Starting phenix.real_space_refine on Tue Sep 15 01:09:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gdb_51260/09_2026/9gdb_51260.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gdb_51260/09_2026/9gdb_51260.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gdb_51260/09_2026/9gdb_51260.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gdb_51260/09_2026/9gdb_51260.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gdb_51260/09_2026/9gdb_51260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gdb_51260/09_2026/9gdb_51260.map" } resolution = 3.8 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= 0.001 sd= 0.011 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 5 6.06 5 P 65 5.49 5 Mg 1 5.21 5 S 143 5.16 5 C 20587 2.51 5 N 5881 2.21 5 O 6491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33173 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1803 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 223} Chain: "B" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1799 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 222} Chain: "C" Number of atoms: 10577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10577 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 54, 'TRANS': 1284} Chain: "D" Number of atoms: 10433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1342, 10433 Classifications: {'peptide': 1342} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1286} Chain breaks: 2 Chain: "E" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 709 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "F" Number of atoms: 6700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 846, 6700 Classifications: {'peptide': 846} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 801} Chain breaks: 1 Chain: "N" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 366 Classifications: {'DNA': 27} Incomplete info: {'p_only': 10} Link IDs: {'rna3p': 26} Unresolved chain links: 10 Unresolved chain link angles: 43 Unresolved chain link dihedrals: 32 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {' DT:plan': 5, ' DA:plan': 2, ' DA:plan2': 2, ' DC:plan': 2, ' DC:plan2': 2, ' DG:plan': 1, ' DG:plan2': 1} Unresolved non-hydrogen planarities: 112 Chain: "R" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 235 Classifications: {'RNA': 11} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna2p': 2, 'rna3p': 8} Chain: "T" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 545 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} 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} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14644 SG CYS D 70 110.990 99.197 87.123 1.00283.83 S ATOM 14658 SG CYS D 72 110.361 102.986 89.229 1.00283.23 S ATOM 14766 SG CYS D 85 112.909 100.412 89.394 1.00270.13 S ATOM 14790 SG CYS D 88 109.465 99.789 90.546 1.00267.52 S ATOM 20478 SG CYS D 814 81.051 38.818 90.874 1.00157.93 S ATOM 21043 SG CYS D 888 80.344 42.426 90.796 1.00154.07 S ATOM 21094 SG CYS D 895 80.637 40.346 87.481 1.00148.93 S ATOM 21115 SG CYS D 898 77.624 39.903 89.613 1.00150.57 S ATOM 29933 SG CYS F 599 130.296 125.262 123.175 1.001043.6 S ATOM 29953 SG CYS F 602 133.284 127.557 123.435 1.001043.6 S ATOM 30073 SG CYS F 619 130.811 127.833 126.044 1.00959.38 S ATOM 30157 SG CYS F 630 129.664 129.019 122.694 1.00932.27 S ATOM 30407 SG CYS F 662 125.600 117.340 146.183 1.00857.67 S ATOM 30429 SG CYS F 665 123.704 118.684 149.189 1.00864.75 S ATOM 30570 SG CYS F 683 122.359 119.207 145.781 1.00876.98 S ATOM 30610 SG CYS F 689 125.365 121.205 146.968 1.00870.83 S ATOM 30786 SG CYS F 711 112.337 113.654 107.187 1.00972.32 S ATOM 30810 SG CYS F 714 114.812 111.630 108.687 1.001007.7 S ATOM 30942 SG CYS F 731 113.525 114.158 110.785 1.001031.5 S ATOM 30981 SG CYS F 736 115.856 114.885 107.032 1.001043.6 S Time building chain proxies: 6.72, per 1000 atoms: 0.20 Number of scatterers: 33173 At special positions: 0 Unit cell: (149.988, 168.952, 189.64, 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 5 29.99 S 143 16.00 P 65 15.00 Mg 1 11.99 O 6491 8.00 N 5881 7.00 C 20587 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.88 Conformation dependent library (CDL) restraints added in 1.3 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 88 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 619 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 602 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 599 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 630 " pdb=" ZN F1002 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 665 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 683 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 689 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 662 " pdb=" ZN F1003 " pdb="ZN ZN F1003 " - pdb=" SG CYS F 714 " pdb="ZN ZN F1003 " - pdb=" SG CYS F 711 " pdb="ZN ZN F1003 " - pdb=" SG CYS F 736 " pdb="ZN ZN F1003 " - pdb=" SG CYS F 731 " Number of angles added : 30 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7556 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 58 sheets defined 41.2% alpha, 18.3% beta 25 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 4.44 Creating SS restraints... Processing helix chain 'A' and resid 34 through 51 removed outlier: 4.011A pdb=" N MET A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 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 154 through 161 Processing helix chain 'A' and resid 191 through 195 Processing helix chain 'A' and resid 212 through 234 removed outlier: 3.772A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 51 removed outlier: 3.591A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N MET B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 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 159 Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 212 through 229 Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.551A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 55 Processing helix chain 'C' and resid 81 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: 3.714A pdb=" N LEU C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG C 247 " --> pdb=" O PRO C 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 242 through 247' Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.578A pdb=" N ILE C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 391 Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 482 removed outlier: 3.705A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 removed outlier: 3.682A pdb=" N MET C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 509 Processing helix chain 'C' and resid 519 through 529 Processing helix chain 'C' and resid 544 through 549 removed outlier: 3.681A pdb=" N ARG C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.676A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 569 removed outlier: 4.400A pdb=" N ASN C 568 " --> pdb=" O GLU C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 614 Processing helix chain 'C' and resid 656 through 661 removed outlier: 4.204A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 668 removed outlier: 4.293A pdb=" N ILE C 668 " --> pdb=" O GLY C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 removed outlier: 3.958A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 712 removed outlier: 4.446A pdb=" N ALA C 707 " --> pdb=" O GLY C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 865 removed outlier: 3.768A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU C 865 " --> pdb=" O ALA C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 Processing helix chain 'C' and resid 942 through 980 Processing helix chain 'C' and resid 985 through 991 Processing helix chain 'C' and resid 993 through 1000 Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1101 through 1107 removed outlier: 4.164A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1108 through 1134 removed outlier: 3.927A pdb=" N ILE C1112 " --> pdb=" O ASN C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.797A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1177 Processing helix chain 'C' and resid 1191 through 1203 Processing helix chain 'C' and resid 1238 through 1242 Processing helix chain 'C' and resid 1271 through 1281 Processing helix chain 'C' and resid 1283 through 1292 removed outlier: 3.622A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) Processing helix chain 'C' and resid 1299 through 1310 Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.667A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 95 through 101 removed outlier: 3.997A pdb=" N ARG D 99 " --> pdb=" O THR D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 119 removed outlier: 3.552A pdb=" N LEU D 117 " --> pdb=" O HIS D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 173 removed outlier: 3.905A pdb=" N GLU D 171 " --> pdb=" O ASP D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 191 Processing helix chain 'D' and resid 193 through 208 removed outlier: 4.052A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 256 through 258 No H-bonds generated for 'chain 'D' and resid 256 through 258' Processing helix chain 'D' and resid 263 through 285 Processing helix chain 'D' and