Starting phenix.real_space_refine on Fri Mar 6 00:14:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q0j_13745/03_2026/7q0j_13745.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q0j_13745/03_2026/7q0j_13745.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7q0j_13745/03_2026/7q0j_13745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q0j_13745/03_2026/7q0j_13745.map" model { file = "/net/cci-nas-00/data/ceres_data/7q0j_13745/03_2026/7q0j_13745.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q0j_13745/03_2026/7q0j_13745.cif" } resolution = 4.3 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= 0.006 sd= 0.049 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 2 6.06 5 P 53 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16157 2.51 5 N 4612 2.21 5 O 5125 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s 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: 26056 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 9, 'TRANS': 218} Chain: "B" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1687 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 8, 'TRANS': 210} Chain breaks: 1 Chain: "C" Number of atoms: 10533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10533 Classifications: {'peptide': 1335} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1278} Chain breaks: 1 Chain: "D" Number of atoms: 10388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10388 Classifications: {'peptide': 1335} Link IDs: {'PTRANS': 55, 'TRANS': 1279} Chain breaks: 2 Chain: "E" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "N" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 336 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "R" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 235 Classifications: {'RNA': 11} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 9} Chain: "T" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 524 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "D" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14451 SG CYS D 72 20.063 57.094 97.238 1.00224.23 S ATOM 14559 SG CYS D 85 17.293 58.484 98.864 1.00251.88 S ATOM 14583 SG CYS D 88 21.411 60.565 98.673 1.00247.24 S ATOM 20271 SG CYS D 814 41.053 125.934 90.059 1.00198.64 S ATOM 20836 SG CYS D 888 42.411 121.476 90.808 1.00192.05 S ATOM 20887 SG CYS D 895 41.450 123.208 87.760 1.00177.56 S Time building chain proxies: 5.34, per 1000 atoms: 0.20 Number of scatterers: 26056 At special positions: 0 Unit cell: (132, 168.3, 168.3, 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 2 29.99 S 106 16.00 P 53 15.00 Mg 1 11.99 O 5125 8.00 N 4612 7.00 C 16157 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5888 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 43 sheets defined 37.6% alpha, 13.6% beta 24 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 2.68 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 4.032A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 removed outlier: 3.517A pdb=" N ILE A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 212 through 230 removed outlier: 3.909A pdb=" N ILE A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ARG A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.676A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 87 removed outlier: 3.507A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 154 through 158 Processing helix chain 'B' and resid 212 through 228 removed outlier: 3.628A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 10 removed outlier: 3.540A pdb=" N ARG C 10 " --> pdb=" O GLU C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 39 Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 82 through 89 Processing helix chain 'C' and resid 206 through 213 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.529A pdb=" N ARG C 245 " --> pdb=" O VAL C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 279 Processing helix chain 'C' and resid 289 through 294 removed outlier: 4.277A pdb=" N GLY C 294 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 327 Processing helix chain 'C' and resid 345 through 353 removed outlier: 4.107A pdb=" N GLU C 349 " --> pdb=" O PRO C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.898A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 422 through 438 Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 480 removed outlier: 3.577A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 526 Processing helix chain 'C' and resid 551 through 555 Processing helix chain 'C' and resid 609 through 614 removed outlier: 3.803A pdb=" N GLY C 612 " --> pdb=" O ILE C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 661 removed outlier: 3.812A pdb=" N GLN C 659 " --> pdb=" O SER C 656 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL C 661 " --> pdb=" O GLN C 658 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 656 through 661' Processing helix chain 'C' and resid 664 through 668 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 826 Processing helix chain 'C' and resid 858 through 864 removed outlier: 4.542A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 907 Processing helix chain 'C' and resid 942 through 979 removed outlier: 4.406A pdb=" N LEU C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY C 970 " --> pdb=" O ILE C 966 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU C 971 " --> pdb=" O LEU C 967 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG C 974 " --> pdb=" O GLY C 970 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE C 975 " --> pdb=" O LEU C 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 992 removed outlier: 4.196A pdb=" N LYS C 991 " --> pdb=" O GLU C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1006 through 1038 removed outlier: 3.589A pdb=" N GLN C1010 " --> pdb=" O GLU C1006 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU C1016 " --> pdb=" O GLU C1012 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN C1017 " --> pdb=" O GLN C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 4.075A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1133 removed outlier: 3.503A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR C1115 " --> pdb=" O GLN C1111 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS C1127 " --> pdb=" O GLY C1123 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 removed outlier: 4.261A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1175 removed outlier: 3.794A pdb=" N ASN C1175 " --> pdb=" O ARG C1171 " (cutoff:3.500A) Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.642A pdb=" N ILE C1195 " --> pdb=" O LYS C1191 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS C1200 " --> pdb=" O LYS C1196 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU C1201 " --> pdb=" O GLU C1197 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY C1202 " --> pdb=" O LEU C1198 " (cutoff:3.500A) Processing helix chain 'C' and resid 1272 through 1281 removed outlier: 3.662A pdb=" N TRP C1276 " --> pdb=" O GLU C1272 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU C1279 " --> pdb=" O VAL C1275 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1284 through 1293 removed outlier: 3.707A pdb=" N LEU C1291 " --> pdb=" O LEU C1287 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL C1293 " --> pdb=" O GLU C1289 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1309 removed outlier: 3.932A pdb=" N ARG C1301 " --> pdb=" O ASP C1297 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL C1309 " --> pdb=" O TYR C1305 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.704A pdb=" N LYS C1328 " --> pdb=" O ASN C1324 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU C1329 " --> pdb=" O VAL C1325 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE C1330 " --> pdb=" O LEU C1326 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 58 through 63 removed outlier: 3.813A pdb=" N PHE D 62 " --> pdb=" O CYS D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.829A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 139 Processing helix chain 'D' and resid 161 through 171 Processing helix chain 'D' and resid 180 through 191 removed outlier: 3.532A pdb=" N ALA D 184 " --> pdb=" O MET D 180 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 208 Processing helix chain 'D' and