Starting phenix.real_space_refine on Sun Sep 13 23:17:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7q0j_13745/09_2026/7q0j_13745.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q0j_13745/09_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_13745/09_2026/7q0j_13745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q0j_13745/09_2026/7q0j_13745.map" model { file = "/net/cci-nas-00/data/ceres_data/7q0j_13745/09_2026/7q0j_13745.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q0j_13745/09_2026/7q0j_13745.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7q0j_13745/09_2026/7q0j_13745.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7q0j_13745/09_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-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: 4.48, per 1000 atoms: 0.17 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: 1.77 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: 2.55 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: 5.44 Time building geometry restraints manager: 2.39 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=" C3' DC T 3 " pdb=" C2' DC T 3 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.63e+01 bond pdb=" C3' DC T 25 " pdb=" C2' DC T 25 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DG N 26 " pdb=" C2' DG N 26 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.88e+00 bond pdb=" C3' DT T 12 " pdb=" C2' DT T 12 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.53e+00 bond pdb=" C3' DC T 14 " pdb=" C2' DC T 14 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.97e+00 ... (remaining 26545 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 35408 2.54 - 5.07: 580 5.07 - 7.61: 77 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=" O4' DG T 19 " pdb=" C4' DG T 19 " pdb=" C3' DG T 19 " ideal model delta sigma weight residual 106.00 103.04 2.96 6.00e-01 2.78e+00 2.44e+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 ... (remaining 36077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.13: 15446 28.13 - 56.27: 677 56.27 - 84.40: 81 84.40 - 112.54: 1 112.54 - 140.67: 2 Dihedral angle restraints: 16207 sinusoidal: 7053 harmonic: 9154 Sorted by residual: dihedral pdb=" C4' C R 5 " pdb=" C3' C R 5 " pdb=" C2' C R 5 " pdb=" C1' C R 5 " ideal model delta sinusoidal sigma weight residual 36.35 -37.09 73.43 1 3.10e+00 1.04e-01 7.14e+02 dihedral pdb=" O4' C R 5 " pdb=" C4' C R 5 " pdb=" C3' C R 5 " pdb=" C2' C R 5 " ideal model delta sinusoidal sigma weight residual -35.15 25.51 -60.66 1 4.00e+00 6.25e-02 3.06e+02 dihedral pdb=" O4' C R 5 " pdb=" C2' C R 5 " pdb=" C1' C R 5 " pdb=" C3' C R 5 " ideal model delta sinusoidal sigma weight residual -94.41 -36.78 -57.63 3 3.80e+00 6.93e-02 1.47e+02 ... (remaining 16204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3292 0.061 - 0.121: 739 0.121 - 0.182: 70 0.182 - 0.242: 18 0.242 - 0.303: 5 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=" C2' C R 5 " pdb=" C3' C R 5 " pdb=" O2' C R 5 " pdb=" C1' C R 5 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" P C R 5 " pdb=" OP1 C R 5 " pdb=" OP2 C R 5 " pdb=" O5' C R 5 " both_signs ideal model delta sigma weight residual True 2.17 -2.45 -0.27 2.00e-01 2.50e+01 1.87e+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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 25.820 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.246 26556 Z= 0.233 Angle : 0.806 12.680 36082 Z= 0.448 Chirality : 0.051 0.303 4124 Planarity : 0.006 0.135 4543 Dihedral : 14.721 140.671 10319 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/Z covalent geometry : bond 0.00373 / 0.21 (26550) covalent geometry : angle 0.80648 / 0.45 (36082) hydrogen bonds : bond 0.23176 / 15.86 ( 962) hydrogen bonds : angle 7.49864 / 5.14 ( 2642) metal coordination : bond 0.18390 / 9.05 ( 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 : 1.077 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: 0.1764 time to fit residues: 60.7632 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 : 1.091 ------------------------------------------------------------------------------- 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... ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.045226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.033020 restraints weight = 213250.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.034110 restraints weight = 130778.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.034851 restraints weight = 93153.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.035422 restraints weight = 72933.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.035787 restraints weight = 61121.928| |-----------------------------------------------------------------------------| r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26556 Z= 0.193 Angle : 0.696 21.046 36082 Z= 0.365 Chirality : 0.047 0.866 4124 Planarity : 0.006 0.138 4543 Dihedral : 12.708 143.155 4073 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.68 % Favored : 93.22 % Rotamer: Outliers : 0.11 % Allowed : 4.67 % Favored : 95.22 % 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: -1.82 (0.14), residues: 3172 helix: 0.01 (0.16), residues: 1060 sheet: -1.62 (0.26), residues: 354 loop : -1.94 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG D 709 TYR 0.023 0.002 TYR C1018 PHE 0.024 0.001 PHE C 337 TRP 0.021 0.002 TRP C1276 HIS 0.010 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.19 (26550) covalent geometry : angle 0.69644 / 0.36 (36082) hydrogen bonds : bond 0.05435 / 3.75 ( 962) hydrogen bonds : angle 5.76785 / 3.95 ( 2642) metal coordination : bond 0.01428 / 0.73 ( 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 190 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 