Starting phenix.real_space_refine on Sat Feb 7 15:21:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gdb_51260/02_2026/9gdb_51260.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gdb_51260/02_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_51260/02_2026/9gdb_51260.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gdb_51260/02_2026/9gdb_51260.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gdb_51260/02_2026/9gdb_51260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gdb_51260/02_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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: 7.03, per 1000 atoms: 0.21 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: 2.61 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: 4.15 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: 9.27 Time building geometry restraints manager: 3.37 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=" CA PRO F 750 " pdb=" C PRO F 750 " ideal model delta sigma weight residual 1.517 1.545 -0.028 9.30e-03 1.16e+04 9.15e+00 bond pdb=" N ARG F 724 " pdb=" CA ARG F 724 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.29e-02 6.01e+03 8.50e+00 bond pdb=" CZ ARG F 793 " pdb=" NH2 ARG F 793 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.30e-02 5.92e+03 8.18e+00 bond pdb=" CZ ARG F 804 " pdb=" NH2 ARG F 804 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.30e-02 5.92e+03 8.13e+00 ... (remaining 33790 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 44757 2.25 - 4.49: 995 4.49 - 6.74: 102 6.74 - 8.98: 11 8.98 - 11.23: 7 Bond angle restraints: 45872 Sorted by residual: 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=" N LEU F 781 " pdb=" CA LEU F 781 " pdb=" C LEU F 781 " ideal model delta sigma weight residual 110.20 120.00 -9.80 1.58e+00 4.01e-01 3.84e+01 angle pdb=" C GLY F 723 " pdb=" N ARG F 724 " pdb=" CA ARG F 724 " ideal model delta sigma weight residual 121.54 132.59 -11.05 1.91e+00 2.74e-01 3.35e+01 angle pdb=" N ARG D 47 " pdb=" CA ARG D 47 " pdb=" C ARG D 47 " ideal model delta sigma weight residual 110.97 105.07 5.90 1.09e+00 8.42e-01 2.93e+01 angle pdb=" N PRO F 751 " pdb=" CA PRO F 751 " pdb=" CB PRO F 751 " ideal model delta sigma weight residual 102.92 105.90 -2.98 5.60e-01 3.19e+00 2.84e+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: 5138 0.149 - 0.298: 40 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 2.35 -2.92 -0.57 2.00e-01 2.50e+01 8.21e+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 2.35 -2.84 -0.50 2.00e-01 2.50e+01 6.18e+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: 4.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.550 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 38.470 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.341 33815 Z= 0.269 Angle : 0.794 22.682 45902 Z= 0.448 Chirality : 0.049 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 covalent geometry : bond 0.00486 (33795) covalent geometry : angle 0.76579 (45872) hydrogen bonds : bond 0.13085 ( 1518) hydrogen bonds : angle 6.58593 ( 4224) metal coordination : bond 0.09804 ( 20) metal coordination : angle 8.28744 ( 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 : 1.087 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: 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: 0.8621 (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: 0.8109 (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: 0.2133 (mtt) REVERT: F 305 MET cc_start: -0.3080 (mmm) cc_final: -0.3291 (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: 0.2259 time to fit residues: 117.7278 Evaluate side-chains 187 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 1.303 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 HIS A 147 GLN B 41 ASN 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 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 HIS C 628 HIS C 688 GLN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1237 HIS C1244 HIS C1264 GLN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN D 477 GLN D 875 ASN D1218 HIS D1227 HIS D1350 ASN E 29 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 240 HIS F 250 ASN F 573 GLN F 681 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.081032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.050241 restraints weight = 216913.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.047706 restraints weight = 115222.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.048119 restraints weight = 75319.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.048504 restraints weight = 58281.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.048440 restraints weight = 49592.183| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 33815 Z= 0.288 Angle : 0.713 13.508 45902 Z= 0.368 Chirality : 0.044 0.204 5182 Planarity : 0.005 0.069 5833 Dihedral : 12.093 172.394 5164 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.36 % Allowed : 10.22 % Favored : 87.41 % 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: 0.33 (0.13), residues: 4066 helix: 1.12 (0.13), residues: 1466 sheet: 0.13 (0.20), residues: 654 loop : -0.36 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 53 TYR 0.022 0.002 TYR D1363 PHE 0.021 0.002 PHE C 514 TRP 0.012 0.002 TRP D 409 HIS 0.008 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00617 (33795) covalent geometry : angle 0.70042 (45872) hydrogen bonds : bond 0.04930 ( 1518) hydrogen bonds : angle 5.39002 ( 4224) metal coordination : bond 0.01189 ( 20) metal coordination : angle 5.28073 ( 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 255 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 173 time to evaluate : 1.274 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: A 142 MET cc_start: 0.9516 (OUTLIER) cc_final: 0.9266 (pmm) REVERT: B 51 MET cc_start: 0.9447 (tpp) cc_final: 0.8935 (mmm) REVERT: C 239 MET cc_start: 0.9190 (ppp) cc_final: 0.8973 (ppp) REVERT: C 369 MET cc_start: 0.9129 (tmm) cc_final: 0.8795 (ppp) REVERT: C 545 PHE cc_start: 0.8483 (m-80) cc_final: 0.8092 (m-10) REVERT: C 696 ASP cc_start: 0.9038 (t0) cc_final: 0.8648 (t0) REVERT: C 742 TYR cc_start: 0.8970 (m-10) cc_final: 0.8632 (m-10) REVERT: C 1290 MET cc_start: 0.9281 (tpp) cc_final: 0.8883 (tpp) REVERT: D 301 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.8810 (mm-30) REVERT: D 304 ASP cc_start: 0.8716 (m-30) cc_final: 0.8323 (m-30) REVERT: D 697 