resid 210 through 230 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 283 removed outlier: 3.790A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 286 No H-bonds generated for 'chain 'D' and resid 284 through 286' Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 337 through 342 Processing helix chain 'D' and resid 370 through 377 removed outlier: 3.645A pdb=" N PHE D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 407 No H-bonds generated for 'chain 'D' and resid 405 through 407' Processing helix chain 'D' and resid 408 through 415 Processing helix chain 'D' and resid 430 through 434 removed outlier: 3.786A pdb=" N ILE D 434 " --> pdb=" O ARG D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 458 removed outlier: 4.126A pdb=" N CYS D 454 " --> pdb=" O HIS D 450 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA D 455 " --> pdb=" O PRO D 451 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 484 Processing helix chain 'D' and resid 504 through 514 removed outlier: 3.764A pdb=" N LEU D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 540 Processing helix chain 'D' and resid 574 through 581 Processing helix chain 'D' and resid 588 through 593 removed outlier: 3.701A pdb=" N ASN D 593 " --> pdb=" O SER D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.667A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 removed outlier: 3.660A pdb=" N MET D 644 " --> pdb=" O ILE D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 669 Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.239A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.899A pdb=" N ILE D 737 " --> pdb=" O SER D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.513A pdb=" N TYR D 772 " --> pdb=" O ASN D 768 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 Processing helix chain 'D' and resid 865 through 874 Processing helix chain 'D' and resid 885 through 888 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 925 removed outlier: 4.257A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 928 No H-bonds generated for 'chain 'D' and resid 926 through 928' Processing helix chain 'D' and resid 1068 through 1073 removed outlier: 4.090A pdb=" N ASP D1073 " --> pdb=" O ALA D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 4.152A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.656A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN D1235 " --> pdb=" O ARG D1231 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU D1236 " --> pdb=" O TYR D1232 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP D1239 " --> pdb=" O ASN D1235 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR D1241 " --> pdb=" O VAL D1237 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 removed outlier: 3.820A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1293 Processing helix chain 'D' and resid 1308 through 1313 Processing helix chain 'D' and resid 1319 through 1324 Processing helix chain 'D' and resid 1328 through 1339 Processing helix chain 'D' and resid 1347 through 1354 Processing helix chain 'D' and resid 1361 through 1373 removed outlier: 4.155A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP D1368 " --> pdb=" O ALA D1364 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG D1373 " --> pdb=" O ARG D1369 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 30 removed outlier: 4.091A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.713A pdb=" N GLU E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 72 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 18 removed outlier: 3.877A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 26 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 28 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LEU A 201 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 101 removed outlier: 7.150A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR A 57 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 53 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.766A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 18 removed outlier: 4.518A pdb=" N LEU B 198 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG B 182 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 60 removed outlier: 3.667A pdb=" N ALA B 55 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AA8, first strand: chain 'B' and resid 108 through 111 removed outlier: 5.943A pdb=" N GLY B 108 " --> pdb=" O HIS B 132 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS B 132 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB1, first strand: chain 'C' and resid 59 through 60 removed outlier: 5.538A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE C 104 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 451 through 453 removed outlier: 6.463A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 155 through 158 removed outlier: 3.531A pdb=" N ASP C 158 " --> pdb=" O ASN C 173 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN C 173 " --> pdb=" O ASP C 158 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE C 195 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 227 through 231 Processing sheet with id=AB5, first strand: chain 'C' and resid 239 through 240 Processing sheet with id=AB6, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.720A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 301 through 302 Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 removed outlier: 6.613A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC1, first strand: chain 'C' and resid 616 through 617 Processing sheet with id=AC2, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.842A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 749 through 752 removed outlier: 3.939A pdb=" N ASP C 749 " --> pdb=" O ILE C 734 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE C 734 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.815A pdb=" N THR C 757 " --> pdb=" O ILE C 765 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE C 765 " --> pdb=" O THR C 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC6, first strand: chain 'C' and resid 1066 through 1067 removed outlier: 3.848A pdb=" N ALA C1067 " --> pdb=" O LEU C1233 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL C1097 " --> pdb=" O LEU C 817 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ILE C 816 " --> pdb=" O LYS C1078 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N ASN C1080 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL C 818 " --> pdb=" O ASN C1080 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 830 through 838 removed outlier: 4.009A pdb=" N LEU C1054 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 882 through 884 removed outlier: 7.035A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 887 through 889 Processing sheet with id=AD1, first strand: chain 'C' and resid 1244 through 1245 removed outlier: 3.609A pdb=" N GLY D 351 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE D 437 " --> pdb=" O VAL D 421 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN D 435 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1244 through 1245 removed outlier: 7.631A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1268 through 1269 removed outlier: 3.958A pdb=" N GLN C1268 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1335 through 1338 removed outlier: 3.616A pdb=" N GLU C1338 " --> pdb=" O LYS D 21 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS D 21 " --> pdb=" O GLU C1338 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 103 through 112 removed outlier: 9.904A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 11.008A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 144 through 145 Processing sheet with id=AD7, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.567A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASP D 558 " --> pdb=" O GLU D 562 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLU D 562 " --> pdb=" O ASP D 558 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 706 through 707 Processing sheet with id=AD9, first strand: chain 'D' and resid 809 through 811 removed outlier: 3.503A pdb=" N THR D 810 " --> pdb=" O VAL D 894 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'D' and resid 819 through 822 removed outlier: 3.552A pdb=" N ILE D 820 " --> pdb=" O VAL D 882 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 949 through 951 removed outlier: 7.017A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 957 through 961 removed outlier: 3.698A pdb=" N LYS D 959 " --> pdb=" O LYS D 983 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1024 through 1028 removed outlier: 4.618A pdb=" N ALA D1122 " --> pdb=" O VAL D1027 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1034 through 1035 removed outlier: 3.512A pdb=" N VAL D1113 " --> pdb=" O VAL D1035 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1162 through 1165 Processing sheet with id=AE7, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 6.367A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) 903 hydrogen bonds defined for protein. 