187 time to evaluate : 1.086 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 194 GLN cc_start: 0.9127 (mp10) cc_final: 0.8756 (pp30) REVERT: A 205 MET cc_start: 0.9473 (ptm) cc_final: 0.8900 (ppp) REVERT: B 51 MET cc_start: 0.9167 (mmm) cc_final: 0.8461 (mmm) REVERT: B 142 MET cc_start: 0.8569 (mmp) cc_final: 0.8183 (mmp) REVERT: C 160 ASP cc_start: 0.8319 (m-30) cc_final: 0.8043 (m-30) REVERT: C 446 ASP cc_start: 0.8210 (p0) cc_final: 0.7987 (p0) REVERT: C 685 MET cc_start: 0.9103 (mtm) cc_final: 0.8684 (mtt) REVERT: C 794 LEU cc_start: 0.9299 (tp) cc_final: 0.9029 (pp) REVERT: C 1025 PHE cc_start: 0.9290 (t80) cc_final: 0.9039 (t80) REVERT: C 1066 MET cc_start: 0.9128 (mmp) cc_final: 0.8776 (mmm) REVERT: C 1119 MET cc_start: 0.9384 (mmp) cc_final: 0.9066 (mmp) REVERT: C 1304 MET cc_start: 0.9444 (ttp) cc_final: 0.9154 (ptm) REVERT: C 1319 MET cc_start: 0.9228 (tmm) cc_final: 0.8977 (tmm) REVERT: D 245 LEU cc_start: 0.9229 (tp) cc_final: 0.8959 (tp) REVERT: D 330 MET cc_start: 0.8919 (mmp) cc_final: 0.8419 (mmp) REVERT: D 429 LEU cc_start: 0.9443 (tp) cc_final: 0.9240 (tp) REVERT: D 449 LEU cc_start: 0.9599 (mm) cc_final: 0.9228 (tp) REVERT: D 454 CYS cc_start: 0.9275 (m) cc_final: 0.8745 (m) REVERT: D 485 MET cc_start: 0.9030 (tpt) cc_final: 0.8792 (tpp) REVERT: D 604 MET cc_start: 0.9469 (mmm) cc_final: 0.8981 (mmm) REVERT: D 608 CYS cc_start: 0.9345 (t) cc_final: 0.9129 (t) REVERT: D 625 MET cc_start: 0.9571 (tmm) cc_final: 0.9344 (tmm) REVERT: D 644 MET cc_start: 0.8989 (mpp) cc_final: 0.8688 (mpp) REVERT: D 698 MET cc_start: 0.9391 (mmm) cc_final: 0.8707 (mmm) REVERT: D 822 MET cc_start: 0.9490 (mmp) cc_final: 0.8836 (mmm) REVERT: D 915 ILE cc_start: 0.9458 (pt) cc_final: 0.9142 (mm) REVERT: D 1025 MET cc_start: 0.8283 (tpt) cc_final: 0.7961 (tpt) REVERT: D 1189 MET cc_start: 0.8645 (tpt) cc_final: 0.8166 (tpp) REVERT: D 1239 ASP cc_start: 0.9279 (m-30) cc_final: 0.9073 (m-30) REVERT: D 1250 ASP cc_start: 0.9415 (m-30) cc_final: 0.8968 (p0) REVERT: D 1326 GLN cc_start: 0.8286 (mt0) cc_final: 0.7850 (mt0) REVERT: E 30 MET cc_start: 0.9147 (mmp) cc_final: 0.8900 (mmp) REVERT: E 36 ASP cc_start: 0.8937 (p0) cc_final: 0.8542 (p0) outliers start: 3 outliers final: 1 residues processed: 190 average time/residue: 0.1651 time to fit residues: 52.4163 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 : 1.017 ------------------------------------------------------------------------------- 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: 20.0000 chunk 206 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 chunk 312 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 155 optimal weight: 10.0000 chunk 252 optimal weight: 5.9990 chunk 251 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ** 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 = 0.3167 r_free = 0.3167 target = 0.045912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.033717 restraints weight = 208246.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.034844 restraints weight = 126276.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.035623 restraints weight = 89162.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.036168 restraints weight = 69175.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.036592 restraints weight = 57902.923| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26556 Z= 0.122 Angle : 0.630 11.246 36082 Z= 0.327 Chirality : 0.045 0.360 4124 Planarity : 0.005 0.083 4543 Dihedral : 12.551 142.241 4073 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.99 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % 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: -1.71 (0.14), residues: 3172 helix: 0.07 (0.16), residues: 1074 sheet: -1.45 (0.26), residues: 335 loop : -1.90 (0.14), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 403 TYR 0.015 0.001 TYR C 367 PHE 0.018 0.001 PHE A 231 TRP 0.014 0.001 TRP C1276 HIS 0.004 0.001 HIS C 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (26550) covalent geometry : angle 0.63014 / 0.33 (36082) hydrogen bonds : bond 0.04910 / 3.38 ( 962) hydrogen bonds : angle 5.32375 / 3.66 ( 2642) metal coordination : bond 0.00124 / 0.07 ( 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 199 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 1.050 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: 0.9464 (ptm) cc_final: 0.8849 (ppp) REVERT: B 51 MET cc_start: 0.9193 (mmm) cc_final: 0.8576 (mmm) REVERT: B 142 MET cc_start: 0.8478 (mmp) cc_final: 0.8190 (mmp) REVERT: C 160 ASP cc_start: 0.8246 (m-30) cc_final: 0.7965 (m-30) REVERT: C 685 MET cc_start: 0.9158 (mtm) cc_final: 0.8735 (mtt) REVERT: C 741 MET cc_start: 0.8734 (ptp) cc_final: 0.8479 (ptt) REVERT: C 794 LEU cc_start: 0.9285 (tp) cc_final: 0.9016 (pp) REVERT: C 1025 PHE cc_start: 0.9217 (t80) cc_final: 0.8979 (t80) REVERT: C 1084 ASP cc_start: 0.9261 (m-30) cc_final: 0.8990 (m-30) REVERT: C 1170 MET cc_start: 0.9443 (mmp) cc_final: 0.9236 (mmm) REVERT: C 1273 MET cc_start: 0.9418 (mmm) cc_final: 0.8886 (mmm) REVERT: C 1279 GLU cc_start: 0.9242 (pm20) cc_final: 0.9038 (pm20) REVERT: C 1304 MET cc_start: 0.9439 (ttp) cc_final: 0.9134 (ptm) REVERT: D 330 MET cc_start: 0.8912 (mmp) cc_final: 0.8396 (mmp) REVERT: D 372 MET cc_start: 0.9085 (mmp) cc_final: 0.8766 (mmt) REVERT: D 608 CYS cc_start: 0.9383 (t) cc_final: 0.9169 (t) REVERT: D 625 MET cc_start: 0.9585 (tmm) cc_final: 0.9316 (tmm) REVERT: D 644 MET cc_start: 0.8982 (mpp) cc_final: 0.8699 (mpp) REVERT: D 697 MET cc_start: 0.9257 (tmm) cc_final: 0.8875 (tmm) REVERT: D 698 MET cc_start: 0.9402 (mmm) cc_final: 0.8702 (mmm) REVERT: D 821 MET cc_start: 0.9036 (mmp) cc_final: 0.8697 (tpp) REVERT: D 822 MET cc_start: 0.9243 (mmp) cc_final: 0.8943 (mmm) REVERT: D 