Starting phenix.real_space_refine on Fri Mar 6 14:12:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7aoz_11848/03_2026/7aoz_11848_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7aoz_11848/03_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_11848/03_2026/7aoz_11848_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7aoz_11848/03_2026/7aoz_11848_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7aoz_11848/03_2026/7aoz_11848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7aoz_11848/03_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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 6.81, per 1000 atoms: 0.22 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: 2.72 Conformation dependent library (CDL) restraints added in 1.2 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: 3.79 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: 6.47 Time building geometry restraints manager: 3.41 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 55 " pdb=" O3' DT N 55 " ideal model delta sigma weight residual 1.422 1.515 -0.093 3.00e-02 1.11e+03 9.62e+00 bond pdb=" C3' DA N 53 " pdb=" O3' DA N 53 " ideal model delta sigma weight residual 1.422 1.514 -0.092 3.00e-02 1.11e+03 9.50e+00 bond pdb=" C3' DC N 54 " pdb=" O3' DC N 54 " ideal model delta sigma weight residual 1.422 1.512 -0.090 3.00e-02 1.11e+03 9.09e+00 bond pdb=" C3' DG N 57 " pdb=" O3' DG N 57 " ideal model delta sigma weight residual 1.422 1.512 -0.090 3.00e-02 1.11e+03 8.96e+00 bond pdb=" C3' DA N 48 " pdb=" O3' DA N 48 " ideal model delta sigma weight residual 1.422 1.512 -0.090 3.00e-02 1.11e+03 8.93e+00 ... (remaining 32230 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 42732 1.77 - 3.54: 813 3.54 - 5.31: 170 5.31 - 7.08: 30 7.08 - 8.84: 2 Bond angle restraints: 43747 Sorted by residual: angle pdb=" C5' DC N 51 " pdb=" C4' DC N 51 " pdb=" O4' DC N 51 " ideal model delta sigma weight residual 109.40 103.02 6.38 1.50e+00 4.44e-01 1.81e+01 angle pdb=" C5' DC N 52 " pdb=" C4' DC N 52 " pdb=" O4' DC N 52 " ideal model delta sigma weight residual 109.40 103.18 6.22 1.50e+00 4.44e-01 1.72e+01 angle pdb=" C5' DG N 57 " pdb=" C4' DG N 57 " pdb=" O4' DG N 57 " ideal model delta sigma weight residual 109.40 103.18 6.22 1.50e+00 4.44e-01 1.72e+01 angle pdb=" C5' DA N 49 " pdb=" C4' DA N 49 " pdb=" O4' DA N 49 " ideal model delta sigma weight residual 109.40 103.48 5.92 1.50e+00 4.44e-01 1.56e+01 angle pdb=" C5' DC N 50 " pdb=" C4' DC N 50 " pdb=" O4' DC N 50 " ideal model delta sigma weight residual 109.40 103.56 5.84 1.50e+00 4.44e-01 1.51e+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 - 0.046: 3700 0.046 - 0.093: 902 0.093 - 0.139: 306 0.139 - 0.186: 33 0.186 - 0.232: 11 Chirality restraints: 4952 Sorted by residual: chirality pdb=" C3' DT N 55 " pdb=" C4' DT N 55 " pdb=" O3' DT N 55 " pdb=" C2' DT N 55 " both_signs ideal model delta sigma weight residual False -2.66 -2.89 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" C3' DT N 56 " pdb=" C4' DT N 56 " pdb=" O3' DT N 56 " pdb=" C2' DT N 56 " both_signs ideal model delta sigma weight residual False -2.66 -2.88 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C3' DA N 53 " pdb=" C4' DA N 53 " pdb=" O3' DA N 53 " pdb=" C2' DA N 53 " both_signs ideal model delta sigma weight residual False -2.66 -2.88 0.22 2.00e-01 2.50e+01 1.19e+00 ... (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: 2.280 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: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 33.620 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 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:5.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 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 0.093 32252 Z= 0.201 Angle : 0.653 8.844 43767 Z= 0.353 Chirality : 0.047 0.232 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 covalent geometry : bond 0.00472 (32235) covalent geometry : angle 0.65105 (43747) SS BOND : bond 0.01003 ( 1) SS BOND : angle 2.13007 ( 2) hydrogen bonds : bond 0.13136 ( 1323) hydrogen bonds : angle 6.11959 ( 3638) metal coordination : bond 0.00640 ( 16) metal coordination : angle 2.25183 ( 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 : 0.961 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: 0.7818 time to fit residues: 465.7646 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 : 1.163 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 114 HIS A 184 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 ASN G 146 GLN I 181 GLN I 626 GLN I 735 ASN I 776 GLN S 90 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.089487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.061723 restraints weight = 63938.663| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 2.45 r_work: 0.2706 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 32252 Z= 0.198 Angle : 0.605 10.993 43767 Z= 0.321 Chirality : 0.046 0.196 4952 Planarity : 0.004 0.046 5392 Dihedral : 11.343 60.874 4638 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.63 % Allowed : 9.95 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.10 (0.14), residues: 3752 helix: 1.14 (0.14), residues: 1377 sheet: -0.64 (0.22), residues: 554 loop : -0.78 (0.15), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 90 TYR 0.021 0.001 TYR S 134 PHE 0.031 0.002 PHE A 938 TRP 0.034 0.001 TRP A1054 HIS 0.009 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00463 (32235) covalent geometry : angle 0.60224 (43747) SS BOND : bond 0.00530 ( 1) SS BOND : angle 2.76758 ( 2) hydrogen bonds : bond 0.04808 ( 1323) hydrogen bonds : angle 5.01967 ( 3638) metal coordination : bond 0.00776 ( 16) metal coordination : angle 2.63324 ( 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 369 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 278 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8703 (pp) REVERT: A 149 VAL cc_start: 0.8683 (m) cc_final: 0.8333 (t) REVERT: A 156 ASP cc_start: 0.8445 (m-30) cc_final: 0.7500 (p0) REVERT: A 246 GLU cc_start: 0.9135 (pt0) cc_final: 0.8841 (pt0) REVERT: A 360 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7072 (pp) REVERT: B 65 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.6959 (ptm-80) REVERT: B 120 TYR cc_start: 0.6905 (t80) cc_final: 0.6546 (t80) REVERT: B 121 