MET cc_start: 0.9219 (ttp) cc_final: 0.9002 (tmm) REVERT: D 743 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.7257 (ttt) REVERT: D 747 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7666 (mtm) REVERT: D 932 MET cc_start: 0.8336 (tmm) cc_final: 0.7743 (tmm) REVERT: D 1146 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8407 (tm-30) REVERT: E 3 ARG cc_start: 0.9012 (tpm-80) cc_final: 0.8665 (tpt90) REVERT: E 30 MET cc_start: 0.8975 (ttm) cc_final: 0.8545 (ttp) REVERT: F 71 MET cc_start: 0.2570 (ptm) cc_final: 0.1884 (ptp) REVERT: F 376 MET cc_start: 0.4012 (mmp) cc_final: 0.3354 (tpt) REVERT: F 403 MET cc_start: -0.2711 (mtp) cc_final: -0.3515 (mmm) REVERT: F 729 MET cc_start: 0.2769 (tpp) cc_final: 0.2492 (mmm) outliers start: 82 outliers final: 37 residues processed: 240 average time/residue: 0.2115 time to fit residues: 83.5680 Evaluate side-chains 192 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 150 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 142 MET 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 100 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1239 VAL 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 321 LYS Chi-restraints excluded: chain D residue 342 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 743 MET Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1146 GLU Chi-restraints excluded: chain D residue 1257 VAL Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 384 GLU 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: 20.0000 chunk 80 optimal weight: 10.0000 chunk 237 optimal weight: 20.0000 chunk 175 optimal weight: 1.9990 chunk 376 optimal weight: 40.0000 chunk 24 optimal weight: 0.4980 chunk 179 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 390 optimal weight: 50.0000 chunk 107 optimal weight: 3.9990 chunk 313 optimal weight: 9.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS C 46 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 518 ASN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN C 965 GLN ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN D1235 ASN D1350 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.088281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.061290 restraints weight = 213420.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.062616 restraints weight = 107822.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.063456 restraints weight = 71447.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.063963 restraints weight = 55439.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.064248 restraints weight = 47496.668| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33815 Z= 0.150 Angle : 0.594 12.349 45902 Z= 0.306 Chirality : 0.042 0.252 5182 Planarity : 0.004 0.058 5833 Dihedral : 11.860 172.759 5153 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.07 % Allowed : 11.52 % Favored : 86.41 % 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: 0.55 (0.13), residues: 4066 helix: 1.49 (0.14), residues: 1460 sheet: -0.04 (0.20), residues: 662 loop : -0.28 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 195 TYR 0.014 0.001 TYR D 795 PHE 0.020 0.001 PHE A 231 TRP 0.017 0.001 TRP F 395 HIS 0.004 0.001 HIS C 447 Details of bonding type rmsd covalent geometry : bond 0.00324 (33795) covalent geometry : angle 0.58348 (45872) hydrogen bonds : bond 0.03821 ( 1518) hydrogen bonds : angle 4.95478 ( 4224) metal coordination : bond 0.00498 ( 20) metal coordination : angle 4.41593 ( 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 240 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 168 time to evaluate : 1.325 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: B 51 MET cc_start: 0.9461 (tpp) cc_final: 0.8892 (mmm) REVERT: C 142 GLU cc_start: 0.8709 (mp0) cc_final: 0.8333 (pm20) REVERT: C 239 MET cc_start: 0.9158 (ppp) cc_final: 0.8940 (ppp) REVERT: C 369 MET cc_start: 0.9217 (tmm) cc_final: 0.8956 (ppp) REVERT: C 515 MET cc_start: 0.8383 (tpp) cc_final: 0.7914 (tpp) REVERT: C 545 PHE cc_start: 0.8469 (m-80) cc_final: 0.8183 (m-10) REVERT: C 696 ASP cc_start: 0.8879 (t0) cc_final: 0.8406 (t0) REVERT: C 1243 MET cc_start: 0.8923 (tmm) cc_final: 0.8556 (ttp) REVERT: D 282 LEU cc_start: 0.9371 (mm) cc_final: 0.8932 (tp) REVERT: D 304 ASP cc_start: 0.8757 (m-30) cc_final: 0.8352 (m-30) REVERT: D 330 MET cc_start: 0.8452 (mmm) cc_final: 0.8045 (mmm) REVERT: D 400 MET cc_start: 0.9291 (tpp) cc_final: 0.9054 (tpp) REVERT: D 424 ASN cc_start: 0.8816 (OUTLIER) cc_final: 0.8080 (t0) REVERT: D 466 MET cc_start: 0.8709 (tpp) cc_final: 0.8437 (mmm) REVERT: D 604 MET cc_start: 0.9501 (tpp) cc_final: 0.9279 (tpp) REVERT: D 724 MET cc_start: 0.9036 (tpp) cc_final: 0.8807 (tpp) REVERT: D 743 MET cc_start: 0.7530 (ppp) cc_final: 0.7009 (ttt) REVERT: D 932 MET cc_start: 0.8472 (tmm) cc_final: 0.7681 (tmm) REVERT: E 3 ARG cc_start: 0.9007 (tpm-80) cc_final: 0.8662 (tpt90) REVERT: E 30 MET cc_start: 0.9007 (ttm) cc_final: 0.8557 (ttp) REVERT: F 71 MET cc_start: -0.3163 (ptm) cc_final: -0.3561 (ptp) REVERT: F 376 MET cc_start: 0.4848 (mmp) cc_final: 0.4198 (tpt) REVERT: F 403 MET cc_start: -0.4175 (mtp) cc_final: -0.4432 (mmm) REVERT: F 729 MET cc_start: 0.3156 (tpp) cc_final: 0.2849 (mmm) REVERT: F 828 MET cc_start: 0.5106 (pmm) cc_final: 0.3578 (tmm) REVERT: F 831 PHE cc_start: 0.1143 (t80) cc_final: 0.0561 (t80) REVERT: F 855 TYR cc_start: 0.5660 (t80) cc_final: 0.4873 (t80) outliers start: 72 outliers final: 35 residues processed: 229 average time/residue: 0.2037 time to fit residues: 78.2470 Evaluate side-chains 191 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 228 LEU 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 160 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 483 ASP 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 1066 MET Chi-restraints excluded: chain C residue 1082 ILE 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 83 VAL Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 424 ASN 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 997 VAL Chi-restraints excluded: chain D residue 1255 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 86 optimal weight: 10.0000 chunk 227 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 302 optimal weight: 4.9990 chunk 146 optimal weight: 20.0000 chunk 181 optimal weight: 2.9990 chunk 338 optimal weight: 50.0000 chunk 207 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 chunk 32 optimal weight: 20.0000 chunk 104 optimal weight: 0.5980 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 GLN ** D 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.087586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.060596 restraints weight = 214302.