915 ILE cc_start: 0.9453 (pt) cc_final: 0.9138 (mm) REVERT: D 1025 MET cc_start: 0.8232 (tpt) cc_final: 0.7919 (tpt) REVERT: D 1189 MET cc_start: 0.8695 (tpt) cc_final: 0.8126 (tpp) REVERT: D 1239 ASP cc_start: 0.9300 (m-30) cc_final: 0.9023 (m-30) REVERT: D 1250 ASP cc_start: 0.9360 (m-30) cc_final: 0.9007 (p0) REVERT: D 1326 GLN cc_start: 0.8384 (mt0) cc_final: 0.7852 (mt0) REVERT: E 30 MET cc_start: 0.9135 (mmp) cc_final: 0.8862 (mmp) REVERT: E 36 ASP cc_start: 0.8904 (p0) cc_final: 0.8523 (p0) REVERT: E 53 GLU cc_start: 0.9399 (mt-10) cc_final: 0.9100 (mm-30) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.1697 time to fit residues: 55.7956 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 : 1.014 ------------------------------------------------------------------------------- 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: 8.9990 chunk 315 optimal weight: 4.9990 chunk 231 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 175 optimal weight: 9.9990 chunk 230 optimal weight: 5.9990 chunk 298 optimal weight: 10.0000 chunk 301 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 3 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.044137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.032206 restraints weight = 215449.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.033263 restraints weight = 132895.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.033984 restraints weight = 95035.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.034479 restraints weight = 74767.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.034897 restraints weight = 62900.581| |-----------------------------------------------------------------------------| r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 26556 Z= 0.230 Angle : 0.690 10.408 36082 Z= 0.358 Chirality : 0.044 0.265 4124 Planarity : 0.005 0.065 4543 Dihedral : 12.579 144.807 4073 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.22 % Favored : 92.69 % Rotamer: Outliers : 0.04 % Allowed : 3.79 % Favored : 96.17 % 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: -1.73 (0.14), residues: 3172 helix: 0.04 (0.15), residues: 1079 sheet: -1.50 (0.26), residues: 353 loop : -1.89 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 709 TYR 0.021 0.002 TYR C1149 PHE 0.018 0.002 PHE A 231 TRP 0.014 0.002 TRP C1276 HIS 0.006 0.001 HIS D 907 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.23 (26550) covalent geometry : angle 0.68967 / 0.36 (36082) hydrogen bonds : bond 0.04942 / 3.40 ( 962) hydrogen bonds : angle 5.35767 / 3.68 ( 2642) metal coordination : bond 0.00766 / 0.44 ( 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 175 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 1.047 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: 0.9505 (ptm) cc_final: 0.8955 (ppp) REVERT: B 142 MET cc_start: 0.8544 (mmp) cc_final: 0.8106 (mmp) REVERT: C 160 ASP cc_start: 0.8279 (m-30) cc_final: 0.7998 (m-30) REVERT: C 685 MET cc_start: 0.9215 (mtm) cc_final: 0.8762 (mtt) REVERT: C 741 MET cc_start: 0.8751 (ptp) cc_final: 0.8545 (ptt) REVERT: C 1008 GLN cc_start: 0.9121 (tp40) cc_final: 0.8869 (pp30) REVERT: C 1025 PHE cc_start: 0.9196 (t80) cc_final: 0.8935 (t80) REVERT: C 1084 ASP cc_start: 0.9251 (m-30) cc_final: 0.9026 (m-30) REVERT: C 1119 MET cc_start: 0.9505 (mmp) cc_final: 0.9075 (mmp) REVERT: C 1170 MET cc_start: 0.9421 (mmp) cc_final: 0.9192 (mmm) REVERT: C 1304 MET cc_start: 0.9441 (ttp) cc_final: 0.9174 (ptm) REVERT: D 124 ILE cc_start: 0.9542 (mp) cc_final: 0.9272 (mp) REVERT: D 180 MET cc_start: 0.7010 (mmm) cc_final: 0.6741 (mmm) REVERT: D 237 MET cc_start: 0.9214 (ttt) cc_final: 0.8692 (tpt) REVERT: D 245 LEU cc_start: 0.9273 (tp) cc_final: 0.9029 (tp) REVERT: D 330 MET cc_start: 0.8970 (mmp) cc_final: 0.8475 (mmp) REVERT: D 372 MET cc_start: 0.9201 (mmp) cc_final: 0.8846 (mmt) REVERT: D 458 ASN cc_start: 0.9775 (t0) cc_final: 0.9572 (t0) REVERT: D 485 MET cc_start: 0.9038 (tpt) cc_final: 0.8761 (tpp) REVERT: D 608 CYS cc_start: 0.9311 (t) cc_final: 0.9108 (t) REVERT: D 625 MET cc_start: 0.9569 (tmm) cc_final: 0.9129 (tmm) REVERT: D 644 MET cc_start: 0.8948 (mpp) cc_final: 0.8583 (mpp) REVERT: D 697 MET cc_start: 0.9316 (tmm) cc_final: 0.8959 (tmm) REVERT: D 698 MET cc_start: 0.9399 (mmm) cc_final: 0.8739 (mmm) REVERT: D 821 MET cc_start: 0.9018 (mmp) cc_final: 0.8765 (tpp) REVERT: D 822 MET cc_start: 0.9263 (mmp) cc_final: 0.9014 (mmm) REVERT: D 915 ILE cc_start: 0.9427 (pt) cc_final: 0.9082 (mm) REVERT: D 1025 MET cc_start: 0.8166 (tpt) cc_final: 0.7877 (tpt) REVERT: D 1189 MET cc_start: 0.8671 (tpt) cc_final: 0.8073 (tpp) REVERT: D 1239 ASP cc_start: 0.9296 (m-30) cc_final: 0.9043 (m-30) REVERT: D 1250 ASP cc_start: 0.9412 (m-30) cc_final: 0.9091 (p0) REVERT: D 1326 GLN cc_start: 0.8400 (mt0) cc_final: 0.8033 (mt0) REVERT: E 30 MET cc_start: 0.9173 (mmp) cc_final: 0.8944 (mmp) REVERT: E 36 ASP cc_start: 0.9014 (p0) cc_final: 0.8581 (p0) REVERT: E 53 GLU cc_start: 0.9472 (mt-10) cc_final: 0.9149 (mm-30) outliers start: 1 outliers final: 0 residues processed: 175 average time/residue: 0.1533 time to fit residues: 45.3472 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 : 1.022 ------------------------------------------------------------------------------- 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: 2.9990 chunk 270 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 141 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 263 optimal weight: 4.9990 chunk 287 optimal weight: 0.0040 chunk 19 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 30.0000 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.045200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.033200 restraints weight = 207400.