Starting phenix.real_space_refine on Tue Sep 15 01:14:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gdh_51264/09_2026/9gdh_51264.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gdh_51264/09_2026/9gdh_51264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gdh_51264/09_2026/9gdh_51264.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gdh_51264/09_2026/9gdh_51264.map" model { file = "/net/cci-nas-00/data/ceres_data/9gdh_51264/09_2026/9gdh_51264.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gdh_51264/09_2026/9gdh_51264.cif" } resolution = 3.9 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= 0.003 sd= 0.044 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 79 5.49 5 Mg 1 5.21 5 S 143 5.16 5 C 20617 2.51 5 N 5892 2.21 5 O 6521 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33258 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': 2, 'PTRANS': 53, '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: 6558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6558 Classifications: {'peptide': 827} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 782} Chain breaks: 3 Chain: "N" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 530 Classifications: {'DNA': 38} Incomplete info: {'p_only': 13} Link IDs: {'rna3p': 37} Unresolved chain links: 13 Unresolved chain link angles: 55 Unresolved chain link dihedrals: 41 Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 397 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {' DT:plan': 8, ' DA:plan': 2, ' DA:plan2': 2, ' DC:plan': 2, ' DC:plan2': 2, ' DG:plan': 1, ' DG:plan2': 1} Unresolved non-hydrogen planarities: 142 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: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 608 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} 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 42.327 107.648 92.245 1.00231.48 S ATOM 14658 SG CYS D 72 40.800 103.969 92.554 1.00224.00 S ATOM 14766 SG CYS D 85 40.243 106.626 95.198 1.00227.91 S ATOM 14790 SG CYS D 88 43.691 105.290 94.734 1.00231.12 S ATOM 20478 SG CYS D 814 66.808 170.179 87.366 1.00184.93 S ATOM 21043 SG CYS D 888 67.717 166.653 87.605 1.00172.65 S ATOM 21094 SG CYS D 895 67.562 168.473 83.951 1.00176.14 S ATOM 21115 SG CYS D 898 70.303 169.115 86.272 1.00184.37 S ATOM 29791 SG CYS F 599 80.710 56.960 180.989 1.00405.08 S ATOM 29811 SG CYS F 602 79.537 57.402 184.552 1.00391.39 S ATOM 29931 SG CYS F 619 77.090 57.980 181.968 1.00394.91 S ATOM 30015 SG CYS F 630 79.821 60.524 182.108 1.00385.92 S ATOM 30265 SG CYS F 662 62.323 44.498 169.821 1.00463.88 S ATOM 30287 SG CYS F 665 59.201 45.383 167.845 1.00474.81 S ATOM 30428 SG CYS F 683 62.218 47.508 167.569 1.00443.42 S ATOM 30468 SG CYS F 689 60.086 47.630 170.712 1.00422.55 S ATOM 30644 SG CYS F 711 96.399 67.153 162.294 1.00571.11 S ATOM 30668 SG CYS F 714 98.023 63.810 162.667 1.00562.80 S ATOM 30800 SG CYS F 731 94.463 64.023 163.548 1.00551.66 S ATOM 30839 SG CYS F 736 96.850 65.846 165.803 1.00555.26 S Time building chain proxies: 6.91, per 1000 atoms: 0.21 Number of scatterers: 33258 At special positions: 0 Unit cell: (151.804, 208.73, 202.738, 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 79 15.00 Mg 1 11.99 O 6521 8.00 N 5892 7.00 C 20617 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: 3.47 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 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " 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 662 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 689 " pdb=" ZN F1003 " pdb="ZN ZN F1003 " - pdb=" SG CYS F 714 " pdb="ZN ZN F1003 " - pdb=" SG CYS F 731 " pdb="ZN ZN F1003 " - pdb=" SG CYS F 711 " pdb="ZN ZN F1003 " - pdb=" SG CYS F 736 " Number of angles added : 30 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7522 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 58 sheets defined 41.0% alpha, 18.9% beta 25 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 3.71 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.636A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.783A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 154 through 160 removed outlier: 3.532A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 233 Processing helix chain 'B' and resid 34 through 51 removed outlier: 4.045A 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 removed outlier: 3.676A pdb=" N ARG B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 166 removed outlier: 4.454A pdb=" N GLU B 165 " --> pdb=" O GLU B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 229 Processing helix chain 'B' and resid 230 through 232 No H-bonds generated for 'chain 'B' and resid 230 through 232' Processing helix chain 'C' and resid 4 through 10 removed outlier: 4.068A pdb=" N ARG C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.825A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 288 through 294 removed outlier: 3.537A pdb=" N ILE C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 345 through 353 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 481 Processing helix chain 'C' and resid 488 through 493 Processing helix chain 'C' and resid 495 through 509 Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 544 through 549 removed outlier: 3.607A pdb=" N ARG C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP C 549 " --> pdb=" O PHE C 545 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 544 through 549' Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.787A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 614 Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 662 through 667 Processing helix chain 'C' and resid 670 through 674 removed outlier: 3.535A pdb=" N ASP C 674 " --> pdb=" O LEU C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 688 Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 826 Processing helix chain 'C' and resid 858 through 865 removed outlier: 4.193A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) removed outlier: 4.046A 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 982 Processing helix chain 'C' and resid 985 through 992 Processing helix chain 'C' and resid 993 through 1000 Processing helix chain 'C' and resid 1005 through 1038 removed outlier: 3.705A pdb=" N ASN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 3.868A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1135 removed outlier: 3.584A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY C1125 " --> pdb=" O ALA C1121 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 Processing helix chain 'C' and resid 1165 through 1176 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1261 through 1265 Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.592A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1284 through 1293 Processing helix chain 'C' and resid 1297 through 1311 Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 3.631A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.508A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 180 through 190 removed outlier: 3.526A pdb=" N ALA D 184 " --> pdb=" O MET D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 Processing helix chain 'D' and resid 210 through 231 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 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 284 removed outlier: 3.856A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 309 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 336 through 342 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 removed outlier: 3.776A pdb=" N ARG D 403 " --> pdb=" O LYS D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 416 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 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 485 through 489 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 582 removed outlier: 4.097A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 593 removed outlier: 3.621A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 613 through 636 Processing helix chain 'D' and resid 640 through 644 Processing helix chain 'D' and resid 648 through 670 removed outlier: 4.279A 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 729 Processing helix chain 'D' and resid 733 through 741 Processing helix chain 'D' and resid 768 through 804 removed outlier: 4.183A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.644A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 884 through 888 removed outlier: 3.545A pdb=" N SER D 887 " --> pdb=" O SER D 884 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N CYS D 888 " --> pdb=" O VAL D 885 " (cutoff:3.500A) No H-bonds generated for '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: 3.896A 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 1136 through 1147 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1245 removed outlier: 3.622A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.449A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (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 removed outlier: 3.529A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1354 Processing helix chain 'D' and resid 1360 through 1376 removed outlier: 4.256A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.035A 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 34 Processing helix chain 'E' and resid 45 through 55 Processing helix chain 'E' and resid 60 through 91 Processing helix chain 'F' and resid 10 through 20 Processing helix chain 'F' and resid 64 through 72 Processing helix chain 'F' and resid 89 through 102 removed outlier: 4.019A pdb=" N GLU F 101 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS F 102 " --> pdb=" O GLN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 128 Processing helix chain 'F' and resid 130 through 132 No H-bonds generated for 'chain 'F' and resid 130 through 132' Processing helix chain 'F' and resid 143 through 153 removed outlier: 4.599A pdb=" N GLN F 149 " --> pdb=" O ASN F 145 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N PHE F 151 " --> pdb=" O ILE F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 187 removed outlier: 3.506A pdb=" N SER F 180 " --> pdb=" O GLY F 176 " (cutoff:3.500A) Proline residue: F 181 - end of helix Processing helix chain 'F' and resid 196 through 213 Processing helix chain 'F' and resid 250 through 264 removed outlier: 3.539A pdb=" N LEU F 260 " --> pdb=" O ALA F 256 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS F 263 " --> pdb=" O SER F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 298 Processing helix chain 'F' and resid 300 through 314 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 401 Processing helix chain 'F' and resid 432 through 437 Processing helix chain 'F' and resid 478 through 489 Processing helix chain 'F' and resid 496 through 507 removed outlier: 3.935A 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 541 through 555 Processing helix chain 'F' and resid 559 through 580 removed outlier: 3.592A pdb=" N LYS F 580 " --> pdb=" O ASP F 576 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 585 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 811 through 817 removed outlier: 3.920A 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 17 removed outlier: 5.101A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.555A 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: 7.795A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (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: 6.183A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (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: 5.596A pdb=" N LEU B 13 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLU B 29 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N THR B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL B 192 " --> pdb=" O THR B 196 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 105 removed outlier: 8.004A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 91 through 92 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 111 Processing sheet with id=AB1, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.165A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.517A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA C 94 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLY C 125 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU C 96 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TYR C 123 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N VAL C 98 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU C 121 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU C 100 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU C 119 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU C 102 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE C 117 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE C 104 " --> pdb=" O LYS C 115 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 454 removed outlier: 4.047A pdb=" N SER C 147 " --> pdb=" O ARG C 529 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 159 removed outlier: 4.732A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 284 through 286 removed outlier: 4.531A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 250 through 251 Processing sheet with id=AB9, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AC1, first strand: chain 'C' and resid 301 through 303 removed outlier: 6.625A pdb=" N TYR C 301 