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.061939 restraints weight = 108228.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.062770 restraints weight = 71139.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.063174 restraints weight = 54812.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.063533 restraints weight = 47571.624| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 33815 Z= 0.177 Angle : 0.584 11.329 45902 Z= 0.300 Chirality : 0.042 0.206 5182 Planarity : 0.004 0.059 5833 Dihedral : 11.760 171.652 5147 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.45 % Allowed : 12.59 % Favored : 84.97 % 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: 0.60 (0.13), residues: 4066 helix: 1.51 (0.13), residues: 1464 sheet: 0.03 (0.20), residues: 656 loop : -0.27 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 158 TYR 0.013 0.001 TYR D1363 PHE 0.023 0.001 PHE A 231 TRP 0.009 0.001 TRP D 580 HIS 0.004 0.001 HIS C 526 Details of bonding type rmsd covalent geometry : bond 0.00383 (33795) covalent geometry : angle 0.57449 (45872) hydrogen bonds : bond 0.03770 ( 1518) hydrogen bonds : angle 4.84520 ( 4224) metal coordination : bond 0.00575 ( 20) metal coordination : angle 4.18288 ( 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 244 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 159 time to evaluate : 1.319 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: B 51 MET cc_start: 0.9418 (tpp) cc_final: 0.9135 (mmm) REVERT: C 239 MET cc_start: 0.9181 (ppp) cc_final: 0.8946 (ppp) REVERT: C 545 PHE cc_start: 0.8533 (m-80) cc_final: 0.8275 (m-10) REVERT: C 696 ASP cc_start: 0.8886 (t0) cc_final: 0.8438 (t0) REVERT: C 918 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9244 (tt) REVERT: C 1131 MET cc_start: 0.9496 (ttt) cc_final: 0.8589 (tmm) REVERT: C 1243 MET cc_start: 0.8987 (tmm) cc_final: 0.8512 (ttp) REVERT: C 1315 MET cc_start: 0.8136 (ttp) cc_final: 0.7782 (ttt) REVERT: D 282 LEU cc_start: 0.9347 (mm) cc_final: 0.8960 (tp) REVERT: D 304 ASP cc_start: 0.8784 (m-30) cc_final: 0.8380 (m-30) REVERT: D 368 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8314 (tt) REVERT: D 581 MET cc_start: 0.9097 (tpp) cc_final: 0.8868 (tpp) REVERT: D 724 MET cc_start: 0.9008 (tpp) cc_final: 0.8748 (tpp) REVERT: D 743 MET cc_start: 0.7438 (OUTLIER) cc_final: 0.7216 (ttp) REVERT: D 747 MET cc_start: 0.7653 (mtm) cc_final: 0.7283 (mtp) REVERT: D 932 MET cc_start: 0.8641 (tmm) cc_final: 0.7829 (tmm) REVERT: E 3 ARG cc_start: 0.9022 (tpm-80) cc_final: 0.8715 (tpt90) REVERT: E 30 MET cc_start: 0.9005 (ttm) cc_final: 0.8231 (mtp) REVERT: F 71 MET cc_start: -0.3308 (ptm) cc_final: -0.3662 (ptp) REVERT: F 376 MET cc_start: 0.5284 (mmp) cc_final: 0.4323 (tpt) REVERT: F 383 MET cc_start: 0.3496 (mmm) cc_final: 0.2990 (mmm) REVERT: F 403 MET cc_start: -0.3982 (mtp) cc_final: -0.4308 (mmm) REVERT: F 729 MET cc_start: 0.3890 (tpp) cc_final: 0.3326 (mmm) REVERT: F 828 MET cc_start: 0.5018 (pmm) cc_final: 0.3902 (ptt) REVERT: F 831 PHE cc_start: 0.1315 (t80) cc_final: 0.0734 (t80) REVERT: F 855 TYR cc_start: 0.5630 (t80) cc_final: 0.4843 (t80) outliers start: 85 outliers final: 46 residues processed: 234 average time/residue: 0.2004 time to fit residues: 80.0452 Evaluate side-chains 200 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 151 time to evaluate : 1.226 ------------------------------------------------------------------------------- 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 142 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 100 LEU 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 62 TYR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 653 MET 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 918 LEU Chi-restraints excluded: chain C residue 1066 MET 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 83 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 283 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 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 790 THR Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain F residue 384 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 201 optimal weight: 5.9990 chunk 311 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 127 optimal weight: 0.0040 chunk 357 optimal weight: 30.0000 chunk 38 optimal weight: 0.3980 chunk 178 optimal weight: 5.9990 chunk 140 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 202 optimal weight: 0.7980 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 GLN C 518 ASN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 673 HIS ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN D1249 ASN D1259 GLN F 158 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.088027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.061138 restraints weight = 214711.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.062487 restraints weight = 107299.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.063320 restraints weight = 70531.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.063827 restraints weight = 54679.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.064091 restraints weight = 46701.707| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 33815 Z= 0.113 Angle : 0.556 10.999 45902 Z= 0.283 Chirality : 0.041 0.265 5182 Planarity : 0.004 0.057 5833 Dihedral : 11.666 171.910 5147 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.07 % Allowed : 13.51 % Favored : 84.42 % 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: 0.66 (0.13), residues: 4066 helix: 1.58 (0.14), residues: 1473 sheet: 0.06 (0.20), residues: 660 loop : -0.25 (0.14), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 821 TYR 0.011 0.001 TYR C 742 PHE 0.024 0.001 PHE C 186 TRP 0.013 0.001 TRP F 395 HIS 0.004 0.001 HIS C 526 Details of bonding type rmsd covalent geometry : bond 0.00246 (33795) covalent geometry : angle 0.54840 (45872) hydrogen bonds : bond 0.03384 ( 1518) hydrogen bonds : angle 4.68885 ( 4224) metal coordination : bond 0.00334 ( 20) metal coordination : angle 3.69990 ( 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 238 