 1.84e-02 5.94e+00 pdb=" CG PHE A 938 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 938 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 938 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 938 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 938 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 938 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 316 " -0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO B 317 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 317 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 317 " -0.028 5.00e-02 4.00e+02 ... (remaining 5389 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 335 2.62 - 3.19: 28079 3.19 - 3.76: 47599 3.76 - 4.33: 70895 4.33 - 4.90: 115641 Nonbonded interactions: 262549 Sorted by model distance: nonbonded pdb=" OD1 ASP A 415 " pdb="MG MG A1301 " model vdw 2.045 2.170 nonbonded pdb=" OD1 ASP A 417 " pdb="MG MG A1301 " model vdw 2.071 2.170 nonbonded pdb=" OG SER A 98 " pdb=" OE1 GLU A 100 " model vdw 2.076 3.040 nonbonded pdb=" OH TYR A 783 " pdb=" OD2 ASP E 177 " model vdw 2.086 3.040 nonbonded pdb=" OG SER A 145 " pdb=" O LYS A 148 " model vdw 2.095 3.040 ... (remaining 262544 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: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 33.170 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 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 : 0.005 0.080 32252 Z= 0.292 Angle : 0.663 8.844 43767 Z= 0.379 Chirality : 0.047 0.170 4952 Planarity : 0.003 0.050 5392 Dihedral : 12.793 89.890 12235 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.42 % Allowed : 4.62 % Favored : 92.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.14), residues: 3752 helix: 0.94 (0.14), residues: 1365 sheet: -0.75 (0.21), residues: 536 loop : -0.87 (0.15), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 163 TYR 0.023 0.001 TYR S 134 PHE 0.042 0.002 PHE A 938 TRP 0.014 0.001 TRP A 365 HIS 0.005 0.001 HIS A 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.29 (32235) covalent geometry : angle 0.66146 / 0.38 (43747) SS BOND : bond 0.01003 / 0.53 ( 1) SS BOND : angle 2.13007 / 1.42 ( 2) hydrogen bonds : bond 0.13136 / 8.30 ( 1323) hydrogen bonds : angle 6.11959 / 4.32 ( 3638) metal coordination : bond 0.00640 / 0.38 ( 16) metal coordination : angle 2.25183 / 1.52 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 446 time to evaluate : 1.157 Fit side-chains revert: symmetry clash REVERT: A 7 VAL cc_start: 0.9438 (t) cc_final: 0.9222 (p) REVERT: A 122 LYS cc_start: 0.8655 (mtmt) cc_final: 0.8228 (ttmm) REVERT: A 155 LEU cc_start: 0.8466 (mp) cc_final: 0.8216 (mm) REVERT: A 156 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7338 (p0) REVERT: A 360 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6992 (pp) REVERT: B 65 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8325 (ptt90) REVERT: B 173 LYS cc_start: 0.8933 (mmmt) cc_final: 0.8686 (mttp) REVERT: B 395 TYR cc_start: 0.7241 (m-80) cc_final: 0.7038 (m-80) REVERT: B 422 SER cc_start: 0.3872 (OUTLIER) cc_final: 0.3544 (p) REVERT: B 506 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7550 (tm-30) REVERT: B 545 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8453 (pt) REVERT: B 600 MET cc_start: 0.8967 (mmm) cc_final: 0.8753 (mmp) REVERT: C 289 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8410 (tptm) REVERT: C 304 ARG cc_start: 0.7836 (ptp90) cc_final: 0.7559 (ptp90) REVERT: E 55 ASP cc_start: 0.8418 (p0) cc_final: 0.8138 (p0) REVERT: E 86 SER cc_start: 0.9300 (m) cc_final: 0.9051 (p) REVERT: G 20 THR cc_start: 0.9166 (OUTLIER) cc_final: 0.8958 (p) REVERT: G 46 LYS cc_start: 0.9140 (mtpt) cc_final: 0.8901 (mmmm) REVERT: G 142 MET cc_start: 0.8277 (mmp) cc_final: 0.7834 (ttt) REVERT: I 758 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8149 (tm-30) REVERT: S 42 GLU cc_start: 0.8626 (tt0) cc_final: 0.8379 (tp30) REVERT: S 78 TYR cc_start: 0.9172 (t80) cc_final: 0.8800 (t80) REVERT: S 93 SER cc_start: 0.9224 (m) cc_final: 0.8985 (p) REVERT: S 116 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7835 (mm-30) REVERT: S 118 LEU cc_start: 0.9296 (mt) cc_final: 0.9009 (mm) REVERT: S 150 VAL cc_start: 0.8011 (p) cc_final: 0.7791 (m) outliers start: 84 outliers final: 18 residues processed: 515 average time/residue: 0.7525 time to fit residues: 451.0907 Evaluate side-chains 293 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 267 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 289 LYS Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 117 PHE Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 758 GLU Chi-restraints excluded: chain S residue 110 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 HIS A 184 GLN A 188 ASN A 853 ASN E 65 ASN G 146 GLN I 181 GLN I 626 GLN I 735 ASN I 776 GLN J 51 GLN S 90 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.089621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.061980 restraints weight = 63890.016| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.43 r_work: 0.2711 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 32252 Z= 0.201 Angle : 0.618 10.797 43767 Z= 0.331 Chirality : 0.046 0.193 4952 Planarity : 0.004 0.047 5392 Dihedral : 11.260 59.913 4638 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.31 % Allowed : 10.24 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.14), residues: 3752 helix: 1.08 (0.14), residues: 1374 sheet: -0.68 (0.22), residues: 554 loop : -0.76 (0.15), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 110 TYR 0.020 0.001 TYR S 134 PHE 0.031 0.002 PHE A 938 TRP 0.037 0.002 TRP A1054 HIS 0.010 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 (32235) covalent geometry : angle 0.61612 / 0.33 (43747) SS BOND : bond 0.00485 / 0.26 ( 1) SS BOND : angle 3.52130 / 2.35 ( 2) hydrogen bonds : bond 0.05175 / 3.46 ( 1323) hydrogen