resid 288 through 309 Processing helix chain 'D' and resid 327 through 331 Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 370 through 388 Proline residue: D 379 - end of helix Processing helix chain 'D' and resid 393 through 403 Processing helix chain 'D' and resid 406 through 416 removed outlier: 3.545A pdb=" N ILE D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 457 removed outlier: 3.604A pdb=" N ALA D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 515 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 583 removed outlier: 4.085A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL D 583 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 613 through 636 removed outlier: 3.686A pdb=" N THR D 617 " --> pdb=" O GLY D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 670 removed outlier: 4.592A pdb=" N GLU D 652 " --> pdb=" O GLU D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 702 Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.902A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.576A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 876 Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 925 removed outlier: 4.150A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 929 Processing helix chain 'D' and resid 1069 through 1074 removed outlier: 4.246A pdb=" N ASP D1073 " --> pdb=" O ALA D1069 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU D1074 " --> pdb=" O GLY D1070 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1069 through 1074' Processing helix chain 'D' and resid 1136 through 1146 Processing helix chain 'D' and resid 1216 through 1245 removed outlier: 7.653A pdb=" N VAL D1226 " --> pdb=" O ARG D1222 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N HIS D1227 " --> pdb=" O LEU D1223 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA D1228 " --> pdb=" O ARG D1224 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 removed outlier: 3.870A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1295 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.964A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1376 removed outlier: 4.305A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 14 Processing helix chain 'E' and resid 15 through 32 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 91 Processing helix chain 'F' and resid 10 through 22 removed outlier: 3.850A pdb=" N TYR F 20 " --> pdb=" O THR F 16 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY F 22 " --> pdb=" O ASN F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 72 Processing helix chain 'F' and resid 88 through 103 removed outlier: 4.487A pdb=" N VAL F 92 " --> pdb=" O GLY F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 128 Processing helix chain 'F' and resid 143 through 153 removed outlier: 3.919A pdb=" N LYS F 153 " --> pdb=" O GLN F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 187 Proline residue: F 181 - end of helix Processing helix chain 'F' and resid 194 through 214 removed outlier: 3.571A pdb=" N VAL F 199 " --> pdb=" O ARG F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 264 Processing helix chain 'F' and resid 285 through 298 Processing helix chain 'F' and resid 300 through 315 removed outlier: 3.658A pdb=" N THR F 304 " --> pdb=" O GLY F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 343 Processing helix chain 'F' and resid 344 through 348 Processing helix chain 'F' and resid 376 through 380 Processing helix chain 'F' and resid 384 through 402 removed outlier: 4.027A pdb=" N GLN F 402 " --> pdb=" O PHE F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 438 removed outlier: 3.701A pdb=" N VAL F 437 " --> pdb=" O GLY F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 478 through 490 Processing helix chain 'F' and resid 496 through 507 removed outlier: 3.867A pdb=" N GLN F 505 " --> pdb=" O ILE F 501 " (cutoff:3.500A) Processing helix chain 'F' and resid 520 through 534 Processing helix chain 'F' and resid 534 through 539 Processing helix chain 'F' and resid 539 through 556 Processing helix chain 'F' and resid 559 through 580 removed outlier: 4.169A pdb=" N LYS F 580 " --> pdb=" O ASP F 576 " (cutoff:3.500A) Processing helix chain 'F' and resid 621 through 624 Processing helix chain 'F' and resid 625 through 629 Processing helix chain 'F' and resid 644 through 648 Processing helix chain 'F' and resid 649 through 659 removed outlier: 4.197A pdb=" N THR F 653 " --> pdb=" O GLU F 649 " (cutoff:3.500A) Processing helix chain 'F' and resid 785 through 790 Processing helix chain 'F' and resid 796 through 803 Processing helix chain 'F' and resid 808 through 810 No H-bonds generated for 'chain 'F' and resid 808 through 810' Processing helix chain 'F' and resid 811 through 817 removed outlier: 3.960A pdb=" N ALA F 815 " --> pdb=" O LEU F 811 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 18 removed outlier: 5.251A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.570A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.709A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 18 removed outlier: 5.677A pdb=" N LEU B 13 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N GLU B 29 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N HIS B 23 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N THR B 207 " --> pdb=" O HIS B 23 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LYS B 25 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N MET B 205 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR B 27 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ILE B 203 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N GLU B 29 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LEU B 201 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS B 200 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL B 187 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL B 202 " --> pdb=" O TYR B 185 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR B 185 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLU B 204 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE B 183 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLU B 206 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 104 removed outlier: 8.389A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 111 removed outlier: 6.291A pdb=" N GLY B 108 " --> pdb=" O HIS B 132 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N HIS B 132 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.139A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 61 removed outlier: 6.739A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA C 94 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLY C 125 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU C 96 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TYR C 123 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N VAL C 98 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU C 121 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU C 100 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLU C 119 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU C 102 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE C 117 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE C 104 " --> pdb=" O LYS C 115 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB4, first strand: chain 'C' and resid 451 through 454 removed outlier: 4.661A pdb=" N SER C 574 " --> pdb=" O CYS C 559 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 160 removed outlier: 3.624A pdb=" N LEU C 171 " --> pdb=" O ASP C 160 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 284 through 286 removed outlier: 4.449A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 250 through 251 removed outlier: 3.741A pdb=" N ARG C 267 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AB9, first strand: chain 'C' and resid 296 through 297 removed outlier: 3.699A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 301 through 303 removed outlier: 6.676A pdb=" N TYR C 301 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE C 310 " --> pdb=" O TYR C 301 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581 removed outlier: 6.536A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC4, first strand: chain 'C' and resid 716 through 717 removed outlier: 7.024A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.651A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.646A pdb=" N THR C 757 " --> pdb=" O ILE C 765 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE C 765 " --> pdb=" O THR C 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC8, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.430A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.650A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AD2, first strand: chain 'C' and resid 882 through 884 removed outlier: 7.185A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD4, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 7.631A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1335 through 1340 removed outlier: 4.015A pdb=" N ALA D 19 " --> pdb=" O GLU C1340 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 103 through 112 removed outlier: 3.531A pdb=" N LEU D 107 