2520 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 63 hydrogen bonds 122 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 5.97 Time building geometry restraints manager: 2.90 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: 8682 1.34 - 1.46: 5130 1.46 - 1.58: 12451 1.58 - 1.70: 103 1.70 - 1.83: 184 Bond restraints: 26550 Sorted by residual: bond pdb=" C VAL C1103 " pdb=" N PRO C1104 " ideal model delta sigma weight residual 1.335 1.366 -0.031 1.30e-02 5.92e+03 5.52e+00 bond pdb=" CG PRO E 40 " pdb=" CD PRO E 40 " ideal model delta sigma weight residual 1.503 1.559 -0.056 3.40e-02 8.65e+02 2.76e+00 bond pdb=" CD GLU D 873 " pdb=" OE1 GLU D 873 " ideal model delta sigma weight residual 1.249 1.218 0.031 1.90e-02 2.77e+03 2.59e+00 bond pdb=" CG GLU E 55 " pdb=" CD GLU E 55 " ideal model delta sigma weight residual 1.516 1.479 0.037 2.50e-02 1.60e+03 2.19e+00 bond pdb=" CG GLU D 873 " pdb=" CD GLU D 873 " ideal model delta sigma weight residual 1.516 1.479 0.037 2.50e-02 1.60e+03 2.18e+00 ... (remaining 26545 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 35449 2.54 - 5.07: 541 5.07 - 7.61: 75 7.61 - 10.14: 13 10.14 - 12.68: 4 Bond angle restraints: 36082 Sorted by residual: angle pdb=" N VAL C 714 " pdb=" CA VAL C 714 " pdb=" C VAL C 714 " ideal model delta sigma weight residual 111.88 104.60 7.28 1.06e+00 8.90e-01 4.72e+01 angle pdb=" C GLU A 163 " pdb=" N ASP A 164 " pdb=" CA ASP A 164 " ideal model delta sigma weight residual 121.54 131.85 -10.31 1.91e+00 2.74e-01 2.91e+01 angle pdb=" C GLU A 165 " pdb=" N ARG A 166 " pdb=" CA ARG A 166 " ideal model delta sigma weight residual 123.21 117.45 5.76 1.19e+00 7.06e-01 2.34e+01 angle pdb=" C GLU E 55 " pdb=" N GLU E 56 " pdb=" CA GLU E 56 " ideal model delta sigma weight residual 121.58 113.13 8.45 1.95e+00 2.63e-01 1.88e+01 angle pdb=" N GLU D 658 " pdb=" CA GLU D 658 " pdb=" CB GLU D 658 " ideal model delta sigma weight residual 110.39 117.28 -6.89 1.66e+00 3.63e-01 1.72e+01 ... (remaining 36077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.13: 15476 28.13 - 56.27: 681 56.27 - 84.40: 100 84.40 - 112.54: 2 112.54 - 140.67: 2 Dihedral angle restraints: 16261 sinusoidal: 7107 harmonic: 9154 Sorted by residual: dihedral pdb=" CA GLN E 72 " pdb=" C GLN E 72 " pdb=" N GLN E 73 " pdb=" CA GLN E 73 " ideal model delta harmonic sigma weight residual 180.00 154.05 25.95 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA GLY C 162 " pdb=" C GLY C 162 " pdb=" N LYS C 163 " pdb=" CA LYS C 163 " ideal model delta harmonic sigma weight residual -180.00 -154.37 -25.63 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA ARG D 47 " pdb=" C ARG D 47 " pdb=" N THR D 48 " pdb=" CA THR D 48 " ideal model delta harmonic sigma weight residual 180.00 155.18 24.82 0 5.00e+00 4.00e-02 2.46e+01 ... (remaining 16258 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3331 0.061 - 0.121: 714 0.121 - 0.182: 69 0.182 - 0.242: 8 0.242 - 0.303: 2 Chirality restraints: 4124 Sorted by residual: chirality pdb=" CG LEU A 171 " pdb=" CB LEU A 171 " pdb=" CD1 LEU A 171 " pdb=" CD2 LEU A 171 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CB VAL D 661 " pdb=" CA VAL D 661 " pdb=" CG1 VAL D 661 " pdb=" CG2 VAL D 661 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB VAL D1353 " pdb=" CA VAL D1353 " pdb=" CG1 VAL D1353 " pdb=" CG2 VAL D1353 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 4121 not shown) Planarity restraints: 4543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C1276 " 0.018 2.00e-02 2.50e+03 2.46e-02 1.52e+01 pdb=" CG TRP C1276 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP C1276 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP C1276 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C1276 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP C1276 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C1276 " 0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1276 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1276 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP C1276 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C1331 " -0.300 9.50e-02 1.11e+02 1.35e-01 1.13e+01 pdb=" NE ARG C1331 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG C1331 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG C1331 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG C1331 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 846 " 0.048 5.00e-02 4.00e+02 7.23e-02 8.37e+00 pdb=" N PRO C 847 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO C 847 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 847 " 0.040 5.00e-02 4.00e+02 ... (remaining 4540 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 513 2.65 - 3.21: 25203 3.21 - 3.77: 41540 3.77 - 4.34: 53693 4.34 - 4.90: 82981 Nonbonded interactions: 203930 Sorted by model distance: nonbonded pdb=" O3' G R 14 " pdb="MG MG D1503 " model vdw 2.083 2.170 nonbonded pdb=" O GLN C1288 " pdb=" OG1 THR C1292 " model vdw 2.148 3.040 nonbonded pdb=" OD2 ASP D 462 " pdb="MG MG D1503 " model vdw 2.151 2.170 nonbonded pdb=" O TYR C 810 " pdb=" OG SER C 815 " model vdw 2.170 3.040 nonbonded pdb=" OH TYR D1186 " pdb=" OE2 GLU D1188 " model vdw 2.196 3.040 ... (remaining 203925 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 158 or resid 169 through 232)) selection = (chain 'B' and resid 7 through 232) } 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 group one per residue 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: 1.260 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: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 28.300 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.246 26556 Z= 0.190 Angle : 0.790 12.680 36082 Z= 0.414 Chirality : 0.048 0.303 4124 Planarity : 0.006 0.135 4543 Dihedral : 15.005 140.671 10373 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.65 % Favored : 93.25 % Rotamer: Outliers : 0.04 % Allowed : 0.33 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: -1.95 (0.14), residues: 3172 helix: -0.20 (0.16), residues: 1023 sheet: -1.62 (0.27), residues: 321 loop : -1.94 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D1242 TYR 0.029 0.002 TYR C1281 PHE 0.024 0.002 PHE C 186 TRP 0.066 0.003 TRP C1276 HIS 0.007 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00354 (26550) covalent geometry : angle 0.79016 (36082) hydrogen bonds : bond 0.23176 ( 962) hydrogen bonds : angle 7.49864 ( 2642) metal coordination : bond 0.18390 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.9146 (ptm) cc_final: 0.8728 (ppp) REVERT: B 142 MET cc_start: 0.8487 (mmp) cc_final: 0.8090 (mmp) REVERT: C 160 ASP cc_start: 0.8296 (m-30) cc_final: 0.8026 (m-30) REVERT: C 370 MET cc_start: 0.8826 (tpt) cc_final: 0.8370 (tpp) REVERT: C 542 ARG cc_start: 0.9138 (mmp80) cc_final: 0.8852 (mmp80) REVERT: C 685 MET cc_start: 0.9144 (mtm) cc_final: 0.8817 (mtt) REVERT: C 741 MET cc_start: 0.8860 (ptp) cc_final: 0.8653 (ptt) REVERT: C 794 LEU cc_start: 0.9372 (tp) cc_final: 0.9031 (pp) REVERT: C 1025 PHE cc_start: 0.9379 (t80) cc_final: 0.9078 (t80) REVERT: C 1170 MET cc_start: 0.9373 (mmp) cc_final: 0.9130 (mmm) REVERT: C 1232 MET cc_start: 0.9332 (mmp) cc_final: 0.9079 (mmm) REVERT: C 1304 MET cc_start: 0.9475 (ttp) cc_final: 0.9135 (ptm) REVERT: D 130 MET cc_start: 0.8507 (mpp) cc_final: 0.8274 (mpp) REVERT: D 330 MET cc_start: 0.8891 (mmp) cc_final: 0.8249 (mmp) REVERT: D 372 MET cc_start: 0.9285 (mmm) cc_final: 0.8984 (mmp) REVERT: D 458 ASN cc_start: 0.9737 (t0) cc_final: 0.9454 (p0) REVERT: D 485 MET cc_start: 0.9173 (tpt) cc_final: 0.8898 (tpp) REVERT: D 608 CYS cc_start: 0.9350 (t) cc_final: 0.9124 (t) REVERT: D 625 MET cc_start: 0.9556 (tmm) cc_final: 0.9336 (tmm) REVERT: D 644 MET cc_start: 0.8997 (mpp) cc_final: 0.8749 (mpp) REVERT: D 822 MET cc_start: 0.9504 (mmp) cc_final: 0.8965 (mmm) REVERT: D 915 ILE cc_start: 0.9556 (pt) cc_final: 0.9355 (mt) REVERT: D 1025 MET cc_start: 0.8497 (tpt) cc_final: 0.8269 (tpt) REVERT: D 1239 ASP cc_start: 0.9136 (m-30) cc_final: 0.8871 (m-30) REVERT: D 1326 GLN cc_start: 0.8277 (mt0) cc_final: 0.7853 (mt0) REVERT: E 30 MET cc_start: 0.9046 (mmp) cc_final: 0.8813 (mmm) REVERT: E 36 ASP cc_start: 0.8932 (p0) cc_final: 0.8601 (p0) outliers start: 1 outliers final: 0 residues processed: 212 average time/residue: 0.1607 time to fit residues: 55.2602 Evaluate side-chains 141 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 0.4980 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN C 955 GLN D 365 GLN ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 594 GLN D 669 GLN D 771 GLN D 921 GLN D1238 GLN D1326 GLN E 61 ASN ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.045013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.032838 restraints weight = 213862.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.033934 restraints weight = 131093.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.034668 restraints weight = 93105.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.035216 restraints weight = 73036.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.035548 restraints weight = 61524.594| |-----------------------------------------------------------------------------| r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 26556 Z= 0.182 Angle : 0.638 9.912 36082 Z= 0.338 Chirality : 0.043 0.169 4124 Planarity : 0.005 0.119 4543 Dihedral : 13.596 144.543 4127 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.40 % Favored : 93.51 % Rotamer: Outliers : 0.18 % Allowed : 5.01 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: -1.74 (0.14), residues: 3172 helix: 0.06 (0.15), residues: 1070 sheet: -1.50 (0.26), residues: 345 loop : -1.92 (0.14), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C1216 TYR 0.016 0.002 TYR C1149 PHE 0.021 0.001 PHE A 231 TRP 0.021 0.002 TRP C1276 HIS 0.008 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00383 (26550) covalent geometry : angle 0.63806 (36082) hydrogen bonds : bond 0.05099 ( 962) hydrogen bonds : angle 5.55525 ( 2642) metal coordination : bond 0.00564 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 191 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.9480 (ptm) cc_final: 0.8897 (ppp) REVERT: B 51 MET cc_start: 0.9174 (mmm) cc_final: 0.8476 (mmm) REVERT: B 142 MET cc_start: 0.8539 (mmp) cc_final: 0.8194 (mmp) REVERT: C 160 ASP cc_start: 0.8277 (m-30) cc_final: 0.8005 (m-30) REVERT: C 370 MET cc_start: 0.9202 (tpt) cc_final: 0.8943 (tpp) REVERT: C 446 ASP cc_start: 0.8073 (p0) cc_final: 0.7869 (p0) REVERT: C 685 MET cc_start: 0.9153 (mtm) cc_final: 0.8724 (mtt) REVERT: C 741 MET cc_start: 0.8795 (ptp) cc_final: 0.8580 (ptt) REVERT: C 794 LEU cc_start: 0.9280 (tp) cc_final: 0.8988 (pp) REVERT: C 1025 PHE cc_start: 0.9231 (t80) cc_final: 0.8970 (t80) REVERT: C 1066 MET cc_start: 0.9140 (mmp) cc_final: 0.8831 (mmm) REVERT: C 1084 ASP cc_start: 0.9227 (m-30) cc_final: 0.9015 (m-30) REVERT: C 1170 MET cc_start: 0.9453 (mmp) cc_final: 0.9230 (mmm) REVERT: C 1304 MET cc_start: 0.9410 (ttp) cc_final: 0.9148 (ptm) REVERT: C 1319 MET cc_start: 0.9186 (tmm) cc_final: 0.8941 (tmm) REVERT: D 245 LEU cc_start: 0.9242 (tp) cc_final: 0.8995 (tp) REVERT: D 330 MET cc_start: 0.8924 (mmp) cc_final: 0.8421 (mmp) REVERT: D 372 MET cc_start: 0.9331 (mmm) cc_final: 0.9093 (mmp) REVERT: D 485 MET cc_start: 0.9013 (tpt) cc_final: 0.8794 (tpp) REVERT: D 604 MET cc_start: 0.9481 (mmm) cc_final: 0.9008 (mmm) REVERT: D 608 CYS cc_start: 0.9340 (t) cc_final: 0.9127 (t) REVERT: D 625 MET cc_start: 0.9582 (tmm) cc_final: 0.9307 (tmm) REVERT: D 644 MET cc_start: 0.8995 (mpp) cc_final: 0.8693 (mpp) REVERT: D 697 MET cc_start: 0.9250 (tmm) cc_final: 0.9026 (tmm) REVERT: D 698 MET cc_start: 0.9357 (mmm) cc_final: 0.8646 (mmm) REVERT: D 822 MET cc_start: 0.9475 (mmp) cc_final: 0.8900 (mmm) REVERT: D 915 ILE cc_start: 0.9481 (pt) cc_final: 0.9148 (mt) REVERT: D 1025 MET cc_start: 0.8188 (tpt) cc_final: 0.7920 (tpt) REVERT: D 1189 MET cc_start: 0.8659 (tpt) cc_final: 0.8275 (tpp) REVERT: D 1250 ASP cc_start: 0.9379 (m-30) cc_final: 0.9013 (p0) REVERT: D 1326 GLN cc_start: 0.8327 (mt0) cc_final: 0.7872 (mt0) REVERT: E 30 MET cc_start: 0.9138 (mmp) cc_final: 0.8893 (mmp) REVERT: E 36 ASP cc_start: 0.8980 (p0) cc_final: 0.8578 (p0) REVERT: E 53 GLU cc_start: 0.9411 (mt-10) cc_final: 0.9021 (mm-30) outliers start: 5 outliers final: 2 residues processed: 196 average time/residue: 0.1611 time to fit residues: 52.5384 Evaluate side-chains 145 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 143 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 284 optimal weight: 30.0000 chunk 206 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 176 optimal weight: 4.9990 chunk 312 optimal weight: 8.9990 chunk 73 optimal weight: 7.9990 chunk 155 optimal weight: 7.9990 chunk 252 optimal weight: 20.0000 chunk 251 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN D 465 GLN ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 921 GLN D1126 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.044104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.032108 restraints weight = 216181.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.033160 restraints weight = 133025.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.033882 restraints weight = 95373.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.034426 restraints weight = 74989.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.034802 restraints weight = 62865.610| |-----------------------------------------------------------------------------| r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26556 Z= 0.204 Angle : 0.644 10.518 36082 Z= 0.339 Chirality : 0.043 0.211 4124 Planarity : 0.005 0.076 4543 Dihedral : 13.581 147.599 4127 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.59 % Favored : 93.32 % Rotamer: Outliers : 0.07 % Allowed : 6.44 % Favored : 93.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: -1.74 (0.14), residues: 3172 helix: 0.00 (0.15), residues: 1081 sheet: -1.39 (0.27), residues: 331 loop : -1.90 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 67 TYR 0.016 0.002 TYR C1149 PHE 0.018 0.002 PHE A 231 TRP 0.015 0.002 TRP C1276 HIS 0.005 0.001 HIS C 551 Details of bonding type rmsd covalent geometry : bond 0.00428 (26550) covalent geometry : angle 0.64420 (36082) hydrogen bonds : bond 0.04793 ( 962) hydrogen bonds : angle 5.29305 ( 2642) metal coordination : bond 0.00597 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 183 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.9498 (ptm) cc_final: 0.8905 (ppp) REVERT: B 51 MET cc_start: 0.9265 (mmm) cc_final: 0.8930 (mmp) REVERT: B 86 LYS cc_start: 0.8898 (tttp) cc_final: 0.8659 (tttp) REVERT: C 160 ASP cc_start: 0.8257 (m-30) cc_final: 0.7984 (m-30) REVERT: C 562 GLU cc_start: 0.9054 (tp30) cc_final: 0.8725 (tp30) REVERT: C 685 MET cc_start: 0.9228 (mtm) cc_final: 0.8806 (mtt) REVERT: C 741 MET cc_start: 0.8787 (ptp) cc_final: 0.8568 (ptt) REVERT: C 1008 GLN cc_start: 0.9134 (tp40) cc_final: 0.8871 (pp30) REVERT: C 1025 PHE cc_start: 0.9213 (t80) cc_final: 0.8953 (t80) REVERT: C 1066 MET cc_start: 0.9203 (mmp) cc_final: 0.8830 (mmm) REVERT: C 1084 ASP cc_start: 0.9237 (m-30) cc_final: 0.8968 (m-30) REVERT: C 1107 MET cc_start: 0.8701 (pmm) cc_final: 0.8425 (pmm) REVERT: C 1119 MET cc_start: 0.9506 (mmp) cc_final: 0.9176 (mmp) REVERT: C 1170 MET cc_start: 0.9406 (mmp) cc_final: 0.9153 (mmm) REVERT: C 1273 MET cc_start: 0.9377 (mmm) cc_final: 0.8818 (mmm) REVERT: C 1304 MET cc_start: 0.9450 (ttp) cc_final: 0.9163 (ptm) REVERT: D 245 LEU cc_start: 0.9307 (tp) cc_final: 0.9020 (tp) REVERT: D 330 MET cc_start: 0.9024 (mmp) cc_final: 0.8564 (mmp) REVERT: D 372 MET cc_start: 0.9345 (mmm) cc_final: 0.9137 (mmp) REVERT: D 608 CYS cc_start: 0.9301 (t) cc_final: 