bonds : angle 5.19247 / 3.65 ( 3638) metal coordination : bond 0.00946 / 0.72 ( 16) metal coordination : angle 2.39556 / 1.76 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 278 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8700 (pp) REVERT: A 156 ASP cc_start: 0.8432 (m-30) cc_final: 0.7490 (p0) REVERT: A 360 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7070 (pp) REVERT: A 1054 TRP cc_start: 0.8879 (p-90) cc_final: 0.8662 (p-90) REVERT: A 1062 ASP cc_start: 0.8164 (OUTLIER) cc_final: 0.7745 (t0) REVERT: B 65 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.6915 (ptm-80) REVERT: B 120 TYR cc_start: 0.6846 (t80) cc_final: 0.6556 (t80) REVERT: B 173 LYS cc_start: 0.9307 (mmmt) cc_final: 0.8880 (mttp) REVERT: B 395 TYR cc_start: 0.7451 (m-80) cc_final: 0.7196 (m-80) REVERT: B 422 SER cc_start: 0.5281 (OUTLIER) cc_final: 0.4670 (p) REVERT: B 506 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8327 (tm-30) REVERT: B 545 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8539 (pt) REVERT: B 600 MET cc_start: 0.9246 (mmm) cc_final: 0.9024 (mmp) REVERT: B 868 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.7630 (mtp85) REVERT: B 1158 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8901 (mp) REVERT: C 239 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7815 (tp30) REVERT: E 18 GLU cc_start: 0.9313 (tp30) cc_final: 0.8706 (tp30) REVERT: E 86 SER cc_start: 0.9408 (m) cc_final: 0.9128 (p) REVERT: E 141 LYS cc_start: 0.9098 (mttt) cc_final: 0.8854 (mttm) REVERT: E 174 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.7474 (tm-30) REVERT: F 103 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7871 (tm-30) REVERT: G 20 THR cc_start: 0.9263 (OUTLIER) cc_final: 0.9036 (p) REVERT: G 46 LYS cc_start: 0.9299 (mtpt) cc_final: 0.9053 (mmmt) REVERT: I 305 ASP cc_start: 0.8669 (m-30) cc_final: 0.7918 (p0) REVERT: I 313 GLU cc_start: 0.8356 (pm20) cc_final: 0.8113 (pm20) REVERT: J 34 SER cc_start: 0.8849 (OUTLIER) cc_final: 0.8443 (p) REVERT: S 42 GLU cc_start: 0.8944 (tt0) cc_final: 0.8559 (tp30) REVERT: S 46 GLU cc_start: 0.8102 (pt0) cc_final: 0.7866 (pt0) REVERT: S 69 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7520 (tm-30) REVERT: S 93 SER cc_start: 0.9381 (m) cc_final: 0.9029 (p) REVERT: S 97 ASN cc_start: 0.7099 (OUTLIER) cc_final: 0.6831 (m-40) REVERT: S 116 GLU cc_start: 0.8304 (mm-30) cc_final: 0.8023 (tp30) REVERT: S 127 CYS cc_start: 0.8600 (m) cc_final: 0.8147 (m) REVERT: S 129 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8410 (ttpt) REVERT: S 150 VAL cc_start: 0.8025 (p) cc_final: 0.7793 (m) outliers start: 80 outliers final: 25 residues processed: 340 average time/residue: 0.7248 time to fit residues: 288.4230 Evaluate side-chains 297 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 258 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1062 ASP Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 868 ARG Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain E residue 174 GLU Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 117 PHE Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain S residue 97 ASN Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain S residue 129 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 286 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 212 optimal weight: 2.9990 chunk 348 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 275 optimal weight: 5.9990 chunk 356 optimal weight: 7.9990 chunk 232 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 HIS A 184 GLN A 853 ASN A 947 HIS B 325 GLN G 146 GLN I 181 GLN I 626 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.089012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.061126 restraints weight = 63867.549| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 2.45 r_work: 0.2691 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 32252 Z= 0.213 Angle : 0.602 9.793 43767 Z= 0.320 Chirality : 0.046 0.196 4952 Planarity : 0.004 0.042 5392 Dihedral : 11.242 59.441 4622 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.65 % Allowed : 10.79 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.14), residues: 3752 helix: 1.15 (0.14), residues: 1377 sheet: -0.52 (0.22), residues: 543 loop : -0.82 (0.15), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 90 TYR 0.020 0.001 TYR S 134 PHE 0.032 0.002 PHE A 938 TRP 0.024 0.001 TRP A1054 HIS 0.012 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.21 (32235) covalent geometry : angle 0.60000 / 0.32 (43747) SS BOND : bond 0.00770 / 0.41 ( 1) SS BOND : angle 2.19633 / 1.46 ( 2) hydrogen bonds : bond 0.04845 / 3.25 ( 1323) hydrogen bonds : angle 5.00886 / 3.52 ( 3638) metal coordination : bond 0.00824 / 0.59 ( 16) metal coordination : angle 2.65928 / 1.95 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 271 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8655 (pp) REVERT: A 136 MET cc_start: 0.8945 (tpp) cc_final: 0.8668 (tpp) REVERT: A 246 GLU cc_start: 0.9199 (pt0) cc_final: 0.8895 (pt0) REVERT: A 347 ARG cc_start: 0.8407 (tmt170) cc_final: 0.8063 (tmt-80) REVERT: A 360 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7089 (pp) REVERT: A 398 GLU cc_start: 0.8716 (pm20) cc_final: 0.8493 (mt-10) REVERT: B 65 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.6959 (ptm-80) REVERT: B 120 TYR cc_start: 0.6923 (t80) cc_final: 0.6674 (t80) REVERT: B 173 LYS cc_start: 0.9307 (mmmt) cc_final: 0.8906 (mttp) REVERT: B 395 TYR cc_start: 0.7422 (m-80) cc_final: 0.7193 (m-80) REVERT: B 422 SER cc_start: 0.5017 (OUTLIER) cc_final: 0.4564 (p) REVERT: B 506 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8308 (tm-30) REVERT: B 868 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.7707 (mtp85) REVERT: B 977 ASN cc_start: 0.8884 (t0) cc_final: 0.8655 (t0) REVERT: B 1158 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9112 (mp) REVERT: C 239 GLU cc_start: 0.8248 (tp30) cc_final: 0.7800 (tp30) REVERT: E 18 GLU cc_start: 0.9330 (tp30) cc_final: 0.8690 (tp30) REVERT: E 141 LYS cc_start: 0.9101 (mttt) cc_final: 0.8864 (mttm) REVERT: F 103 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7683 (tm-30) REVERT: G 20 THR cc_start: 0.9218 (OUTLIER) cc_final: 0.8969 (p) REVERT: G 142 MET cc_start: 0.9058 (mmp) cc_final: 0.8742 (mmm) REVERT: J 34 SER cc_start: 0.8857 (OUTLIER) cc_final: 0.8452 (p) REVERT: S 42 GLU cc_start: 0.8923 (tt0) cc_final: 0.8544 (tp30) REVERT: S 69 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7453 (tm-30) REVERT: S 93 SER cc_start: 0.9383 (m) cc_final: 0.9136 (p) REVERT: S 106 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.7327 (mtm) REVERT: S 116 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7676 (mm-30) REVERT: S 127 CYS cc_start: 0.8660 (m) cc_final: 0.8219 (m) REVERT: S 150 VAL cc_start: 0.8092 (p) cc_final: 0.7874 (m) outliers start: 92 outliers final: 41 residues processed: 348 average time/residue: 0.7186 time to fit residues: 293.6116 Evaluate side-chains 305 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 255 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1062 ASP Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 868 ARG Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 117 PHE Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 261 LYS Chi-restraints excluded: chain I residue 319 VAL Chi-restraints excluded: chain I residue 661 HIS Chi-restraints excluded: chain J residue 26 LYS Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain S residue 106 MET Chi-restraints excluded: chain S residue 122 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 342 optimal weight: 8.9990 chunk 243 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 200 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 236 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 237 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 174 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 HIS A 853 ASN G 146 GLN I 181 GLN I 626 GLN ** S 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.090283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.062537 restraints weight = 63233.118| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.45 r_work: 0.2728 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32252 Z= 0.129 Angle : 0.553 10.922 43767 Z= 0.295 Chirality : 0.044 0.197 4952 Planarity : 0.004 0.045 5392 Dihedral : 11.131 59.872 4621 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.16 % Allowed : 11.68 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.14), residues: 3752 helix: 1.30 (0.14), residues: 1374 sheet: -0.44 (0.22), residues: 552 loop : -0.78 (0.15), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 110 TYR 0.019 0.001 TYR S 134 PHE 0.029 0.001 PHE A 938 TRP 0.032 0.001 TRP A1054 HIS 0.012 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (32235) covalent geometry : angle 0.55000 / 0.29 (43747) SS BOND : bond 0.02820 / 1.48 ( 1) SS BOND : angle 3.32766 / 2.22 ( 2) hydrogen bonds : bond 0.04210 / 2.84 ( 1323) hydrogen bonds : angle 4.84133 / 3.39 ( 3638) metal coordination : bond 0.00585 / 0.41 ( 16) metal coordination : angle 2.46534 / 1.80 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 276 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8686 (pp) REVERT: A 246 GLU cc_start: 0.9162 (pt0) cc_final: 0.8843 (pt0) REVERT: A 347 ARG cc_start: 0.8417 (tmt170) cc_final: 0.8098 (tmt-80) REVERT: A 360 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.7053 (pp) REVERT: B 59 PHE cc_start: 0.8559 (m-80) cc_final: 0.7843 (m-80) REVERT: B 120 TYR cc_start: 0.6874 (t80) cc_final: 0.6611 (t80) REVERT: B 160 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8122 (ptpt) REVERT: B 173 LYS cc_start: 0.9335 (mmmt) cc_final: 0.8893 (mttp) REVERT: B 395 TYR cc_start: 0.7399 (m-80) cc_final: 0.7138 (m-80) REVERT: B 422 SER cc_start: 0.4694 (OUTLIER) cc_final: 0.4365 (p) REVERT: B 506 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8254 (tm-30) REVERT: B 544 MET cc_start: 0.9285 (mtp) cc_final: 0.9075 (mtm) REVERT: B 977 ASN cc_start: 0.8912 (t0) cc_final: 0.8694 (t0) REVERT: B 1158 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9104 (mp) REVERT: C 239 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7741 (tp30) REVERT: E 18 GLU cc_start: 0.9323 (tp30) cc_final: 0.8722 (tp30) REVERT: E 141 LYS cc_start: 0.9093 (mttt) cc_final: 0.8848 (mttm) REVERT: F 81 GLU cc_start: 0.9249 (OUTLIER) cc_final: 0.8959 (mp0) REVERT: F 103 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7667 (tm-30) REVERT: G 20 THR cc_start: 0.9216 (OUTLIER) cc_final: 0.8938 (p) REVERT: G 142 MET cc_start: 0.9028 (mmp) cc_final: 0.8703 (mmm) REVERT: I 305 ASP cc_start: 0.8662 (m-30) cc_final: 0.7808 (p0) REVERT: I 790 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8469 (mpp) REVERT: J 34 SER cc_start: 0.8850 (OUTLIER) cc_final: 0.8425 (p) REVERT: S 39 ASP cc_start: 0.8674 (m-30) cc_final: 0.8352 (m-30) REVERT: S 42 GLU cc_start: 0.8957 (tt0) cc_final: 0.8445 (pt0) REVERT: S 69 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7382 (tm-30) REVERT: S 84 ASN cc_start: 0.9076 (m-40) cc_final: 0.8856 (m110) REVERT: S 93 SER cc_start: 0.9333 (m) cc_final: 0.9107 (p) REVERT: S 103 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7386 (mm) REVERT: S 106 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7325 (mtm) REVERT: S 116 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7628 (mm-30) REVERT: S 118 LEU cc_start: 0.9087 (mt) cc_final: 0.8879 (mm) REVERT: S 127 CYS cc_start: 0.8634 (m) cc_final: 0.8210 (m) REVERT: S 150 VAL cc_start: 0.8145 (p) cc_final: 0.7925 (m) outliers start: 75 outliers final: 36 residues processed: 338 average time/residue: 0.7181 time to fit residues: 285.0992 