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.458A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.179A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AD8, first strand: chain 'D' and resid 252 through 254 Processing sheet with id=AD9, first strand: chain 'D' and resid 367 through 369 Processing sheet with id=AE1, first strand: chain 'D' and resid 526 through 527 removed outlier: 7.226A pdb=" N LEU D 527 " --> pdb=" O ARG D 551 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N THR D 553 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 703 through 707 Processing sheet with id=AE3, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE4, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE5, first strand: chain 'D' and resid 825 through 827 removed outlier: 6.364A pdb=" N VAL D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 848 through 849 removed outlier: 6.453A pdb=" N VAL D 848 " --> pdb=" O LEU D 857 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 949 through 951 removed outlier: 4.165A pdb=" N ALA D1018 " --> pdb=" O ILE D 950 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 991 through 997 removed outlier: 6.342A pdb=" N LEU D 984 " --> pdb=" O LYS D 992 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER D 994 " --> pdb=" O LEU D 982 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU D 982 " --> pdb=" O SER D 994 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LYS D 996 " --> pdb=" O THR D 980 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N THR D 980 " --> pdb=" O LYS D 996 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1028 through 1029 Processing sheet with id=AF1, first strand: chain 'D' and resid 1098 through 1100 Processing sheet with id=AF2, first strand: chain 'D' and resid 1046 through 1050 removed outlier: 3.852A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 1186 through 1191 Processing sheet with id=AF4, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 6.741A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 25 through 29 removed outlier: 6.266A pdb=" N ALA F 4 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LYS F 28 " --> pdb=" O ALA F 4 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL F 6 " --> pdb=" O LYS F 28 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU F 5 " --> pdb=" O TYR F 107 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 244 through 245 removed outlier: 14.840A pdb=" N ALA F 233 " --> pdb=" O ARG F 427 " (cutoff:3.500A) removed outlier: 12.295A pdb=" N ARG F 427 " --> pdb=" O ALA F 233 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N ALA F 235 " --> pdb=" O ARG F 425 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ARG F 425 " --> pdb=" O ALA F 235 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ARG F 421 " --> pdb=" O THR F 239 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LYS F 407 " --> pdb=" O ARG F 430 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA F 406 " --> pdb=" O THR F 277 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR F 277 " --> pdb=" O ALA F 406 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N TYR F 408 " --> pdb=" O PRO F 275 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER F 410 " --> pdb=" O ASP F 273 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASP F 273 " --> pdb=" O SER F 410 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR F 412 " --> pdb=" O ARG F 271 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ARG F 271 " --> pdb=" O THR F 412 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR F 414 " --> pdb=" O LEU F 269 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 244 through 245 removed outlier: 4.627A pdb=" N VAL F 222 " --> pdb=" O VAL F 238 " (cutoff:3.500A) removed outlier: 9.358A pdb=" N HIS F 240 " --> pdb=" O TRP F 220 " (cutoff:3.500A) removed outlier: 12.766A pdb=" N TRP F 220 " --> pdb=" O HIS F 240 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N SER F 225 " --> pdb=" O GLU F 463 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLU F 463 " --> pdb=" O SER F 225 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N THR F 227 " --> pdb=" O LEU F 461 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEU F 461 " --> pdb=" O THR F 227 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 510 through 513 Processing sheet with id=AF9, first strand: chain 'F' and resid 593 through 595 removed outlier: 3.969A pdb=" N VAL F 593 " --> pdb=" O ILE F 608 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 637 through 638 removed outlier: 3.743A pdb=" N VAL F 637 " --> pdb=" O LEU F 673 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 709 through 710 removed outlier: 7.319A pdb=" N LYS F 727 " --> pdb=" O ILE F 742 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE F 742 " --> pdb=" O LYS F 727 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LEU F 743 " --> pdb=" O GLU F 747 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLU F 747 " --> pdb=" O LEU F 743 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 756 through 762 removed outlier: 3.877A pdb=" N PHE F 770 " --> pdb=" O LEU F 758 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 827 through 831 removed outlier: 3.739A pdb=" N SER F 842 " --> pdb=" O TRP F 851 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N TRP F 851 " --> pdb=" O SER F 842 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LYS F 844 " --> pdb=" O THR F 849 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N THR F 849 " --> pdb=" O LYS F 844 " (cutoff:3.500A) 1460 hydrogen bonds defined for protein. 4092 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 9.21 Time building geometry restraints manager: 3.79 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: 11118 1.34 - 1.46: 6607 1.46 - 1.58: 15735 1.58 - 1.70: 91 1.70 - 1.82: 244 Bond restraints: 33795 Sorted by residual: bond pdb=" C TYR F 704 " pdb=" N ASP F 705 " ideal model delta sigma weight residual 1.330 1.224 0.106 1.24e-02 6.50e+03 7.31e+01 bond pdb=" C3' DT T 12 " pdb=" O3' DT T 12 " ideal model delta sigma weight residual 1.435 1.374 0.061 1.30e-02 5.92e+03 2.22e+01 bond pdb=" C3' DG N 39 " pdb=" O3' DG N 39 " ideal model delta sigma weight residual 1.435 1.376 0.059 1.30e-02 5.92e+03 2.04e+01 bond pdb=" C3' DC T 15 " pdb=" O3' DC T 15 " ideal model delta sigma weight residual 1.435 1.378 0.057 1.30e-02 5.92e+03 1.90e+01 bond pdb=" C3' DA T 7 " pdb=" O3' DA T 7 " ideal model delta sigma weight residual 1.435 1.380 0.055 1.30e-02 5.92e+03 1.81e+01 ... (remaining 33790 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 44709 2.25 - 4.49: 1036 4.49 - 6.74: 109 6.74 - 8.98: 11 8.98 - 11.23: 7 Bond angle restraints: 45872 Sorted by residual: angle pdb=" O4' DA N 50 " pdb=" C1' DA N 50 " pdb=" N9 DA N 50 " ideal model delta sigma weight residual 108.00 101.98 6.02 7.00e-01 2.04e+00 7.41e+01 angle pdb=" C1' C R 11 " pdb=" N1 C R 11 " pdb=" C2 C R 11 " ideal model delta sigma weight residual 118.80 128.19 -9.39 1.10e+00 8.26e-01 7.29e+01 angle pdb=" O4' DC N 49 " pdb=" C1' DC N 49 " pdb=" N1 DC N 49 " ideal model delta sigma weight residual 108.00 102.37 5.63 7.00e-01 2.04e+00 6.46e+01 angle pdb=" N GLY F 726 " pdb=" CA GLY F 726 " pdb=" C GLY F 726 " ideal model delta sigma weight residual 110.75 121.98 -11.23 1.46e+00 4.69e-01 5.91e+01 angle pdb=" O4' DC T 15 " pdb=" C4' DC T 15 " pdb=" C3' DC T 15 " ideal model delta sigma weight residual 106.00 110.34 -4.34 6.00e-01 2.78e+00 5.23e+01 ... (remaining 45867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.78: 20175 34.78 - 69.55: 521 69.55 - 104.33: 24 104.33 - 139.10: 0 139.10 - 173.88: 1 Dihedral angle restraints: 20721 sinusoidal: 8976 harmonic: 11745 Sorted by residual: dihedral pdb=" C LEU F 781 " pdb=" N LEU F 781 " pdb=" CA LEU F 781 " pdb=" CB LEU F 781 " ideal model delta harmonic sigma weight residual -122.60 -141.30 18.70 0 2.50e+00 1.60e-01 5.60e+01 dihedral pdb=" N LEU F 781 " pdb=" C LEU F 781 " pdb=" CA LEU F 781 " pdb=" CB LEU F 781 " ideal model delta harmonic sigma weight residual 122.80 140.07 -17.27 0 2.50e+00 1.60e-01 4.77e+01 dihedral pdb=" CA GLY F 726 " pdb=" C GLY F 726 " pdb=" N LYS F 727 " pdb=" CA LYS F 727 " ideal model delta harmonic sigma weight residual 180.00 150.86 29.14 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 20718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 5128 0.149 - 0.298: 50 0.298 - 0.447: 1 0.447 - 0.596: 2 0.596 - 0.745: 1 Chirality restraints: 5182 Sorted by residual: chirality pdb=" CA LEU F 781 " pdb=" N LEU F 781 " pdb=" C LEU F 781 " pdb=" CB LEU F 781 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.75 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" P DA T 17 " pdb=" OP1 DA T 17 " pdb=" OP2 DA T 17 " pdb=" O5' DA T 17 " both_signs ideal model delta sigma weight residual True 2.34 -2.92 -0.58 2.00e-01 2.50e+01 8.51e+00 chirality pdb=" P DG T 16 " pdb=" OP1 DG T 16 " pdb=" OP2 DG T 16 " pdb=" O5' DG T 16 " both_signs ideal model delta sigma weight residual True 2.34 -2.84 -0.51 2.00e-01 2.50e+01 6.43e+00 ... (remaining 5179 not shown) Planarity restraints: 5833 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 860 " -0.032 2.00e-02 2.50e+03 3.22e-02 2.59e+01 