0.9091 (t) REVERT: D 625 MET cc_start: 0.9604 (tmm) cc_final: 0.9370 (tmm) REVERT: D 644 MET cc_start: 0.8947 (mpp) cc_final: 0.8573 (mpp) REVERT: D 697 MET cc_start: 0.9288 (tmm) cc_final: 0.8943 (tmm) REVERT: D 698 MET cc_start: 0.9363 (mmm) cc_final: 0.8707 (mmm) REVERT: D 821 MET cc_start: 0.8977 (mmp) cc_final: 0.8732 (tpt) REVERT: D 822 MET cc_start: 0.9269 (mmp) cc_final: 0.9061 (mmm) REVERT: D 915 ILE cc_start: 0.9430 (pt) cc_final: 0.9095 (mt) REVERT: D 932 MET cc_start: 0.8741 (tmm) cc_final: 0.8524 (tmm) REVERT: D 1025 MET cc_start: 0.8112 (tpt) cc_final: 0.7823 (tpt) REVERT: D 1189 MET cc_start: 0.8709 (tpt) cc_final: 0.8178 (tpp) REVERT: D 1239 ASP cc_start: 0.9300 (m-30) cc_final: 0.9065 (m-30) REVERT: D 1250 ASP cc_start: 0.9394 (m-30) cc_final: 0.9081 (p0) REVERT: D 1326 GLN cc_start: 0.8482 (mt0) cc_final: 0.8196 (mt0) REVERT: E 30 MET cc_start: 0.9177 (mmp) cc_final: 0.8957 (mmp) REVERT: E 36 ASP cc_start: 0.9033 (p0) cc_final: 0.8626 (p0) REVERT: E 53 GLU cc_start: 0.9486 (mt-10) cc_final: 0.9070 (mm-30) outliers start: 2 outliers final: 1 residues processed: 185 average time/residue: 0.1522 time to fit residues: 46.6444 Evaluate side-chains 145 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 177 optimal weight: 2.9990 chunk 315 optimal weight: 7.9990 chunk 231 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 230 optimal weight: 5.9990 chunk 298 optimal weight: 5.9990 chunk 301 optimal weight: 8.9990 chunk 127 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 GLN C 760 ASN ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 GLN ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 921 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.044470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.032500 restraints weight = 208604.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.033557 restraints weight = 128775.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.034322 restraints weight = 91906.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.034828 restraints weight = 72240.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.035258 restraints weight = 60607.352| |-----------------------------------------------------------------------------| r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26556 Z= 0.146 Angle : 0.605 11.189 36082 Z= 0.315 Chirality : 0.043 0.171 4124 Planarity : 0.004 0.060 4543 Dihedral : 13.551 147.164 4127 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.31 % Favored : 93.60 % Rotamer: Outliers : 0.07 % Allowed : 3.31 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: -1.61 (0.14), residues: 3172 helix: 0.13 (0.15), residues: 1088 sheet: -1.31 (0.26), residues: 337 loop : -1.85 (0.14), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1331 TYR 0.016 0.001 TYR C 367 PHE 0.015 0.001 PHE A 231 TRP 0.020 0.001 TRP C1276 HIS 0.004 0.001 HIS D 777 Details of bonding type rmsd covalent geometry : bond 0.00311 (26550) covalent geometry : angle 0.60451 (36082) hydrogen bonds : bond 0.04275 ( 962) hydrogen bonds : angle 5.02202 ( 2642) metal coordination : bond 0.00359 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 187 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.9034 (tppt) cc_final: 0.8795 (tptt) REVERT: A 205 MET cc_start: 0.9453 (ptm) cc_final: 0.8874 (ppp) REVERT: B 51 MET cc_start: 0.9153 (mmm) cc_final: 0.8792 (mmt) REVERT: C 160 ASP cc_start: 0.8215 (m-30) cc_final: 0.7930 (m-30) REVERT: C 488 MET cc_start: 0.8243 (ppp) cc_final: 0.7913 (ppp) REVERT: C 492 MET cc_start: 0.9495 (pmm) cc_final: 0.8938 (pmm) REVERT: C 562 GLU cc_start: 0.9054 (tp30) cc_final: 0.8680 (tp30) REVERT: C 685 MET cc_start: 0.9269 (mtm) cc_final: 0.8812 (mtt) REVERT: C 741 MET cc_start: 0.8693 (ptp) cc_final: 0.8479 (ptt) REVERT: C 1008 GLN cc_start: 0.9110 (tp40) cc_final: 0.8802 (pp30) REVERT: C 1025 PHE cc_start: 0.9193 (t80) cc_final: 0.8905 (t80) REVERT: C 1066 MET cc_start: 0.9275 (mmp) cc_final: 0.8951 (mmm) REVERT: C 1084 ASP cc_start: 0.9283 (m-30) cc_final: 0.8948 (m-30) REVERT: C 1107 MET cc_start: 0.8723 (pmm) cc_final: 0.8461 (pmm) REVERT: C 1119 MET cc_start: 0.9470 (mmp) cc_final: 0.9044 (mmp) REVERT: C 1170 MET cc_start: 0.9389 (mmp) cc_final: 0.9139 (mmm) REVERT: C 1273 MET cc_start: 0.9339 (mmm) cc_final: 0.8822 (mmm) REVERT: C 1304 MET cc_start: 0.9463 (ttp) cc_final: 0.9199 (ptm) REVERT: D 130 MET cc_start: 0.8763 (mmp) cc_final: 0.8339 (mmm) REVERT: D 180 MET cc_start: 0.7044 (mmm) cc_final: 0.6759 (mmm) REVERT: D 237 MET cc_start: 0.9139 (ttt) cc_final: 0.8653 (tpt) REVERT: D 245 LEU cc_start: 0.9344 (tp) cc_final: 0.9064 (tp) REVERT: D 330 MET cc_start: 0.9059 (mmp) cc_final: 0.8685 (mmp) REVERT: D 608 CYS cc_start: 0.9284 (t) cc_final: 0.9070 (t) REVERT: D 625 MET cc_start: 0.9580 (tmm) cc_final: 0.9302 (tmm) REVERT: D 644 MET cc_start: 0.8954 (mpp) cc_final: 0.8624 (mpp) REVERT: D 697 MET cc_start: 0.9247 (tmm) cc_final: 0.8704 (tmm) REVERT: D 698 MET cc_start: 0.9410 (mmm) cc_final: 0.8717 (mmm) REVERT: D 822 MET cc_start: 0.9250 (mmp) cc_final: 0.9047 (mmm) REVERT: D 915 ILE cc_start: 0.9404 (pt) cc_final: 0.9059 (mt) REVERT: D 932 MET cc_start: 0.8668 (tmm) cc_final: 0.8406 (tmm) REVERT: D 1025 MET cc_start: 0.8166 (tpt) cc_final: 0.7877 (tpt) REVERT: D 1189 MET cc_start: 0.8746 (tpt) cc_final: 0.8171 (tpp) REVERT: D 1239 ASP cc_start: 0.9326 (m-30) cc_final: 0.9074 (m-30) REVERT: D 1250 ASP cc_start: 0.9339 (m-30) cc_final: 0.9060 (p0) REVERT: E 36 ASP cc_start: 0.9053 (p0) cc_final: 0.8634 (p0) REVERT: E 53 GLU cc_start: 0.9486 (mt-10) cc_final: 0.9246 (mm-30) outliers start: 2 outliers final: 1 residues processed: 189 average time/residue: 0.1539 time to fit residues: 48.3599 Evaluate side-chains 146 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 214 optimal weight: 3.9990 chunk 270 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 141 optimal weight: 30.0000 chunk 81 optimal weight: 9.9990 chunk 263 optimal weight: 0.5980 chunk 287 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 35 optimal weight: 30.0000 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 737 ASN ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.043530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.031712 restraints weight = 215261.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.032740 restraints weight = 133282.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.033457 restraints weight = 95260.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.033984 restraints weight = 74714.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.034353 restraints weight = 62489.379| |-----------------------------------------------------------------------------| r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 26556 Z= 0.199 Angle : 0.637 11.084 36082 Z= 0.332 Chirality : 0.043 0.167 4124 Planarity : 0.004 0.059 4543 Dihedral : 13.577 149.336 4127 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.00 % Favored : 92.91 % Rotamer: Outliers : 0.07 % Allowed : 3.50 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: -1.64 (0.14), residues: 3172 helix: 0.11 (0.15), residues: 1091 sheet: -1.41 (0.26), residues: 342 loop : -1.86 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1269 TYR 0.018 0.002 TYR C1149 PHE 0.014 0.001 PHE A 231 TRP 0.023 0.002 TRP C1276 HIS 0.006 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00417 (26550) covalent geometry : angle 0.63657 (36082) hydrogen bonds : bond 0.04450 ( 962) hydrogen bonds : angle 5.05083 ( 2642) metal coordination : bond 0.00455 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 179 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.9453 (ptm) cc_final: 0.8894 (ppp) REVERT: B 51 MET cc_start: 0.9156 (mmm) cc_final: 0.8778 (mmt) REVERT: C 160 ASP cc_start: 0.8199 (m-30) cc_final: 0.7892 (m-30) REVERT: C 562 GLU cc_start: 0.9014 (tp30) cc_final: 0.8679 (tp30) REVERT: C 685 MET cc_start: 0.9285 (mtm) cc_final: 0.8864 (mtt) REVERT: C 741 MET cc_start: 0.8674 (ptp) cc_final: 0.8465 (ptt) REVERT: C 1025 PHE cc_start: 0.9209 (t80) cc_final: 0.8917 (t80) REVERT: C 1084 ASP cc_start: 0.9298 (m-30) cc_final: 0.8965 (m-30) REVERT: C 1170 MET cc_start: 0.9356 (mmp) cc_final: 0.9109 (mmm) REVERT: C 1304 MET cc_start: 0.9462 (ttp) cc_final: 0.9198 (ptm) REVERT: D 130 MET