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581 removed outlier: 6.538A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 4.208A 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 623 through 624 Processing sheet with id=AC5, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.387A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.565A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC8, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC9, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 3.574A pdb=" N ALA C1067 " --> pdb=" O LEU C1233 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.765A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AD3, first strand: chain 'C' and resid 882 through 884 removed outlier: 7.152A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1213 through 1214 Processing sheet with id=AD5, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 6.334A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1335 through 1340 removed outlier: 3.916A pdb=" N ILE D 20 " --> pdb=" O ASP D1342 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP D1342 " --> pdb=" O ILE D 20 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 34 through 37 removed outlier: 6.962A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 10.467A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 11.068A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 159 through 160 removed outlier: 5.559A pdb=" N VAL D 146 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LYS D 179 " --> pdb=" O VAL D 146 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 252 through 254 Processing sheet with id=AE1, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.512A pdb=" N ARG D 551 " --> 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 removed outlier: 3.740A pdb=" N THR D 810 " --> pdb=" O VAL D 894 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 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: 6.596A 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 Processing sheet with id=AE7, first strand: chain 'D' and resid 991 through 997 removed outlier: 6.113A pdb=" N LEU D 984 " --> pdb=" O LYS D 992 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER D 994 " --> pdb=" O LEU D 982 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU D 982 " --> pdb=" O SER D 994 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N LYS D 996 " --> pdb=" O THR D 980 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N THR D 980 " --> pdb=" O LYS D 996 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AE9, first strand: chain 'D' and resid 1024 through 1027 removed outlier: 3.761A pdb=" N VAL D1027 " --> pdb=" O ALA D1122 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA D1122 " --> pdb=" O VAL D1027 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1098 through 1099 Processing sheet with id=AF2, first strand: chain 'D' and resid 1046 through 1050 Processing sheet with id=AF3, first strand: chain 'D' and resid 1186 through 1191 removed outlier: 6.300A pdb=" N LYS D1172 " --> pdb=" O GLU D1168 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLU D1168 " --> pdb=" O LYS D1172 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ARG D1174 " --> pdb=" O GLY D1166 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 4.633A pdb=" N LYS D1263 " --> pdb=" O ASP D1305 " (cutoff:3.500A) removed outlier: 6.647A 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: 6.710A pdb=" N ALA F 4 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N LYS F 28 " --> pdb=" O ALA F 4 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL F 6 " --> pdb=" O LYS F 28 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LYS F 3 " --> pdb=" O HIS F 105 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N TYR F 107 " --> pdb=" O LYS F 3 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU F 5 " --> pdb=" O TYR F 107 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 35 through 36 Processing sheet with id=AF7, first strand: chain 'F' and resid 244 through 245 removed outlier: 15.291A pdb=" N ALA F 233 " --> pdb=" O ARG F 427 " (cutoff:3.500A) removed outlier: 12.172A pdb=" N ARG F 427 " --> pdb=" O ALA F 233 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ALA F 235 " --> pdb=" O ARG F 425 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ARG F 425 " --> pdb=" O ALA F 235 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ARG F 421 " --> pdb=" O THR F 239 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LYS F 407 " --> pdb=" O ARG F 430 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLY F 416 " --> pdb=" O VAL F 268 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL F 268 " --> pdb=" O GLY F 416 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR F 266 " --> pdb=" O LEU F 459 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER F 225 " --> pdb=" O VAL F 462 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU F 464 " --> pdb=" O ASP F 223 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASP F 223 " --> pdb=" O LEU F 464 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLU F 221 " --> pdb=" O PRO F 466 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLN F 468 " --> pdb=" O PHE F 219 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N PHE F 219 " --> pdb=" O GLN F 468 " (cutoff:3.500A) removed outlier: 13.359A pdb=" N TRP F 220 " --> pdb=" O HIS F 240 " (cutoff:3.500A) removed outlier: 9.912A pdb=" N HIS F 240 " --> pdb=" O TRP F 220 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL F 222 " --> pdb=" O VAL F 238 " (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: 3.784A 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: 3.734A 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 Processing sheet with id=AG3, first strand: chain 'F' and resid 753 through 762 removed outlier: 6.075A pdb=" N ASP F 754 " --> pdb=" O ASP F 774 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ASP F 774 " --> pdb=" O ASP F 754 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE F 770 " --> pdb=" O LEU F 758 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 826 through 831 removed outlier: 4.676A pdb=" N LYS F 826 " --> pdb=" O GLU F 843 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU F 843 " --> pdb=" O LYS F 826 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N GLN F 838 " --> pdb=" O ALA F 853 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ALA F 853 " --> pdb=" O GLN F 838 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL F 840 " --> pdb=" O TRP F 851 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N TRP F 851 " --> pdb=" O VAL F 840 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N SER F 842 " --> pdb=" O THR F 849 " (cutoff:3.500A) 1474 hydrogen bonds defined for protein. 