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 166 time to evaluate : 1.241 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: B 51 MET cc_start: 0.9437 (tpp) cc_final: 0.8855 (mmm) REVERT: C 142 GLU cc_start: 0.8744 (mp0) cc_final: 0.8405 (pm20) REVERT: C 239 MET cc_start: 0.9124 (ppp) cc_final: 0.8863 (ppp) REVERT: C 369 MET cc_start: 0.9146 (tmm) cc_final: 0.8803 (ppp) REVERT: C 429 MET cc_start: 0.9246 (mmt) cc_final: 0.8873 (mmt) REVERT: C 545 PHE cc_start: 0.8532 (m-80) cc_final: 0.8270 (m-10) REVERT: C 696 ASP cc_start: 0.8726 (t0) cc_final: 0.8245 (t0) REVERT: C 918 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9256 (tt) REVERT: C 1119 MET cc_start: 0.9315 (tpp) cc_final: 0.8665 (tpp) REVERT: C 1131 MET cc_start: 0.9459 (ttt) cc_final: 0.8583 (tmm) REVERT: C 1243 MET cc_start: 0.8983 (tmm) cc_final: 0.8500 (ttm) REVERT: C 1272 GLU cc_start: 0.7365 (tp30) cc_final: 0.6440 (tp30) REVERT: C 1276 TRP cc_start: 0.8910 (m-10) cc_final: 0.8222 (m-10) REVERT: D 38 VAL cc_start: 0.9602 (OUTLIER) cc_final: 0.9347 (p) REVERT: D 282 LEU cc_start: 0.9350 (mm) cc_final: 0.8941 (tp) REVERT: D 304 ASP cc_start: 0.8777 (m-30) cc_final: 0.8363 (m-30) REVERT: D 368 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8370 (tt) REVERT: D 400 MET cc_start: 0.9396 (tpp) cc_final: 0.9186 (tpp) REVERT: D 466 MET cc_start: 0.8706 (tpp) cc_final: 0.8446 (mmm) REVERT: D 581 MET cc_start: 0.9090 (tpp) cc_final: 0.8818 (tpp) REVERT: D 604 MET cc_start: 0.9559 (tpp) cc_final: 0.9266 (tpt) REVERT: D 697 MET cc_start: 0.9306 (tmm) cc_final: 0.8816 (tmm) REVERT: D 743 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.7165 (ppp) REVERT: D 747 MET cc_start: 0.7576 (mtm) cc_final: 0.7257 (mtp) REVERT: D 822 MET cc_start: 0.9266 (tpp) cc_final: 0.8942 (tpp) REVERT: D 932 MET cc_start: 0.8627 (tmm) cc_final: 0.7837 (tmm) REVERT: E 3 ARG cc_start: 0.8996 (tpm-80) cc_final: 0.8714 (tpt90) REVERT: E 30 MET cc_start: 0.9013 (ttm) cc_final: 0.8166 (mtp) REVERT: F 71 MET cc_start: -0.3280 (ptm) cc_final: -0.3659 (ptp) REVERT: F 376 MET cc_start: 0.5329 (mmp) cc_final: 0.4518 (mmm) REVERT: F 403 MET cc_start: -0.3817 (mtp) cc_final: -0.4193 (mmm) REVERT: F 709 VAL cc_start: 0.7776 (OUTLIER) cc_final: 0.7262 (m) REVERT: F 729 MET cc_start: 0.3710 (tpp) cc_final: 0.3322 (mmm) REVERT: F 828 MET cc_start: 0.5194 (pmm) cc_final: 0.4266 (ptt) REVERT: F 831 PHE cc_start: 0.1160 (t80) cc_final: 0.0610 (t80) REVERT: F 855 TYR cc_start: 0.5533 (t80) cc_final: 0.4773 (t80) outliers start: 72 outliers final: 45 residues processed: 231 average time/residue: 0.2013 time to fit residues: 78.3979 Evaluate side-chains 205 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 155 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 48 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 B residue 196 THR Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 680 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 918 LEU Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1203 ASP 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 124 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 249 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 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 743 MET Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 964 LYS Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1249 ASN 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 709 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 209 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 356 optimal weight: 50.0000 chunk 225 optimal weight: 5.9990 chunk 183 optimal weight: 20.0000 chunk 264 optimal weight: 6.9990 chunk 70 optimal weight: 0.1980 chunk 150 optimal weight: 0.4980 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** 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 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN D1249 ASN D1259 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.085580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.053569 restraints weight = 250005.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 75)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.051132 restraints weight = 148084.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.050285 restraints weight = 106202.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.050757 restraints weight = 85756.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.050412 restraints weight = 69327.582| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 33815 Z= 0.181 Angle : 0.575 12.396 45902 Z= 0.294 Chirality : 0.041 0.205 5182 Planarity : 0.004 0.059 5833 Dihedral : 11.676 170.808 5146 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.59 % Allowed : 13.62 % Favored : 83.78 % 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: 0.65 (0.13), residues: 4066 helix: 1.55 (0.14), residues: 1478 sheet: 0.09 (0.20), residues: 639 loop : -0.26 (0.14), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1231 TYR 0.012 0.001 TYR D1363 PHE 0.016 0.001 PHE C 186 TRP 0.021 0.001 TRP F 395 HIS 0.004 0.001 HIS C 526 Details of bonding type rmsd covalent geometry : bond 0.00391 (33795) covalent geometry : angle 0.56683 (45872) hydrogen bonds : bond 0.03641 ( 1518) hydrogen bonds : angle 4.70676 ( 4224) metal coordination : bond 0.00573 ( 20) metal coordination : angle 3.79237 ( 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 244 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 154 time to evaluate : 1.322 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: 0.9064 (mmm) cc_final: 0.8746 (mmp) REVERT: B 51 MET cc_start: 0.9384 (tpp) cc_final: 0.8851 (mmm) REVERT: C 239 MET cc_start: 0.9267 (ppp) cc_final: 0.8901 (ppp) REVERT: C 369 MET cc_start: 0.9204 (tmm) cc_final: 0.8905 (ppp) REVERT: C 429 MET cc_start: 0.9267 (mmt) cc_final: 0.8930 (mmm) REVERT: C 545 PHE cc_start: 0.8517 (m-80) cc_final: 0.8301 (m-10) REVERT: C 696 ASP cc_start: 0.8896 (t0) cc_final: 0.8506 (t0) REVERT: C 918 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9232 (tt) REVERT: C 1119 MET cc_start: 0.9307 (tpp) cc_final: 0.8698 (tpp) REVERT: C 1131 MET cc_start: 0.9370 (ttt) cc_final: 0.8482 (tmm) REVERT: C 1243 MET cc_start: 0.8953 (tmm) cc_final: 0.8496 (ttp) REVERT: C 1272 GLU cc_start: 0.7430 (tp30) cc_final: 0.6554 (tp30) REVERT: C 1276 TRP cc_start: 0.8999 (m-10) cc_final: 0.8267 (m-10) REVERT: C 1315 MET cc_start: 