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.034286 restraints weight = 126893.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.035067 restraints weight = 90255.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.035619 restraints weight = 70204.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.035967 restraints weight = 58462.428| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1822 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= 0.120 Angle : 0.624 11.838 36082 Z= 0.322 Chirality : 0.044 0.274 4124 Planarity : 0.004 0.059 4543 Dihedral : 12.504 144.354 4073 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.90 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % 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: -1.59 (0.14), residues: 3172 helix: 0.15 (0.16), residues: 1082 sheet: -1.42 (0.26), residues: 350 loop : -1.81 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1301 TYR 0.016 0.001 TYR D 679 PHE 0.015 0.001 PHE A 231 TRP 0.016 0.001 TRP C1276 HIS 0.004 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (26550) covalent geometry : angle 0.62447 / 0.32 (36082) hydrogen bonds : bond 0.04422 / 3.04 ( 962) hydrogen bonds : angle 5.07117 / 3.49 ( 2642) metal coordination : bond 0.00181 / 0.10 ( 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 191 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.9467 (ptm) cc_final: 0.8904 (ppp) REVERT: B 51 MET cc_start: 0.9155 (mmm) cc_final: 0.8493 (mmm) REVERT: C 160 ASP cc_start: 0.8240 (m-30) cc_final: 0.7966 (m-30) REVERT: C 685 MET cc_start: 0.9259 (mtm) cc_final: 0.8765 (mtt) REVERT: C 741 MET cc_start: 0.8687 (ptp) cc_final: 0.8459 (ptt) REVERT: C 794 LEU cc_start: 0.9275 (tp) cc_final: 0.8996 (pp) REVERT: C 1008 GLN cc_start: 0.9114 (tp40) cc_final: 0.8867 (pp30) REVERT: C 1025 PHE cc_start: 0.9195 (t80) cc_final: 0.8934 (t80) REVERT: C 1084 ASP cc_start: 0.9239 (m-30) cc_final: 0.8994 (m-30) REVERT: C 1107 MET cc_start: 0.8670 (pmm) cc_final: 0.8459 (pmm) REVERT: C 1119 MET cc_start: 0.9466 (mmp) cc_final: 0.9086 (mmp) REVERT: C 1170 MET cc_start: 0.9420 (mmp) cc_final: 0.9176 (mmm) REVERT: C 1304 MET cc_start: 0.9416 (ttp) cc_final: 0.9089 (ptm) REVERT: D 124 ILE cc_start: 0.9530 (mp) cc_final: 0.9300 (mp) REVERT: D 180 MET cc_start: 0.6992 (mmm) cc_final: 0.6689 (mmm) REVERT: D 237 MET cc_start: 0.9185 (ttt) cc_final: 0.8557 (tpt) REVERT: D 330 MET cc_start: 0.9019 (mmp) cc_final: 0.8552 (mmp) REVERT: D 458 ASN cc_start: 0.9774 (t0) cc_final: 0.9549 (t0) REVERT: D 485 MET cc_start: 0.8975 (tpt) cc_final: 0.8733 (tpp) REVERT: D 604 MET cc_start: 0.9480 (mmt) cc_final: 0.9179 (mmm) REVERT: D 608 CYS cc_start: 0.9325 (t) cc_final: 0.9100 (t) REVERT: D 625 MET cc_start: 0.9570 (tmm) cc_final: 0.9182 (tmm) REVERT: D 644 MET cc_start: 0.8991 (mpp) cc_final: 0.8659 (mpp) REVERT: D 697 MET cc_start: 0.9275 (tmm) cc_final: 0.8788 (tmm) REVERT: D 698 MET cc_start: 0.9426 (mmm) cc_final: 0.8727 (mmm) REVERT: D 821 MET cc_start: 0.8981 (mmp) cc_final: 0.8770 (tpp) REVERT: D 822 MET cc_start: 0.9237 (mmp) cc_final: 0.8995 (mmm) REVERT: D 915 ILE cc_start: 0.9434 (pt) cc_final: 0.9089 (mt) REVERT: D 1025 MET cc_start: 0.8165 (tpt) cc_final: 0.7892 (tpt) REVERT: D 1189 MET cc_start: 0.8673 (tpt) cc_final: 0.8086 (tpp) REVERT: D 1239 ASP cc_start: 0.9282 (m-30) cc_final: 0.9011 (m-30) REVERT: D 1250 ASP cc_start: 0.9321 (m-30) cc_final: 0.9027 (p0) REVERT: D 1326 GLN cc_start: 0.8392 (mt0) cc_final: 0.7960 (mt0) REVERT: E 5 THR cc_start: 0.9326 (p) cc_final: 0.8887 (p) REVERT: E 30 MET cc_start: 0.9130 (mmp) cc_final: 0.8906 (mmp) REVERT: E 36 ASP cc_start: 0.9031 (p0) cc_final: 0.8627 (p0) REVERT: E 53 GLU cc_start: 0.9433 (mt-10) cc_final: 0.9149 (mm-30) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.1531 time to fit residues: 49.0517 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 : 1.008 ------------------------------------------------------------------------------- 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: 5.9990 chunk 20 optimal weight: 20.0000 chunk 153 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 294 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 chunk 288 optimal weight: 30.0000 chunk 52 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN D 771 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.044350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.032561 restraints weight = 214631.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.033596 restraints weight = 132317.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.034313 restraints weight = 93877.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.034847 restraints weight = 73443.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.035164 restraints weight = 61407.168| |-----------------------------------------------------------------------------| r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 26556 Z= 0.189 Angle : 0.652 11.100 36082 Z= 0.337 Chirality : 0.044 0.272 4124 Planarity : 0.004 0.055 4543 Dihedral : 12.517 145.128 4073 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.87 % Favored : 93.03 % Rotamer: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % 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: -1.59 (0.14), residues: 3172 helix: 0.15 (0.16), residues: 1088 sheet: -1.37 (0.27), residues: 343 loop : -1.83 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 67 TYR 0.018 0.001 TYR C1149 PHE 0.032 0.001 PHE C 136 TRP 0.015 0.001 TRP C1276 HIS 0.004 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.19 (26550) covalent geometry : angle 0.65178 / 0.34 (36082) hydrogen bonds : bond 0.04510 / 3.09 ( 962) hydrogen bonds : angle 5.12406 / 3.53 ( 2642) metal coordination : bond 0.00566 / 0.33 ( 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 