pdb=" CG TRP F 860 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP F 860 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP F 860 " -0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP F 860 " 0.047 2.00e-02 2.50e+03 pdb=" CE2 TRP F 860 " -0.020 2.00e-02 2.50e+03 pdb=" CE3 TRP F 860 " 0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 860 " -0.045 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 860 " 0.036 2.00e-02 2.50e+03 pdb=" CH2 TRP F 860 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 770 " -0.059 2.00e-02 2.50e+03 3.65e-02 2.33e+01 pdb=" CG PHE F 770 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE F 770 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE F 770 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 PHE F 770 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE F 770 " -0.019 2.00e-02 2.50e+03 pdb=" CZ PHE F 770 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 803 " -0.057 2.00e-02 2.50e+03 3.59e-02 2.26e+01 pdb=" CG PHE F 803 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE F 803 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE F 803 " 0.046 2.00e-02 2.50e+03 pdb=" CE1 PHE F 803 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE F 803 " -0.020 2.00e-02 2.50e+03 pdb=" CZ PHE F 803 " -0.030 2.00e-02 2.50e+03 ... (remaining 5830 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 322 2.55 - 3.14: 27583 3.14 - 3.72: 53570 3.72 - 4.31: 70697 4.31 - 4.90: 116581 Nonbonded interactions: 268753 Sorted by model distance: nonbonded pdb=" OD2 ASP D 460 " pdb="MG MG D1500 " model vdw 1.961 2.170 nonbonded pdb=" N4 DC N 38 " pdb=" O6 DG T 16 " model vdw 2.022 3.120 nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D1500 " model vdw 2.025 2.170 nonbonded pdb=" O CYS D 85 " pdb=" O CYS D 88 " model vdw 2.107 3.040 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1500 " model vdw 2.156 2.170 ... (remaining 268748 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 4 through 235) selection = chain 'B' } 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: 4.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 39.550 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.080 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 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 : 0.006 0.341 33815 Z= 0.326 Angle : 0.802 22.682 45902 Z= 0.497 Chirality : 0.050 0.745 5182 Planarity : 0.006 0.084 5833 Dihedral : 14.096 173.877 13165 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.07 % Favored : 96.85 % Rotamer: Outliers : 1.24 % Allowed : 6.42 % Favored : 92.34 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.13), residues: 4066 helix: 0.64 (0.13), residues: 1454 sheet: 0.33 (0.21), residues: 597 loop : -0.39 (0.13), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 136 TYR 0.057 0.002 TYR F 839 PHE 0.077 0.003 PHE F 786 TRP 0.047 0.003 TRP F 860 HIS 0.010 0.001 HIS F 719 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.32 (33795) covalent geometry : angle 0.77390 / 0.50 (45872) hydrogen bonds : bond 0.13085 / 8.79 ( 1518) hydrogen bonds : angle 6.58593 / 4.56 ( 4224) metal coordination : bond 0.09804 / 5.72 ( 20) metal coordination : angle 8.28744 / 5.74 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 291 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: 0.9442 (tpp) cc_final: 0.8759 (mmm) REVERT: C 142 GLU cc_start: 0.8828 (mp0) cc_final: 0.8620 (pm20) REVERT: C 239 MET cc_start: 0.9262 (ppp) cc_final: 0.9002 (ppp) REVERT: C 541 GLU cc_start: 0.9198 (mp0) cc_final: 0.8970 (tm-30) REVERT: C 545 PHE cc_start: 0.8629 (m-80) cc_final: 0.8110 (m-10) REVERT: C 742 TYR cc_start: 0.9028 (m-10) cc_final: 0.8784 (m-10) REVERT: C 1170 MET cc_start: 0.9087 (tpp) cc_final: 0.8385 (mmm) REVERT: C 1243 MET cc_start: 0.8587 (ttp) cc_final: 0.8213 (ttp) REVERT: C 1273 MET cc_start: 0.9424 (mmm) cc_final: 0.9167 (mmm) REVERT: C 1315 MET cc_start: 0.8073 (ttp) cc_final: 0.7142 (ttp) REVERT: D 282 LEU cc_start: 0.9448 (mm) cc_final: 0.8982 (tp) REVERT: D 304 ASP cc_start: 0.8620 (m-30) cc_final: 0.8120 (m-30) REVERT: D 466 MET cc_start: 0.8767 (ttm) cc_final: 0.8559 (tpp) REVERT: D 697 MET cc_start: 0.9185 (ttp) cc_final: 0.8836 (tmm) REVERT: D 743 MET cc_start: 0.7696 (ppp) cc_final: 0.7289 (ttt) REVERT: D 807 LEU cc_start: 0.9411 (tp) cc_final: 0.9101 (tp) REVERT: E 7 GLN cc_start: 0.9329 (tm-30) cc_final: 0.9127 (tm-30) REVERT: E 18 ASP cc_start: 0.9040 (t0) cc_final: 0.8611 (t0) REVERT: E 30 MET cc_start: 0.8967 (ttm) cc_final: 0.8702 (ttp) REVERT: E 65 ASP cc_start: 0.9753 (t0) cc_final: 0.9537 (t0) REVERT: F 95 GLU cc_start: 0.3700 (mt-10) cc_final: 0.3471 (pp20) REVERT: F 171 MET cc_start: 0.2547 (mtp) cc_final: 0.2132 (mtt) REVERT: F 305 MET cc_start: -0.3080 (mmm) cc_final: -0.3292 (mmp) REVERT: F 376 MET cc_start: 0.4498 (mmp) cc_final: 0.4037 (tpp) REVERT: F 403 MET cc_start: -0.2828 (mtp) cc_final: -0.3350 (mmm) REVERT: F 546 MET cc_start: 0.3932 (tpt) cc_final: 0.2764 (mtt) REVERT: F 729 MET cc_start: 0.4754 (tpp) cc_final: 0.4483 (mmm) outliers start: 43 outliers final: 15 residues processed: 331 average time/residue: 0.2296 time to fit residues: 119.2842 Evaluate side-chains 186 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain D residue 85 CYS Chi-restraints excluded: chain D residue 312 ARG Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 672 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN B 66 HIS C 46 GLN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 HIS C 686 GLN C 688 GLN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1237 HIS C1244 HIS ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN D 477 GLN D 951 GLN D1218 HIS ** D1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 240 HIS F 250 ASN F 681 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.086365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.051343 restraints weight = 252808.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 76)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.048503 restraints weight = 142199.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.048397 restraints weight = 96630.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.048496 restraints weight = 75315.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.048688 restraints weight = 65169.221| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 33815 Z= 0.287 Angle : 0.734 12.144 45902 Z= 0.381 Chirality : 0.045 0.401 5182 Planarity : 0.005 0.077 5833 Dihedral : 12.179 178.646 5164 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.10 % Allowed : 10.11 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.13), residues: 4066 helix: 1.02 (0.13), residues: 1479 sheet: 0.22 (0.20), residues: 634 loop : -0.42 (0.14), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 69 TYR 0.022 0.002 TYR D 795 PHE 0.021 0.002 PHE C 514 TRP 0.011 0.002 TRP D 409 HIS 0.007 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.29 (33795) covalent geometry : angle 0.72069 / 0.38 (45872) hydrogen bonds : bond 0.05076 / 3.46 ( 1518) hydrogen bonds : angle 5.54856 / 3.84 ( 4224) metal coordination : bond 0.01090 / 0.75 ( 20) metal coordination : angle 5.56145 / 3.54 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 171 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.9356 (mmm) cc_final: 0.8794 (mpp) REVERT: B 51 MET cc_start: 0.9467 (tpp) cc_final: 0.8768 (mmm) REVERT: B 205 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7637 (ttm) REVERT: C 142 GLU cc_start: 0.8736 (mp0) cc_final: 0.8382 (pm20) REVERT: C 545 PHE cc_start: 0.8439 (m-80) cc_final: 0.8058 (m-10) REVERT: C 696 ASP cc_start: 0.9024 (t0) cc_final: 0.8655 (t0) REVERT: C 742 TYR cc_start: 0.8962 (m-10) cc_final: 0.8606 (m-10) REVERT: C 1170 MET cc_start: 0.9097 (tpp) cc_final: 0.8451 (mmm) REVERT: C 1243 MET cc_start: 0.8707 (ttp) cc_final: 0.8391 (ttp) REVERT: C 1290 MET cc_start: 0.9216 (tpp) cc_final: 0.8484 (tpp) REVERT: C 1315 MET cc_start: 0.8117 (ttp) cc_final: 0.7833 (ttt) REVERT: D 282 LEU cc_start: 0.9471 (mm) cc_final: 0.9018 (tp) REVERT: D 301 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8707 (mm-30) REVERT: D 304 ASP cc_start: 0.8791 (m-30) cc_final: 0.8406 (m-30) REVERT: D 697 MET cc_start: 0.9239 (ttp) cc_final: 0.8950 (tmm) REVERT: D 743 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.7330 (ttt) REVERT: D 799 ARG cc_start: 0.9324 (OUTLIER) cc_final: 0.8980 (mtm-85) REVERT: D 932 MET cc_start: 0.8064 (tmm) cc_final: 0.7380 (tmm) REVERT: E 3 ARG cc_start: 0.8995 (tpm-80) cc_final: 0.8529 (tpt90) REVERT: E 7 GLN cc_start: 0.9323 (tm-30) cc_final: 0.9110 (tm-30) REVERT: E 18 ASP cc_start: 0.9167 (t0) cc_final: 0.8729 (t0) REVERT: E 30 MET cc_start: 0.8993 (ttm) cc_final: 0.8584 (ttp) REVERT: F 376 MET cc_start: 0.3986 (mmp) cc_final: 0.3412 (tpt) REVERT: F 403 MET cc_start: -0.2202 (mtp) cc_final: -0.3095 (mmm) REVERT: F 729 MET cc_start: 0.3587 (tpp) cc_final: 0.3377 (mmm) outliers start: 73 outliers final: 32 residues processed: 228 average time/residue: 0.2095 time to fit residues: 78.8787 Evaluate side-chains 185 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 662 SER Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 53 ARG Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 599 LYS Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 799 ARG Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1257 VAL Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 672 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 68 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 237 optimal weight: 20.0000 chunk 175 optimal weight: 1.9990 chunk 376 optimal weight: 40.0000 chunk 24 optimal weight: 0.0170 chunk 179 optimal weight: 0.9990 chunk 221 optimal weight: 8.9990 chunk 390 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 313 optimal weight: 1.