0.8140 (ttp) cc_final: 0.7855 (ttt) REVERT: D 38 VAL cc_start: 0.9552 (OUTLIER) cc_final: 0.9327 (p) REVERT: D 139 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9196 (mm) REVERT: D 282 LEU cc_start: 0.9390 (mm) cc_final: 0.8958 (tp) REVERT: D 304 ASP cc_start: 0.8816 (m-30) cc_final: 0.8397 (m-30) REVERT: D 368 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8574 (tt) REVERT: D 581 MET cc_start: 0.9029 (tpp) cc_final: 0.8791 (tpp) REVERT: D 697 MET cc_start: 0.9311 (tmm) cc_final: 0.8849 (tmm) REVERT: D 743 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.7119 (ttp) REVERT: D 747 MET cc_start: 0.7694 (mtm) cc_final: 0.7279 (mtp) REVERT: D 932 MET cc_start: 0.8648 (tmm) cc_final: 0.7942 (tmm) REVERT: D 1249 ASN cc_start: 0.9233 (OUTLIER) cc_final: 0.8935 (t0) REVERT: D 1260 MET cc_start: 0.9015 (tpp) cc_final: 0.8538 (tpt) REVERT: E 3 ARG cc_start: 0.8991 (tpm-80) cc_final: 0.8756 (tpt90) REVERT: E 30 MET cc_start: 0.9039 (ttm) cc_final: 0.8268 (mtp) REVERT: F 71 MET cc_start: 0.2860 (ptm) cc_final: 0.2169 (ptp) REVERT: F 178 MET cc_start: 0.2831 (mpp) cc_final: 0.2608 (mpp) REVERT: F 376 MET cc_start: 0.5368 (mmp) cc_final: 0.4954 (tpt) REVERT: F 403 MET cc_start: -0.1344 (mtp) cc_final: -0.2337 (mmm) REVERT: F 828 MET cc_start: 0.5071 (pmm) cc_final: 0.4843 (ptt) REVERT: F 855 TYR cc_start: 0.6508 (t80) cc_final: 0.6097 (t80) outliers start: 90 outliers final: 58 residues processed: 236 average time/residue: 0.1884 time to fit residues: 76.1773 Evaluate side-chains 211 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 147 time to evaluate : 1.322 ------------------------------------------------------------------------------- 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 142 MET Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 48 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 B residue 196 THR Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 158 ASP 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 662 SER Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 724 VAL 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 918 LEU Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1203 ASP 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 C residue 1308 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 249 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 412 LEU 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 724 MET Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 964 LYS Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1249 ASN Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1357 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 216 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 170 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 chunk 344 optimal weight: 30.0000 chunk 206 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 chunk 325 optimal weight: 20.0000 chunk 304 optimal weight: 9.9990 chunk 223 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN D1249 ASN ** 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 = 0.3984 r_free = 0.3984 target = 0.085571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.058354 restraints weight = 247717.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.056740 restraints weight = 160407.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.057585 restraints weight = 109543.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.056806 restraints weight = 77936.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.056692 restraints weight = 76834.640| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3096 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= 0.116 Angle : 0.560 13.049 45902 Z= 0.284 Chirality : 0.041 0.211 5182 Planarity : 0.004 0.058 5833 Dihedral : 11.634 171.168 5146 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.16 % Allowed : 14.31 % Favored : 83.53 % 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: 0.68 (0.13), residues: 4066 helix: 1.60 (0.14), residues: 1475 sheet: 0.03 (0.21), residues: 644 loop : -0.23 (0.14), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 281 TYR 0.011 0.001 TYR C 742 PHE 0.013 0.001 PHE D1034 TRP 0.012 0.001 TRP F 395 HIS 0.003 0.001 HIS C 526 Details of bonding type rmsd covalent geometry : bond 0.00256 (33795) covalent geometry : angle 0.55305 (45872) hydrogen bonds : bond 0.03328 ( 1518) hydrogen bonds : angle 4.61079 ( 4224) metal coordination : bond 0.00374 ( 20) metal coordination : angle 3.50182 ( 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: 75 poor density : 154 time to evaluate : 1.273 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: B 51 MET cc_start: 0.9366 (tpp) cc_final: 0.8791 (mmm) REVERT: C 239 MET cc_start: 0.9230 (ppp) cc_final: 0.8849 (ppp) REVERT: C 369 MET cc_start: 0.9261 (tmm) cc_final: 0.8949 (ppp) REVERT: C 429 MET cc_start: 0.9279 (mmt) cc_final: 0.8939 (mmm) REVERT: C 545 PHE cc_start: 0.8536 (m-80) cc_final: 0.8291 (m-10) REVERT: C 696 ASP cc_start: 0.8739 (t0) cc_final: 0.8263 (t0) REVERT: C 918 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9271 (tt) REVERT: C 1119 MET cc_start: 0.9306 (tpp) cc_final: 0.8637 (tpp) REVERT: C 1131 MET cc_start: 0.9403 (ttt) cc_final: 0.8493 (tmm) REVERT: C 1232 MET cc_start: 0.9161 (mmm) cc_final: 0.8739 (mmm) REVERT: C 1243 MET cc_start: 0.8984 (tmm) cc_final: 0.8526 (ttp) REVERT: C 1272 GLU cc_start: 0.7429 (tp30) cc_final: 0.6581 (tp30) REVERT: C 1276 TRP cc_start: 0.8896 (m-10) cc_final: 0.8201 (m-10) REVERT: C 1315 MET cc_start: 0.8186 (ttp) cc_final: 0.7863 (ttt) REVERT: D 38 VAL cc_start: 0.9547 (OUTLIER) cc_final: 0.9317 (p) REVERT: D 139 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9205 (mm) REVERT: D 282 LEU cc_start: 0.9351 (mm) cc_final: 0.8923 (tp) REVERT: D 304 ASP cc_start: 0.8774 (m-30) cc_final: 0.8433 (m-30) REVERT: D 368 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8448 (tt) REVERT: D 400 MET cc_start: 0.9379 (tpp) cc_final: 0.9137 (tpp) REVERT: D 581 MET cc_start: 0.9021 (tpp) cc_final: 0.8743 (tpp) REVERT: D 697 MET cc_start: 0.9297 (tmm) cc_final: 0.8868 (tmm) REVERT: D 724 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8845 (tpp) REVERT: D 743 MET cc_start: 0.7300 (OUTLIER) cc_final: 0.7072 (ttp) REVERT: D 747 MET cc_start: 0.7615 (mtm) cc_final: 0.7197 (mtp) REVERT: D 932 MET cc_start: 0.8744 (tmm) cc_final: 0.7999 (tmm) REVERT: E 3 ARG cc_start: 0.9011 (tpm-80) cc_final: 0.8802 (tpt90) REVERT: E 30 MET cc_start: 0.9021 (ttm) cc_final: 0.8197 (mtp) REVERT: F 71 MET cc_start: -0.0491 (ptm) cc_final: -0.1769 (ptt) REVERT: F 376 MET cc_start: 0.5514 (mmp) cc_final: 0.4992 (tpt) REVERT: F 403 MET cc_start: -0.2348 (mtp) cc_final: -0.3146 (mmm) REVERT: F 828 MET cc_start: 0.5315 (pmm) cc_final: 0.4902 (ptt) REVERT: F 855 TYR cc_start: 0.5974 (t80) cc_final: 0.5366 (t80) outliers start: 75 outliers final: 58 residues processed: 221 average time/residue: 0.1859 time to fit residues: 69.6259 Evaluate side-chains 212 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 148 time to evaluate : 1.248 ------------------------------------------------------------------------------- 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 48 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 B residue 196 THR Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 176 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 662 SER Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 680 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 918 LEU Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1203 ASP 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 C residue 1308 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 249 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 412 LEU 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 724 MET Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1249 ASN 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 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: 9.9990 chunk 155 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 261 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 210 optimal weight: 30.0000 chunk 243 optimal weight: 6.9990 chunk 391 optimal weight: 20.0000 chunk 55 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN D1249 ASN ** 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 = 0.3810 r_free = 0.3810 target = 0.080869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.045465 restraints weight = 219264.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.045278 restraints weight = 114872.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.045763 restraints weight = 76684.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.045967 restraints weight = 61090.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.046127 restraints weight = 56407.572| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3228 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= 0.205 Angle : 0.602 13.753 45902 Z= 0.306 Chirality : 0.041 0.204 5182 Planarity : 0.004 0.057 5833 Dihedral : 11.689 170.103 5146 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.48 % Allowed : 14.31 % Favored : 83.21 % 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: 0.61 (0.13), residues: 4066 helix: 1.54 (0.14), residues: 1475 sheet: -0.00 (0.21), residues: 632 loop : -0.27 (0.14), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 425 TYR 0.013 0.001 TYR C 742 PHE 0.014 0.001 PHE C 812 TRP 0.014 0.001 TRP F 395 HIS 0.004 0.001 HIS C 526 Details of bonding type rmsd covalent geometry : bond 0.00442 (33795) covalent geometry : angle 0.59397 (45872) hydrogen bonds : bond 0.03685 ( 1518) hydrogen bonds : angle 4.70835 ( 4224) metal coordination : bond 0.00684 ( 20) metal coordination : angle 3.78132 ( 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 235 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 149 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: A 51 MET cc_start: 0.9086 (mmm) cc_final: 0.8738 (mmm) REVERT: C 239 MET cc_start: 0.9123 (ppp) cc_final: 0.8759 (ppp) REVERT: C 369 MET cc_start: 0.9251 (tmm) cc_final: 0.8966 (ppp) REVERT: C 429 MET cc_start: 0.9323 (mmt) cc_final: 0.8986 (mmm) REVERT: C 545 PHE cc_start: 0.8581 (m-80) cc_final: 0.8350 (m-10) REVERT: C 696 ASP cc_start: 0.8890 (t0) cc_final: 0.8446 (t0) REVERT: C 918 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9232 (tt) REVERT: C 1119 MET cc_start: 0.9320 (tpp) cc_final: 0.8680 (tpp) REVERT: C 1131 MET cc_start: 0.9436 (ttt) cc_final: 0.8507 (tmm) REVERT: C 1243 MET cc_start: 0.9026 (tmm) cc_final: 0.8568 (ttp) REVERT: C 1276 TRP cc_start: 0.8985 (m-10) cc_final: 0.8239 (m-10) REVERT: C 1315 MET cc_start: 0.8194 (ttp) cc_final: 0.7900 (ttt) REVERT: D 38 VAL cc_start: 0.9543 (OUTLIER) cc_final: 0.9341 (p) REVERT: D 139 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9227 (mm) REVERT: D 252 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8441 (tp) REVERT: D 282 LEU cc_start: 0.9343 (mm) cc_final: 0.8902 (tp) REVERT: D 304 ASP cc_start: 0.8743 (m-30) cc_final: 0.8404 (m-30) REVERT: D 368 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8440 (tt) REVERT: D 400 MET cc_start: 0.9422 (tpp) cc_final: 0.9173 (tpp) REVERT: D 581 MET cc_start: 0.9078 (tpp) cc_final: 0.8744 (tpp) REVERT: D 697 MET cc_start: 0.9326 (tmm) cc_final: 0.8911 (tmm) REVERT: D 932 MET cc_start: 0.8856 (tmm) cc_final: 0.8133 (tmm) REVERT: E 3 ARG cc_start: 0.9058 (tpm-80) cc_final: 0.8791 (tpt90) REVERT: E 30 MET cc_start: 0.9019 (ttm) cc_final: 0.8244 (mtp) REVERT: F 71 MET cc_start: 0.2342 (ptm) cc_final: 0.1576 (ptt) REVERT: F 376 MET cc_start: 0.5416 (mmp) cc_final: 0.4983 (tpt) REVERT: F 403 MET cc_start: -0.1856 (mtp) cc_final: -0.2646 (mmm) REVERT: F 587 MET cc_start: 0.3191 (ttt) cc_final: 0.2920 (mtp) REVERT: F 828 MET cc_start: 0.5278 (pmm) cc_final: 0.5026 (ptt) REVERT: F 855 TYR cc_start: 0.6233 (t80) cc_final: 0.5797 (t80) REVERT: F 859 LYS cc_start: 0.6758 (OUTLIER) cc_final: 0.6439 (pttt) outliers start: 86 outliers final: 63 residues processed: 229 average time/residue: 0.1860 time to fit residues: 72.5323 Evaluate side-chains 213 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 144 time to evaluate : 1.247 ------------------------------------------------------------------------------- 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 153 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 563 THR 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 680 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 918 LEU Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1203 ASP Chi-restraints excluded: chain C residue 1235 LEU 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 C residue 1308 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 252 LEU 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 412 LEU 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 724 MET Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1249 ASN 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 859 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 317 optimal weight: 1.9990 chunk 378 optimal weight: 50.0000 chunk 154 optimal weight: 0.6980 chunk 326 optimal weight: 0.9990 chunk 166 optimal weight: 6.9990 chunk 365 optimal weight: 30.0000 chunk 8 optimal weight: 6.9990 chunk 291 optimal weight: 8.9990 chunk 294 optimal weight: 20.0000 chunk 290 optimal weight: 3.9990 chunk 330 optimal weight: 6.