4125 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 63 hydrogen bonds 122 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 9.76 Time building geometry restraints manager: 4.34 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: 11175 1.34 - 1.47: 7267 1.47 - 1.59: 15103 1.59 - 1.72: 113 1.72 - 1.84: 244 Bond restraints: 33902 Sorted by residual: bond pdb=" O3' DC T 18 " pdb=" P DG T 19 " ideal model delta sigma weight residual 1.607 1.558 0.049 1.20e-02 6.94e+03 1.66e+01 bond pdb=" O3' DG T 19 " pdb=" P DC T 20 " ideal model delta sigma weight residual 1.607 1.565 0.042 1.20e-02 6.94e+03 1.24e+01 bond pdb=" N TYR F 319 " pdb=" CA TYR F 319 " ideal model delta sigma weight residual 1.457 1.503 -0.045 1.29e-02 6.01e+03 1.23e+01 bond pdb=" CA THR F 318 " pdb=" C THR F 318 " ideal model delta sigma weight residual 1.527 1.576 -0.049 1.41e-02 5.03e+03 1.18e+01 bond pdb=" N ILE F 34 " pdb=" CA ILE F 34 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.07e+01 ... (remaining 33897 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 44991 2.16 - 4.32: 978 4.32 - 6.48: 85 6.48 - 8.64: 8 8.64 - 10.80: 4 Bond angle restraints: 46066 Sorted by residual: angle pdb=" N PRO F 751 " pdb=" CA PRO F 751 " pdb=" C PRO F 751 " ideal model delta sigma weight residual 111.21 122.01 -10.80 1.59e+00 3.96e-01 4.61e+01 angle pdb=" N PRO F 750 " pdb=" CA PRO F 750 " pdb=" C PRO F 750 " ideal model delta sigma weight residual 110.70 102.59 8.11 1.22e+00 6.72e-01 4.42e+01 angle pdb=" N TRP F 560 " pdb=" CA TRP F 560 " pdb=" C TRP F 560 " ideal model delta sigma weight residual 111.07 117.85 -6.78 1.07e+00 8.73e-01 4.02e+01 angle pdb=" N ILE F 187 " pdb=" CA ILE F 187 " pdb=" C ILE F 187 " ideal model delta sigma weight residual 111.48 117.35 -5.87 9.40e-01 1.13e+00 3.90e+01 angle pdb=" N ILE F 285 " pdb=" CA ILE F 285 " pdb=" C ILE F 285 " ideal model delta sigma weight residual 110.05 103.66 6.39 1.09e+00 8.42e-01 3.43e+01 ... (remaining 46061 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.20: 19871 27.20 - 54.40: 755 54.40 - 81.61: 117 81.61 - 108.81: 11 108.81 - 136.01: 2 Dihedral angle restraints: 20756 sinusoidal: 9066 harmonic: 11690 Sorted by residual: dihedral pdb=" O4' U R 4 " pdb=" C1' U R 4 " pdb=" N1 U R 4 " pdb=" C2 U R 4 " ideal model delta sinusoidal sigma weight residual -128.00 -37.50 -90.50 1 1.70e+01 3.46e-03 3.35e+01 dihedral pdb=" CA ASP F 670 " pdb=" C ASP F 670 " pdb=" N SER F 671 " pdb=" CA SER F 671 " ideal model delta harmonic sigma weight residual 180.00 -151.72 -28.28 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA MET F 718 " pdb=" C MET F 718 " pdb=" N HIS F 719 " pdb=" CA HIS F 719 " ideal model delta harmonic sigma weight residual -180.00 -153.49 -26.51 0 5.00e+00 4.00e-02 2.81e+01 ... (remaining 20753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 4677 0.087 - 0.173: 487 0.173 - 0.260: 37 0.260 - 0.347: 6 0.347 - 0.433: 1 Chirality restraints: 5208 Sorted by residual: chirality pdb=" C3' DT N 21 " pdb=" C4' DT N 21 " pdb=" O3' DT N 21 " pdb=" C2' DT N 21 " both_signs ideal model delta sigma weight residual False -2.73 -2.30 -0.43 2.00e-01 2.50e+01 4.70e+00 chirality pdb=" CA VAL F 510 " pdb=" N VAL F 510 " pdb=" C VAL F 510 " pdb=" CB VAL F 510 " both_signs ideal model delta sigma weight residual False 2.44 2.75 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA ASP F 24 " pdb=" N ASP F 24 " pdb=" C ASP F 24 " pdb=" CB ASP F 24 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 5205 not shown) Planarity restraints: 5815 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA F 400 " 0.025 2.00e-02 2.50e+03 5.09e-02 2.59e+01 pdb=" C ALA F 400 " -0.088 2.00e-02 2.50e+03 pdb=" O ALA F 400 " 0.034 2.00e-02 2.50e+03 pdb=" N CYS F 401 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA F 749 " 0.023 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" C ALA F 749 " -0.079 2.00e-02 2.50e+03 pdb=" O ALA F 749 " 0.029 2.00e-02 2.50e+03 pdb=" N PRO F 750 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 566 " 0.047 2.00e-02 2.50e+03 3.51e-02 1.85e+01 pdb=" CG HIS F 566 " -0.049 2.00e-02 2.50e+03 pdb=" ND1 HIS F 566 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 HIS F 566 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 HIS F 566 " 0.023 2.00e-02 2.50e+03 pdb=" NE2 HIS F 566 " 0.031 2.00e-02 2.50e+03 ... (remaining 5812 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.30: 62 2.30 - 2.95: 16471 2.95 - 3.60: 52323 3.60 - 4.25: 78857 4.25 - 4.90: 127231 Nonbonded interactions: 274944 Sorted by model distance: nonbonded pdb=" O THR F 404 " pdb=" N TRP F 434 " model vdw 1.644 3.120 nonbonded pdb=" O LYS F 212 " pdb=" CB ALA F 668 " model vdw 1.898 3.460 nonbonded pdb=" CD PRO F 473 " pdb=" CA THR F 653 " model vdw 1.975 3.870 nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1500 " model vdw 1.987 2.170 nonbonded pdb=" OD2 ASP D 462 " pdb="MG MG D1500 " model vdw 2.066 2.170 ... (remaining 274939 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: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.050 Process input model: 39.760 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 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 0.068 33922 Z= 0.302 Angle : 0.728 10.799 46096 Z= 0.455 Chirality : 0.052 0.433 5208 Planarity : 0.005 0.059 5815 Dihedral : 14.396 136.011 13234 Min Nonbonded Distance : 1.644 Molprobity Statistics. All-atom Clashscore : 20.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.71 % Favored : 96.22 % Rotamer: Outliers : 2.63 % Allowed : 7.99 % Favored : 89.38 % 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: 4043 helix: 0.86 (0.14), residues: 1457 sheet: -0.26 (0.20), residues: 660 loop : -0.36 (0.15), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 833 TYR 0.051 0.003 TYR F 355 PHE 0.030 0.002 PHE F 343 TRP 0.022 0.002 TRP F 560 HIS 0.005 0.001 HIS D1252 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.30 (33902) covalent geometry : angle 0.71912 / 0.46 (46066) hydrogen bonds : bond 0.16636 / 11.37 ( 1535) hydrogen bonds : angle 6.72486 / 4.69 ( 4247) metal coordination : bond 0.01945 / 1.23 ( 20) metal coordination : angle 4.48405 / 3.07 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 266 time to evaluate : 1.185 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: A 25 LYS cc_start: 0.9411 (tttt) cc_final: 0.9198 (tmmt) REVERT: A 194 GLN cc_start: 0.9356 (tm-30) cc_final: 0.9097 (tm-30) REVERT: B 25 LYS cc_start: 0.9458 (mmmt) cc_final: 0.9153 (mmtm) REVERT: B 51 MET cc_start: 0.9446 (tpp) cc_final: 0.9171 (tpp) REVERT: B 74 VAL cc_start: 0.8890 (OUTLIER) cc_final: 0.8682 (p) REVERT: C 47 TYR cc_start: 0.8793 (m-80) cc_final: 0.8347 (m-80) REVERT: C 465 ARG cc_start: 0.9306 (OUTLIER) cc_final: 0.8816 (ttm-80) REVERT: C 492 MET cc_start: 0.9332 (mmt) cc_final: 0.8966 (mmt) REVERT: C 538 LEU cc_start: 0.9634 (mp) cc_final: 0.9237 (tp) REVERT: C 653 MET cc_start: 0.9042 (ttm) cc_final: 0.8754 (tpp) REVERT: C 686 GLN cc_start: 0.9544 (mt0) cc_final: 0.9274 (mt0) REVERT: C 1131 MET cc_start: 0.9144 (ttt) cc_final: 0.8783 (ttt) REVERT: C 1170 MET cc_start: 0.9411 (mmm) cc_final: 0.8886 (mmp) REVERT: C 1200 LYS cc_start: 0.9669 (tttt) cc_final: 0.9468 (tppp) REVERT: C 1230 MET cc_start: 0.8375 (tpt) cc_final: 0.8161 (tpp) REVERT: C 1232 MET cc_start: 0.8771 (mmm) cc_final: 0.8523 (mmm) REVERT: C 1243 MET cc_start: 0.9059 (tmm) cc_final: 0.8578 (tmm) REVERT: C 1273 MET cc_start: 0.9253 (mmm) cc_final: 0.9028 (mmm) REVERT: C 1279 GLU cc_start: 0.9370 (mt-10) cc_final: 0.9135 (mt-10) REVERT: C 1304 MET cc_start: 0.9532 (tpp) cc_final: 0.9214 (tpp) REVERT: D 29 MET cc_start: 0.9467 (ptm) cc_final: 0.9253 (ptp) REVERT: D 180 MET cc_start: 0.7080 (mmt) cc_final: 0.6826 (mmt) REVERT: D 485 MET cc_start: 0.9119 (mmm) cc_final: 0.8879 (mmm) REVERT: D 513 MET cc_start: 0.9228 (ttp) cc_final: 0.9012 (ttp) REVERT: D 625 MET cc_start: 0.9292 (tpp) cc_final: 0.8883 (tpp) REVERT: D 629 PHE cc_start: 0.9070 (OUTLIER) cc_final: 0.8867 (m-80) REVERT: D 1208 ASP cc_start: 0.9309 (t0) cc_final: 0.9055 (m-30) REVERT: D 1260 MET cc_start: 0.8836 (mtp) cc_final: 0.8414 (mtp) REVERT: E 30 MET cc_start: 0.8898 (mmm) cc_final: 0.8402 (mpp) REVERT: E 58 LEU cc_start: 0.9081 (mp) cc_final: 0.8584 (tt) REVERT: E 67 ARG cc_start: 0.9699 (mmm-85) cc_final: 0.9424 (mmm-85) REVERT: F 78 ASN cc_start: 0.8798 (OUTLIER) cc_final: 0.8235 (p0) REVERT: F 130 ASP cc_start: 0.9249 (t70) cc_final: 0.9030 (p0) REVERT: F 145 ASN cc_start: 0.9064 (t0) cc_final: 0.8636 (p0) REVERT: F 157 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.6926 (mp) REVERT: F 217 GLU cc_start: 0.9366 (mt-10) cc_final: 0.9133 (tp30) REVERT: F 345 LYS cc_start: 0.9498 (OUTLIER) cc_final: 0.9286 (tppt) REVERT: F 507 ARG cc_start: 0.4095 (OUTLIER) cc_final: 0.3810 (mmp80) REVERT: F 539 ASN cc_start: 0.8805 (OUTLIER) cc_final: 0.8511 (t0) REVERT: F 592 MET cc_start: 0.7662 (tpt) cc_final: 0.7446 (tpp) REVERT: F 669 MET cc_start: 0.4469 (mtm) cc_final: 0.3475 (ttp) REVERT: F 747 GLU cc_start: 0.8394 (tp30) cc_final: 0.7948 (pm20) outliers start: 91 outliers final: 30 residues processed: 347 average time/residue: 0.2083 time to fit residues: 117.8443 Evaluate side-chains 225 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1064 ASP Chi-restraints excluded: chain C residue 1240 ASP Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 85 CYS Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 629 PHE Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 345 LYS Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 472 LYS Chi-restraints excluded: chain F residue 493 ARG Chi-restraints excluded: chain F residue 507 ARG Chi-restraints excluded: chain F residue 539 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 0.8980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 0.6980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 HIS A 66 HIS B 66 HIS B 93 GLN B 132 HIS B 147 GLN C 36 GLN ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS C 406 ASN C 686 GLN C 808 ASN C 832 HIS C 955 GLN C1061 GLN ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1136 GLN C1175 ASN C1256 GLN C1257 GLN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN D 365 GLN D 448 GLN D 450 HIS ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 665 GLN D 777 HIS D 951 GLN D 962 ASN D1010 GLN D1108 GLN D1295 ASN E 31 GLN F 78 ASN F 140 ASN F 145 ASN F 152 ASN F 163 ASN F 197 GLN F 242 ASN F 253 GLN F 353 ASN F 533 ASN F 548 ASN F 681 HIS F 738 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.052889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.034906 restraints weight = 266304.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.035993 restraints weight = 144515.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.036728 restraints weight = 96746.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.037217 restraints weight = 74314.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.037517 restraints weight = 62420.567| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33922 Z= 0.159 Angle : 0.643 12.729 46096 Z= 0.335 Chirality : 0.043 0.210 5208 Planarity : 0.005 0.048 5815 Dihedral : 13.257 136.702 5321 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.79 % Favored : 97.18 % Rotamer: Outliers : 2.49 % Allowed : 10.13 % Favored : 87.38 % 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: 0.46 (0.13), residues: 4043 helix: 1.16 (0.13), residues: 1486 sheet: -0.01 (0.20), residues: 629 loop : -0.15 (0.15), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 310 TYR 0.022 0.001 TYR D 631 PHE 0.022 0.001 PHE F 477 TRP 0.009 0.001 TRP F 79 HIS 0.005 0.001 HIS F 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.16 (33902) covalent geometry : angle 0.62913 / 0.33 (46066) hydrogen bonds : bond 0.05036 / 3.40 ( 1535) hydrogen bonds : angle 5.32494 / 3.68 ( 4247) metal coordination : bond 0.00919 / 0.56 ( 20) metal coordination : angle 5.20176 / 3.38 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 201 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLN cc_start: 0.8739 (pt0) cc_final: 0.8531 (pp30) REVERT: C 47 TYR cc_start: 0.8777 (m-80) cc_final: 0.8368 (m-80) REVERT: C 465 ARG cc_start: 0.9280 (OUTLIER) cc_final: 0.8790 (ttm-80) REVERT: C 492 MET cc_start: 0.9362 (mmt) cc_final: 0.9030 (mmt) REVERT: C 538 LEU cc_start: 0.9589 (mp) cc_final: 0.9251 (tp) REVERT: C 1131 MET cc_start: 0.8887 (ttt) cc_final: 0.8529 (ttt) REVERT: C 1170 MET cc_start: 0.9318 (mmm) cc_final: 0.8856 (mmp) REVERT: C 1230 MET cc_start: 0.8022 (tpt) cc_final: 0.7772 (tpp) REVERT: C 1279 GLU cc_start: 0.9240 (mt-10) cc_final: 0.9023 (mt-10) REVERT: C 1304 MET cc_start: 0.9417 (tpp) cc_final: 0.9089 (tpp) REVERT: D 29 MET cc_start: 0.9315 (ptm) cc_final: 0.9103 (ptp) REVERT: D 180 MET cc_start: 0.7281 (mmt) cc_final: 0.6996 (mmt) REVERT: D 282 LEU cc_start: 0.9681 (tp) cc_final: 0.9421 (tt) REVERT: D 466 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7875 (tpt) REVERT: D 485 MET cc_start: 0.9051 (mmm) cc_final: 0.8770 (mmm) REVERT: D 535 ARG cc_start: 0.9507 (OUTLIER) cc_final: 0.8656 (ptp-110) REVERT: D 625 MET cc_start: 0.9086 (tpp) cc_final: 0.8720 (tpp) REVERT: D 629 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.8730 (m-80) REVERT: D 724 MET cc_start: 0.9259 (ttm) cc_final: 0.8877 (mtp) REVERT: D 736 GLN cc_start: 0.9520 (OUTLIER) cc_final: 0.9275 (mt0) REVERT: D 747 