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 HIS C 46 GLN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 GLN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 ASN D1350 ASN E 81 GLN F 573 GLN F 733 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.087409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.051844 restraints weight = 250911.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.051916 restraints weight = 138014.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 73)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.049714 restraints weight = 101122.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.049830 restraints weight = 79959.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.049883 restraints weight = 67582.093| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33815 Z= 0.143 Angle : 0.629 12.608 45902 Z= 0.324 Chirality : 0.044 0.405 5182 Planarity : 0.004 0.069 5833 Dihedral : 12.027 178.464 5152 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.96 % Allowed : 11.00 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.13), residues: 4066 helix: 1.33 (0.13), residues: 1468 sheet: 0.03 (0.20), residues: 665 loop : -0.35 (0.14), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 158 TYR 0.021 0.001 TYR D 795 PHE 0.018 0.001 PHE D 116 TRP 0.017 0.002 TRP F 395 HIS 0.003 0.001 HIS C 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (33795) covalent geometry : angle 0.61734 / 0.32 (45872) hydrogen bonds : bond 0.04246 / 2.90 ( 1518) hydrogen bonds : angle 5.15265 / 3.56 ( 4224) metal coordination : bond 0.00614 / 0.42 ( 20) metal coordination : angle 4.66559 / 2.97 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 163 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 142 MET cc_start: 0.9092 (pmm) cc_final: 0.8428 (pmm) REVERT: B 51 MET cc_start: 0.9439 (tpp) cc_final: 0.8655 (mmm) REVERT: C 142 GLU cc_start: 0.8548 (mp0) cc_final: 0.8165 (pm20) REVERT: C 545 PHE cc_start: 0.8345 (m-80) cc_final: 0.7965 (m-10) REVERT: C 685 MET cc_start: 0.8711 (mtp) cc_final: 0.8497 (ttm) REVERT: C 696 ASP cc_start: 0.8940 (t0) cc_final: 0.8517 (t0) REVERT: C 1243 MET cc_start: 0.8680 (ttp) cc_final: 0.8216 (ttp) REVERT: D 282 LEU cc_start: 0.9403 (mm) cc_final: 0.8907 (tp) REVERT: D 301 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8711 (mm-30) REVERT: D 304 ASP cc_start: 0.8755 (m-30) cc_final: 0.8348 (m-30) REVERT: D 330 MET cc_start: 0.8288 (mmm) cc_final: 0.7923 (mmm) REVERT: D 368 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8599 (tt) REVERT: D 400 MET cc_start: 0.9256 (tpp) cc_final: 0.9029 (tpp) REVERT: D 724 MET cc_start: 0.9055 (tpp) cc_final: 0.8794 (tpp) REVERT: D 743 MET cc_start: 0.7628 (ppp) cc_final: 0.7341 (ttt) REVERT: D 747 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7621 (mtm) REVERT: D 807 LEU cc_start: 0.9460 (tp) cc_final: 0.9174 (tp) REVERT: D 932 MET cc_start: 0.8181 (tmm) cc_final: 0.7540 (tmm) REVERT: E 3 ARG cc_start: 0.8966 (tpm-80) cc_final: 0.8654 (tpt90) REVERT: E 7 GLN cc_start: 0.9324 (tm-30) cc_final: 0.9122 (tm-30) REVERT: E 30 MET cc_start: 0.8991 (ttm) cc_final: 0.8541 (ttp) REVERT: F 71 MET cc_start: 0.2353 (ptm) cc_final: 0.2065 (ptp) REVERT: F 376 MET cc_start: 0.4856 (mmp) cc_final: 0.4442 (tpt) REVERT: F 403 MET cc_start: -0.2392 (mtp) cc_final: -0.3112 (mmm) REVERT: F 729 MET cc_start: 0.3569 (tpp) cc_final: 0.3347 (mmm) REVERT: F 831 PHE cc_start: 0.2650 (t80) cc_final: 0.2439 (t80) outliers start: 68 outliers final: 32 residues processed: 222 average time/residue: 0.1962 time to fit residues: 72.8934 Evaluate side-chains 191 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 599 LYS Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1257 VAL Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain F residue 384 GLU Chi-restraints excluded: chain F residue 672 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 86 optimal weight: 4.9990 chunk 227 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 302 optimal weight: 9.9990 chunk 146 optimal weight: 20.0000 chunk 181 optimal weight: 3.9990 chunk 338 optimal weight: 50.0000 chunk 207 optimal weight: 0.0370 chunk 154 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 103 ASN A 128 HIS ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 GLN D 951 GLN D1019 ASN D1227 HIS D1350 ASN E 81 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.088597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.061546 restraints weight = 213033.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.062887 restraints weight = 108092.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.063727 restraints weight = 71607.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.064265 restraints weight = 55921.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.064537 restraints weight = 47648.659| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 33815 Z= 0.159 Angle : 0.605 11.098 45902 Z= 0.313 Chirality : 0.043 0.401 5182 Planarity : 0.004 0.049 5833 Dihedral : 11.908 177.046 5147 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.28 % Allowed : 11.69 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.13), residues: 4066 helix: 1.44 (0.14), residues: 1469 sheet: -0.05 (0.20), residues: 669 loop : -0.31 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 158 TYR 0.016 0.001 TYR D 795 PHE 0.027 0.001 PHE C 186 TRP 0.018 0.001 TRP F 395 HIS 0.004 0.001 HIS C 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (33795) covalent geometry : angle 0.59541 / 0.31 (45872) hydrogen bonds : bond 0.03987 / 2.72 ( 1518) hydrogen bonds : angle 5.01530 / 3.45 ( 4224) metal coordination : bond 0.00596 / 0.42 ( 20) metal coordination : angle 4.18844 / 2.67 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 160 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.9362 (pmm) cc_final: 0.8627 (pmm) REVERT: B 51 MET cc_start: 0.9490 (tpp) cc_final: 0.8710 (mmm) REVERT: C 142 GLU cc_start: 0.8709 (mp0) cc_final: 0.8267 (pm20) REVERT: C 429 MET cc_start: 0.9362 (mmm) cc_final: 0.9099 (mmt) REVERT: C 545 PHE cc_start: 0.8449 (m-80) cc_final: 0.8172 (m-10) REVERT: C 685 MET cc_start: 0.8614 (mtp) cc_final: 0.8409 (ttm) REVERT: C 696 ASP cc_start: 0.8897 (t0) cc_final: 0.8438 (t0) REVERT: C 1119 MET cc_start: 0.9204 (tpp) cc_final: 0.8549 (tpp) REVERT: C 1243 MET cc_start: 0.8717 (ttp) cc_final: 0.8353 (ttp) REVERT: C 1315 MET cc_start: 0.8098 (ttp) cc_final: 0.7896 (ttp) REVERT: D 282 LEU cc_start: 0.9372 (mm) cc_final: 0.8940 (tp) REVERT: D 304 ASP cc_start: 0.8767 (m-30) cc_final: 0.8382 (m-30) REVERT: D 330 MET cc_start: 0.8392 (mmm) cc_final: 0.8009 (mmm) REVERT: D 466 MET cc_start: 0.8260 (mmm) cc_final: 0.7888 (tpt) REVERT: D 724 MET cc_start: 0.8983 (tpp) cc_final: 0.8714 (tpp) REVERT: D 743 MET cc_start: 0.7523 (OUTLIER) cc_final: 0.7143 (ttt) REVERT: D 747 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7532 (mtm) REVERT: D 932 MET cc_start: 0.8354 (tmm) cc_final: 0.7547 (tmm) REVERT: E 3 ARG cc_start: 0.9012 (tpm-80) cc_final: 0.8661 (tpt90) REVERT: E 30 MET cc_start: 0.9018 (ttm) cc_final: 0.8518 (ttp) REVERT: F 71 MET cc_start: -0.3435 (ptm) cc_final: -0.3795 (ptp) REVERT: F 376 MET cc_start: 0.5029 (mmp) cc_final: 0.4349 (tpt) REVERT: F 709 VAL cc_start: 0.8001 (OUTLIER) cc_final: 0.7539 (m) REVERT: F 729 MET cc_start: 0.3131 (tpp) cc_final: 0.2803 (mmm) REVERT: F 831 PHE cc_start: 0.1405 (t80) cc_final: 0.0785 (t80) outliers start: 79 outliers final: 41 residues processed: 228 average time/residue: 0.1987 time to fit residues: 76.6396 Evaluate side-chains 192 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 848 GLU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 53 ARG Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 599 LYS Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1257 VAL Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain F residue 384 GLU Chi-restraints excluded: chain F residue 709 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 201 optimal weight: 3.9990 chunk 311 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 357 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 178 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 202 optimal weight: 8.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 ASN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 518 ASN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1264 GLN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.087479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.060563 restraints weight = 216555.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.061857 restraints weight = 109237.