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7545 (tm-30) REVERT: B 173 LYS cc_start: 0.9297 (mmmt) cc_final: 0.8872 (mttp) REVERT: B 395 TYR cc_start: 0.7454 (m-80) cc_final: 0.7222 (m-80) REVERT: B 422 SER cc_start: 0.5106 (OUTLIER) cc_final: 0.4587 (p) REVERT: B 478 ARG cc_start: 0.7714 (mtm110) cc_final: 0.7502 (mtm110) REVERT: B 506 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8289 (tm-30) REVERT: B 600 MET cc_start: 0.9261 (mmm) cc_final: 0.9056 (mmp) REVERT: B 868 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.7696 (mtp85) REVERT: B 1158 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9113 (mp) REVERT: C 239 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7801 (tp30) REVERT: E 18 GLU cc_start: 0.9332 (tp30) cc_final: 0.8733 (tp30) REVERT: E 40 GLU cc_start: 0.7546 (pp20) cc_final: 0.7323 (pp20) REVERT: F 103 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7854 (tm-30) REVERT: G 20 THR cc_start: 0.9258 (OUTLIER) cc_final: 0.9028 (p) REVERT: G 46 LYS cc_start: 0.9293 (mtpt) cc_final: 0.9039 (mmmt) REVERT: I 305 ASP cc_start: 0.8657 (m-30) cc_final: 0.7886 (p0) REVERT: J 34 SER cc_start: 0.8869 (OUTLIER) cc_final: 0.8462 (p) REVERT: S 42 GLU cc_start: 0.8933 (tt0) cc_final: 0.8571 (tp30) REVERT: S 69 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7635 (tm-30) REVERT: S 93 SER cc_start: 0.9389 (m) cc_final: 0.9133 (p) REVERT: S 97 ASN cc_start: 0.7151 (OUTLIER) cc_final: 0.6841 (m-40) REVERT: S 116 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7723 (mm-30) REVERT: S 118 LEU cc_start: 0.9144 (mt) cc_final: 0.8841 (mm) REVERT: S 127 CYS cc_start: 0.8597 (m) cc_final: 0.8177 (m) REVERT: S 150 VAL cc_start: 0.8054 (p) cc_final: 0.7839 (m) outliers start: 91 outliers final: 34 residues processed: 353 average time/residue: 0.7507 time to fit residues: 308.3468 Evaluate side-chains 294 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 250 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 971 SER Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1062 ASP Chi-restraints excluded: chain A residue 1064 ASP Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 162 SER 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 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 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 211 CYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain E residue 54 ILE 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 202 ILE 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 J residue 34 SER Chi-restraints excluded: chain S residue 97 ASN Chi-restraints excluded: chain S residue 110 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 286 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 212 optimal weight: 0.7980 chunk 348 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 171 optimal weight: 0.6980 chunk 275 optimal weight: 1.9990 chunk 356 optimal weight: 0.9990 chunk 232 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 ASN B 325 GLN E 65 ASN G 146 GLN I 181 GLN I 626 GLN I 776 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.090343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.062699 restraints weight = 63486.634| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.45 r_work: 0.2732 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1740 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= 0.138 Angle : 0.551 11.403 43767 Z= 0.292 Chirality : 0.044 0.211 4952 Planarity : 0.004 0.043 5392 Dihedral : 11.101 59.560 4623 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.25 % Allowed : 11.08 % Favored : 86.67 % 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: 0.05 (0.14), residues: 3752 helix: 1.30 (0.14), residues: 1376 sheet: -0.50 (0.22), residues: 554 loop : -0.75 (0.15), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 110 TYR 0.020 0.001 TYR S 134 PHE 0.030 0.001 PHE A 938 TRP 0.028 0.001 TRP A1054 HIS 0.009 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00314 (32235) covalent geometry : angle 0.54831 (43747) SS BOND : bond 0.00645 ( 1) SS BOND : angle 1.56963 ( 2) hydrogen bonds : bond 0.04213 ( 1323) hydrogen bonds : angle 4.82818 ( 3638) metal coordination : bond 0.00624 ( 16) metal coordination : angle 2.43419 ( 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 352 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 274 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8679 (pp) REVERT: A 148 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8501 (ptmt) REVERT: A 149 VAL cc_start: 0.8550 (m) cc_final: 0.8284 (t) REVERT: A 246 GLU cc_start: 0.9131 (pt0) cc_final: 0.8778 (pt0) REVERT: A 347 ARG cc_start: 0.8355 (tmt170) cc_final: 0.8028 (tmt-80) REVERT: A 360 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.7017 (pp) REVERT: A 398 GLU cc_start: 0.8777 (pm20) cc_final: 0.8463 (pt0) REVERT: A 1062 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7598 (t0) REVERT: B 59 PHE cc_start: 0.8544 (m-80) cc_final: 0.7813 (m-80) REVERT: B 120 TYR cc_start: 0.6906 (t80) cc_final: 0.6578 (t80) REVERT: B 160 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8107 (ptpt) REVERT: B 173 LYS cc_start: 0.9312 (mmmt) cc_final: 0.8896 (mttp) REVERT: B 306 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7726 (pm20) REVERT: B 395 TYR cc_start: 0.7380 (m-80) cc_final: 0.7131 (m-80) REVERT: B 422 SER cc_start: 0.4706 (OUTLIER) cc_final: 0.4390 (p) REVERT: B 506 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8234 (tm-30) REVERT: B 977 ASN cc_start: 0.8928 (t0) cc_final: 0.8656 (t0) REVERT: B 1043 GLU cc_start: 0.8642 (tt0) cc_final: 0.8142 (pm20) REVERT: B 1158 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9109 (mp) REVERT: C 239 GLU cc_start: 0.8194 (tp30) cc_final: 0.7760 (tp30) REVERT: E 18 GLU cc_start: 0.9324 (tp30) cc_final: 0.8754 (tp30) REVERT: E 40 GLU cc_start: 0.7712 (pp20) cc_final: 0.7509 (pp20) REVERT: F 81 GLU cc_start: 0.9255 (OUTLIER) cc_final: 0.8979 (mp0) REVERT: F 103 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7763 (tm-30) REVERT: G 20 THR cc_start: 0.9217 (OUTLIER) cc_final: 0.8934 (p) REVERT: G 46 LYS cc_start: 0.9310 (mtpt) cc_final: 0.9094 (mmmt) REVERT: G 142 MET cc_start: 0.9029 (mmp) cc_final: 0.8764 (mmm) REVERT: I 305 ASP cc_start: 0.8658 (m-30) cc_final: 0.7845 (p0) REVERT: J 34 SER cc_start: 0.8840 (OUTLIER) cc_final: 0.8417 (p) REVERT: S 39 ASP cc_start: 0.8728 (m-30) cc_final: 0.8355 (m-30) REVERT: S 42 GLU cc_start: 0.8982 (tt0) cc_final: 0.8493 (pt0) REVERT: S 69 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7379 (tm-30) REVERT: S 77 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8827 (mm-30) REVERT: S 93 SER cc_start: 0.9349 (m) cc_final: 0.9126 (p) REVERT: S 97 ASN cc_start: 0.7058 (OUTLIER) cc_final: 0.6770 (m-40) REVERT: S 103 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7569 (mm) REVERT: S 106 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.7251 (mtm) REVERT: S 116 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7630 (mm-30) REVERT: S 127 CYS cc_start: 0.8646 (m) cc_final: 0.8213 (m) REVERT: S 150 VAL cc_start: 0.8142 (p) cc_final: 0.7925 (m) outliers start: 78 outliers final: 29 residues processed: 338 average time/residue: 0.7507 time to fit residues: 295.1918 Evaluate side-chains 297 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 254 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 148 LYS 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 971 SER Chi-restraints excluded: chain A residue 1062 ASP 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 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 234 VAL 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 626 GLN Chi-restraints excluded: chain I residue 661 HIS Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain S residue 81 ASP Chi-restraints excluded: chain S residue 97 ASN Chi-restraints excluded: chain S residue 103 LEU 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: 3.9990 chunk 193 optimal weight: 0.9980 chunk 200 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 236 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 237 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 ASN A 947 HIS G 146 GLN I 181 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 = 0.3386 r_free = 0.3386 target = 0.089090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.061359 restraints weight = 63571.648| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 2.44 r_work: 0.2699 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 32252 Z= 0.200 Angle : 0.574 9.947 43767 Z= 0.304 Chirality : 0.045 0.206 4952 Planarity : 0.004 0.061 5392 Dihedral : 11.009 59.971 4616 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.63 % Allowed : 11.22 % 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: 1.26 (0.14), residues: 1384 sheet: -0.41 (0.23), residues: 531 loop : -0.77 (0.15), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG S 83 TYR 0.019 0.001 TYR S 134 PHE 0.032 0.002 PHE A 938 TRP 0.029 0.001 TRP A1054 HIS 0.009 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00467 (32235) covalent geometry : angle 0.57103 (43747) SS BOND : bond 0.00460 ( 1) SS BOND : angle 3.64536 ( 2) hydrogen bonds : bond 0.04517 ( 1323) hydrogen bonds : angle 4.82636 ( 3638) metal coordination : bond 0.00836 ( 16) metal coordination : angle 2.72615 ( 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 357 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 266 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8766 (pp) REVERT: A 148 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8502 (ptmt) REVERT: A 149 VAL cc_start: 0.8613 (m) cc_final: 0.8312 (t) REVERT: A 246 GLU cc_start: 0.9139 (pt0) cc_final: 0.8788 (pt0) REVERT: A 347 ARG cc_start: 0.8416 (tmt170) cc_final: 0.8059 (tmt-80) REVERT: A 360 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7111 (pp) REVERT: A 398 GLU cc_start: 0.8767 (pm20) cc_final: 0.8543 (pt0) REVERT: A 1062 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.7787 (t0) REVERT: B 59 PHE cc_start: 0.8593 (m-80) cc_final: 0.7891 (m-80) REVERT: B 120 TYR cc_start: 0.7024 (t80) cc_final: 0.6818 (t80) REVERT: B 121 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7494 (tm-30) REVERT: B 173 LYS cc_start: 0.9321 (mmmt) cc_final: 0.8911 (mttp) REVERT: B 395 TYR cc_start: 0.7335 (m-80) cc_final: 0.7026 (m-80) REVERT: B 422 SER cc_start: 0.4823 (OUTLIER) cc_final: 0.4479 (p) REVERT: B 506 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8215 (tm-30) REVERT: B 977 ASN cc_start: 0.8981 (t0) cc_final: 0.8744 (t0) REVERT: B 979 LYS cc_start: 0.8810 (pmmt) cc_final: 0.8525 (pmmt) REVERT: B 1158 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9153 (mp) REVERT: C 239 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7822 (tp30) REVERT: E 18 GLU cc_start: 0.9335 (tp30) cc_final: 0.8759 (tp30) REVERT: E 120 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8785 (mt-10) REVERT: F 81 GLU cc_start: 0.9278 (OUTLIER) cc_final: 0.9031 (mp0) REVERT: F 103 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7703 (tm-30) REVERT: G 20 THR cc_start: 0.9235 (OUTLIER) cc_final: 0.8956 (p) REVERT: G 142 MET cc_start: 0.9060 (mmp) cc_final: 0.8728 (mmm) REVERT: I 179 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7943 (tm) REVERT: I 305 ASP cc_start: 0.8662 (m-30) cc_final: 0.7835 (p0) REVERT: J 34 SER cc_start: 0.8886 (OUTLIER) cc_final: 0.8499 (p) REVERT: S 42 GLU cc_start: 0.8959 (tt0) cc_final: 0.8477 (pt0) REVERT: S 67 LYS cc_start: 0.8797 (tmmt) cc_final: 0.8581 (tptt) REVERT: S 69 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7563 (tm-30) REVERT: S 77 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8840 (mm-30) REVERT: S 93 SER cc_start: 0.9346 (m) cc_final: 0.9135 (p) REVERT: S 97 ASN cc_start: 0.7162 (OUTLIER) cc_final: 0.6899 (m-40) REVERT: S 106 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.7404 (mtm) REVERT: S 116 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7635 (mm-30) REVERT: S 127 CYS cc_start: 0.8709 (m) cc_final: 0.8290 (m) outliers start: 91 outliers final: 44 residues processed: 339 average time/residue: 0.7040 time to fit residues: 279.6161 Evaluate side-chains 315 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 256 time to evaluate : 1.246 ------------------------------------------------------------------------------- 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 148 LYS 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 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 121 GLU 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 225 THR 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 