173 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.9003 (tppt) cc_final: 0.8791 (tptt) REVERT: A 205 MET cc_start: 0.9433 (ptm) cc_final: 0.8905 (ppp) REVERT: B 51 MET cc_start: 0.9177 (mmm) cc_final: 0.8542 (mmm) REVERT: C 160 ASP cc_start: 0.8264 (m-30) cc_final: 0.7977 (m-30) REVERT: C 685 MET cc_start: 0.9308 (mtm) cc_final: 0.8851 (mtt) REVERT: C 741 MET cc_start: 0.8698 (ptp) cc_final: 0.8494 (ptt) REVERT: C 1008 GLN cc_start: 0.9136 (tp40) cc_final: 0.8861 (pp30) REVERT: C 1025 PHE cc_start: 0.9180 (t80) cc_final: 0.8901 (t80) REVERT: C 1084 ASP cc_start: 0.9263 (m-30) cc_final: 0.8978 (m-30) REVERT: C 1119 MET cc_start: 0.9453 (mmp) cc_final: 0.9008 (mmp) REVERT: C 1170 MET cc_start: 0.9402 (mmp) cc_final: 0.9145 (mmm) REVERT: C 1232 MET cc_start: 0.9321 (mmm) cc_final: 0.9051 (mmm) REVERT: C 1304 MET cc_start: 0.9419 (ttp) cc_final: 0.9174 (ptm) REVERT: D 237 MET cc_start: 0.9123 (ttt) cc_final: 0.8608 (tpt) REVERT: D 245 LEU cc_start: 0.9320 (tp) cc_final: 0.9104 (tp) REVERT: D 298 MET cc_start: 0.9348 (ttp) cc_final: 0.8641 (tmm) REVERT: D 330 MET cc_start: 0.9039 (mmp) cc_final: 0.8594 (mmp) REVERT: D 372 MET cc_start: 0.9154 (mmp) cc_final: 0.8779 (mmt) REVERT: D 458 ASN cc_start: 0.9775 (t0) cc_final: 0.9555 (t0) REVERT: D 608 CYS cc_start: 0.9250 (t) cc_final: 0.9039 (t) REVERT: D 625 MET cc_start: 0.9572 (tmm) cc_final: 0.9195 (tmm) REVERT: D 644 MET cc_start: 0.8935 (mpp) cc_final: 0.8588 (mpp) REVERT: D 697 MET cc_start: 0.9261 (tmm) cc_final: 0.8860 (tmm) REVERT: D 698 MET cc_start: 0.9405 (mmm) cc_final: 0.8747 (mmm) REVERT: D 747 MET cc_start: 0.8977 (tpp) cc_final: 0.8707 (tpp) REVERT: D 821 MET cc_start: 0.9003 (mmp) cc_final: 0.8795 (tpp) REVERT: D 822 MET cc_start: 0.9221 (mmp) cc_final: 0.8957 (mmm) REVERT: D 915 ILE cc_start: 0.9414 (pt) cc_final: 0.9081 (mt) REVERT: D 1025 MET cc_start: 0.8204 (tpt) cc_final: 0.7901 (tpt) REVERT: D 1189 MET cc_start: 0.8653 (tpt) cc_final: 0.8053 (tpp) REVERT: D 1239 ASP cc_start: 0.9300 (m-30) cc_final: 0.9035 (m-30) REVERT: D 1250 ASP cc_start: 0.9342 (m-30) cc_final: 0.9040 (p0) REVERT: D 1326 GLN cc_start: 0.8535 (mt0) cc_final: 0.8164 (mt0) REVERT: E 30 MET cc_start: 0.9128 (mmp) cc_final: 0.8849 (mmp) REVERT: E 36 ASP cc_start: 0.8977 (p0) cc_final: 0.8522 (p0) REVERT: E 53 GLU cc_start: 0.9459 (mt-10) cc_final: 0.9176 (mm-30) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1505 time to fit residues: 43.9846 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 : 0.859 ------------------------------------------------------------------------------- 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: 0.5980 chunk 119 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 236 optimal weight: 7.9990 chunk 241 optimal weight: 5.9990 chunk 306 optimal weight: 0.0370 chunk 162 optimal weight: 5.9990 overall best weight: 2.9264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN D 739 GLN ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.044636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.032681 restraints weight = 212008.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.033746 restraints weight = 129942.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.034483 restraints weight = 92711.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.035039 restraints weight = 72726.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.035386 restraints weight = 60902.165| |-----------------------------------------------------------------------------| r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 26556 Z= 0.149 Angle : 0.635 11.912 36082 Z= 0.327 Chirality : 0.044 0.276 4124 Planarity : 0.004 0.056 4543 Dihedral : 12.493 144.425 4073 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.18 % Favored : 93.76 % Rotamer: Outliers : 0.04 % Allowed : 1.66 % Favored : 98.31 % 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: -1.58 (0.14), residues: 3172 helix: 0.15 (0.15), residues: 1088 sheet: -1.28 (0.27), residues: 345 loop : -1.83 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 67 TYR 0.016 0.001 TYR C 367 PHE 0.014 0.001 PHE A 231 TRP 0.018 0.001 TRP C1276 HIS 0.004 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (26550) covalent geometry : angle 0.63475 / 0.33 (36082) hydrogen bonds : bond 0.04282 / 2.93 ( 962) hydrogen bonds : angle 5.04043 / 3.48 ( 2642) metal coordination : bond 0.00361 / 0.21 ( 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 178 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.9010 (tppt) cc_final: 0.8780 (tptt) REVERT: A 205 MET cc_start: 0.9379 (ptm) cc_final: 0.8906 (ppp) REVERT: B 51 MET cc_start: 0.9143 (mmm) cc_final: 0.8495 (mmm) REVERT: C 160 ASP cc_start: 0.8206 (m-30) cc_final: 0.7924 (m-30) REVERT: C 492 MET cc_start: 0.9507 (pmm) cc_final: 0.8901 (pmm) REVERT: C 685 MET cc_start: 0.9335 (mtm) cc_final: 0.8868 (mtt) REVERT: C 741 MET cc_start: 0.8680 (ptp) cc_final: 0.8478 (ptt) REVERT: C 1008 GLN cc_start: 0.9134 (tp40) cc_final: 0.8820 (pp30) REVERT: C 1025 PHE cc_start: 0.9191 (t80) cc_final: 0.8931 (t80) REVERT: C 1084 ASP cc_start: 0.9267 (m-30) cc_final: 0.8964 (m-30) REVERT: C 1119 MET cc_start: 0.9469 (mmp) cc_final: 0.8996 (mmp) REVERT: C 1170 MET cc_start: 0.9389 (mmp) cc_final: 0.9132 (mmm) REVERT: C 1281 TYR cc_start: 0.8178 (m-10) cc_final: 0.7831 (m-10) REVERT: C 1304 MET cc_start: 0.9434 (ttp) cc_final: 0.9179 (ptm) REVERT: D 180 MET cc_start: 0.7129 (mmm) cc_final: 0.6900 (mmm) REVERT: D 237 MET cc_start: 0.9094 (ttt) cc_final: 0.8605 (tpt) REVERT: D 245 LEU cc_start: 0.9329 (tp) cc_final: 0.9103 (tp) REVERT: D 330 MET cc_start: 0.9098 (mmp) cc_final: 0.8691 (mmp) REVERT: D 372 MET cc_start: 0.9181 (mmp) cc_final: 0.8797 (mmt) REVERT: D 458 ASN cc_start: 