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.062700 restraints weight = 72216.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.063225 restraints weight = 55857.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.063449 restraints weight = 47334.996| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 33815 Z= 0.198 Angle : 0.615 11.411 45902 Z= 0.316 Chirality : 0.043 0.396 5182 Planarity : 0.004 0.059 5833 Dihedral : 11.923 175.727 5145 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.13 % Allowed : 13.02 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.13), residues: 4066 helix: 1.46 (0.14), residues: 1465 sheet: -0.11 (0.19), residues: 675 loop : -0.31 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 158 TYR 0.016 0.001 TYR F 855 PHE 0.024 0.001 PHE A 231 TRP 0.010 0.001 TRP D 580 HIS 0.006 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.20 (33795) covalent geometry : angle 0.60673 / 0.32 (45872) hydrogen bonds : bond 0.04000 / 2.74 ( 1518) hydrogen bonds : angle 4.97904 / 3.41 ( 4224) metal coordination : bond 0.00715 / 0.49 ( 20) metal coordination : angle 4.01677 / 2.59 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 152 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.9447 (pmm) cc_final: 0.8640 (pmm) REVERT: B 51 MET cc_start: 0.9466 (tpp) cc_final: 0.9218 (mmm) REVERT: C 429 MET cc_start: 0.9354 (mmm) cc_final: 0.9085 (mmt) REVERT: C 545 PHE cc_start: 0.8495 (m-80) cc_final: 0.8237 (m-10) REVERT: C 653 MET cc_start: 0.8770 (tpt) cc_final: 0.8123 (tpp) REVERT: C 696 ASP cc_start: 0.8949 (t0) cc_final: 0.8529 (t0) REVERT: C 1119 MET cc_start: 0.9276 (tpp) cc_final: 0.8626 (tpp) REVERT: C 1243 MET cc_start: 0.8735 (ttp) cc_final: 0.8387 (ttp) REVERT: D 237 MET cc_start: 0.9427 (ttt) cc_final: 0.9174 (tmm) REVERT: D 282 LEU cc_start: 0.9387 (mm) cc_final: 0.8941 (tp) REVERT: D 304 ASP cc_start: 0.8807 (m-30) cc_final: 0.8408 (m-30) REVERT: D 368 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8388 (tt) REVERT: D 400 MET cc_start: 0.9409 (tpp) cc_final: 0.8934 (tpp) REVERT: D 466 MET cc_start: 0.8229 (mmm) cc_final: 0.7725 (tpt) REVERT: D 697 MET cc_start: 0.9324 (tmm) cc_final: 0.8927 (tmm) REVERT: D 724 MET cc_start: 0.9003 (tpp) cc_final: 0.8721 (tpp) REVERT: D 743 MET cc_start: 0.7506 (OUTLIER) cc_final: 0.7069 (ttt) REVERT: D 932 MET cc_start: 0.8532 (tmm) cc_final: 0.7761 (tmm) REVERT: D 1260 MET cc_start: 0.9037 (tpp) cc_final: 0.8784 (mmt) REVERT: E 3 ARG cc_start: 0.9028 (tpm-80) cc_final: 0.8732 (tpt90) REVERT: E 30 MET cc_start: 0.9025 (ttm) cc_final: 0.8543 (ttp) REVERT: F 71 MET cc_start: -0.3344 (ptm) cc_final: -0.3570 (ptp) REVERT: F 376 MET cc_start: 0.5112 (mmp) cc_final: 0.4405 (tpt) REVERT: F 709 VAL cc_start: 0.7912 (OUTLIER) cc_final: 0.7438 (m) REVERT: F 729 MET cc_start: 0.2975 (tpp) cc_final: 0.2654 (mmm) REVERT: F 831 PHE cc_start: 0.1323 (t80) cc_final: 0.0763 (t80) outliers start: 74 outliers final: 44 residues processed: 217 average time/residue: 0.1963 time to fit residues: 72.4853 Evaluate side-chains 195 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 148 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 599 LYS Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 964 LYS Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1257 VAL Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain F residue 384 GLU Chi-restraints excluded: chain F residue 709 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 209 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 356 optimal weight: 0.0870 chunk 225 optimal weight: 10.0000 chunk 183 optimal weight: 0.9980 chunk 264 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 150 optimal weight: 0.8980 overall best weight: 1.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 518 ASN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1008 GLN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN ** E 81 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 = 0.3854 r_free = 0.3854 target = 0.088074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.061194 restraints weight = 214181.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.062588 restraints weight = 107385.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.063460 restraints weight = 70755.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.063948 restraints weight = 54390.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.064205 restraints weight = 46492.919| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33815 Z= 0.122 Angle : 0.593 11.871 45902 Z= 0.300 Chirality : 0.043 0.449 5182 Planarity : 0.004 0.099 5833 Dihedral : 11.859 175.984 5145 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.87 % Allowed : 14.23 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.13), residues: 4066 helix: 1.53 (0.14), residues: 1461 sheet: -0.09 (0.20), residues: 677 loop : -0.28 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG F 336 TYR 0.016 0.001 TYR F 855 PHE 0.015 0.001 PHE A 231 TRP 0.013 0.001 TRP F 395 HIS 0.006 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (33795) covalent geometry : angle 0.58513 / 0.30 (45872) hydrogen bonds : bond 0.03571 / 2.43 ( 1518) hydrogen bonds : angle 4.83562 / 3.31 ( 4224) metal coordination : bond 0.00363 / 0.26 ( 20) metal coordination : angle 3.75515 / 2.38 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 167 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.9537 (mmt) cc_final: 0.9005 (tmm) REVERT: A 142 MET cc_start: 0.9418 (pmm) cc_final: 0.8689 (pmm) REVERT: B 51 MET cc_start: 0.9424 (tpp) cc_final: 0.9129 (mmm) REVERT: C 142 GLU cc_start: 0.8703 (mp0) cc_final: 0.8340 (pm20) REVERT: C 429 MET cc_start: 0.9378 (mmm) cc_final: 0.9115 (mmt) REVERT: C 459 MET cc_start: 0.9005 (mtm) cc_final: 0.8725 (mtm) REVERT: C 545 PHE cc_start: 0.8499 (m-80) cc_final: 0.8238 (m-10) REVERT: C 623 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9142 (mt) REVERT: C 653 MET cc_start: 0.8708 (tpt) cc_final: 0.8096 (tpp) REVERT: C 696 ASP cc_start: 0.8804 (t0) cc_final: 0.8315 (t0) REVERT: C 741 MET cc_start: 0.7975 (ttt) cc_final: 0.7557 (tpp) REVERT: C 838 CYS cc_start: 0.8314 (OUTLIER) cc_final: 0.8007 (p) REVERT: C 1119 MET cc_start: 0.9283 (tpp) cc_final: 0.8603 (tpp) REVERT: C 1243 MET cc_start: 0.8722 (ttp) cc_final: 0.8231 (ttp) REVERT: C 1272 GLU cc_start: 0.7315 (tp30) cc_final: 0.6265 (tp30) REVERT: C 1276 TRP cc_start: 0.8998 (m-10) cc_final: 0.8311 (m-10) REVERT: C 1315 MET cc_start: 0.8164 (ttp) cc_final: 0.7712 (ttt) REVERT: D 237 MET cc_start: 0.9381 (ttt) cc_final: 0.8918 (tmm) REVERT: D 282 LEU cc_start: 0.9324 (mm) cc_final: 0.8892 (tp) REVERT: D 304 ASP cc_start: 0.8808 (m-30) cc_final: 0.8409 (m-30) REVERT: D 330 MET cc_start: 0.8310 (mmm) cc_final: 0.7966 (mmm) REVERT: D 368 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8315 (tt) REVERT: D 466 MET cc_start: 0.8266 (mmm) cc_final: 0.7777 (tpt) REVERT: D 697 MET cc_start: 0.9299 (tmm) cc_final: 0.8786 (tmm) REVERT: D 724 MET cc_start: 0.9006 (tpp) cc_final: 0.8725 (tpp) REVERT: D 747 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.7157 (mtp) REVERT: D 932 MET cc_start: 0.8601 (tmm) cc_final: 0.7831 (tmm) REVERT: D 1260 MET cc_start: 0.9008 (tpp) cc_final: 0.8777 (mmt) REVERT: E 3 ARG cc_start: 0.9012 (tpm-80) cc_final: 0.8702 (tpt90) REVERT: E 30 MET cc_start: 0.9003 (ttm) cc_final: 0.8468 (ttp) REVERT: F 71 MET cc_start: -0.3482 (ptm) cc_final: -0.3792 (ptp) REVERT: F 376 MET cc_start: 0.5280 (mmp) cc_final: 0.4528 (tpt) REVERT: F 729 MET cc_start: 0.3018 (tpp) cc_final: 0.2191 (mmm) REVERT: F 831 PHE cc_start: 0.1355 (t80) cc_final: 0.0795 (t80) outliers start: 65 outliers final: 38 residues processed: 223 average time/residue: 0.2049 time to fit residues: 76.6055 Evaluate side-chains 194 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 53 ARG Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 599 LYS Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 964 LYS Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 384 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 216 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 chunk 170 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 344 optimal weight: 9.9990 chunk 206 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 325 optimal weight: 20.0000 chunk 304 optimal weight: 10.0000 chunk 223 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN C 518 ASN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.080375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.047848 restraints weight = 220293.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.048203 restraints weight = 119822.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.048358 restraints weight = 91664.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.048310 restraints weight = 70880.