cc_start: 0.8823 (mmp) cc_final: 0.8547 (mmm) REVERT: D 237 MET cc_start: 0.9099 (ttt) cc_final: 0.8700 (tpt) REVERT: D 245 LEU cc_start: 0.9419 (tp) cc_final: 0.9144 (tp) REVERT: D 330 MET cc_start: 0.9086 (mmp) cc_final: 0.8678 (mmp) REVERT: D 372 MET cc_start: 0.9103 (mmp) cc_final: 0.8838 (mmt) REVERT: D 458 ASN cc_start: 0.9786 (t0) cc_final: 0.9573 (t0) REVERT: D 608 CYS cc_start: 0.9256 (t) cc_final: 0.9051 (t) REVERT: D 625 MET cc_start: 0.9611 (tmm) cc_final: 0.9330 (tmm) REVERT: D 644 MET cc_start: 0.8875 (mpp) cc_final: 0.8536 (mpp) REVERT: D 697 MET cc_start: 0.9238 (tmm) cc_final: 0.8815 (tmm) REVERT: D 698 MET cc_start: 0.9373 (mmm) cc_final: 0.8702 (mmm) REVERT: D 822 MET cc_start: 0.9392 (mmp) cc_final: 0.8877 (mmm) REVERT: D 915 ILE cc_start: 0.9394 (pt) cc_final: 0.9018 (mt) REVERT: D 1025 MET cc_start: 0.8215 (tpt) cc_final: 0.7934 (tpt) REVERT: D 1099 TYR cc_start: 0.9558 (m-80) cc_final: 0.9347 (m-80) REVERT: D 1189 MET cc_start: 0.8729 (tpt) cc_final: 0.8171 (tpp) REVERT: D 1239 ASP cc_start: 0.9307 (m-30) cc_final: 0.9084 (m-30) REVERT: D 1250 ASP cc_start: 0.9381 (m-30) cc_final: 0.9103 (p0) REVERT: E 36 ASP cc_start: 0.9084 (p0) cc_final: 0.8705 (p0) REVERT: E 53 GLU cc_start: 0.9490 (mt-10) cc_final: 0.9212 (mm-30) outliers start: 2 outliers final: 0 residues processed: 181 average time/residue: 0.1510 time to fit residues: 45.5364 Evaluate side-chains 144 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 298 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 153 optimal weight: 0.0470 chunk 4 optimal weight: 4.9990 chunk 294 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 34 optimal weight: 0.0980 chunk 117 optimal weight: 3.9990 chunk 288 optimal weight: 0.0370 chunk 52 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 overall best weight: 1.0360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1257 GLN D 365 GLN ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.044867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.032933 restraints weight = 205199.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.034036 restraints weight = 124617.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.034818 restraints weight = 88408.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.035367 restraints weight = 68727.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.035785 restraints weight = 57057.246| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 26556 Z= 0.112 Angle : 0.611 11.938 36082 Z= 0.315 Chirality : 0.043 0.175 4124 Planarity : 0.004 0.049 4543 Dihedral : 13.488 146.786 4127 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.74 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: -1.52 (0.14), residues: 3172 helix: 0.19 (0.15), residues: 1090 sheet: -1.19 (0.26), residues: 362 loop : -1.81 (0.14), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 687 TYR 0.016 0.001 TYR C 367 PHE 0.016 0.001 PHE C 337 TRP 0.018 0.001 TRP C1276 HIS 0.003 0.001 HIS D1218 Details of bonding type rmsd covalent geometry : bond 0.00240 (26550) covalent geometry : angle 0.61102 (36082) hydrogen bonds : bond 0.04029 ( 962) hydrogen bonds : angle 4.72026 ( 2642) metal coordination : bond 0.00071 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: 0.9094 (mmm) cc_final: 0.8477 (mmm) REVERT: C 160 ASP cc_start: 0.8109 (m-30) cc_final: 0.7807 (m-30) REVERT: C 492 MET cc_start: 0.9474 (pmm) cc_final: 0.8733 (pmm) REVERT: C 562 GLU cc_start: 0.8671 (tp30) cc_final: 0.8470 (tp30) REVERT: C 685 MET cc_start: 0.9245 (mtm) cc_final: 0.8789 (mtp) REVERT: C 741 MET cc_start: 0.8596 (ptp) cc_final: 0.8369 (ptt) REVERT: C 1025 PHE cc_start: 0.9153 (t80) cc_final: 0.8884 (t80) REVERT: C 1066 MET cc_start: 0.9236 (mmp) cc_final: 0.8904 (mmm) REVERT: C 1084 ASP cc_start: 0.9265 (m-30) cc_final: 0.8917 (m-30) REVERT: C 1119 MET cc_start: 0.9375 (mmp) cc_final: 0.9053 (mmp) REVERT: C 1170 MET cc_start: 0.9346 (mmp) cc_final: 0.9089 (mmm) REVERT: C 1304 MET cc_start: 0.9399 (ttp) cc_final: 0.9150 (ptm) REVERT: D 130 MET cc_start: 0.8824 (mmp) cc_final: 0.8537 (mmm) REVERT: D 180 MET cc_start: 0.7087 (mmm) cc_final: 0.6870 (mmm) REVERT: D 237 MET cc_start: 0.9064 (ttt) cc_final: 0.8575 (tpt) REVERT: D 298 MET cc_start: 0.9298 (ttp) cc_final: 0.8623 (tmm) REVERT: D 330 MET cc_start: 0.9063 (mmp) cc_final: 0.8672 (mmp) REVERT: D 372 MET cc_start: 0.9133 (mmp) cc_final: 0.8797 (mmt) REVERT: D 458 ASN cc_start: 0.9778 (t0) cc_final: 0.9564 (t0) REVERT: D 604 MET cc_start: 0.9491 (mmt) cc_final: 0.9058 (mmm) REVERT: D 625 MET cc_start: 0.9554 (tmm) cc_final: 0.9243 (tmm) REVERT: D 644 MET cc_start: 0.8929 (mpp) cc_final: 0.8698 (mpp) REVERT: D 697 MET cc_start: 0.9171 (tmm) cc_final: 0.8660 (ppp) REVERT: D 698 MET cc_start: 0.9409 (mmm) cc_final: 0.8702 (mmt) REVERT: D 821 MET cc_start: 0.8958 (mmp) cc_final: 0.8749 (tpp) REVERT: D 915 ILE cc_start: 0.9392 (pt) cc_final: 0.8978 (mt) REVERT: D 1025 MET cc_start: 0.8176 (tpt) cc_final: 0.7918 (tpt) REVERT: D 1189 MET cc_start: 0.8729 (tpt) cc_final: 0.8195 (tpp) REVERT: D 1239 ASP cc_start: 0.9302 (m-30) cc_final: 0.9040 (m-30) REVERT: D 1250 ASP cc_start: 0.9311 (m-30) cc_final: 0.9037 (p0) REVERT: D 1326 GLN cc_start: 0.8973 (pp30) cc_final: 0.8717 (pp30) REVERT: E 30 MET cc_start: 0.9022 (mmp) cc_final: 0.8777 (mmp) REVERT: E 36 ASP cc_start: 0.9056 (p0) cc_final: 0.8632 (p0) REVERT: E 53 GLU cc_start: 0.9386 (mt-10) cc_final: 0.8976 (mm-30) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1651 time to fit residues: 52.4974 Evaluate side-chains 140 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 117 optimal weight: 9.9990 chunk 197 optimal weight: 2.9990 chunk 199 optimal weight: 0.2980 chunk 119 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 20 optimal weight: 0.0980 chunk 236 optimal weight: 8.9990 chunk 241 optimal weight: 10.0000 chunk 306 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN D 667 GLN ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN D1252 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.045212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.033316 restraints weight = 206408.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.034397 restraints weight = 125701.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.035180 restraints weight = 89247.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.035649 restraints weight = 69597.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.036046 restraints weight = 58919.926| |-----------------------------------------------------------------------------| r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 26556 Z= 0.110 Angle : 0.608 12.693 36082 Z= 0.310 Chirality : 0.043 0.232 4124 Planarity : 0.004 0.048 4543 Dihedral : 13.389 145.294 4127 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.02 % Favored : 93.88 % Rotamer: Outliers : 0.04 % Allowed : 1.55 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: -1.44 (0.14), residues: 3172 helix: 0.23 (0.16), residues: 1084 sheet: -0.99 (0.26), residues: 350 loop : -1.77 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 191 TYR 0.032 0.001 TYR D 457 PHE 0.012 0.001 PHE A 231 TRP 0.016 0.001 TRP C1276 HIS 0.003 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00240 (26550) covalent geometry : angle 0.60810 (36082) hydrogen bonds : bond 0.03877 ( 962) hydrogen bonds : angle 4.62003 ( 2642) metal coordination : bond 0.00062 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.9301 (p0) cc_final: 0.9090 (p0) REVERT: B 51 MET cc_start: 0.9074 (mmm) cc_final: 0.8692 (mmt) REVERT: C 160 ASP cc_start: 0.8165 (m-30) cc_final: 0.7842 (m-30) REVERT: C 403 MET cc_start: 0.9065 (tpt) cc_final: 0.8850 (mmm) REVERT: C 492 MET cc_start: 0.9512 (pmm) cc_final: 0.8818 (pmm) REVERT: C 562 GLU cc_start: 0.8692 (tp30) cc_final: 0.8446 (tp30) REVERT: C 685 MET cc_start: 0.9263 (mtm) cc_final: 0.8817 (mtp) REVERT: C 741 MET cc_start: 0.8554 (ptp) cc_final: 0.8303 (ptt) REVERT: C 1025 PHE cc_start: 0.9140 (t80) cc_final: 0.8929 (t80) REVERT: C 1066 MET cc_start: 0.9238 (mmp) cc_final: 0.8890 (mmm) REVERT: C 1084 ASP cc_start: 0.9258 (m-30) cc_final: 0.8934 (m-30) REVERT: C 1085 MET cc_start: 0.9425 (mmm) cc_final: 0.8932 (mmm) REVERT: C 1119 MET cc_start: 0.9399 (mmp) cc_final: 0.9074 (mmp) REVERT: C 1170 MET cc_start: 