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.8049 (mmp) REVERT: D 895 CYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7667 (p) REVERT: D 915 ILE cc_start: 0.9732 (OUTLIER) cc_final: 0.9349 (mt) REVERT: D 1254 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8758 (pt0) REVERT: E 30 MET cc_start: 0.8715 (mmm) cc_final: 0.8206 (mmm) REVERT: E 58 LEU cc_start: 0.8934 (mp) cc_final: 0.8386 (tt) REVERT: E 67 ARG cc_start: 0.9697 (mmm-85) cc_final: 0.9414 (mmm-85) REVERT: F 145 ASN cc_start: 0.9113 (t0) cc_final: 0.8704 (p0) REVERT: F 171 MET cc_start: 0.7864 (mtt) cc_final: 0.7661 (mmm) REVERT: F 217 GLU cc_start: 0.9307 (mt-10) cc_final: 0.9007 (tm-30) REVERT: F 539 ASN cc_start: 0.8716 (OUTLIER) cc_final: 0.8484 (p0) REVERT: F 592 MET cc_start: 0.7324 (tpt) cc_final: 0.6949 (tpt) REVERT: F 669 MET cc_start: 0.5060 (mtm) cc_final: 0.4610 (mtm) REVERT: F 747 GLU cc_start: 0.8232 (tp30) cc_final: 0.7800 (pm20) outliers start: 86 outliers final: 33 residues processed: 274 average time/residue: 0.2089 time to fit residues: 94.8983 Evaluate side-chains 220 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 178 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1138 VAL Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 535 ARG Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 629 PHE Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 472 LYS Chi-restraints excluded: chain F residue 507 ARG Chi-restraints excluded: chain F residue 539 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 186 optimal weight: 0.9990 chunk 384 optimal weight: 8.9990 chunk 406 optimal weight: 30.0000 chunk 234 optimal weight: 0.6980 chunk 106 optimal weight: 8.9990 chunk 334 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 chunk 361 optimal weight: 50.0000 chunk 92 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 338 optimal weight: 8.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 ASN B 132 HIS ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 HIS C1220 GLN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 ASN D1238 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.051952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.033983 restraints weight = 271353.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.035080 restraints weight = 146624.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.035804 restraints weight = 97999.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.036290 restraints weight = 75154.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.036617 restraints weight = 63290.215| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 33922 Z= 0.212 Angle : 0.635 12.969 46096 Z= 0.329 Chirality : 0.042 0.197 5208 Planarity : 0.004 0.055 5815 Dihedral : 13.145 130.487 5284 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.14 % Favored : 96.83 % Rotamer: Outliers : 2.34 % Allowed : 11.66 % Favored : 86.00 % 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: 0.47 (0.13), residues: 4043 helix: 1.23 (0.13), residues: 1478 sheet: -0.18 (0.19), residues: 656 loop : -0.13 (0.15), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 158 TYR 0.021 0.001 TYR D 631 PHE 0.014 0.001 PHE C 514 TRP 0.013 0.001 TRP C 183 HIS 0.012 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.21 (33902) covalent geometry : angle 0.62610 / 0.33 (46066) hydrogen bonds : bond 0.04625 / 3.12 ( 1535) hydrogen bonds : angle 5.17954 / 3.58 ( 4247) metal coordination : bond 0.01029 / 0.64 ( 20) metal coordination : angle 4.27544 / 2.70 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 180 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLN cc_start: 0.8786 (pt0) cc_final: 0.8507 (pp30) REVERT: B 46 ILE cc_start: 0.9712 (OUTLIER) cc_final: 0.9472 (tt) REVERT: C 47 TYR cc_start: 0.8805 (m-80) cc_final: 0.8356 (m-80) REVERT: C 429 MET cc_start: 0.9522 (mpp) cc_final: 0.9298 (mpp) REVERT: C 465 ARG cc_start: 0.9288 (OUTLIER) cc_final: 0.8786 (ttm-80) REVERT: C 492 MET cc_start: 0.9407 (mmt) cc_final: 0.9087 (mmt) REVERT: C 538 LEU cc_start: 0.9580 (mp) cc_final: 0.9235 (tp) REVERT: C 611 GLU cc_start: 0.9043 (tt0) cc_final: 0.8789 (tm-30) REVERT: C 697 LYS cc_start: 0.9295 (OUTLIER) cc_final: 0.9073 (pptt) REVERT: C 1131 MET cc_start: 0.8937 (ttt) cc_final: 0.8569 (ttt) REVERT: C 1170 MET cc_start: 0.9339 (mmm) cc_final: 0.8873 (mmp) REVERT: C 1304 MET cc_start: 0.9405 (tpp) cc_final: 0.9093 (tpp) REVERT: D 29 MET cc_start: 0.9345 (ptm) cc_final: 0.9136 (ptp) REVERT: D 180 MET cc_start: 0.7575 (mmt) cc_final: 0.7277 (mmt) REVERT: D 466 MET cc_start: 0.8131 (ttt) cc_final: 0.7835 (tpt) REVERT: D 485 MET cc_start: 0.9046 (mmm) cc_final: 0.8814 (mmm) REVERT: D 535 ARG cc_start: 0.9524 (OUTLIER) cc_final: 0.8681 (ptp-170) REVERT: D 625 MET cc_start: 0.9106 (tpp) cc_final: 0.8720 (tpp) REVERT: D 629 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.8664 (m-80) REVERT: D 724 MET cc_start: 0.9249 (ttm) cc_final: 0.8862 (mtp) REVERT: D 747 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.8088 (mmp) REVERT: D 822 MET cc_start: 0.9042 (tpt) cc_final: 0.8709 (tpp) REVERT: D 895 CYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7747 (p) REVERT: D 915 ILE cc_start: 0.9727 (OUTLIER) cc_final: 0.9331 (mt) REVERT: D 1208 ASP cc_start: 0.9277 (t0) cc_final: 0.9062 (m-30) REVERT: E 30 MET cc_start: 0.8688 (mmm) cc_final: 0.8292 (tpp) REVERT: E 58 LEU cc_start: 0.8952 (mp) cc_final: 0.8406 (tt) REVERT: F 145 ASN cc_start: 0.9175 (t0) cc_final: 0.8868 (p0) REVERT: F 217 GLU cc_start: 0.9335 (mt-10) cc_final: 0.9058 (tm-30) REVERT: F 438 MET cc_start: 0.4891 (mtt) cc_final: 0.4424 (tpt) REVERT: F 539 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8495 (p0) REVERT: F 592 MET cc_start: 0.7640 (tpt) cc_final: 0.7277 (tpp) REVERT: F 669 MET cc_start: 0.5548 (mtm) cc_final: 0.5277 (mtm) REVERT: F 747 GLU cc_start: 0.8326 (tp30) cc_final: 0.7926 (pm20) outliers start: 81 outliers final: 45 residues processed: 251 average time/residue: 0.1965 time to fit residues: 84.5357 Evaluate side-chains 225 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 171 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1138 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 535 ARG Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 629 PHE Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 472 LYS Chi-restraints excluded: chain F residue 539 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 299 optimal weight: 6.9990 chunk 57 optimal weight: 20.0000 chunk 60 optimal weight: 8.9990 chunk 257 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 152 optimal weight: 20.0000 chunk 295 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 348 optimal weight: 3.9990 chunk 153 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 673 HIS ** C 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1366 HIS F 309 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.051957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.034075 restraints weight = 269898.