0.9781 (t0) cc_final: 0.9559 (t0) REVERT: D 604 MET cc_start: 0.9465 (mmt) cc_final: 0.9143 (mmm) REVERT: D 608 CYS cc_start: 0.9288 (t) cc_final: 0.9081 (t) REVERT: D 625 MET cc_start: 0.9551 (tmm) cc_final: 0.9037 (tmm) REVERT: D 644 MET cc_start: 0.8918 (mpp) cc_final: 0.8586 (mpp) REVERT: D 697 MET cc_start: 0.9245 (tmm) cc_final: 0.8725 (tmm) REVERT: D 698 MET cc_start: 0.9413 (mmm) cc_final: 0.8702 (mmm) REVERT: D 747 MET cc_start: 0.9055 (tpp) cc_final: 0.8727 (tpp) REVERT: D 822 MET cc_start: 0.9206 (mmp) cc_final: 0.8919 (mmm) REVERT: D 915 ILE cc_start: 0.9406 (pt) cc_final: 0.9069 (mt) REVERT: D 1025 MET cc_start: 0.8233 (tpt) cc_final: 0.7931 (tpt) REVERT: D 1189 MET cc_start: 0.8655 (tpt) cc_final: 0.8060 (tpp) REVERT: D 1239 ASP cc_start: 0.9297 (m-30) cc_final: 0.9055 (m-30) REVERT: D 1250 ASP cc_start: 0.9332 (m-30) cc_final: 0.9032 (p0) REVERT: D 1326 GLN cc_start: 0.8527 (mt0) cc_final: 0.8061 (tt0) REVERT: E 3 ARG cc_start: 0.8316 (tpp-160) cc_final: 0.8104 (tpm170) REVERT: E 5 THR cc_start: 0.9338 (p) cc_final: 0.8908 (p) REVERT: E 30 MET cc_start: 0.9085 (mmp) cc_final: 0.8822 (mmp) REVERT: E 36 ASP cc_start: 0.9061 (p0) cc_final: 0.8627 (p0) REVERT: E 53 GLU cc_start: 0.9445 (mt-10) cc_final: 0.9171 (mm-30) outliers start: 1 outliers final: 0 residues processed: 178 average time/residue: 0.1632 time to fit residues: 48.6082 Evaluate side-chains 142 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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: 0.7980 chunk 252 optimal weight: 7.9990 chunk 194 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 2 optimal weight: 0.4980 chunk 207 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 230 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 74 optimal weight: 30.0000 chunk 231 optimal weight: 3.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1257 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 = 0.3134 r_free = 0.3134 target = 0.044566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.032612 restraints weight = 212900.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.033680 restraints weight = 130088.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.034464 restraints weight = 92590.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.034977 restraints weight = 72221.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.035331 restraints weight = 60607.902| |-----------------------------------------------------------------------------| r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26556 Z= 0.150 Angle : 0.633 12.159 36082 Z= 0.325 Chirality : 0.044 0.276 4124 Planarity : 0.004 0.053 4543 Dihedral : 12.474 144.219 4073 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.75 % Favored : 93.19 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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: -1.55 (0.14), residues: 3172 helix: 0.15 (0.15), residues: 1094 sheet: -1.22 (0.26), residues: 348 loop : -1.81 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 275 TYR 0.031 0.001 TYR C1285 PHE 0.016 0.001 PHE C 337 TRP 0.024 0.001 TRP C1276 HIS 0.003 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (26550) covalent geometry : angle 0.63350 / 0.33 (36082) hydrogen bonds : bond 0.04213 / 2.88 ( 962) hydrogen bonds : angle 4.94649 / 3.41 ( 2642) metal coordination : bond 0.00342 / 0.20 ( 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 174 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.9420 (ptm) cc_final: 0.8973 (ppp) REVERT: B 51 MET cc_start: 0.9159 (mmm) cc_final: 0.8518 (mmm) REVERT: C 160 ASP cc_start: 0.8250 (m-30) cc_final: 0.7940 (m-30) REVERT: C 492 MET cc_start: 0.9525 (pmm) cc_final: 0.8864 (pmm) REVERT: C 685 MET cc_start: 0.9340 (mtm) cc_final: 0.8913 (mtt) REVERT: C 1008 GLN cc_start: 0.9164 (tp40) cc_final: 0.8826 (pp30) REVERT: C 1025 PHE cc_start: 0.9162 (t80) cc_final: 0.8921 (t80) REVERT: C 1084 ASP cc_start: 0.9255 (m-30) cc_final: 0.8947 (m-30) REVERT: C 1170 MET cc_start: 0.9374 (mmp) cc_final: 0.9117 (mmm) REVERT: C 1273 MET cc_start: 0.9428 (mmp) cc_final: 0.8867 (mmm) REVERT: C 1278 LEU cc_start: 0.9763 (tp) cc_final: 0.9561 (tp) REVERT: C 1304 MET cc_start: 0.9430 (ttp) cc_final: 0.9187 (ptm) REVERT: D 180 MET cc_start: 0.7127 (mmm) cc_final: 0.6891 (mmm) REVERT: D 237 MET cc_start: 0.9121 (ttt) cc_final: 0.8653 (tpt) REVERT: D 245 LEU cc_start: 0.9342 (tp) cc_final: 0.9112 (tp) REVERT: D 298 MET cc_start: 0.9235 (ttp) cc_final: 0.8737 (tmm) REVERT: D 330 MET cc_start: 0.9047 (mmp) cc_final: 0.8710 (mmp) REVERT: D 458 ASN cc_start: 0.9770 (t0) cc_final: 0.9553 (t0) REVERT: D 479 GLU cc_start: 0.8905 (tt0) cc_final: 0.7953 (pt0) REVERT: D 604 MET cc_start: 0.9473 (mmt) cc_final: 0.9128 (mmm) REVERT: D 608 CYS cc_start: 0.9282 (t) cc_final: 0.9077 (t) REVERT: D 625 MET cc_start: 0.9562 (tmm) cc_final: 0.9269 (tmm) REVERT: D 644 MET cc_start: 0.8912 (mpp) cc_final: 0.8588 (mpp) REVERT: D 697 MET cc_start: 0.9245 (tmm) cc_final: 0.8720 (tmm) REVERT: D 698 MET cc_start: 0.9420 (mmm) cc_final: 0.8703 (mmm) REVERT: D 747 MET cc_start: 0.9078 (tpp) cc_final: 0.8737 (tpp) REVERT: D 822 MET cc_start: 0.9388 (mmp) cc_final: 0.8902 (mmm) REVERT: D 915 ILE cc_start: 0.9397 (pt) cc_final: 0.9055 (mt) REVERT: D 1025 MET cc_start: 0.8194 (tpt) cc_final: 0.7890 (tpt) REVERT: D 1189 MET cc_start: 0.8664 (tpt) cc_final: 0.8069 (tpp) REVERT: D 1239 ASP cc_start: 0.9288 (m-30) cc_final: 0.9069 (m-30) REVERT: D 1250 ASP cc_start: 0.9339 (m-30) cc_final: 0.9042 (p0) REVERT: D 1326 GLN cc_start: 0.8627 (mt0) cc_final: 0.8341 (mt0) REVERT: E 3 ARG cc_start: 0.8343 (tpp-160) cc_final: 0.7952 (tpm170) REVERT: E 5 THR cc_start: 0.9370 (p) cc_final: 0.9039 (p) REVERT: E 30 MET cc_start: 0.9090 (mmp) cc_final: 0.8874 (mmp) REVERT: E 36 ASP cc_start: 0.9059 (p0) cc_final: 0.8646 (p0) REVERT: E 53 GLU cc_start: 0.9437 (mt-10) cc_final: 0.9163 (mm-30) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1595 time to fit residues: 46.6051 Evaluate side-chains 142 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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: 1.9990 chunk 248 optimal weight: 8.9990 chunk 130 optimal weight: 8.9990 chunk 264 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 221 optimal weight: 0.9990 chunk 141 optimal weight: 7.9990 chunk 208 optimal weight: 0.8980 chunk 86 optimal weight: 8.9990 chunk 193 optimal weight: 0.9980 chunk 289 optimal weight: 8.