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN D1249 ASN D1259 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 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 = 0.3836 r_free = 0.3836 target = 0.086618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.060513 restraints weight = 222458.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.061614 restraints weight = 116103.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.062245 restraints weight = 82879.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.062639 restraints weight = 57261.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.062617 restraints weight = 50150.778| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33815 Z= 0.146 Angle : 0.584 13.991 45902 Z= 0.296 Chirality : 0.041 0.311 5182 Planarity : 0.004 0.058 5833 Dihedral : 11.702 170.380 5146 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.10 % Allowed : 14.72 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.13), residues: 4066 helix: 1.54 (0.14), residues: 1474 sheet: 0.01 (0.21), residues: 629 loop : -0.26 (0.14), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 281 TYR 0.013 0.001 TYR C 742 PHE 0.013 0.001 PHE D1034 TRP 0.016 0.001 TRP F 395 HIS 0.006 0.001 HIS D 450 Details of bonding type rmsd covalent geometry : bond 0.00320 (33795) covalent geometry : angle 0.57751 (45872) hydrogen bonds : bond 0.03421 ( 1518) hydrogen bonds : angle 4.65282 ( 4224) metal coordination : bond 0.00448 ( 20) metal coordination : angle 3.44469 ( 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 222 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 149 time to evaluate : 1.366 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: B 51 MET cc_start: 0.9135 (mmm) cc_final: 0.8329 (mmm) REVERT: C 239 MET cc_start: 0.9118 (ppp) cc_final: 0.8726 (ppp) REVERT: C 369 MET cc_start: 0.9272 (tmm) cc_final: 0.8979 (ppp) REVERT: C 429 MET cc_start: 0.9315 (mmt) cc_final: 0.8968 (mmm) REVERT: C 545 PHE cc_start: 0.8587 (m-80) cc_final: 0.8363 (m-10) REVERT: C 696 ASP cc_start: 0.8745 (t0) cc_final: 0.8314 (t0) REVERT: C 918 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9275 (tt) REVERT: C 1119 MET cc_start: 0.9327 (tpp) cc_final: 0.8680 (tpp) REVERT: C 1131 MET cc_start: 0.9450 (ttt) cc_final: 0.8495 (tmm) REVERT: C 1232 MET cc_start: 0.9220 (mmm) cc_final: 0.8792 (mmm) REVERT: C 1243 MET cc_start: 0.9041 (tmm) cc_final: 0.8613 (ttp) REVERT: C 1272 GLU cc_start: 0.7356 (tp30) cc_final: 0.6466 (tp30) REVERT: C 1276 TRP cc_start: 0.8910 (m-10) cc_final: 0.8254 (m-10) REVERT: C 1315 MET cc_start: 0.8174 (ttp) cc_final: 0.7856 (ttt) REVERT: D 38 VAL cc_start: 0.9545 (OUTLIER) cc_final: 0.9332 (p) REVERT: D 139 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9212 (mm) REVERT: D 252 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8565 (tp) REVERT: D 304 ASP cc_start: 0.8746 (m-30) cc_final: 0.8404 (m-30) REVERT: D 368 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8329 (tt) REVERT: D 400 MET cc_start: 0.9394 (tpp) cc_final: 0.9128 (tpp) REVERT: D 581 MET cc_start: 0.9053 (tpp) cc_final: 0.8711 (tpp) REVERT: D 697 MET cc_start: 0.9293 (tmm) cc_final: 0.8890 (tmm) REVERT: D 724 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8793 (tpp) REVERT: D 822 MET cc_start: 0.8695 (tpt) cc_final: 0.7895 (tmm) REVERT: D 932 MET cc_start: 0.8696 (tmm) cc_final: 0.8023 (tmm) REVERT: E 3 ARG cc_start: 0.9069 (tpm-80) cc_final: 0.8818 (tpt90) REVERT: E 30 MET cc_start: 0.9024 (ttm) cc_final: 0.8193 (mtp) REVERT: F 71 MET cc_start: -0.3537 (ptm) cc_final: -0.3761 (ptt) REVERT: F 376 MET cc_start: 0.5528 (mmp) cc_final: 0.4785 (tpt) REVERT: F 828 MET cc_start: 0.5289 (pmm) cc_final: 0.4620 (ptt) REVERT: F 855 TYR cc_start: 0.5613 (t80) cc_final: 0.4919 (t80) REVERT: F 859 LYS cc_start: 0.4642 (OUTLIER) cc_final: 0.4090 (pttt) outliers start: 73 outliers final: 62 residues processed: 217 average time/residue: 0.1937 time to fit residues: 71.7912 Evaluate side-chains 214 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 145 time to evaluate : 1.274 ------------------------------------------------------------------------------- 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 48 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 B residue 196 THR Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 176 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 662 SER Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 680 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 918 LEU Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1203 ASP 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 C residue 1308 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 252 LEU 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 412 LEU 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 724 MET Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1249 ASN Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1357 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 859 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 42 optimal weight: 0.7980 chunk 394 optimal weight: 0.3980 chunk 279 optimal weight: 20.0000 chunk 307 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 172 optimal weight: 10.0000 chunk 230 optimal weight: 0.0870 chunk 244 optimal weight: 9.9990 chunk 389 optimal weight: 30.0000 chunk 407 optimal weight: 50.0000 overall best weight: 1.0560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN D1249 ASN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 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 = 0.3856 r_free = 0.3856 target = 0.087948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.061140 restraints weight = 215347.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.062451 restraints weight = 107941.