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.048369 restraints weight = 66044.108| |-----------------------------------------------------------------------------| r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 33815 Z= 0.275 Angle : 0.676 11.383 45902 Z= 0.346 Chirality : 0.043 0.389 5182 Planarity : 0.004 0.060 5833 Dihedral : 11.953 173.733 5145 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.36 % Allowed : 14.31 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.13), residues: 4066 helix: 1.38 (0.14), residues: 1466 sheet: -0.13 (0.20), residues: 670 loop : -0.37 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 378 TYR 0.018 0.001 TYR D1363 PHE 0.017 0.002 PHE C 812 TRP 0.015 0.001 TRP F 395 HIS 0.007 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.27 (33795) covalent geometry : angle 0.66791 / 0.35 (45872) hydrogen bonds : bond 0.04343 / 3.00 ( 1518) hydrogen bonds : angle 5.02363 / 3.44 ( 4224) metal coordination : bond 0.00980 / 0.66 ( 20) metal coordination : angle 4.04049 / 2.76 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 147 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.9507 (mmt) cc_final: 0.9232 (mmm) REVERT: A 142 MET cc_start: 0.9509 (pmm) cc_final: 0.8748 (pmm) REVERT: B 51 MET cc_start: 0.9407 (tpp) cc_final: 0.9112 (mmm) REVERT: C 239 MET cc_start: 0.8080 (ppp) cc_final: 0.7763 (ppp) REVERT: C 429 MET cc_start: 0.9383 (mmm) cc_final: 0.9121 (mmt) REVERT: C 545 PHE cc_start: 0.8579 (m-80) cc_final: 0.8334 (m-10) REVERT: C 623 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9158 (mt) REVERT: C 653 MET cc_start: 0.8640 (tpt) cc_final: 0.7958 (tpt) REVERT: C 696 ASP cc_start: 0.8968 (t0) cc_final: 0.8566 (t0) REVERT: C 741 MET cc_start: 0.7854 (ttt) cc_final: 0.7525 (tpp) REVERT: C 838 CYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7865 (p) REVERT: C 1119 MET cc_start: 0.9336 (tpp) cc_final: 0.8688 (tpp) REVERT: D 38 VAL cc_start: 0.9543 (OUTLIER) cc_final: 0.9333 (p) REVERT: D 282 LEU cc_start: 0.9384 (mm) cc_final: 0.8962 (tp) REVERT: D 304 ASP cc_start: 0.8788 (m-30) cc_final: 0.8384 (m-30) REVERT: D 368 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8524 (tt) REVERT: D 400 MET cc_start: 0.9422 (tpp) cc_final: 0.9215 (tpp) REVERT: D 466 MET cc_start: 0.8257 (mmm) cc_final: 0.7604 (tpt) REVERT: D 697 MET cc_start: 0.9344 (tmm) cc_final: 0.8870 (tmm) REVERT: D 747 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7330 (mtp) REVERT: D 932 MET cc_start: 0.8854 (tmm) cc_final: 0.8107 (tmm) REVERT: E 3 ARG cc_start: 0.9060 (tpm-80) cc_final: 0.8784 (tpt90) REVERT: E 30 MET cc_start: 0.9041 (ttm) cc_final: 0.8301 (mtp) REVERT: F 71 MET cc_start: 0.2640 (ptm) cc_final: 0.2172 (ptp) REVERT: F 376 MET cc_start: 0.5409 (mmp) cc_final: 0.4961 (tpt) REVERT: F 438 MET cc_start: 0.3692 (mmm) cc_final: 0.3210 (mmm) outliers start: 82 outliers final: 53 residues processed: 221 average time/residue: 0.1970 time to fit residues: 73.6668 Evaluate side-chains 197 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 139 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 662 SER Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 53 ARG Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 599 LYS Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 964 LYS Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1257 VAL Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 384 GLU Chi-restraints excluded: chain F residue 460 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 137 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 210 optimal weight: 7.9990 chunk 243 optimal weight: 7.9990 chunk 391 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN D 951 GLN D1098 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.085760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.050489 restraints weight = 251209.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.047093 restraints weight = 143083.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.047153 restraints weight = 98159.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.047218 restraints weight = 78452.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.047206 restraints weight = 67631.803| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33815 Z= 0.147 Angle : 0.598 11.871 45902 Z= 0.305 Chirality : 0.042 0.396 5182 Planarity : 0.004 0.060 5833 Dihedral : 11.937 174.382 5145 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.07 % Allowed : 14.80 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.13), residues: 4066 helix: 1.46 (0.14), residues: 1465 sheet: -0.09 (0.20), residues: 654 loop : -0.33 (0.14), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 336 TYR 0.017 0.001 TYR F 855 PHE 0.015 0.001 PHE D1034 TRP 0.015 0.001 TRP F 395 HIS 0.006 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (33795) covalent geometry : angle 0.58997 / 0.30 (45872) hydrogen bonds : bond 0.03676 / 2.50 ( 1518) hydrogen bonds : angle 4.87423 / 3.34 ( 4224) metal coordination : bond 0.00492 / 0.34 ( 20) metal coordination : angle 3.89726 / 2.54 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 150 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.9498 (mmt) cc_final: 0.9284 (mmm) REVERT: A 142 MET cc_start: 0.9433 (pmm) cc_final: 0.8717 (pmm) REVERT: B 51 MET cc_start: 0.9401 (tpp) cc_final: 0.8807 (mmm) REVERT: C 239 MET cc_start: 0.8293 (ppp) cc_final: 0.7951 (ppp) REVERT: C 369 MET cc_start: 0.9147 (tmm) cc_final: 0.8678 (ppp) REVERT: C 429 MET cc_start: 0.9358 (mmm) cc_final: 0.9119 (mmt) REVERT: C 545 PHE cc_start: 0.8493 (m-80) cc_final: 0.8257 (m-10) REVERT: C 623 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9137 (mt) REVERT: C 653 MET cc_start: 0.8475 (tpt) cc_final: 0.7859 (tpt) REVERT: C 696 ASP cc_start: 0.8852 (t0) cc_final: 0.8431 (t0) REVERT: C 741 MET cc_start: 0.8003 (ttt) cc_final: 0.7546 (tpp) REVERT: C 838 CYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7856 (p) REVERT: C 1119 MET cc_start: 0.9309 (tpp) cc_final: 0.8657 (tpp) REVERT: C 1232 MET cc_start: 0.9152 (mmm) cc_final: 0.8605 (mmm) REVERT: C 1243 MET cc_start: 0.8788 (tmm) cc_final: 0.8472 (ttp) REVERT: C 1315 MET cc_start: 0.8154 (ttp) cc_final: 0.7844 (ttt) REVERT: D 282 LEU cc_start: 0.9369 (mm) cc_final: 0.8932 (tp) REVERT: D 304 ASP cc_start: 0.8780 (m-30) cc_final: 0.8448 (m-30) REVERT: D 368 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8568 (tt) REVERT: D 400 MET cc_start: 0.9373 (tpp) cc_final: 0.9114 (tpp) REVERT: D 424 ASN cc_start: 0.8722 (OUTLIER) cc_final: 0.8425 (t0) REVERT: D 466 MET cc_start: 0.8287 (mmm) cc_final: 0.7655 (tpt) REVERT: D 697 MET cc_start: 0.9282 (tmm) cc_final: 0.8783 (tmm) REVERT: D 932 MET cc_start: 0.8749 (tmm) cc_final: 0.8028 (tmm) REVERT: D 1260 MET cc_start: 0.8914 (tpp) cc_final: 0.8648 (mmt) REVERT: E 3 ARG cc_start: 0.9006 (tpm-80) cc_final: 0.8751 (tpt90) REVERT: E 30 MET cc_start: 0.8965 (ttm) cc_final: 0.8184 (mtp) REVERT: F 71 MET cc_start: 0.2924 (ptm) cc_final: 0.2109 (ptt) REVERT: F 376 MET cc_start: 0.5322 (mmp) cc_final: 0.4888 (tpt) REVERT: F 438 MET cc_start: 0.3949 (mmm) cc_final: 0.3505 (mmm) REVERT: F 828 MET cc_start: 0.4600 (pmm) cc_final: 0.4272 (ptt) outliers start: 72 outliers final: 51 residues processed: 216 average time/residue: 0.1929 time to fit residues: 71.5051 Evaluate side-chains 200 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 145 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 662 SER Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain D residue 53 ARG Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 599 LYS Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 384 GLU Chi-restraints excluded: chain F residue 460 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 317 optimal weight: 0.7980 chunk 378 optimal weight: 20.0000 chunk 154 optimal weight: 2.9990 chunk 326 optimal weight: 5.9990 chunk 166 optimal weight: 0.0770 chunk 365 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 291 optimal weight: 6.9990 chunk 294 optimal weight: 1.9990 chunk 290 optimal weight: 5.9990 chunk 330 optimal weight: 8.9990 overall best weight: 2.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN ** E 81 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 = 0.3841 r_free = 0.3841 target = 0.087712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.060895 restraints weight = 213956.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.062201 restraints weight = 107882.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.062995 restraints weight = 70874.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.063486 restraints weight = 54998.