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 E residue 120 GLU 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 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 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 34 SER Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 81 ASP Chi-restraints excluded: chain S residue 97 ASN Chi-restraints excluded: chain S residue 106 MET Chi-restraints excluded: chain S residue 128 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 124 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 244 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 267 optimal weight: 0.9980 chunk 123 optimal weight: 0.5980 chunk 271 optimal weight: 0.8980 chunk 215 optimal weight: 0.5980 chunk 283 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 958 ASN F 161 GLN G 146 GLN I 181 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 = 0.3417 r_free = 0.3417 target = 0.091106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.063529 restraints weight = 63665.775| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.45 r_work: 0.2746 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32252 Z= 0.115 Angle : 0.529 9.614 43767 Z= 0.279 Chirality : 0.043 0.208 4952 Planarity : 0.003 0.055 5392 Dihedral : 10.801 59.981 4615 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.14 % Allowed : 12.03 % Favored : 85.83 % 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: 1.44 (0.14), residues: 1381 sheet: -0.28 (0.23), residues: 538 loop : -0.72 (0.15), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG S 83 TYR 0.019 0.001 TYR S 134 PHE 0.029 0.001 PHE A 938 TRP 0.033 0.001 TRP A1054 HIS 0.010 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00255 (32235) covalent geometry : angle 0.52598 (43747) SS BOND : bond 0.00640 ( 1) SS BOND : angle 1.83466 ( 2) hydrogen bonds : bond 0.03806 ( 1323) hydrogen bonds : angle 4.65269 ( 3638) metal coordination : bond 0.00466 ( 16) metal coordination : angle 2.78316 ( 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 353 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 279 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8216 (ptp) cc_final: 0.7946 (pmt) REVERT: A 91 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8765 (pp) REVERT: A 149 VAL cc_start: 0.8585 (m) cc_final: 0.8353 (t) REVERT: A 246 GLU cc_start: 0.9102 (pt0) cc_final: 0.8703 (pt0) REVERT: A 347 ARG cc_start: 0.8347 (tmt170) cc_final: 0.7953 (tpt90) REVERT: A 360 LEU cc_start: 0.7005 (OUTLIER) cc_final: 0.6756 (pp) REVERT: A 398 GLU cc_start: 0.8802 (pm20) cc_final: 0.8551 (pt0) REVERT: A 1062 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.7755 (t0) REVERT: A 1100 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8539 (pttp) REVERT: A 1128 MET cc_start: 0.9171 (tpp) cc_final: 0.8876 (tpt) REVERT: B 59 PHE cc_start: 0.8556 (m-80) cc_final: 0.7901 (m-80) REVERT: B 74 LYS cc_start: 0.9382 (mmmm) cc_final: 0.9035 (mmtm) REVERT: B 120 TYR cc_start: 0.6948 (t80) cc_final: 0.6738 (t80) REVERT: B 160 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8089 (ptpt) REVERT: B 173 LYS cc_start: 0.9318 (mmmt) cc_final: 0.8876 (mttp) REVERT: B 395 TYR cc_start: 0.7257 (m-80) cc_final: 0.6977 (m-80) REVERT: B 422 SER cc_start: 0.4573 (OUTLIER) cc_final: 0.4234 (p) REVERT: B 460 ARG cc_start: 0.8628 (mtt90) cc_final: 0.8363 (mtt90) REVERT: B 506 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8226 (tm-30) REVERT: B 544 MET cc_start: 0.9297 (mtp) cc_final: 0.9088 (mtm) REVERT: B 545 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8550 (pt) REVERT: B 872 MET cc_start: 0.9195 (mtt) cc_final: 0.8973 (mtt) REVERT: B 977 ASN cc_start: 0.8959 (t0) cc_final: 0.8729 (t0) REVERT: B 979 LYS cc_start: 0.8835 (pmmt) cc_final: 0.8560 (pmmt) REVERT: B 1100 ILE cc_start: 0.9046 (mp) cc_final: 0.8743 (tp) REVERT: C 77 MET cc_start: 0.8235 (ttp) cc_final: 0.8009 (ttp) REVERT: C 103 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.9049 (tt) REVERT: C 239 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7761 (tp30) REVERT: E 18 GLU cc_start: 0.9312 (tp30) cc_final: 0.8778 (tp30) REVERT: F 81 GLU cc_start: 0.9230 (OUTLIER) cc_final: 0.8988 (mp0) REVERT: F 103 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7680 (tm-30) REVERT: G 20 THR cc_start: 0.9188 (OUTLIER) cc_final: 0.8912 (p) REVERT: G 142 MET cc_start: 0.8987 (mmp) cc_final: 0.8622 (mmm) REVERT: I 179 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7907 (tm) REVERT: I 305 ASP cc_start: 0.8636 (m-30) cc_final: 0.7835 (p0) REVERT: S 39 ASP cc_start: 0.8693 (m-30) cc_final: 0.8360 (m-30) REVERT: S 42 GLU cc_start: 0.8927 (tt0) cc_final: 0.8482 (pt0) REVERT: S 69 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7526 (tm-30) REVERT: S 77 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8745 (mm-30) REVERT: S 106 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7364 (mtm) REVERT: S 116 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7576 (mm-30) REVERT: S 118 LEU cc_start: 0.9088 (mt) cc_final: 0.8838 (mm) REVERT: S 127 CYS cc_start: 0.8695 (m) cc_final: 0.8258 (m) outliers start: 74 outliers final: 29 residues processed: 340 average time/residue: 0.7508 time to fit residues: 297.1163 Evaluate side-chains 300 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 258 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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 555 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 1100 LYS Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 217 LEU 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 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 103 ILE 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 62 VAL Chi-restraints excluded: chain G residue 117 PHE Chi-restraints excluded: chain I residue 144 TYR Chi-restraints excluded: chain I residue 179 LEU 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 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: 0.8980 chunk 46 optimal weight: 3.9990 chunk 175 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 266 optimal weight: 4.9990 chunk 231 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 209 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 GLN I 181 GLN ** S 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.091703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.063902 