0.9356 (mmp) cc_final: 0.9089 (mmm) REVERT: C 1304 MET cc_start: 0.9423 (ttp) cc_final: 0.9148 (ptm) REVERT: D 130 MET cc_start: 0.8823 (mmp) cc_final: 0.8595 (mmm) REVERT: D 180 MET cc_start: 0.7027 (mmm) cc_final: 0.6776 (mmm) REVERT: D 237 MET cc_start: 0.9102 (ttt) cc_final: 0.8625 (tpt) REVERT: D 245 LEU cc_start: 0.9368 (tp) cc_final: 0.9132 (tp) REVERT: D 298 MET cc_start: 0.9546 (ttp) cc_final: 0.9338 (ttp) REVERT: D 330 MET cc_start: 0.9017 (mmp) cc_final: 0.8741 (mmm) REVERT: D 372 MET cc_start: 0.9195 (mmp) cc_final: 0.8737 (mmt) REVERT: D 458 ASN cc_start: 0.9763 (t0) cc_final: 0.9548 (t0) REVERT: D 479 GLU cc_start: 0.9022 (tt0) cc_final: 0.8131 (pt0) REVERT: D 604 MET cc_start: 0.9488 (mmt) cc_final: 0.9038 (mmm) REVERT: D 608 CYS cc_start: 0.9319 (t) cc_final: 0.9100 (t) REVERT: D 625 MET cc_start: 0.9550 (tmm) cc_final: 0.9247 (tmm) REVERT: D 644 MET cc_start: 0.8918 (mpp) cc_final: 0.8687 (mpp) REVERT: D 821 MET cc_start: 0.9034 (mmp) cc_final: 0.8769 (tpp) REVERT: D 822 MET cc_start: 0.9266 (mmp) cc_final: 0.9001 (mmm) REVERT: D 915 ILE cc_start: 0.9385 (pt) cc_final: 0.8981 (mt) REVERT: D 1025 MET cc_start: 0.8240 (tpt) cc_final: 0.7947 (tpt) REVERT: D 1189 MET cc_start: 0.8715 (tpt) cc_final: 0.8160 (tpp) REVERT: D 1239 ASP cc_start: 0.9310 (m-30) cc_final: 0.9045 (m-30) REVERT: D 1250 ASP cc_start: 0.9325 (m-30) cc_final: 0.9054 (p0) REVERT: D 1326 GLN cc_start: 0.8993 (pp30) cc_final: 0.8716 (pp30) REVERT: E 30 MET cc_start: 0.9056 (mmp) cc_final: 0.8840 (mmm) REVERT: E 36 ASP cc_start: 0.9069 (p0) cc_final: 0.8674 (p0) REVERT: E 53 GLU cc_start: 0.9364 (mt-10) cc_final: 0.9156 (mm-30) outliers start: 1 outliers final: 1 residues processed: 187 average time/residue: 0.1676 time to fit residues: 51.5093 Evaluate side-chains 147 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 146 optimal weight: 7.9990 chunk 252 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 230 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 231 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1313 HIS D 365 GLN D 489 ASN ** D 771 GLN ** 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 = 0.3105 r_free = 0.3105 target = 0.043674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.031949 restraints weight = 214445.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.032985 restraints weight = 131836.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.033746 restraints weight = 93740.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.034225 restraints weight = 73326.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.034617 restraints weight = 61617.482| |-----------------------------------------------------------------------------| r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26556 Z= 0.189 Angle : 0.645 12.076 36082 Z= 0.334 Chirality : 0.043 0.199 4124 Planarity : 0.004 0.053 4543 Dihedral : 13.389 146.841 4127 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.06 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: -1.47 (0.14), residues: 3172 helix: 0.17 (0.16), residues: 1086 sheet: -0.96 (0.27), residues: 345 loop : -1.78 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 744 TYR 0.019 0.002 TYR C1285 PHE 0.023 0.001 PHE D 763 TRP 0.013 0.001 TRP C1276 HIS 0.005 0.001 HIS D 777 Details of bonding type rmsd covalent geometry : bond 0.00397 (26550) covalent geometry : angle 0.64464 (36082) hydrogen bonds : bond 0.04232 ( 962) hydrogen bonds : angle 4.87000 ( 2642) metal coordination : bond 0.00412 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.9533 (ppp) cc_final: 0.9045 (ppp) REVERT: B 51 MET cc_start: 0.9136 (mmm) cc_final: 0.8762 (mmt) REVERT: C 133 ASN cc_start: 0.9204 (t0) cc_final: 0.8821 (t0) REVERT: C 160 ASP cc_start: 0.8179 (m-30) cc_final: 0.7879 (m-30) REVERT: C 562 GLU cc_start: 0.8705 (tp30) cc_final: 0.8419 (tp30) REVERT: C 685 MET cc_start: 0.9280 (mtm) cc_final: 0.8847 (mtp) REVERT: C 741 MET cc_start: 0.8583 (ptp) cc_final: 0.8361 (ptt) REVERT: C 1008 GLN cc_start: 0.9147 (tp40) cc_final: 0.8676 (pp30) REVERT: C 1025 PHE cc_start: 0.9131 (t80) cc_final: 0.8919 (t80) REVERT: C 1066 MET cc_start: 0.9271 (mmp) cc_final: 0.8875 (mmm) REVERT: C 1084 ASP cc_start: 0.9296 (m-30) cc_final: 0.8947 (m-30) REVERT: C 1170 MET cc_start: 0.9329 (mmp) cc_final: 0.9036 (mmm) REVERT: C 1304 MET cc_start: 0.9408 (ttp) cc_final: 0.9170 (ptm) REVERT: D 130 MET cc_start: 0.8862 (mmp) cc_final: 0.8528 (mmm) REVERT: D 237 MET cc_start: 0.9143 (ttt) cc_final: 0.8792 (tpt) REVERT: D 245 LEU cc_start: 0.9338 (tp) cc_final: 0.9122 (tp) REVERT: D 298 MET cc_start: 0.9591 (ttp) cc_final: 0.9169 (ttp) REVERT: D 330 MET cc_start: 0.9062 (mmp) cc_final: 0.8793 (mmm) REVERT: D 372 MET cc_start: 0.9197 (mmp) cc_final: 0.8772 (mmt) REVERT: D 449 LEU cc_start: 0.9464 (mm) cc_final: 0.9050 (tp) REVERT: D 454 CYS cc_start: 0.9164 (m) cc_final: 0.8557 (m) REVERT: D 604 MET cc_start: 0.9453 (mmt) cc_final: 0.9010 (mmm) REVERT: D 608 CYS cc_start: 0.9281 (t) cc_final: 0.9016 (t) REVERT: D 625 MET cc_start: 0.9590 (tmm) cc_final: 0.9304 (tmm) REVERT: D 644 MET cc_start: 0.8960 (mpp) cc_final: 0.8577 (mpp) REVERT: D 697 MET cc_start: 0.9246 (tmm) cc_final: 0.8574 (ppp) REVERT: D 698 MET cc_start: 0.9384 (mmm) cc_final: 0.8739 (mmm) REVERT: D 821 MET cc_start: 0.8987 (mmp) cc_final: 0.8752 (tpp) REVERT: D 822 MET cc_start: 0.9268 (mmp) cc_final: 0.8921 (mmm) REVERT: D 915 ILE cc_start: 0.9369 (pt) cc_final: 0.8991 (mt) REVERT: D 1025 MET cc_start: 0.8188 (tpt) cc_final: 0.7892 (tpt) REVERT: D 1189 MET cc_start: 0.8673 (tpt) cc_final: 0.8115 (tpp) REVERT: D 1239 ASP cc_start: 0.9308 (m-30) cc_final: 0.9081 (m-30) REVERT: D 1250 ASP cc_start: 0.9372 (m-30) cc_final: 0.9114 (p0) REVERT: D 1326 GLN cc_start: 0.9027 (pp30) cc_final: 0.8740 (pp30) REVERT: E 30 MET cc_start: 0.9045 (mmp) cc_final: 0.8826 (mmp) REVERT: E 36 ASP cc_start: 0.9080 (p0) cc_final: 0.8657 (p0) REVERT: E 53 GLU cc_start: 0.9417 (mt-10) cc_final: 0.9003 (mm-30) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1634 time to fit residues: 45.6569 Evaluate side-chains 141 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 78 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 264 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 221 optimal weight: 5.9990 chunk 141 optimal weight: 0.1980 chunk 208 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 193 optimal weight: 8.9990 chunk 289 optimal weight: 9.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.044219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.032608 restraints weight = 208231.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.033623 restraints weight = 125021.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.034370 restraints weight = 88608.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.034894 restraints weight = 68817.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.035285 restraints weight = 57266.544| |-----------------------------------------------------------------------------| r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26556 Z= 0.139 Angle : 0.621 12.968 36082 Z= 0.318 Chirality : 0.043 0.192 4124 Planarity : 0.004 0.053 4543 Dihedral : 13.373 145.511 4127 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.37 % Favored : 93.54 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: -1.50 (0.14), residues: 3172 helix: 0.10 (0.15), residues: 1103 sheet: -0.94 (0.26), residues: 353 loop : -1.78 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 191 TYR 0.019 0.001 TYR C1018 PHE 0.020 0.001 PHE D 763 TRP 0.012 0.001 TRP C1276 HIS 0.003 0.001 HIS D 777 Details of bonding type rmsd covalent geometry : bond 0.00301 (26550) covalent geometry : angle 0.62079 (36082) hydrogen bonds : bond 0.03942 ( 962) hydrogen bonds : angle 4.77137 ( 2642) metal coordination : bond 0.00205 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.9564 (ppp) cc_final: 0.9058 (ppp) REVERT: B 51 MET cc_start: 0.9077 (mmm) cc_final: 0.8729 (mmt) REVERT: C 133 ASN cc_start: 0.9243 (t0) cc_final: 0.8842 (t0) REVERT: C 160 ASP cc_start: 0.8141 (m-30) cc_final: 0.7847 (m-30) REVERT: C 562 GLU cc_start: 0.8667 (tp30) cc_final: 0.8378 (tp30) REVERT: C 685 MET cc_start: 0.9269 (mtm) cc_final: 0.8823 (mtp) REVERT: C 741 MET cc_start: 0.8525 (ptp) cc_final: 