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.035170 restraints weight = 145820.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.035900 restraints weight = 97500.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.036393 restraints weight = 74567.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.036730 restraints weight = 62581.755| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 33922 Z= 0.183 Angle : 0.604 10.347 46096 Z= 0.312 Chirality : 0.042 0.196 5208 Planarity : 0.004 0.056 5815 Dihedral : 13.109 123.904 5279 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.97 % Favored : 97.01 % Rotamer: Outliers : 2.46 % Allowed : 12.15 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.13), residues: 4043 helix: 1.28 (0.13), residues: 1483 sheet: -0.09 (0.20), residues: 629 loop : -0.19 (0.15), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 944 TYR 0.020 0.001 TYR D 631 PHE 0.015 0.001 PHE C 514 TRP 0.010 0.001 TRP F 79 HIS 0.020 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.18 (33902) covalent geometry : angle 0.59496 / 0.31 (46066) hydrogen bonds : bond 0.04163 / 2.80 ( 1535) hydrogen bonds : angle 5.00225 / 3.45 ( 4247) metal coordination : bond 0.00895 / 0.55 ( 20) metal coordination : angle 4.13126 / 2.60 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 178 time to evaluate : 1.283 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: A 147 GLN cc_start: 0.8796 (pt0) cc_final: 0.8519 (pp30) REVERT: C 47 TYR cc_start: 0.8787 (m-80) cc_final: 0.8333 (m-80) REVERT: C 429 MET cc_start: 0.9540 (mpp) cc_final: 0.9308 (mpp) REVERT: C 465 ARG cc_start: 0.9286 (OUTLIER) cc_final: 0.8789 (ttm-80) REVERT: C 492 MET cc_start: 0.9384 (mmt) cc_final: 0.9094 (mmt) REVERT: C 538 LEU cc_start: 0.9580 (mp) cc_final: 0.9233 (tp) REVERT: C 611 GLU cc_start: 0.9043 (tt0) cc_final: 0.8763 (tm-30) REVERT: C 1131 MET cc_start: 0.8977 (ttt) cc_final: 0.8593 (ttt) REVERT: C 1170 MET cc_start: 0.9324 (mmm) cc_final: 0.8860 (mmp) REVERT: C 1304 MET cc_start: 0.9408 (tpp) cc_final: 0.9082 (tpp) REVERT: D 29 MET cc_start: 0.9334 (ptm) cc_final: 0.9132 (ptp) REVERT: D 180 MET cc_start: 0.7643 (mmt) cc_final: 0.7347 (mmt) REVERT: D 192 MET cc_start: 0.7811 (ppp) cc_final: 0.6612 (ppp) REVERT: D 485 MET cc_start: 0.9047 (mmm) cc_final: 0.8841 (mmm) REVERT: D 625 MET cc_start: 0.9106 (tpp) cc_final: 0.8720 (tpp) REVERT: D 629 PHE cc_start: 0.8923 (OUTLIER) cc_final: 0.8692 (m-80) REVERT: D 724 MET cc_start: 0.9243 (ttm) cc_final: 0.8862 (mtp) REVERT: D 822 MET cc_start: 0.9012 (tpt) cc_final: 0.8627 (tpp) REVERT: D 895 CYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7745 (p) REVERT: D 915 ILE cc_start: 0.9715 (OUTLIER) cc_final: 0.9307 (mt) REVERT: D 1251 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.9002 (mtpp) REVERT: E 30 MET cc_start: 0.8672 (mmm) cc_final: 0.8271 (tpp) REVERT: E 58 LEU cc_start: 0.8966 (mp) cc_final: 0.8412 (tt) REVERT: F 71 MET cc_start: 0.8609 (tmm) cc_final: 0.8192 (tmm) REVERT: F 145 ASN cc_start: 0.9114 (t0) cc_final: 0.8744 (p0) REVERT: F 217 GLU cc_start: 0.9358 (mt-10) cc_final: 0.9050 (tm-30) REVERT: F 438 MET cc_start: 0.4880 (mtt) cc_final: 0.4470 (tpt) REVERT: F 539 ASN cc_start: 0.8801 (OUTLIER) cc_final: 0.8570 (p0) REVERT: F 592 MET cc_start: 0.7559 (tpt) cc_final: 0.7262 (tpp) REVERT: F 669 MET cc_start: 0.5724 (mtm) cc_final: 0.5381 (mtm) REVERT: F 747 GLU cc_start: 0.8260 (tp30) cc_final: 0.7908 (pm20) outliers start: 85 outliers final: 50 residues processed: 253 average time/residue: 0.1906 time to fit residues: 82.2952 Evaluate side-chains 225 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 169 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1138 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 629 PHE Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1041 ILE Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1251 LYS Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 472 LYS Chi-restraints excluded: chain F residue 539 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 202 optimal weight: 7.9990 chunk 220 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 258 optimal weight: 9.9990 chunk 228 optimal weight: 8.9990 chunk 406 optimal weight: 50.0000 chunk 396 optimal weight: 50.0000 chunk 328 optimal weight: 4.9990 chunk 288 optimal weight: 20.0000 chunk 377 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 132 HIS ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS C 808 ASN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.051105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.033389 restraints weight = 269408.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.034439 restraints weight = 147393.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.035145 restraints weight = 99414.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.035634 restraints weight = 76529.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.035963 restraints weight = 64107.549| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 33922 Z= 0.249 Angle : 0.643 9.475 46096 Z= 0.333 Chirality : 0.042 0.223 5208 Planarity : 0.004 0.054 5815 Dihedral : 13.143 120.344 5279 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.46 % Favored : 96.51 % Rotamer: Outliers : 2.72 % Allowed : 12.99 % Favored : 84.29 % 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: 0.38 (0.13), residues: 4043 helix: 1.20 (0.13), residues: 1474 sheet: -0.21 (0.20), residues: 651 loop : -0.24 (0.15), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 53 TYR 0.022 0.001 TYR D 631 PHE 0.013 0.001 PHE C 230 TRP 0.013 0.001 TRP F 79 HIS 0.018 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.25 (33902) covalent geometry : angle 0.63450 / 0.33 (46066) hydrogen bonds : bond 0.04284 / 2.86 ( 1535) hydrogen bonds : angle 5.08938 / 3.51 ( 4247) metal coordination : bond 0.01112 / 0.70 ( 20) metal coordination : angle 4.09776 / 2.58 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 168 time to evaluate : 1.398 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 147 GLN cc_start: 0.8854 (pt0) cc_final: 0.8542 (pp30) REVERT: B 46 ILE cc_start: 0.9713 (OUTLIER) cc_final: 0.9475 (tt) REVERT: C 395 TYR cc_start: 0.7503 (t80) cc_final: 0.7233 (t80) REVERT: C 429 MET cc_start: 0.9575 (mpp) cc_final: 0.9337 (mpp) REVERT: C 492 MET cc_start: 0.9377 (mmt) cc_final: 0.9097 (mmt) REVERT: C 538 LEU cc_start: 0.9598 (mp) cc_final: 0.9251 (tp) REVERT: C 611 GLU cc_start: 0.9064 (tt0) cc_final: 