restraints weight = 63571.667| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.47 r_work: 0.2758 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 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 0.042 32252 Z= 0.118 Angle : 0.526 12.209 43767 Z= 0.277 Chirality : 0.043 0.211 4952 Planarity : 0.003 0.050 5392 Dihedral : 10.633 59.984 4611 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.99 % Allowed : 12.38 % Favored : 85.63 % 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: 0.27 (0.14), residues: 3752 helix: 1.53 (0.14), residues: 1381 sheet: -0.27 (0.23), residues: 540 loop : -0.70 (0.15), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 110 TYR 0.019 0.001 TYR S 134 PHE 0.029 0.001 PHE A 938 TRP 0.041 0.001 TRP A1054 HIS 0.012 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00263 (32235) covalent geometry : angle 0.52366 (43747) SS BOND : bond 0.00650 ( 1) SS BOND : angle 1.38834 ( 2) hydrogen bonds : bond 0.03746 ( 1323) hydrogen bonds : angle 4.57314 ( 3638) metal coordination : bond 0.00455 ( 16) metal coordination : angle 2.56471 ( 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 342 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 273 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8167 (ptp) cc_final: 0.7925 (pmt) REVERT: A 91 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8754 (pp) REVERT: A 136 MET cc_start: 0.8844 (tpp) cc_final: 0.8261 (mtm) REVERT: A 226 MET cc_start: 0.8572 (mmp) cc_final: 0.8243 (mmm) REVERT: A 246 GLU cc_start: 0.9088 (pt0) cc_final: 0.8700 (pt0) REVERT: A 347 ARG cc_start: 0.8346 (tmt170) cc_final: 0.7945 (tpt90) REVERT: A 360 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6829 (pp) REVERT: A 398 GLU cc_start: 0.8802 (pm20) cc_final: 0.8550 (pt0) REVERT: A 1062 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.7815 (t70) REVERT: B 59 PHE cc_start: 0.8578 (m-80) cc_final: 0.7878 (m-80) REVERT: B 160 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8071 (ptpt) REVERT: B 173 LYS cc_start: 0.9293 (mmmt) cc_final: 0.8861 (mttp) REVERT: B 395 TYR cc_start: 0.7245 (m-80) cc_final: 0.6962 (m-80) REVERT: B 422 SER cc_start: 0.4598 (OUTLIER) cc_final: 0.4224 (p) REVERT: B 506 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8193 (tm-30) REVERT: B 544 MET cc_start: 0.9250 (mtp) cc_final: 0.9047 (mtm) REVERT: B 545 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8566 (pt) REVERT: B 872 MET cc_start: 0.9185 (mtt) cc_final: 0.8967 (mtt) REVERT: B 1100 ILE cc_start: 0.9039 (mp) cc_final: 0.8754 (tp) REVERT: C 77 MET cc_start: 0.8404 (ttp) cc_final: 0.8133 (ttp) REVERT: C 103 ILE cc_start: 0.9311 (OUTLIER) cc_final: 0.9064 (tt) REVERT: C 239 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7746 (tp30) REVERT: E 18 GLU cc_start: 0.9329 (tp30) cc_final: 0.8777 (tp30) REVERT: F 81 GLU cc_start: 0.9203 (OUTLIER) cc_final: 0.8958 (mp0) REVERT: F 103 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7601 (tm-30) REVERT: G 20 THR cc_start: 0.9201 (OUTLIER) cc_final: 0.8930 (p) REVERT: G 142 MET cc_start: 0.9019 (mmp) cc_final: 0.8656 (mmm) REVERT: I 179 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7992 (tm) REVERT: I 305 ASP cc_start: 0.8679 (m-30) cc_final: 0.7852 (p0) REVERT: S 42 GLU cc_start: 0.8937 (tt0) cc_final: 0.8602 (pt0) REVERT: S 62 ASN cc_start: 0.7301 (m-40) cc_final: 0.6969 (m-40) REVERT: S 69 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7534 (tm-30) REVERT: S 77 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8760 (mm-30) REVERT: S 116 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7652 (mm-30) REVERT: S 118 LEU cc_start: 0.9058 (mt) cc_final: 0.8820 (mm) REVERT: S 127 CYS cc_start: 0.8697 (m) cc_final: 0.8259 (m) outliers start: 69 outliers final: 34 residues processed: 325 average time/residue: 0.7518 time to fit residues: 283.6586 Evaluate side-chains 300 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 255 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 555 ILE Chi-restraints excluded: chain A residue 653 LEU 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 B residue 79 ASP 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 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 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 103 ILE 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 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 Chi-restraints excluded: chain S residue 122 LEU 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: 3.9990 chunk 202 optimal weight: 0.6980 chunk 233 optimal weight: 1.9990 chunk 145 optimal weight: 0.0370 chunk 374 optimal weight: 8.9990 chunk 266 optimal weight: 4.9990 chunk 260 optimal weight: 4.9990 chunk 243 optimal weight: 0.7980 chunk 136 optimal weight: 3.9990 chunk 220 optimal weight: 5.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3422 r_free = 0.3422 target = 0.091696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.063858 restraints weight = 64160.657| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.50 r_work: 0.2755 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32252 Z= 0.125 Angle : 0.537 11.235 43767 Z= 0.282 Chirality : 0.043 0.222 4952 Planarity : 0.003 0.052 5392 Dihedral : 10.586 59.908 4611 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.08 % Allowed : 12.67 % 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: 0.34 (0.14), residues: 3752 helix: 1.58 (0.14), residues: 1376 sheet: -0.22 (0.23), residues: 541 loop : -0.66 (0.15), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG G 86 TYR 0.018 0.001 TYR S 134 PHE 0.029 0.001 PHE A 938 TRP 0.043 0.001 TRP A1054 HIS 0.012 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00283 (32235) covalent geometry : angle 0.53339 (43747) SS BOND : bond 0.01233 ( 1) SS BOND : angle 5.13636 ( 2) hydrogen bonds : bond 0.03766 ( 1323) hydrogen bonds : angle 4.54917 ( 3638) metal coordination : bond 0.00436 ( 16) metal coordination : angle 2.45466 ( 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: 72 poor density : 274 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8722 (pp) REVERT: A 136 MET cc_start: 0.8868 (tpp) cc_final: 0.8246 (mtm) REVERT: A 226 MET cc_start: 0.8537 (mmp) cc_final: 0.8320 (mmm) REVERT: A 347 ARG cc_start: 0.8353 (tmt170) cc_final: 0.7954 (tpt90) REVERT: A 360 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6828 (pp) REVERT: A 398 GLU cc_start: 0.8781 (pm20) cc_final: 0.8551 (pt0) REVERT: A 1062 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.7861 (t70) REVERT: A 1128 MET cc_start: 0.9140 (tpp) cc_final: 0.8775 (tpt) REVERT: B 59 PHE cc_start: 0.8583 (m-80) cc_final: 0.7908 (m-80) REVERT: B 116 LYS cc_start: 0.8168 (tmmt) cc_final: 0.7922 (tptp) REVERT: B 120 TYR cc_start: 0.6786 (t80) cc_final: 0.6558 (t80) REVERT: B 160 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8090 (ptpt) REVERT: B 173 LYS cc_start: 0.9262 (mmmt) cc_final: 0.8830 (mttp) REVERT: B 395 TYR cc_start: 0.7217 (m-80) cc_final: 0.6995 (m-80) REVERT: B 506 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8165 (tm-30) REVERT: B 544 MET cc_start: 0.9267 (mtp) cc_final: 0.9066 (mtm) REVERT: B 545 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8578 (pt) REVERT: B 872 MET cc_start: 0.9189 (mtt) cc_final: 0.8967 (mtm) REVERT: B 1100 ILE cc_start: 0.9031 (mp) cc_final: 0.8760 (tp) REVERT: C 77 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.8235 (ttp) REVERT: C 103 ILE cc_start: 0.9332 (OUTLIER) cc_final: 0.9110 (tt) REVERT: C 239 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7736 (tp30) REVERT: E 18 GLU cc_start: 0.9336 (tp30) cc_final: 0.8761 (tp30) REVERT: E 138 ARG cc_start: 0.8812 (mtt-85) cc_final: 0.8350 (mmm-85) REVERT: F 81 GLU cc_start: 0.9184 (OUTLIER) cc_final: 0.8953 (mp0) REVERT: F 103 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7592 (tm-30) REVERT: G 20 THR cc_start: 0.9194 (OUTLIER) cc_final: 0.8924 (p) REVERT: G 142 MET cc_start: 0.9020 (mmp) cc_final: 0.8649 (mmm) REVERT: I 305 ASP cc_start: 0.8675 (m-30) cc_final: 0.7857 (p0) REVERT: S 42 GLU cc_start: 0.8915 (tt0) cc_final: 0.8622 (pt0) REVERT: S 62 ASN cc_start: 0.7226 (m-40) cc_final: 0.6471 (m-40) REVERT: S 69 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7504 (tm-30) REVERT: S 77 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8756 (mm-30) REVERT: S 116 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7735 (mm-30) REVERT: S 118 LEU cc_start: 0.9042 (mt) cc_final: 0.8790 (mm) REVERT: S 127 CYS cc_start: 0.8710 (m) cc_final: 0.8245 (m) outliers start: 72 outliers final: 42 residues processed: 329 average time/residue: 0.7645 time to fit residues: 293.5257 Evaluate side-chains 312 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 260 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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 555 ILE Chi-restraints excluded: chain A residue 653 LEU 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 107 MET 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 304 ILE Chi-restraints excluded: chain B residue 397 VAL 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 103 ILE 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 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 117 PHE Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 189 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 Chi-restraints excluded: chain S residue 122 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 159 optimal weight: 0.0970 chunk 46 optimal weight: 3.9990 chunk 366 optimal weight: 3.9990 chunk 234 optimal weight: 5.9990 chunk 347 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 327 optimal weight: 9.9990 chunk 274 optimal weight: 5.9990 chunk 170 optimal weight: 0.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1081 ASN G 146 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 = 0.3387 r_free = 0.3387 target = 0.089692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.061633 restraints weight = 63832.017| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 2.47 r_work: 0.2706 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2210 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= 0.200 Angle : 0.578 11.197 43767 Z= 0.304 Chirality : 0.045 0.220 4952 Planarity : 0.004 0.058 5392 Dihedral : 10.668 59.855 4610 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.99 % Allowed : 12.87 % Favored : 85.14 % 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: 0.24 (0.14), residues: 3752 helix: 1.49 (0.14), residues: 1371 sheet: -0.29 (0.23), residues: 538 loop : -0.70 (0.15), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG S 83 TYR 0.022 0.001 TYR S 120 PHE 0.031 0.002 PHE A 938 TRP 0.044 0.001 TRP A1054 HIS 0.012 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00468 (32235) covalent geometry : angle 0.57508 (43747) SS BOND : bond 0.01364 ( 1) SS BOND : angle 4.20318 ( 2) hydrogen bonds : bond 0.04384 ( 1323) hydrogen bonds : angle 4.66503 ( 3638) metal coordination : bond 0.00636 ( 16) metal coordination : angle 2.44011 ( 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 328 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 259 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8700 (pp) REVERT: A 347 ARG cc_start: 0.8346 (tmt170) cc_final: 0.7936 (tpt90) REVERT: A 360 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6928 (pp) REVERT: A 398 GLU cc_start: 0.8838 (pm20) cc_final: 0.8612 (pt0) REVERT: A 1062 ASP cc_start: 0.8571 (OUTLIER) cc_final: 0.7895 (t70) REVERT: A 1128 MET cc_start: 0.9194 (tpp) cc_final: 0.8734 (tpt) REVERT: B 59 PHE cc_start: 0.8579 (m-80) cc_final: 0.7905 (m-80) REVERT: B 173 LYS cc_start: 0.9267 (mmmt) cc_final: 0.8838 (mttp) REVERT: B 506 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8234 (tm-30) REVERT: C 239 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7705 (tp30) REVERT: E 18 GLU cc_start: 0.9344 (tp30) cc_final: 0.8710 (tp30) REVERT: E 138 ARG cc_start: 0.8836 (mtt-85) cc_final: 0.8316 (mmm-85) REVERT: F 81 GLU cc_start: 0.9200 (OUTLIER) cc_final: 0.8966 (mp0) REVERT: F 103 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7709 (tm-30) REVERT: G 20 THR cc_start: 0.9215 (OUTLIER) cc_final: 0.8951 (p) REVERT: G 142 MET cc_start: 0.9071 (mmp) cc_final: 0.8668 (mmm) REVERT: I 305 ASP cc_start: 0.8690 (m-30) cc_final: 0.7822 (p0) REVERT: S 42 GLU cc_start: 0.8881 (tt0) cc_final: 0.8579 (pt0) REVERT: S 62 ASN cc_start: 0.7149 (m-40) cc_final: 0.6624 (t0) REVERT: S 69 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7659 (tm-30) REVERT: S 77 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8775 (mm-30) REVERT: S 116 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7726 (mm-30) REVERT: S 118 LEU cc_start: 0.9009 (mt) cc_final: 0.8775 (mm) REVERT: S 127 CYS cc_start: 0.8747 (m) cc_final: 0.8304 (m) outliers start: 69 outliers final: 42 residues processed: 310 average time/residue: 0.7432 time to fit residues: 269.1961 Evaluate side-chains 303 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 254 time to evaluate : 1.343 ------------------------------------------------------------------------------- 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 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 653 LEU 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 68 ILE Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 107 MET 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 397 VAL Chi-restraints excluded: chain B residue 545 ILE 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 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 98 THR Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 189 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 Chi-restraints excluded: chain S residue 69 GLU Chi-restraints excluded: chain S residue 122 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 376 optimal weight: 10.0000 chunk 206 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 237 optimal weight: 0.0980 chunk 94 optimal weight: 4.9990 chunk 170 optimal weight: 0.6980 chunk 319 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 271 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN B 47 HIS G 146 GLN I 181 GLN I 626 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.091241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.063491 restraints weight = 63823.661| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.46 r_work: 0.2750 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2316 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= 0.128 Angle : 0.545 11.140 43767 Z= 0.285 Chirality : 0.043 0.227 4952 Planarity : 0.003 0.058 5392 Dihedral : 10.535 59.844 4608 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.50 % Allowed : 13.50 % Favored : 85.00 % 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: 0.31 (0.14), residues: 3752 helix: 1.59 (0.14), residues: 1372 sheet: -0.25 (0.23), residues: 533 loop : -0.70 (0.15), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 110 TYR 0.016 0.001 TYR S 120 PHE 0.030 0.001 PHE A 938 TRP 0.053 0.001 TRP A1054 HIS 0.003 0.001 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.00290 (32235) covalent geometry : angle 0.54198 (43747) SS BOND : bond 0.00982 ( 1) SS BOND : angle 3.31653 ( 2) hydrogen bonds : bond 0.03849 ( 1323) hydrogen bonds : angle 4.57004 ( 3638) metal coordination : bond 0.00461 ( 16) metal coordination : angle 2.43231 ( 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 314 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 262 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8723 (pp) REVERT: A 136 MET cc_start: 0.8743 (mmm) cc_final: 0.8400 (mmm) REVERT: A 347 ARG cc_start: 0.8321 (tmt170) cc_final: 0.7909 (tpt90) REVERT: A 360 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6744 (pp) REVERT: A 398 GLU cc_start: 0.8819 (pm20) cc_final: 0.8606 (pt0) REVERT: A 1062 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.7937 (t70) REVERT: B 59 PHE cc_start: 0.8502 (m-80) cc_final: 0.7888 (m-80) REVERT: B 116 LYS cc_start: 0.8105 (tmmt) cc_final: 0.7858 (tptp) REVERT: B 120 TYR cc_start: 0.6803 (t80) cc_final: 0.6559 (t80) REVERT: B 173 LYS cc_start: 0.9264 (mmmt) cc_final: 0.8837 (mttp) REVERT: B 506 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8200 (tm-30) REVERT: B 544 MET cc_start: 0.9297 (mtp) cc_final: 0.9095 (mtm) REVERT: B 545 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8594 (pt) REVERT: B 719 GLU cc_start: 0.9209 (OUTLIER) cc_final: 0.8966 (pt0) REVERT: B 872 MET cc_start: 0.9211 (mtt) cc_final: 0.8981 (mtm) REVERT: C 239 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7689 (tp30) REVERT: E 18 GLU cc_start: 0.9340 (tp30) cc_final: 0.8794 (tp30) REVERT: E 138 ARG cc_start: 0.8803 (mtt-85) cc_final: 0.8285 (mmm-85) REVERT: F 81 GLU cc_start: 0.9169 (OUTLIER) cc_final: 0.8942 (mp0) REVERT: F 103 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7592 (tm-30) REVERT: F 109 MET cc_start: 0.8558 (mmt) cc_final: 0.8155 (mmt) REVERT: G 20 THR cc_start: 0.9215 (OUTLIER) cc_final: 0.8950 (p) REVERT: G 142 MET cc_start: 0.9016 (mmp) cc_final: 0.8641 (mmm) REVERT: I 235 VAL cc_start: 0.9108 (OUTLIER) cc_final: 0.8825 (p) REVERT: I 305 ASP cc_start: 0.8675 (m-30) cc_final: 0.7834 (p0) REVERT: I 313 GLU cc_start: 0.8383 (pm20) cc_final: 0.7870 (mp0) REVERT: I 626 GLN cc_start: 0.6792 (tt0) cc_final: 0.6576 (tt0) REVERT: S 42 GLU cc_start: 0.8887 (tt0) cc_final: 0.8594 (pt0) REVERT: S 69 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7539 (tm-30) REVERT: S 77 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8759 (mm-30) REVERT: S 114 GLU cc_start: 0.8562 (pm20) cc_final: 0.8353 (pm20) REVERT: S 116 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7714 (mp0) REVERT: S 127 CYS cc_start: 0.8745 (m) cc_final: 0.8300 (m) outliers start: 52 outliers final: 36 residues processed: 301 average time/residue: 0.7531 time to fit residues: 264.2513 Evaluate side-chains 301 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 255 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 298 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 653 LEU 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 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 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 397 VAL 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 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 I residue 140 VAL Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 189 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 J residue 26 LYS Chi-restraints excluded: chain S residue 69 GLU Chi-restraints excluded: chain S residue 122 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 359 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 237 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 307 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 282 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 chunk 256 