Evaluate side-chains 306 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 258 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1062 ASP Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 117 PHE Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 261 LYS Chi-restraints excluded: chain I residue 319 VAL Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 661 HIS Chi-restraints excluded: chain I residue 790 MET Chi-restraints excluded: chain J residue 26 LYS Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 106 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 124 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 244 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 267 optimal weight: 0.8980 chunk 123 optimal weight: 0.3980 chunk 271 optimal weight: 0.9980 chunk 215 optimal weight: 6.9990 chunk 283 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 HIS G 146 GLN I 181 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.090828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.063012 restraints weight = 63574.407| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.47 r_work: 0.2737 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32252 Z= 0.120 Angle : 0.540 10.387 43767 Z= 0.287 Chirality : 0.043 0.210 4952 Planarity : 0.004 0.072 5392 Dihedral : 11.033 59.786 4616 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.16 % Allowed : 12.03 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.14), residues: 3752 helix: 1.38 (0.14), residues: 1384 sheet: -0.39 (0.22), residues: 540 loop : -0.74 (0.15), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG S 83 TYR 0.019 0.001 TYR S 134 PHE 0.029 0.001 PHE A 938 TRP 0.031 0.001 TRP A1054 HIS 0.012 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (32235) covalent geometry : angle 0.53770 / 0.29 (43747) SS BOND : bond 0.00574 / 0.30 ( 1) SS BOND : angle 2.14422 / 1.43 ( 2) hydrogen bonds : bond 0.04018 / 2.71 ( 1323) hydrogen bonds : angle 4.74407 / 3.32 ( 3638) metal coordination : bond 0.00469 / 0.29 ( 16) metal coordination : angle 2.30717 / 1.68 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 280 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8712 (pp) REVERT: A 246 GLU cc_start: 0.9170 (pt0) cc_final: 0.8828 (pt0) REVERT: A 347 ARG cc_start: 0.8395 (tmt170) cc_final: 0.8072 (tmt-80) REVERT: A 360 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.7068 (pp) REVERT: B 59 PHE cc_start: 0.8575 (m-80) cc_final: 0.7910 (m-80) REVERT: B 120 TYR cc_start: 0.6841 (t80) cc_final: 0.6595 (t80) REVERT: B 160 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8105 (ptpt) REVERT: B 173 LYS cc_start: 0.9328 (mmmt) cc_final: 0.8895 (mttp) REVERT: B 395 TYR cc_start: 0.7265 (m-80) cc_final: 0.7043 (m-80) REVERT: B 422 SER cc_start: 0.4663 (OUTLIER) cc_final: 0.4303 (p) REVERT: B 460 ARG cc_start: 0.8623 (mtt90) cc_final: 0.8415 (mtt90) REVERT: B 506 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8274 (tm-30) REVERT: B 544 MET cc_start: 0.9268 (mtp) cc_final: 0.9060 (mtm) REVERT: B 545 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8541 (pt) REVERT: B 977 ASN cc_start: 0.8927 (t0) cc_final: 0.8719 (t0) REVERT: B 1158 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9027 (mp) REVERT: C 239 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7781 (tp30) REVERT: E 18 GLU cc_start: 0.9321 (tp30) cc_final: 0.8747 (tp30) REVERT: E 141 LYS cc_start: 0.9105 (mttt) cc_final: 0.8879 (mttm) REVERT: F 81 GLU cc_start: 0.9240 (OUTLIER) cc_final: 0.8974 (mp0) REVERT: F 103 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7630 (tm-30) REVERT: G 20 THR cc_start: 0.9215 (OUTLIER) cc_final: 0.8938 (p) REVERT: G 86 ARG cc_start: 0.8247 (ttm110) cc_final: 0.7982 (mtp-110) REVERT: G 142 MET cc_start: 0.9034 (mmp) cc_final: 0.8728 (mmm) REVERT: I 305 ASP cc_start: 0.8673 (m-30) cc_final: 0.7841 (p0) REVERT: S 42 GLU cc_start: 0.8955 (tt0) cc_final: 0.8523 (pt0) REVERT: S 69 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7404 (tm-30) REVERT: S 77 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8811 (mm-30) REVERT: S 93 SER cc_start: 0.9333 (m) cc_final: 0.9097 (p) REVERT: S 103 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7366 (mm) REVERT: S 106 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7215 (mtm) REVERT: S 114 GLU cc_start: 0.8682 (pm20) cc_final: 0.8464 (pm20) REVERT: S 116 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7618 (mm-30) REVERT: S 118 LEU cc_start: 0.9062 (mt) cc_final: 0.8857 (mm) REVERT: S 127 CYS cc_start: 0.8643 (m) cc_final: 0.8213 (m) REVERT: S 150 VAL cc_start: 0.8162 (p) cc_final: 0.7933 (m) outliers start: 75 outliers final: 34 residues processed: 338 average time/residue: 0.7188 time to fit residues: 285.3463 Evaluate side-chains 303 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 258 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1062 ASP Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 117 PHE Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 319 VAL Chi-restraints excluded: chain I residue 661 HIS Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 106 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 289 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 266 optimal weight: 4.9990 chunk 231 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 209 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 146 GLN I 181 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.089314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.061520 restraints weight = 63876.046| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.43 r_work: 0.2698 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 32252 Z= 0.196 Angle : 0.577 9.510 43767 Z= 0.306 Chirality : 0.045 0.202 4952 Planarity : 0.004 0.058 5392 Dihedral : 11.062 59.882 4616 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.28 % Allowed : 12.32 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.14), residues: 3752 helix: 1.39 (0.14), residues: 1378 sheet: -0.37 (0.23), residues: 542 loop : -0.73 (0.15), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 110 TYR 0.017 0.001 TYR S 134 PHE 0.033 0.001 PHE A 938 TRP 0.033 0.001 TRP A1054 HIS 0.004 0.001 HIS A 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 (32235) covalent geometry : angle 0.57452 / 0.31 (43747) SS BOND : bond 0.00758 / 0.40 ( 1) SS BOND : angle 2.05451 / 1.37 ( 2) hydrogen bonds : bond 0.04415 / 2.97 ( 1323) hydrogen bonds : angle 4.77694 / 3.34 ( 3638) metal coordination : bond 0.00654 / 0.45 ( 16) metal coordination : angle 2.48337 / 1.80 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 267 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8339 (ptp) cc_final: 0.8115 (pmt) REVERT: A 91 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8741 (pp) REVERT: A 246 GLU cc_start: 0.9170 (pt0) cc_final: 0.8807 (pt0) REVERT: A 347 ARG cc_start: 0.8403 (tmt170) cc_final: 0.7992 (tpt90) REVERT: A 360 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.7088 (pp) REVERT: A 1128 MET cc_start: 0.9121 (tpp) cc_final: 0.8892 (tpt) REVERT: A 1202 LYS cc_start: 0.8794 (mmtp) cc_final: 0.8558 (mmtm) REVERT: B 59 PHE cc_start: 0.8574 (m-80) cc_final: 0.7888 (m-80) REVERT: B 120 TYR cc_start: 0.7018 (t80) cc_final: 0.6801 (t80) REVERT: B 173 LYS cc_start: 0.9307 (mmmt) cc_final: 0.8882 (mttp) REVERT: B 395 TYR cc_start: 0.7261 (m-80) cc_final: 0.7028 (m-80) REVERT: B 422 SER cc_start: 0.4738 (OUTLIER) cc_final: 0.4382 (p) REVERT: B 506 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8206 (tm-30) REVERT: B 544 MET cc_start: 0.9320 (mtp) cc_final: 0.9106 (mtm) REVERT: C 239 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7794 (tp30) REVERT: E 18 GLU cc_start: 0.9329 (tp30) cc_final: 0.8670 (tp30) REVERT: E 141 LYS cc_start: 0.9083 (mttt) cc_final: 0.8834 (mttm) REVERT: F 81 GLU cc_start: 0.9249 (OUTLIER) cc_final: 0.8987 (mp0) REVERT: F 103 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7666 (tm-30) REVERT: G 20 THR cc_start: 0.9171 (OUTLIER) cc_final: 0.8895 (p) REVERT: G 142 MET cc_start: 0.8996 (mmp) cc_final: 0.8604 (mmm) REVERT: I 305 ASP cc_start: 0.8656 (m-30) cc_final: 0.7796 (p0) REVERT: S 42 GLU cc_start: 0.8914 (tt0) cc_final: 0.8516 (tp30) REVERT: S 69 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7547 (tm-30) REVERT: S 77 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8800 (mm-30) REVERT: S 93 SER cc_start: 0.9338 (m) cc_final: 0.9110 (p) REVERT: S 103 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7404 (mm) REVERT: S 106 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7279 (mtm) REVERT: S 116 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7584 (mm-30) REVERT: S 127 CYS cc_start: 0.8630 (m) cc_final: 0.8200 (m) outliers start: 79 outliers final: 47 residues processed: 332 average time/residue: 0.6790 time to fit residues: 265.3960 Evaluate side-chains 317 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 262 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1062 ASP Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 117 PHE Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 319 VAL Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 661 HIS Chi-restraints excluded: chain J residue 26 LYS Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 106 MET Chi-restraints excluded: chain S residue 128 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 110 optimal weight: 0.9990 chunk 179 optimal weight: 1.9990 chunk 202 optimal weight: 0.9990 chunk 233 optimal weight: 0.0070 chunk 145 optimal weight: 3.9990 chunk 374 optimal weight: 9.9990 chunk 266 optimal weight: 3.9990 chunk 260 optimal weight: 4.9990 chunk 243 optimal weight: 1.9990 chunk 136 optimal weight: 0.0170 chunk 220 optimal weight: 4.9990 overall best weight: 0.8042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 HIS G 146 GLN I 181 GLN I 626 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.091151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.063248 restraints weight = 63842.749| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.49 r_work: 0.2739 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32252 Z= 0.121 Angle : 0.546 11.866 43767 Z= 0.290 Chirality : 0.044 0.323 4952 Planarity : 0.004 0.096 5392 Dihedral : 10.987 59.978 4616 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.05 % Allowed : 12.69 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.14), residues: 3752 helix: 1.47 (0.14), residues: 1376 sheet: -0.31 (0.23), residues: 539 loop : -0.71 (0.15), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG S 83 TYR 0.015 0.001 TYR C 170 PHE 0.027 0.001 PHE A 938 TRP 0.036 0.001 TRP A1054 HIS 0.011 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (32235) covalent geometry : angle 0.54286 / 0.29 (43747) SS BOND : bond 0.00345 / 0.18 ( 1) SS BOND : angle 4.44834 / 2.97 ( 2) hydrogen bonds : bond 0.03975 / 2.69 ( 1323) hydrogen bonds : angle 4.69476 / 3.28 ( 3638) metal coordination : bond 0.00443 / 0.26 ( 16) metal coordination : angle 2.37787 / 1.72 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 275 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8763 (pp) REVERT: A 136 MET cc_start: 0.8890 (tpp) cc_final: 0.8269 (mtm) REVERT: A 248 ASP cc_start: 0.8703 (t0) cc_final: 0.8403 (t0) REVERT: A 347 ARG cc_start: 0.8383 (tmt170) cc_final: 0.7980 (tpt90) REVERT: A 360 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.6993 (pp) REVERT: B 59 PHE cc_start: 0.8609 (m-80) cc_final: 0.7955 (m-80) REVERT: B 74 LYS cc_start: 0.9389 (mmmm) cc_final: 0.9043 (mmtm) REVERT: B 120 TYR cc_start: 0.6858 (t80) cc_final: 0.6651 (t80) REVERT: B 160 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.8062 (ptpt) REVERT: B 173 LYS cc_start: 0.9293 (mmmt) cc_final: 0.8872 (mttp) REVERT: B 306 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7747 (pm20) REVERT: B 395 TYR cc_start: 0.7241 (m-80) cc_final: 0.7006 (m-80) REVERT: B 422 SER cc_start: 0.4689 (OUTLIER) cc_final: 0.4316 (p) REVERT: B 460 ARG cc_start: 0.8587 (mtt90) cc_final: 0.8364 (mtt90) REVERT: B 506 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8217 (tm-30) REVERT: B 544 MET cc_start: 0.9270 (mtp) cc_final: 0.9069 (mtm) REVERT: B 545 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8566 (pt) REVERT: C 231 MET cc_start: 0.8325 (tpt) cc_final: 0.8036 (ppp) REVERT: C 239 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7765 (tp30) REVERT: E 18 GLU cc_start: 0.9329 (tp30) cc_final: 0.8733 (tp30) REVERT: E 141 LYS cc_start: 0.9103 (mttt) cc_final: 0.8860 (mttm) REVERT: F 81 GLU cc_start: 0.9226 (OUTLIER) cc_final: 0.8962 (mp0) REVERT: F 103 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7669 (tm-30) REVERT: G 20 THR cc_start: 0.9192 (OUTLIER) cc_final: 0.8916 (p) REVERT: G 86 ARG cc_start: 0.7974 (ttm110) cc_final: 0.7757 (mtp-110) REVERT: G 142 MET cc_start: 0.9030 (mmp) cc_final: 0.8665 (mmm) REVERT: I 305 ASP cc_start: 0.8650 (m-30) cc_final: 0.7820 (p0) REVERT: S 42 GLU cc_start: 0.8909 (tt0) cc_final: 0.8488 (pt0) REVERT: S 62 ASN cc_start: 0.7324 (m-40) cc_final: 0.7012 (m-40) REVERT: S 69 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7537 (tm-30) REVERT: S 77 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8769 (mm-30) REVERT: S 106 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7408 (mtm) REVERT: S 116 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7583 (mm-30) REVERT: S 127 CYS cc_start: 0.8665 (m) cc_final: 0.8239 (m) outliers start: 71 outliers final: 42 residues processed: 328 average time/residue: 0.7148 time to fit residues: 275.4511 Evaluate side-chains 317 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 265 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1062 ASP Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 117 PHE Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 319 VAL Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 661 HIS Chi-restraints excluded: chain J residue 26 LYS Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 106 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 159 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 366 optimal weight: 2.9990 chunk 234 optimal weight: 0.9990 chunk 347 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 327 optimal weight: 10.0000 chunk 274 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 146 GLN I 181 GLN I 626 GLN S 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.089490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.061702 restraints weight = 63911.942| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.43 r_work: 0.2703 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 32252 Z= 0.186 Angle : 0.575 11.594 43767 Z= 0.304 Chirality : 0.044 0.224 4952 Planarity : 0.004 0.072 5392 Dihedral : 10.964 59.998 4612 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.88 % Allowed : 13.24 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.14), residues: 3752 helix: 1.47 (0.14), residues: 1374 sheet: -0.30 (0.23), residues: 530 loop : -0.75 (0.15), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 90 TYR 0.022 0.001 TYR S 134 PHE 0.032 0.001 PHE A 938 TRP 0.038 0.001 TRP A1054 HIS 0.004 0.001 HIS A 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (32235) covalent geometry : angle 0.57283 / 0.30 (43747) SS BOND : bond 0.01290 / 0.68 ( 1) SS BOND : angle 3.79172 / 2.53 ( 2) hydrogen bonds : bond 0.04302 / 2.90 ( 1323) hydrogen bonds : angle 4.71901 / 3.30 ( 3638) metal coordination : bond 0.00596 / 0.39 ( 16) metal coordination : angle 2.32746 / 1.70 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 266 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8775 (pp) REVERT: A 136 MET cc_start: 0.8906 (tpp) cc_final: 0.8267 (mtm) REVERT: A 246 GLU cc_start: 0.9180 (pt0) cc_final: 0.8814 (pt0) REVERT: A 248 ASP cc_start: 0.8728 (t0) cc_final: 0.8432 (t0) REVERT: A 347 ARG cc_start: 0.8393 (tmt170) cc_final: 0.7982 (tpt90) REVERT: A 360 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6982 (pp) REVERT: A 1128 MET cc_start: 0.9171 (tpp) cc_final: 0.8829 (tpt) REVERT: A 1202 LYS cc_start: 0.8823 (mmtp) cc_final: 0.8561 (mmtm) REVERT: B 59 PHE cc_start: 0.8588 (m-80) cc_final: 0.7913 (m-80) REVERT: B 120 TYR cc_start: 0.6918 (t80) cc_final: 0.6678 (t80) REVERT: B 173 LYS cc_start: 0.9270 (mmmt) cc_final: 0.8858 (mttp) REVERT: B 395 TYR cc_start: 0.7238 (m-80) cc_final: 0.6941 (m-80) REVERT: B 422 SER cc_start: 0.4712 (OUTLIER) cc_final: 0.4361 (p) REVERT: B 506 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8227 (tm-30) REVERT: B 544 MET cc_start: 0.9313 (mtp) cc_final: 0.9100 (mtm) REVERT: C 231 MET cc_start: 0.8402 (tpt) cc_final: 0.8078 (ppp) REVERT: C 239 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7736 (tp30) REVERT: E 18 GLU cc_start: 0.9322 (tp30) cc_final: 0.8725 (tp30) REVERT: E 138 ARG cc_start: 0.8793 (mtt-85) cc_final: 0.8290 (mmm-85) REVERT: E 141 LYS cc_start: 0.9084 (mttt) cc_final: 0.8841 (mttm) REVERT: F 81 GLU cc_start: 0.9236 (OUTLIER) cc_final: 0.8985 (mp0) REVERT: F 103 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7738 (tm-30) REVERT: G 20 THR cc_start: 0.9175 (OUTLIER) cc_final: 0.8900 (p) REVERT: G 86 ARG cc_start: 0.7953 (ttm110) cc_final: 0.7704 (mtp-110) REVERT: G 142 MET cc_start: 0.9031 (mmp) cc_final: 0.8637 (mmm) REVERT: I 305 ASP cc_start: 0.8674 (m-30) cc_final: 0.7804 (p0) REVERT: I 336 MET cc_start: 0.2837 (mmp) cc_final: 0.2602 (tpt) REVERT: S 42 GLU cc_start: 0.8938 (tt0) cc_final: 0.8606 (pt0) REVERT: S 62 ASN cc_start: 0.7277 (m-40) cc_final: 0.6580 (m-40) REVERT: S 69 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7509 (tm-30) REVERT: S 77 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8718 (mm-30) REVERT: S 106 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7416 (mtm) REVERT: S 116 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7742 (mp0) REVERT: S 127 CYS cc_start: 0.8665 (m) cc_final: 0.8232 (m) outliers start: 65 outliers final: 50 residues processed: 317 average time/residue: 0.6986 time to fit residues: 260.0507 Evaluate side-chains 322 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 265 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1062 ASP Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 117 PHE Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 319 VAL Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 661 HIS Chi-restraints excluded: chain J residue 26 LYS Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 106 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 376 optimal weight: 30.0000 chunk 206 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 chunk 237 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 170 optimal weight: 0.3980 chunk 319 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 271 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 HIS A 140 GLN B 47 HIS F 161 GLN G 146 GLN I 626 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.091157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.063371 restraints weight = 63512.493| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.47 r_work: 0.2745 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32252 Z= 0.119 Angle : 0.552 12.957 43767 Z= 0.291 Chirality : 0.044 0.547 4952 Planarity : 0.004 0.075 5392 Dihedral : 10.891 59.504 4612 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.90 % Allowed : 13.21 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.14), residues: 3752 helix: 1.51 (0.14), residues: 1374 sheet: -0.30 (0.23), residues: 534 loop : -0.70 (0.15), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 110 TYR 0.021 0.001 TYR S 134 PHE 0.028 0.001 PHE A 938 TRP 0.047 0.001 TRP A1054 HIS 0.012 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (32235) covalent geometry : angle 0.54931 / 0.29 (43747) SS BOND : bond 0.00803 / 0.42 ( 1) SS BOND : angle 2.96434 / 1.98 ( 2) hydrogen bonds : bond 0.03934 / 2.66 ( 1323) hydrogen bonds : angle 4.66305 / 3.26 ( 3638) metal coordination : bond 0.00444 / 0.27 ( 16) metal coordination : angle 2.29219 / 1.65 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 274 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8790 (pp) REVERT: A 136 MET cc_start: 0.8876 (tpp) cc_final: 0.8238 (mtm) REVERT: A 248 ASP cc_start: 0.8676 (t0) cc_final: 0.8391 (t0) REVERT: A 347 ARG cc_start: 0.8352 (tmt170) cc_final: 0.7942 (tpt90) REVERT: A 360 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6666 (pp) REVERT: A 1062 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.7718 (t70) REVERT: A 1128 MET cc_start: 0.9169 (tpp) cc_final: 0.8780 (tpt) REVERT: B 59 PHE cc_start: 0.8614 (m-80) cc_final: 0.7977 (m-80) REVERT: B 160 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8054 (ptpt) REVERT: B 173 LYS cc_start: 0.9260 (mmmt) cc_final: 0.8845 (mttp) REVERT: B 306 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7730 (pm20) REVERT: B 395 TYR cc_start: 0.7243 (m-80) cc_final: 0.6958 (m-80) REVERT: B 422 SER cc_start: 0.4653 (OUTLIER) cc_final: 0.4289 (p) REVERT: B 460 ARG cc_start: 0.8604 (mtt90) cc_final: 0.8378 (mtt90) REVERT: B 478 ARG cc_start: 0.7437 (mtm110) cc_final: 0.7186 (mtm110) REVERT: B 506 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8181 (tm-30) REVERT: B 544 MET cc_start: 0.9275 (mtp) cc_final: 0.9074 (mtm) REVERT: B 545 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8572 (pt) REVERT: C 239 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7759 (tp30) REVERT: E 18 GLU cc_start: 0.9329 (tp30) cc_final: 0.8736 (tp30) REVERT: E 138 ARG cc_start: 0.8798 (mtt-85) cc_final: 0.8283 (mmm-85) REVERT: E 141 LYS cc_start: 0.9119 (mttt) cc_final: 0.8898 (mttm) REVERT: F 81 GLU cc_start: 0.9214 (OUTLIER) cc_final: 0.8953 (mp0) REVERT: F 103 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7653 (tm-30) REVERT: G 20 THR cc_start: 0.9193 (OUTLIER) cc_final: 0.8920 (p) REVERT: G 86 ARG cc_start: 0.7918 (ttm110) cc_final: 0.7697 (mtp-110) REVERT: G 142 MET cc_start: 0.9027 (mmp) cc_final: 0.8651 (mmm) REVERT: I 305 ASP cc_start: 0.8653 (m-30) cc_final: 0.7817 (p0) REVERT: I 626 GLN cc_start: 0.6962 (tt0) cc_final: 0.6702 (tt0) REVERT: S 42 GLU cc_start: 0.8911 (tt0) cc_final: 0.8618 (pt0) REVERT: S 62 ASN cc_start: 0.7274 (m-40) cc_final: 0.6563 (m-40) REVERT: S 69 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7466 (tm-30) REVERT: S 77 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8764 (mm-30) REVERT: S 116 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7716 (mp0) REVERT: S 127 CYS cc_start: 0.8702 (m) cc_final: 0.8273 (m) outliers start: 66 outliers final: 45 residues processed: 323 average time/residue: 0.7089 time to fit residues: 269.1600 Evaluate side-chains 317 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 262 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1062 ASP Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 117 PHE Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 258 ASP Chi-restraints excluded: chain I residue 319 VAL Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 661 HIS Chi-restraints excluded: chain J residue 26 LYS Chi-restraints excluded: chain S residue 66 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 359 optimal weight: 2.9990 chunk 204 optimal weight: 0.5980 chunk 237 optimal weight: 3.9990 chunk 124 optimal weight: 0.0010 chunk 307 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 282 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 256 optimal weight: 0.0870 overall