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.063273 restraints weight = 71043.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.063772 restraints weight = 54789.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.064066 restraints weight = 46778.478| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 33815 Z= 0.105 Angle : 0.579 15.006 45902 Z= 0.291 Chirality : 0.041 0.294 5182 Planarity : 0.004 0.056 5833 Dihedral : 11.597 170.850 5146 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.87 % Allowed : 15.01 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.13), residues: 4066 helix: 1.62 (0.14), residues: 1473 sheet: 0.08 (0.21), residues: 636 loop : -0.25 (0.14), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 312 TYR 0.018 0.001 TYR C 742 PHE 0.012 0.001 PHE D1034 TRP 0.016 0.001 TRP F 395 HIS 0.007 0.001 HIS D 450 Details of bonding type rmsd covalent geometry : bond 0.00231 (33795) covalent geometry : angle 0.57248 (45872) hydrogen bonds : bond 0.03236 ( 1518) hydrogen bonds : angle 4.54904 ( 4224) metal coordination : bond 0.00364 ( 20) metal coordination : angle 3.50473 ( 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 220 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 155 time to evaluate : 1.339 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: B 51 MET cc_start: 0.9226 (mmm) cc_final: 0.8454 (mmm) REVERT: C 142 GLU cc_start: 0.8732 (mp0) cc_final: 0.8434 (pm20) REVERT: C 239 MET cc_start: 0.9024 (ppp) cc_final: 0.8666 (ppp) REVERT: C 429 MET cc_start: 0.9302 (mmt) cc_final: 0.8961 (mmm) REVERT: C 545 PHE cc_start: 0.8529 (m-80) cc_final: 0.8301 (m-10) REVERT: C 623 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9140 (mt) REVERT: C 696 ASP cc_start: 0.8641 (t0) cc_final: 0.8184 (t0) REVERT: C 918 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9274 (tt) REVERT: C 1119 MET cc_start: 0.9306 (tpp) cc_final: 0.8601 (tpp) REVERT: C 1131 MET cc_start: 0.9432 (ttt) cc_final: 0.8494 (tmm) REVERT: C 1232 MET cc_start: 0.9171 (mmm) cc_final: 0.8758 (mmm) REVERT: C 1243 MET cc_start: 0.9043 (tmm) cc_final: 0.8587 (ttp) REVERT: D 139 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9207 (mm) REVERT: D 252 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8568 (tp) REVERT: D 304 ASP cc_start: 0.8744 (m-30) cc_final: 0.8397 (m-30) REVERT: D 368 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8302 (tt) REVERT: D 400 MET cc_start: 0.9313 (tpp) cc_final: 0.9044 (tpp) REVERT: D 466 MET cc_start: 0.9047 (tpt) cc_final: 0.8833 (tpp) REVERT: D 484 MET cc_start: 0.8684 (mtm) cc_final: 0.7996 (mtm) REVERT: D 581 MET cc_start: 0.9027 (tpp) cc_final: 0.8720 (tpp) REVERT: D 697 MET cc_start: 0.9281 (tmm) cc_final: 0.8887 (tmm) REVERT: D 822 MET cc_start: 0.8723 (tpt) cc_final: 0.8513 (mmm) REVERT: D 932 MET cc_start: 0.8674 (tmm) cc_final: 0.7990 (tmm) REVERT: E 3 ARG cc_start: 0.9042 (tpm-80) cc_final: 0.8817 (tpt90) REVERT: E 30 MET cc_start: 0.9019 (ttm) cc_final: 0.8130 (mtp) REVERT: F 376 MET cc_start: 0.5612 (mmp) cc_final: 0.4863 (tpt) REVERT: F 828 MET cc_start: 0.5163 (pmm) cc_final: 0.4396 (ptt) REVERT: F 855 TYR cc_start: 0.5198 (t80) cc_final: 0.4515 (t80) REVERT: F 859 LYS cc_start: 0.3714 (OUTLIER) cc_final: 0.3004 (pttt) outliers start: 65 outliers final: 53 residues processed: 215 average time/residue: 0.2012 time to fit residues: 73.0557 Evaluate side-chains 205 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 146 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 48 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 B residue 196 THR Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 662 SER Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 702 THR 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 918 LEU Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1235 LEU 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 C residue 1308 ILE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 252 LEU 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 412 LEU Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 599 LYS Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1249 ASN Chi-restraints excluded: chain D residue 1357 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 859 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 145 optimal weight: 0.9980 chunk 142 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 193 optimal weight: 8.9990 chunk 358 optimal weight: 50.0000 chunk 146 optimal weight: 2.9990 chunk 71 optimal weight: 20.0000 chunk 111 optimal weight: 2.9990 chunk 161 optimal weight: 20.0000 chunk 205 optimal weight: 9.9990 chunk 310 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 HIS ** 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 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN D1249 ASN D1259 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 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 = 0.3828 r_free = 0.3828 target = 0.086583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.059896 restraints weight = 221846.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.061238 restraints weight = 110167.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.062070 restraints weight = 71726.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.062494 restraints weight = 54889.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.062836 restraints weight = 47173.407| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 33815 Z= 0.184 Angle : 0.608 14.142 45902 Z= 0.308 Chirality : 0.042 0.296 5182 Planarity : 0.004 0.136 5833 Dihedral : 11.651 169.779 5145 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.90 % Allowed : 15.09 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.13), residues: 4066 helix: 1.55 (0.14), residues: 1471 sheet: -0.03 (0.21), residues: 639 loop : -0.23 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 281 TYR 0.019 0.001 TYR C 742 PHE 0.013 0.001 PHE D1034 TRP 0.014 0.001 TRP F 395 HIS 0.007 0.001 HIS D 450 Details of bonding type rmsd covalent geometry : bond 0.00398 (33795) covalent geometry : angle 0.60082 (45872) hydrogen bonds : bond 0.03573 ( 1518) hydrogen bonds : angle 4.65621 ( 4224) metal coordination : bond 0.00644 ( 20) metal coordination : angle 3.64229 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8856.64 seconds wall clock time: 152 minutes 44.66 seconds (9164.66 seconds total)