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.063747 restraints weight = 47072.915| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33815 Z= 0.135 Angle : 0.597 13.906 45902 Z= 0.305 Chirality : 0.042 0.398 5182 Planarity : 0.004 0.059 5833 Dihedral : 11.876 174.299 5145 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.84 % Allowed : 15.09 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.13), residues: 4066 helix: 1.48 (0.14), residues: 1465 sheet: -0.06 (0.20), residues: 651 loop : -0.32 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 336 TYR 0.021 0.001 TYR F 855 PHE 0.013 0.001 PHE D1034 TRP 0.013 0.001 TRP F 395 HIS 0.006 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (33795) covalent geometry : angle 0.58985 / 0.30 (45872) hydrogen bonds : bond 0.03547 / 2.41 ( 1518) hydrogen bonds : angle 4.80222 / 3.29 ( 4224) metal coordination : bond 0.00422 / 0.29 ( 20) metal coordination : angle 3.70171 / 2.40 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 151 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.9480 (pmm) cc_final: 0.8751 (pmm) REVERT: B 51 MET cc_start: 0.9418 (tpp) cc_final: 0.8770 (mmm) REVERT: C 239 MET cc_start: 0.8399 (ppp) cc_final: 0.8032 (ppp) REVERT: C 369 MET cc_start: 0.9187 (tmm) cc_final: 0.8734 (ppp) REVERT: C 429 MET cc_start: 0.9389 (mmm) cc_final: 0.9146 (mmt) REVERT: C 545 PHE cc_start: 0.8541 (m-80) cc_final: 0.8308 (m-10) REVERT: C 623 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9147 (mt) REVERT: C 653 MET cc_start: 0.8737 (tpt) cc_final: 0.7992 (tpt) REVERT: C 696 ASP cc_start: 0.8784 (t0) cc_final: 0.8328 (t0) REVERT: C 741 MET cc_start: 0.8019 (ttt) cc_final: 0.7572 (tpp) REVERT: C 1119 MET cc_start: 0.9314 (tpp) cc_final: 0.8649 (tpp) REVERT: C 1131 MET cc_start: 0.9480 (OUTLIER) cc_final: 0.8837 (tmm) REVERT: C 1232 MET cc_start: 0.9202 (mmm) cc_final: 0.8674 (mmm) REVERT: C 1243 MET cc_start: 0.8888 (tmm) cc_final: 0.8482 (ttp) REVERT: C 1276 TRP cc_start: 0.8981 (m-10) cc_final: 0.8438 (m-10) REVERT: C 1315 MET cc_start: 0.8166 (ttp) cc_final: 0.7839 (ttt) REVERT: D 237 MET cc_start: 0.9334 (tmm) cc_final: 0.8957 (tmm) REVERT: D 282 LEU cc_start: 0.9346 (mm) cc_final: 0.8913 (tp) REVERT: D 304 ASP cc_start: 0.8741 (m-30) cc_final: 0.8402 (m-30) REVERT: D 368 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8339 (tt) REVERT: D 400 MET cc_start: 0.9345 (tpp) cc_final: 0.9076 (tpp) REVERT: D 424 ASN cc_start: 0.8713 (OUTLIER) cc_final: 0.8513 (t0) REVERT: D 466 MET cc_start: 0.8287 (mmm) cc_final: 0.7785 (tpt) REVERT: D 604 MET cc_start: 0.9619 (tpp) cc_final: 0.9354 (tpt) REVERT: D 697 MET cc_start: 0.9270 (tmm) cc_final: 0.8821 (tmm) REVERT: D 822 MET cc_start: 0.8776 (tpt) cc_final: 0.8040 (tmm) REVERT: D 932 MET cc_start: 0.8699 (tmm) cc_final: 0.8022 (tmm) REVERT: D 1260 MET cc_start: 0.8943 (tpp) cc_final: 0.8672 (mmt) REVERT: E 3 ARG cc_start: 0.9034 (tpm-80) cc_final: 0.8746 (tpt90) REVERT: E 30 MET cc_start: 0.9063 (ttm) cc_final: 0.8203 (mtp) REVERT: F 71 MET cc_start: -0.3648 (ptm) cc_final: -0.3946 (ptt) REVERT: F 376 MET cc_start: 0.5218 (mmp) cc_final: 0.4465 (tpt) REVERT: F 383 MET cc_start: 0.3367 (mmm) cc_final: 0.2765 (mmm) REVERT: F 403 MET cc_start: -0.3960 (mmm) cc_final: -0.4676 (mmp) REVERT: F 828 MET cc_start: 0.4976 (pmm) cc_final: 0.3623 (ptt) outliers start: 64 outliers final: 53 residues processed: 210 average time/residue: 0.2051 time to fit residues: 72.4833 Evaluate side-chains 204 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 147 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 662 SER Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain D residue 53 ARG Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 599 LYS Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 384 GLU Chi-restraints excluded: chain F residue 460 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 42 optimal weight: 5.9990 chunk 394 optimal weight: 50.0000 chunk 279 optimal weight: 5.9990 chunk 307 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 222 optimal weight: 3.9990 chunk 172 optimal weight: 7.9990 chunk 230 optimal weight: 8.9990 chunk 244 optimal weight: 8.9990 chunk 389 optimal weight: 40.0000 chunk 407 optimal weight: 60.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.080913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.045419 restraints weight = 218109.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.046034 restraints weight = 114521.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.046062 restraints weight = 80294.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.046381 restraints weight = 61584.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.046677 restraints weight = 54247.841| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 33815 Z= 0.197 Angle : 0.627 13.757 45902 Z= 0.320 Chirality : 0.042 0.391 5182 Planarity : 0.004 0.059 5833 Dihedral : 11.899 173.351 5145 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.87 % Allowed : 15.09 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.13), residues: 4066 helix: 1.43 (0.14), residues: 1466 sheet: -0.10 (0.20), residues: 659 loop : -0.39 (0.14), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D1231 TYR 0.020 0.001 TYR F 855 PHE 0.014 0.001 PHE C 812 TRP 0.016 0.001 TRP F 395 HIS 0.006 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.20 (33795) covalent geometry : angle 0.61956 / 0.32 (45872) hydrogen bonds : bond 0.03794 / 2.59 ( 1518) hydrogen bonds : angle 4.86038 / 3.33 ( 4224) metal coordination : bond 0.00680 / 0.47 ( 20) metal coordination : angle 3.74601 / 2.50 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 147 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.9501 (pmm) cc_final: 0.8760 (pmm) REVERT: C 130 MET cc_start: 0.8315 (tpp) cc_final: 0.8011 (tpp) REVERT: C 135 THR cc_start: 0.9413 (OUTLIER) cc_final: 0.9081 (p) REVERT: C 239 MET cc_start: 0.8411 (ppp) cc_final: 0.8051 (ppp) REVERT: C 369 MET cc_start: 0.9184 (tmm) cc_final: 0.8772 (ppp) REVERT: C 429 MET cc_start: 0.9384 (mmm) cc_final: 0.9139 (mmt) REVERT: C 545 PHE cc_start: 0.8548 (m-80) cc_final: 0.8315 (m-10) REVERT: C 623 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9149 (mt) REVERT: C 653 MET cc_start: 0.8571 (tpt) cc_final: 0.7898 (tpt) REVERT: C 696 ASP cc_start: 0.8884 (t0) cc_final: 0.8465 (t0) REVERT: C 741 MET cc_start: 0.8053 (ttt) cc_final: 0.7525 (tpp) REVERT: C 1119 MET cc_start: 0.9322 (tpp) cc_final: 0.8677 (tpp) REVERT: C 1131 MET cc_start: 0.9443 (OUTLIER) cc_final: 0.8832 (tmm) REVERT: C 1232 MET cc_start: 0.9233 (mmm) cc_final: 0.8696 (mmm) REVERT: C 1243 MET cc_start: 0.8865 (tmm) cc_final: 0.8511 (ttp) REVERT: C 1272 GLU cc_start: 0.7450 (tp30) cc_final: 0.6423 (tp30) REVERT: C 1276 TRP cc_start: 0.9046 (m-10) cc_final: 0.8388 (m-10) REVERT: C 1315 MET cc_start: 0.8115 (ttp) cc_final: 0.7807 (ttt) REVERT: D 282 LEU cc_start: 0.9375 (mm) cc_final: 0.8904 (tp) REVERT: D 304 ASP cc_start: 0.8734 (m-30) cc_final: 0.8393 (m-30) REVERT: D 368 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8465 (tt) REVERT: D 400 MET cc_start: 0.9407 (tpp) cc_final: 0.9151 (tpp) REVERT: D 424 ASN cc_start: 0.8749 (OUTLIER) cc_final: 0.8401 (t0) REVERT: D 466 MET cc_start: 0.8294 (mmm) cc_final: 0.7669 (tpt) REVERT: D 604 MET cc_start: 0.9597 (tpp) cc_final: 0.9353 (tpp) REVERT: D 697 MET cc_start: 0.9291 (tmm) cc_final: 0.8844 (tmm) REVERT: D 822 MET cc_start: 0.8838 (tpt) cc_final: 0.8178 (tmm) REVERT: D 932 MET cc_start: 0.8832 (tmm) cc_final: 0.8084 (tmm) REVERT: E 3 ARG cc_start: 0.9046 (tpm-80) cc_final: 0.8766 (tpt90) REVERT: E 30 MET cc_start: 0.9037 (ttm) cc_final: 0.8244 (mtp) REVERT: F 71 MET cc_start: 0.2041 (ptm) cc_final: 0.1391 (ptt) REVERT: F 376 MET cc_start: 0.5224 (mmp) cc_final: 0.4750 (tpt) REVERT: F 828 MET cc_start: 0.4858 (pmm) cc_final: 0.4488 (ptt) outliers start: 65 outliers final: 55 residues processed: 209 average time/residue: 0.1864 time to fit residues: 67.0079 Evaluate side-chains 203 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 143 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 662 SER Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain D residue 53 ARG Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 599 LYS Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 384 GLU Chi-restraints excluded: chain F residue 460 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 145 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 193 optimal weight: 7.9990 chunk 358 optimal weight: 0.7980 chunk 146 optimal weight: 4.9990 chunk 71 optimal weight: 30.0000 chunk 111 optimal weight: 3.9990 chunk 161 optimal weight: 10.0000 chunk 205 optimal weight: 0.9990 chunk 310 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.086680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.060085 restraints weight = 219693.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.061397 restraints weight = 109050.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.062207 restraints weight = 71200.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.062709 restraints weight = 54657.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.063006 restraints weight = 46431.201| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33815 Z= 0.141 Angle : 0.607 14.090 45902 Z= 0.308 Chirality : 0.042 0.395 5182 Planarity : 0.004 0.083 5833 Dihedral : 11.880 173.707 5145 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.84 % Allowed : 15.21 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.13), residues: 4066 helix: 1.50 (0.14), residues: 1465 sheet: -0.11 (0.20), residues: 641 loop : -0.34 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 202 TYR 0.020 0.001 TYR F 855 PHE 0.014 0.001 PHE D1034 TRP 0.020 0.001 TRP F 395 HIS 0.007 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (33795) covalent geometry : angle 0.59999 / 0.31 (45872) hydrogen bonds : bond 0.03524 / 2.39 ( 1518) hydrogen bonds : angle 4.77857 / 3.27 ( 4224) metal coordination : bond 0.00450 / 0.31 ( 20) metal coordination : angle 3.72641 / 2.44 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9718.31 seconds wall clock time: 166 minutes 55.08 seconds (10015.08 seconds total)