0.8309 (ptt) REVERT: C 1008 GLN cc_start: 0.9161 (tp40) cc_final: 0.8685 (pp30) REVERT: C 1025 PHE cc_start: 0.9123 (t80) cc_final: 0.8907 (t80) REVERT: C 1066 MET cc_start: 0.9263 (mmp) cc_final: 0.8946 (mmm) REVERT: C 1084 ASP cc_start: 0.9277 (m-30) cc_final: 0.8941 (m-30) REVERT: C 1085 MET cc_start: 0.9389 (mmm) cc_final: 0.8941 (mmm) REVERT: C 1131 MET cc_start: 0.9163 (ptp) cc_final: 0.8884 (ppp) REVERT: C 1170 MET cc_start: 0.9331 (mmp) cc_final: 0.9075 (mmm) REVERT: C 1304 MET cc_start: 0.9433 (ttp) cc_final: 0.9200 (ptm) REVERT: D 130 MET cc_start: 0.8800 (mmp) cc_final: 0.8440 (mmm) REVERT: D 180 MET cc_start: 0.7221 (mmm) cc_final: 0.7008 (mmm) REVERT: D 237 MET cc_start: 0.9133 (ttt) cc_final: 0.8889 (tpp) REVERT: D 245 LEU cc_start: 0.9346 (tp) cc_final: 0.9133 (tp) REVERT: D 298 MET cc_start: 0.9585 (ttp) cc_final: 0.9117 (ttp) REVERT: D 330 MET cc_start: 0.9047 (mmp) cc_final: 0.8804 (mmm) REVERT: D 604 MET cc_start: 0.9467 (mmt) cc_final: 0.9006 (mmm) REVERT: D 608 CYS cc_start: 0.9297 (t) cc_final: 0.9033 (t) REVERT: D 625 MET cc_start: 0.9585 (tmm) cc_final: 0.9299 (tmm) REVERT: D 644 MET cc_start: 0.8969 (mpp) cc_final: 0.8632 (mpp) REVERT: D 697 MET cc_start: 0.9229 (tmm) cc_final: 0.9008 (ppp) REVERT: D 821 MET cc_start: 0.8963 (mmp) cc_final: 0.8726 (tpp) REVERT: D 822 MET cc_start: 0.9244 (mmp) cc_final: 0.8961 (mmm) REVERT: D 915 ILE cc_start: 0.9366 (pt) cc_final: 0.8982 (mt) REVERT: D 1025 MET cc_start: 0.8229 (tpt) cc_final: 0.7959 (tpt) REVERT: D 1189 MET cc_start: 0.8690 (tpt) cc_final: 0.8182 (tpp) REVERT: D 1239 ASP cc_start: 0.9302 (m-30) cc_final: 0.9070 (m-30) REVERT: D 1326 GLN cc_start: 0.9018 (pp30) cc_final: 0.8723 (pp30) REVERT: E 36 ASP cc_start: 0.9078 (p0) cc_final: 0.8697 (p0) REVERT: E 53 GLU cc_start: 0.9390 (mt-10) cc_final: 0.9108 (mm-30) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1648 time to fit residues: 48.0637 Evaluate side-chains 146 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 32 optimal weight: 0.4980 chunk 316 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 279 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 238 optimal weight: 9.9990 chunk 253 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 272 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1111 GLN D 365 GLN ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.044370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.032629 restraints weight = 209892.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.033713 restraints weight = 127740.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.034472 restraints weight = 90644.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.035009 restraints weight = 70637.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.035372 restraints weight = 58795.770| |-----------------------------------------------------------------------------| r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 26556 Z= 0.127 Angle : 0.623 13.210 36082 Z= 0.318 Chirality : 0.043 0.193 4124 Planarity : 0.004 0.049 4543 Dihedral : 13.316 145.123 4127 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.53 % Favored : 93.41 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: -1.45 (0.14), residues: 3172 helix: 0.11 (0.15), residues: 1097 sheet: -0.83 (0.27), residues: 348 loop : -1.75 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 191 TYR 0.016 0.001 TYR C 367 PHE 0.019 0.001 PHE D 763 TRP 0.019 0.001 TRP C1276 HIS 0.003 0.001 HIS D 777 Details of bonding type rmsd covalent geometry : bond 0.00276 (26550) covalent geometry : angle 0.62341 (36082) hydrogen bonds : bond 0.03905 ( 962) hydrogen bonds : angle 4.69876 ( 2642) metal coordination : bond 0.00158 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.9575 (ppp) cc_final: 0.9055 (ppp) REVERT: B 51 MET cc_start: 0.9083 (mmm) cc_final: 0.8723 (mmt) REVERT: B 142 MET cc_start: 0.8749 (tpt) cc_final: 0.8163 (mmm) REVERT: C 133 ASN cc_start: 0.9247 (t0) cc_final: 0.8864 (p0) REVERT: C 160 ASP cc_start: 0.8179 (m-30) cc_final: 0.7870 (m-30) REVERT: C 562 GLU cc_start: 0.8681 (tp30) cc_final: 0.8410 (tp30) REVERT: C 685 MET cc_start: 0.9270 (mtm) cc_final: 0.8803 (mtp) REVERT: C 741 MET cc_start: 0.8495 (ptp) cc_final: 0.8268 (ptt) REVERT: C 1008 GLN cc_start: 0.9159 (tp40) cc_final: 0.8673 (pp30) REVERT: C 1025 PHE cc_start: 0.9133 (t80) cc_final: 0.8923 (t80) REVERT: C 1084 ASP cc_start: 0.9263 (m-30) cc_final: 0.8926 (m-30) REVERT: C 1085 MET cc_start: 0.9351 (mmm) cc_final: 0.8894 (mmm) REVERT: C 1119 MET cc_start: 0.9342 (mmp) cc_final: 0.9124 (mmp) REVERT: C 1131 MET cc_start: 0.9077 (ptp) cc_final: 0.8803 (ppp) REVERT: C 1170 MET cc_start: 0.9338 (mmp) cc_final: 0.9075 (mmm) REVERT: C 1281 TYR cc_start: 0.8129 (m-10) cc_final: 0.7855 (m-10) REVERT: C 1304 MET cc_start: 0.9471 (ttp) cc_final: 0.9209 (ptm) REVERT: D 130 MET cc_start: 0.8776 (mmp) cc_final: 0.8436 (mmm) REVERT: D 237 MET cc_start: 0.9147 (ttt) cc_final: 0.8922 (tpp) REVERT: D 245 LEU cc_start: 0.9386 (tp) cc_final: 0.9164 (tp) REVERT: D 298 MET cc_start: 0.9605 (ttp) cc_final: 0.9116 (ttp) REVERT: D 330 MET cc_start: 0.9044 (mmp) cc_final: 0.8788 (mmm) REVERT: D 372 MET cc_start: 0.9100 (mmp) cc_final: 0.8748 (mmt) REVERT: D 604 MET cc_start: 0.9468 (mmt) cc_final: 0.9000 (mmm) REVERT: D 608 CYS cc_start: 0.9308 (t) cc_final: 0.9054 (t) REVERT: D 625 MET cc_start: 0.9571 (tmm) cc_final: 0.9282 (tmm) REVERT: D 644 MET cc_start: 0.8966 (mpp) cc_final: 0.8619 (mpp) REVERT: D 697 MET cc_start: 0.9217 (tmm) cc_final: 0.9003 (ppp) REVERT: D 743 MET cc_start: 0.7715 (mmp) cc_final: 0.7508 (mmp) REVERT: D 821 MET cc_start: 0.9002 (mmp) cc_final: 0.8741 (tpp) REVERT: D 822 MET cc_start: 0.9231 (mmp) cc_final: 0.8916 (mmm) REVERT: D 915 ILE cc_start: 0.9364 (pt) cc_final: 0.8974 (mt) REVERT: D 1025 MET cc_start: 0.8242 (tpt) cc_final: 0.7974 (tpt) REVERT: D 1189 MET cc_start: 0.8670 (tpt) cc_final: 0.8243 (tpp) REVERT: D 1239 ASP cc_start: 0.9301 (m-30) cc_final: 0.9062 (m-30) REVERT: D 1326 GLN cc_start: 0.9053 (pp30) cc_final: 0.8757 (pp30) REVERT: E 30 MET cc_start: 0.9045 (mmp) cc_final: 0.8814 (mmm) REVERT: E 36 ASP cc_start: 0.9067 (p0) cc_final: 0.8647 (p0) REVERT: E 53 GLU cc_start: 0.9308 (mt-10) cc_final: 0.9080 (mm-30) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1639 time to fit residues: 47.4053 Evaluate side-chains 144 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 116 optimal weight: 20.0000 chunk 148 optimal weight: 8.9990 chunk 215 optimal weight: 1.9990 chunk 197 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 214 optimal weight: 2.9990 chunk 297 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 107 optimal weight: 0.0010 chunk 114 optimal weight: 10.0000 chunk 199 optimal weight: 0.3980 overall best weight: 1.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.044868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.033026 restraints weight = 206821.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.034134 restraints weight = 124751.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.034932 restraints weight = 87513.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.035450 restraints weight = 67938.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.035861 restraints weight = 56725.265| |-----------------------------------------------------------------------------| r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 26556 Z= 0.111 Angle : 0.612 13.457 36082 Z= 0.311 Chirality : 0.043 0.190 4124 Planarity : 0.004 0.048 4543 Dihedral : 13.224 144.321 4127 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.96 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: -1.42 (0.14), residues: 3172 helix: 0.12 (0.15), residues: 1100 sheet: -0.80 (0.27), residues: 349 loop : -1.72 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 709 TYR 0.019 0.001 TYR C1018 PHE 0.017 0.001 PHE D 763 TRP 0.025 0.001 TRP C1276 HIS 0.003 0.001 HIS D 777 Details of bonding type rmsd covalent geometry : bond 0.00243 (26550) covalent geometry : angle 0.61248 (36082) hydrogen bonds : bond 0.03776 ( 962) hydrogen bonds : angle 4.60326 ( 2642) metal coordination : bond 0.00081 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3763.69 seconds wall clock time: 66 minutes 12.79 seconds (3972.79 seconds total)