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS A 140 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1020 HIS G 37 HIS G 146 GLN ** S 62 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 = 0.3430 r_free = 0.3430 target = 0.092013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.064435 restraints weight = 63864.979| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.47 r_work: 0.2766 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2415 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= 0.113 Angle : 0.543 12.192 43767 Z= 0.282 Chirality : 0.043 0.391 4952 Planarity : 0.004 0.068 5392 Dihedral : 10.427 59.990 4608 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.50 % Allowed : 13.62 % 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: 0.37 (0.14), residues: 3752 helix: 1.65 (0.14), residues: 1375 sheet: -0.20 (0.23), residues: 527 loop : -0.67 (0.15), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG S 83 TYR 0.017 0.001 TYR S 120 PHE 0.028 0.001 PHE A 938 TRP 0.061 0.002 TRP A1054 HIS 0.012 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00251 (32235) covalent geometry : angle 0.54102 (43747) SS BOND : bond 0.00895 ( 1) SS BOND : angle 2.93341 ( 2) hydrogen bonds : bond 0.03643 ( 1323) hydrogen bonds : angle 4.49475 ( 3638) metal coordination : bond 0.00415 ( 16) metal coordination : angle 2.16442 ( 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 315 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 263 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8729 (pp) REVERT: A 136 MET cc_start: 0.8785 (mmm) cc_final: 0.8422 (mmm) REVERT: A 226 MET cc_start: 0.8556 (mmp) cc_final: 0.8342 (mmm) REVERT: A 347 ARG cc_start: 0.8310 (tmt170) cc_final: 0.7906 (tpt90) REVERT: A 360 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6722 (pp) REVERT: A 398 GLU cc_start: 0.8820 (pm20) cc_final: 0.8594 (pt0) REVERT: A 1062 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.7931 (t70) REVERT: A 1128 MET cc_start: 0.9193 (tpp) cc_final: 0.8912 (mmm) REVERT: B 59 PHE cc_start: 0.8457 (m-80) cc_final: 0.7848 (m-80) REVERT: B 120 TYR cc_start: 0.6817 (t80) cc_final: 0.6554 (t80) REVERT: B 160 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8081 (ptpt) REVERT: B 173 LYS cc_start: 0.9251 (mmmt) cc_final: 0.8800 (mttp) REVERT: B 478 ARG cc_start: 0.7503 (mtm110) cc_final: 0.7126 (mtp85) REVERT: B 506 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8142 (tm-30) REVERT: B 544 MET cc_start: 0.9246 (mtp) cc_final: 0.9039 (mtm) REVERT: B 545 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8566 (pt) REVERT: B 719 GLU cc_start: 0.9251 (OUTLIER) cc_final: 0.8985 (pt0) REVERT: B 1100 ILE cc_start: 0.9009 (mp) cc_final: 0.8778 (tp) REVERT: C 239 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7636 (tp30) REVERT: E 18 GLU cc_start: 0.9331 (tp30) cc_final: 0.8732 (tp30) REVERT: E 138 ARG cc_start: 0.8775 (mtt-85) cc_final: 0.8190 (mmm-85) REVERT: F 103 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7520 (tm-30) REVERT: F 109 MET cc_start: 0.8564 (mmt) cc_final: 0.8150 (mmt) REVERT: G 20 THR cc_start: 0.9194 (OUTLIER) cc_final: 0.8923 (p) REVERT: I 235 VAL cc_start: 0.9039 (OUTLIER) cc_final: 0.8743 (p) REVERT: I 305 ASP cc_start: 0.8666 (m-30) cc_final: 0.7825 (p0) REVERT: I 313 GLU cc_start: 0.8362 (pm20) cc_final: 0.7881 (mp0) REVERT: S 42 GLU cc_start: 0.8899 (tt0) cc_final: 0.8597 (pt0) REVERT: S 69 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7452 (tm-30) REVERT: S 77 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8752 (mm-30) REVERT: S 116 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7720 (mm-30) REVERT: S 127 CYS cc_start: 0.8702 (m) cc_final: 0.8256 (m) outliers start: 52 outliers final: 37 residues processed: 303 average time/residue: 0.7389 time to fit residues: 262.1767 Evaluate side-chains 299 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 252 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 114 HIS Chi-restraints excluded: chain A residue 156 ASP 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 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 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 243 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 397 VAL 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 113 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 126 SER 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 I residue 140 VAL Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 189 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 69 GLU Chi-restraints excluded: chain S residue 122 LEU Chi-restraints excluded: chain S residue 128 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 251 optimal weight: 1.9990 chunk 193 optimal weight: 4.9990 chunk 341 optimal weight: 0.7980 chunk 355 optimal weight: 0.9990 chunk 368 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 chunk 233 optimal weight: 2.9990 chunk 232 optimal weight: 6.9990 chunk 322 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN B 977 ASN I 181 GLN I 626 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.090681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.062906 restraints weight = 64106.618| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.46 r_work: 0.2737 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 32252 Z= 0.167 Angle : 0.569 12.926 43767 Z= 0.296 Chirality : 0.044 0.272 4952 Planarity : 0.004 0.064 5392 Dihedral : 10.440 59.869 4605 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.36 % Allowed : 13.94 % 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: 0.35 (0.14), residues: 3752 helix: 1.61 (0.14), residues: 1375 sheet: -0.23 (0.23), residues: 537 loop : -0.67 (0.15), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG G 110 TYR 0.020 0.001 TYR S 120 PHE 0.031 0.001 PHE A 938 TRP 0.063 0.002 TRP A1054 HIS 0.017 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00389 (32235) covalent geometry : angle 0.56731 (43747) SS BOND : bond 0.01049 ( 1) SS BOND : angle 3.03042 ( 2) hydrogen bonds : bond 0.04019 ( 1323) hydrogen bonds : angle 4.57093 ( 3638) metal coordination : bond 0.00545 ( 16) metal coordination : angle 2.15985 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12303.16 seconds wall clock time: 209 minutes 38.46 seconds (12578.46 seconds total)