best weight: 1.3368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 385 HIS G 146 GLN I 181 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.090584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.062616 restraints weight = 63715.272| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.47 r_work: 0.2729 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 32252 Z= 0.153 Angle : 0.569 12.099 43767 Z= 0.298 Chirality : 0.044 0.245 4952 Planarity : 0.004 0.087 5392 Dihedral : 10.872 59.594 4612 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.76 % Allowed : 13.47 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.14), residues: 3752 helix: 1.53 (0.14), residues: 1370 sheet: -0.33 (0.23), residues: 536 loop : -0.70 (0.15), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG C 90 TYR 0.041 0.001 TYR S 78 PHE 0.030 0.001 PHE A 938 TRP 0.052 0.002 TRP A1054 HIS 0.003 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (32235) covalent geometry : angle 0.56678 / 0.30 (43747) SS BOND : bond 0.00932 / 0.49 ( 1) SS BOND : angle 2.96734 / 1.98 ( 2) hydrogen bonds : bond 0.04080 / 2.75 ( 1323) hydrogen bonds : angle 4.65570 / 3.25 ( 3638) metal coordination : bond 0.00522 / 0.33 ( 16) metal coordination : angle 2.23029 / 1.61 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 262 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8796 (pp) REVERT: A 136 MET cc_start: 0.8884 (tpp) cc_final: 0.8240 (mtm) REVERT: A 248 ASP cc_start: 0.8677 (t0) cc_final: 0.8389 (t0) REVERT: A 347 ARG cc_start: 0.8352 (tmt170) cc_final: 0.7943 (tpt90) REVERT: A 360 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6732 (pp) REVERT: A 1062 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.7771 (t70) REVERT: A 1128 MET cc_start: 0.9137 (tpp) cc_final: 0.8749 (tpt) REVERT: B 59 PHE cc_start: 0.8585 (m-80) cc_final: 0.7929 (m-80) REVERT: B 160 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8085 (ptpt) REVERT: B 173 LYS cc_start: 0.9267 (mmmt) cc_final: 0.8852 (mttp) REVERT: B 306 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7755 (pm20) REVERT: B 395 TYR cc_start: 0.7199 (m-80) cc_final: 0.6973 (m-80) REVERT: B 422 SER cc_start: 0.4652 (OUTLIER) cc_final: 0.4320 (p) REVERT: B 460 ARG cc_start: 0.8597 (mtt90) cc_final: 0.8366 (mtt90) REVERT: B 506 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8160 (tm-30) REVERT: C 239 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7762 (tp30) REVERT: E 18 GLU cc_start: 0.9329 (tp30) cc_final: 0.8706 (tp30) REVERT: E 138 ARG cc_start: 0.8816 (mtt-85) cc_final: 0.8307 (mmm-85) REVERT: E 141 LYS cc_start: 0.9125 (mttt) cc_final: 0.8910 (mttm) REVERT: F 81 GLU cc_start: 0.9217 (OUTLIER) cc_final: 0.8963 (mp0) REVERT: F 103 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7671 (tm-30) REVERT: G 20 THR cc_start: 0.9189 (OUTLIER) cc_final: 0.8925 (p) REVERT: G 86 ARG cc_start: 0.7960 (ttm110) cc_final: 0.7709 (mtp-110) REVERT: G 142 MET cc_start: 0.9019 (mmp) cc_final: 0.8642 (mmm) REVERT: I 179 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7956 (tm) REVERT: I 305 ASP cc_start: 0.8685 (m-30) cc_final: 0.7828 (p0) REVERT: I 313 GLU cc_start: 0.8430 (pm20) cc_final: 0.7988 (mp0) REVERT: S 42 GLU cc_start: 0.8888 (tt0) cc_final: 0.8593 (pt0) REVERT: S 62 ASN cc_start: 0.7238 (m-40) cc_final: 0.6546 (m-40) REVERT: S 69 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7392 (tm-30) REVERT: S 77 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8742 (mm-30) REVERT: S 116 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7744 (mp0) REVERT: S 127 CYS cc_start: 0.8720 (m) cc_final: 0.8281 (m) outliers start: 61 outliers final: 48 residues processed: 312 average time/residue: 0.7069 time to fit residues: 259.9833 Evaluate side-chains 314 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 256 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1062 ASP Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 117 PHE Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 319 VAL Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 661 HIS Chi-restraints excluded: chain J residue 26 LYS Chi-restraints excluded: chain S residue 66 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 251 optimal weight: 4.9990 chunk 193 optimal weight: 3.9990 chunk 341 optimal weight: 0.0570 chunk 355 optimal weight: 0.8980 chunk 368 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 chunk 233 optimal weight: 2.9990 chunk 232 optimal weight: 5.9990 chunk 322 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 HIS B 408 ASN I 626 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.089896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.061875 restraints weight = 64001.653| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 2.47 r_work: 0.2712 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 32252 Z= 0.184 Angle : 0.586 13.496 43767 Z= 0.307 Chirality : 0.045 0.418 4952 Planarity : 0.004 0.085 5392 Dihedral : 10.895 59.840 4612 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.85 % Allowed : 13.44 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.14), residues: 3752 helix: 1.47 (0.14), residues: 1374 sheet: -0.30 (0.23), residues: 525 loop : -0.72 (0.15), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG G 110 TYR 0.024 0.001 TYR S 120 PHE 0.032 0.001 PHE A 938 TRP 0.053 0.002 TRP A1054 HIS 0.012 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (32235) covalent geometry : angle 0.58379 / 0.31 (43747) SS BOND : bond 0.01169 / 0.62 ( 1) SS BOND : angle 2.86370 / 1.91 ( 2) hydrogen bonds : bond 0.04288 / 2.89 ( 1323) hydrogen bonds : angle 4.68961 / 3.28 ( 3638) metal coordination : bond 0.00595 / 0.39 ( 16) metal coordination : angle 2.31144 / 1.67 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11382.88 seconds wall clock time: 194 minutes 25.07 seconds (11665.07 seconds total)