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1257 GLN D 365 GLN ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 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 = 0.3140 r_free = 0.3140 target = 0.044745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.032776 restraints weight = 211780.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.033863 restraints weight = 129474.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.034602 restraints weight = 91907.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.035155 restraints weight = 72129.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.035512 restraints weight = 60311.065| |-----------------------------------------------------------------------------| r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 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 : 0.003 0.041 26556 Z= 0.131 Angle : 0.636 12.750 36082 Z= 0.324 Chirality : 0.044 0.277 4124 Planarity : 0.004 0.050 4543 Dihedral : 12.441 144.001 4073 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.34 % Favored : 93.60 % 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: -1.49 (0.14), residues: 3172 helix: 0.14 (0.15), residues: 1093 sheet: -1.01 (0.27), residues: 335 loop : -1.77 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 220 TYR 0.017 0.001 TYR C 367 PHE 0.015 0.001 PHE C 337 TRP 0.025 0.001 TRP C1276 HIS 0.003 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (26550) covalent geometry : angle 0.63560 / 0.32 (36082) hydrogen bonds : bond 0.04148 / 2.84 ( 962) hydrogen bonds : angle 4.89293 / 3.38 ( 2642) metal coordination : bond 0.00220 / 0.13 ( 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 172 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: 0.9175 (mmm) cc_final: 0.8724 (mmm) REVERT: C 160 ASP cc_start: 0.8237 (m-30) cc_final: 0.7927 (m-30) REVERT: C 492 MET cc_start: 0.9525 (pmm) cc_final: 0.8890 (pmm) REVERT: C 515 MET cc_start: 0.8527 (tmm) cc_final: 0.8304 (tmm) REVERT: C 653 MET cc_start: 0.8548 (tpp) cc_final: 0.8316 (tpp) REVERT: C 685 MET cc_start: 0.9379 (mtm) cc_final: 0.8910 (mtt) REVERT: C 741 MET cc_start: 0.8524 (ptp) cc_final: 0.8290 (ptt) REVERT: C 1025 PHE cc_start: 0.9152 (t80) cc_final: 0.8904 (t80) REVERT: C 1084 ASP cc_start: 0.9250 (m-30) cc_final: 0.8918 (m-30) REVERT: C 1170 MET cc_start: 0.9368 (mmp) cc_final: 0.9111 (mmm) REVERT: C 1273 MET cc_start: 0.9449 (mmp) cc_final: 0.8884 (mmm) REVERT: C 1278 LEU cc_start: 0.9767 (tp) cc_final: 0.9564 (tp) REVERT: C 1281 TYR cc_start: 0.8290 (m-10) cc_final: 0.7977 (m-10) REVERT: C 1304 MET cc_start: 0.9444 (ttp) cc_final: 0.9188 (ptm) REVERT: D 180 MET cc_start: 0.7148 (mmm) cc_final: 0.6904 (mmm) REVERT: D 237 MET cc_start: 0.9122 (ttt) cc_final: 0.8652 (tpt) REVERT: D 245 LEU cc_start: 0.9377 (tp) cc_final: 0.9169 (tp) REVERT: D 298 MET cc_start: 0.9254 (ttp) cc_final: 0.8732 (tmm) REVERT: D 330 MET cc_start: 0.9067 (mmp) cc_final: 0.8727 (mmp) REVERT: D 458 ASN cc_start: 0.9767 (t0) cc_final: 0.9544 (t0) REVERT: D 479 GLU cc_start: 0.8900 (tt0) cc_final: 0.8022 (pt0) REVERT: D 604 MET cc_start: 0.9472 (mmt) cc_final: 0.9133 (mmm) REVERT: D 608 CYS cc_start: 0.9272 (t) cc_final: 0.9068 (t) REVERT: D 625 MET cc_start: 0.9560 (tmm) cc_final: 0.9269 (tmm) REVERT: D 644 MET cc_start: 0.8919 (mpp) cc_final: 0.8626 (mpp) REVERT: D 697 MET cc_start: 0.9248 (tmm) cc_final: 0.8850 (ppp) REVERT: D 698 MET cc_start: 0.9430 (mmm) cc_final: 0.8795 (mmm) REVERT: D 747 MET cc_start: 0.9088 (tpp) cc_final: 0.8734 (tpp) REVERT: D 822 MET cc_start: 0.9414 (mmp) cc_final: 0.8989 (mmm) REVERT: D 915 ILE cc_start: 0.9386 (pt) cc_final: 0.9047 (mt) REVERT: D 1025 MET cc_start: 0.8211 (tpt) cc_final: 0.7914 (tpt) REVERT: D 1189 MET cc_start: 0.8684 (tpt) cc_final: 0.8080 (tpp) REVERT: D 1239 ASP cc_start: 0.9286 (m-30) cc_final: 0.9066 (m-30) REVERT: D 1250 ASP cc_start: 0.9326 (m-30) cc_final: 0.9033 (p0) REVERT: E 5 THR cc_start: 0.9418 (p) cc_final: 0.8899 (p) REVERT: E 30 MET cc_start: 0.9076 (mmp) cc_final: 0.8861 (mmp) REVERT: E 36 ASP cc_start: 0.9053 (p0) cc_final: 0.8653 (p0) REVERT: E 53 GLU cc_start: 0.9420 (mt-10) cc_final: 0.9013 (mm-30) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1602 time to fit residues: 46.4771 Evaluate side-chains 143 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 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: 0.9990 chunk 316 optimal weight: 40.0000 chunk 33 optimal weight: 1.9990 chunk 279 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 238 optimal weight: 8.9990 chunk 253 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 272 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1313 HIS D 365 GLN ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.044541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.032693 restraints weight = 212294.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.033732 restraints weight = 130430.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.034472 restraints weight = 92750.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.035002 restraints weight = 72267.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.035358 restraints weight = 60501.081| |-----------------------------------------------------------------------------| r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 26556 Z= 0.145 Angle : 0.640 12.868 36082 Z= 0.327 Chirality : 0.044 0.277 4124 Planarity : 0.004 0.052 4543 Dihedral : 12.433 144.434 4073 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.59 % Favored : 93.35 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: -1.49 (0.14), residues: 3172 helix: 0.12 (0.15), residues: 1095 sheet: -1.09 (0.26), residues: 353 loop : -1.74 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1262 TYR 0.032 0.001 TYR D 457 PHE 0.015 0.001 PHE C 828 TRP 0.027 0.001 TRP C1276 HIS 0.003 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (26550) covalent geometry : angle 0.63979 / 0.33 (36082) hydrogen bonds : bond 0.04167 / 2.85 ( 962) hydrogen bonds : angle 4.88963 / 3.37 ( 2642) metal coordination : bond 0.00306 / 0.18 ( 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 173 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: 0.9165 (mmm) cc_final: 0.8713 (mmm) REVERT: B 142 MET cc_start: 0.8703 (tpt) cc_final: 0.8057 (tpp) REVERT: C 160 ASP cc_start: 0.8245 (m-30) cc_final: 0.7935 (m-30) REVERT: C 492 MET cc_start: 0.9530 (pmm) cc_final: 0.8879 (pmm) REVERT: C 685 MET cc_start: 0.9371 (mtm) cc_final: 0.8918 (mtt) REVERT: C 741 MET cc_start: 0.8517 (ptp) cc_final: 0.8251 (ptt) REVERT: C 1025 PHE cc_start: 0.9182 (t80) cc_final: 0.8935 (t80) REVERT: C 1084 ASP cc_start: 0.9245 (m-30) cc_final: 0.8919 (m-30) REVERT: C 1170 MET cc_start: 0.9374 (mmp) cc_final: 0.9117 (mmm) REVERT: C 1180 MET cc_start: 0.8911 (tpp) cc_final: 0.8667 (tpp) REVERT: C 1273 MET cc_start: 0.9463 (mmp) cc_final: 0.8900 (mmm) REVERT: C 1281 TYR cc_start: 0.8215 (m-10) cc_final: 0.7913 (m-10) REVERT: C 1285 TYR cc_start: 0.8282 (m-80) cc_final: 0.7998 (m-80) REVERT: C 1304 MET cc_start: 0.9424 (ttp) cc_final: 0.9179 (ptm) REVERT: D 180 MET cc_start: 0.7143 (mmm) cc_final: 0.6889 (mmm) REVERT: D 237 MET cc_start: 0.9118 (ttt) cc_final: 0.8644 (tpt) REVERT: D 245 LEU cc_start: 0.9400 (tp) cc_final: 0.9198 (tp) REVERT: D 298 MET cc_start: 0.9539 (ttp) cc_final: 0.8819 (tmm) REVERT: D 330 MET cc_start: 0.9060 (mmp) cc_final: 0.8725 (mmp) REVERT: D 372 MET cc_start: 0.9177 (mmp) cc_final: 0.8799 (mmt) REVERT: D 458 ASN cc_start: 0.9764 (t0) cc_final: 0.9536 (t0) REVERT: D 479 GLU cc_start: 0.8947 (tt0) cc_final: 0.7848 (pt0) REVERT: D 604 MET cc_start: 0.9474 (mmt) cc_final: 0.9136 (mmm) REVERT: D 608 CYS cc_start: 0.9280 (t) cc_final: 0.9073 (t) REVERT: D 625 MET cc_start: 0.9576 (tmm) cc_final: 0.9279 (tmm) REVERT: D 644 MET cc_start: 0.8921 (mpp) cc_final: 0.8609 (mpp) REVERT: D 697 MET cc_start: 0.9252 (tmm) cc_final: 0.8862 (tmm) REVERT: D 698 MET cc_start: 0.9426 (mmm) cc_final: 0.8731 (mmm) REVERT: D 747 MET cc_start: 0.9082 (tpp) cc_final: 0.8730 (tpp) REVERT: D 821 MET cc_start: 0.9022 (mmp) cc_final: 0.8745 (tpp) REVERT: D 822 MET cc_start: 0.9215 (mmp) cc_final: 0.9012 (mmm) REVERT: D 915 ILE cc_start: 0.9386 (pt) cc_final: 0.9035 (mt) REVERT: D 1025 MET cc_start: 0.8236 (tpt) cc_final: 0.7935 (tpt) REVERT: D 1189 MET cc_start: 0.8682 (tpt) cc_final: 0.8082 (tpp) REVERT: D 1239 ASP cc_start: 0.9292 (m-30) cc_final: 0.9076 (m-30) REVERT: D 1250 ASP cc_start: 0.9359 (m-30) cc_final: 0.9055 (p0) REVERT: D 1326 GLN cc_start: 0.8983 (pp30) cc_final: 0.8764 (pp30) REVERT: E 30 MET cc_start: 0.9102 (mmp) cc_final: 0.8878 (mmp) REVERT: E 36 ASP cc_start: 0.9055 (p0) cc_final: 0.8655 (p0) REVERT: E 53 GLU cc_start: 0.9361 (mt-10) cc_final: 0.8924 (mm-30) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1527 time to fit residues: 44.8441 Evaluate side-chains 139 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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: 2.9990 chunk 148 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 214 optimal weight: 1.9990 chunk 297 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 114 optimal weight: 20.0000 chunk 199 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 737 ASN 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 = 0.3138 r_free = 0.3138 target = 0.044626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.032712 restraints weight = 206738.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.033800 restraints weight = 126370.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.034565 restraints weight = 90008.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.035081 restraints weight = 70206.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.035505 restraints weight = 58907.744| |-----------------------------------------------------------------------------| r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 26556 Z= 0.128 Angle : 0.632 13.055 36082 Z= 0.322 Chirality : 0.044 0.278 4124 Planarity : 0.004 0.052 4543 Dihedral : 12.407 144.805 4073 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.18 % Favored : 93.79 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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: 0.17 (0.16), residues: 1087 sheet: -1.13 (0.26), residues: 361 loop : -1.69 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1331 TYR 0.017 0.001 TYR C 367 PHE 0.014 0.001 PHE C 337 TRP 0.028 0.001 TRP C1276 HIS 0.003 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (26550) covalent geometry : angle 0.63173 / 0.32 (36082) hydrogen bonds : bond 0.04065 / 2.78 ( 962) hydrogen bonds : angle 4.81514 / 3.32 ( 2642) metal coordination : bond 0.00223 / 0.13 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3896.03 seconds wall clock time: 68 minutes 39.67 seconds (4119.67 seconds total)