0.8800 (tm-30) REVERT: C 1094 VAL cc_start: 0.9340 (OUTLIER) cc_final: 0.8977 (p) REVERT: C 1131 MET cc_start: 0.9045 (ttt) cc_final: 0.8642 (ttt) REVERT: C 1170 MET cc_start: 0.9365 (mmm) cc_final: 0.8880 (mmp) REVERT: C 1304 MET cc_start: 0.9445 (tpp) cc_final: 0.9118 (tpp) REVERT: D 29 MET cc_start: 0.9379 (ptm) cc_final: 0.9166 (ptp) REVERT: D 180 MET cc_start: 0.7764 (mmt) cc_final: 0.7441 (mmt) REVERT: D 192 MET cc_start: 0.7986 (ppp) cc_final: 0.6740 (ppp) REVERT: D 400 MET cc_start: 0.9274 (mpp) cc_final: 0.8868 (pmm) REVERT: D 466 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7887 (tpt) REVERT: D 485 MET cc_start: 0.9091 (mmm) cc_final: 0.8861 (mmm) REVERT: D 513 MET cc_start: 0.9115 (ttp) cc_final: 0.8829 (tpp) REVERT: D 535 ARG cc_start: 0.9544 (OUTLIER) cc_final: 0.8700 (ptp-170) REVERT: D 625 MET cc_start: 0.9172 (tpp) cc_final: 0.8791 (tpp) REVERT: D 629 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.8722 (m-80) REVERT: D 724 MET cc_start: 0.9293 (ttm) cc_final: 0.8834 (mtp) REVERT: D 743 MET cc_start: 0.9276 (mtp) cc_final: 0.8939 (mmm) REVERT: D 822 MET cc_start: 0.9012 (tpt) cc_final: 0.8638 (tpp) REVERT: D 915 ILE cc_start: 0.9739 (OUTLIER) cc_final: 0.9308 (mt) REVERT: D 932 MET cc_start: 0.6906 (ptp) cc_final: 0.6683 (pmm) REVERT: D 1251 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.9073 (mtpp) REVERT: E 30 MET cc_start: 0.8715 (mmm) cc_final: 0.8313 (tpp) REVERT: E 58 LEU cc_start: 0.8984 (mp) cc_final: 0.8456 (tt) REVERT: F 71 MET cc_start: 0.8676 (tmm) cc_final: 0.8195 (tmm) REVERT: F 145 ASN cc_start: 0.9104 (t0) cc_final: 0.8729 (p0) REVERT: F 217 GLU cc_start: 0.9343 (mt-10) cc_final: 0.8988 (tm-30) REVERT: F 539 ASN cc_start: 0.8845 (OUTLIER) cc_final: 0.8614 (p0) REVERT: F 592 MET cc_start: 0.7375 (tpt) cc_final: 0.7098 (tpp) REVERT: F 606 MET cc_start: -0.0880 (tpt) cc_final: -0.1155 (tpp) REVERT: F 669 MET cc_start: 0.6153 (mtm) cc_final: 0.5813 (mtm) REVERT: F 747 GLU cc_start: 0.8269 (tp30) cc_final: 0.7884 (pm20) outliers start: 94 outliers final: 59 residues processed: 252 average time/residue: 0.1953 time to fit residues: 84.4804 Evaluate side-chains 229 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 162 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1138 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 535 ARG Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 629 PHE Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1251 LYS Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 472 LYS Chi-restraints excluded: chain F residue 507 ARG Chi-restraints excluded: chain F residue 539 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 263 optimal weight: 9.9990 chunk 315 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 362 optimal weight: 30.0000 chunk 408 optimal weight: 40.0000 chunk 105 optimal weight: 0.9990 chunk 269 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 409 optimal weight: 40.0000 chunk 70 optimal weight: 1.9990 chunk 297 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 132 HIS ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.051471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.033618 restraints weight = 271132.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.034686 restraints weight = 147029.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.035409 restraints weight = 98831.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.035897 restraints weight = 76011.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.036179 restraints weight = 63892.325| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 33922 Z= 0.188 Angle : 0.616 11.770 46096 Z= 0.316 Chirality : 0.042 0.309 5208 Planarity : 0.004 0.056 5815 Dihedral : 13.111 119.349 5275 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.94 % Favored : 97.03 % Rotamer: Outliers : 2.86 % Allowed : 13.51 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.13), residues: 4043 helix: 1.28 (0.13), residues: 1470 sheet: -0.25 (0.20), residues: 652 loop : -0.20 (0.15), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 169 TYR 0.019 0.001 TYR D 631 PHE 0.012 0.001 PHE C 230 TRP 0.010 0.001 TRP F 79 HIS 0.016 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.19 (33902) covalent geometry : angle 0.60365 / 0.31 (46066) hydrogen bonds : bond 0.04019 / 2.70 ( 1535) hydrogen bonds : angle 4.95572 / 3.41 ( 4247) metal coordination : bond 0.01317 / 0.82 ( 20) metal coordination : angle 4.84189 / 2.94 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 170 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLN cc_start: 0.8818 (pt0) cc_final: 0.8514 (pp30) REVERT: B 46 ILE cc_start: 0.9707 (OUTLIER) cc_final: 0.9476 (tt) REVERT: C 47 TYR cc_start: 0.8816 (m-80) cc_final: 0.8347 (m-80) REVERT: C 429 MET cc_start: 0.9565 (mpp) cc_final: 0.9316 (mpp) REVERT: C 492 MET cc_start: 0.9391 (mmt) cc_final: 0.9090 (mmt) REVERT: C 538 LEU cc_start: 0.9594 (mp) cc_final: 0.9245 (tp) REVERT: C 611 GLU cc_start: 0.9042 (tt0) cc_final: 0.8757 (tm-30) REVERT: C 1094 VAL cc_start: 0.9331 (OUTLIER) cc_final: 0.8971 (p) REVERT: C 1131 MET cc_start: 0.9072 (ttt) cc_final: 0.8651 (ttt) REVERT: C 1170 MET cc_start: 0.9344 (mmm) cc_final: 0.8861 (mmp) REVERT: C 1304 MET cc_start: 0.9431 (tpp) cc_final: 0.9095 (tpp) REVERT: D 29 MET cc_start: 0.9366 (ptm) cc_final: 0.9161 (ptp) REVERT: D 192 MET cc_start: 0.7964 (ppp) cc_final: 0.6691 (ppp) REVERT: D 466 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7884 (tpt) REVERT: D 513 MET cc_start: 0.9089 (ttp) cc_final: 0.8855 (tpp) REVERT: D 535 ARG cc_start: 0.9532 (OUTLIER) cc_final: 0.8699 (ptp-170) REVERT: D 625 MET cc_start: 0.9145 (tpp) cc_final: 0.8762 (tpp) REVERT: D 629 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.8700 (m-80) REVERT: D 724 MET cc_start: 0.9271 (ttm) cc_final: 0.8830 (mtp) REVERT: D 743 MET cc_start: 0.9290 (mtp) cc_final: 0.8951 (mmm) REVERT: D 915 ILE cc_start: 0.9742 (OUTLIER) cc_final: 0.9340 (mt) REVERT: D 1040 MET cc_start: 0.7981 (tmm) cc_final: 0.7647 (tpp) REVERT: E 8 ASP cc_start: 0.9461 (OUTLIER) cc_final: 0.9056 (p0) REVERT: E 30 MET cc_start: 0.8658 (mmm) cc_final: 0.8246 (tpp) REVERT: E 58 LEU cc_start: 0.8994 (mp) cc_final: 0.8456 (tt) REVERT: F 71 MET cc_start: 0.8679 (tmm) cc_final: 0.8200 (tmm) REVERT: F 145 ASN cc_start: 0.9130 (t0) cc_final: 0.8719 (p0) REVERT: F 217 GLU cc_start: 0.9329 (mt-10) cc_final: 0.8967 (tm-30) REVERT: F 438 MET cc_start: 0.4624 (mtt) cc_final: 0.4313 (tpt) REVERT: F 507 ARG cc_start: 0.5565 (OUTLIER) cc_final: 0.4970 (mmm160) REVERT: F 539 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8605 (p0) REVERT: F 592 MET cc_start: 0.7418 (tpt) cc_final: 0.7127 (tpp) REVERT: F 669 MET cc_start: 0.6212 (mtm) cc_final: 0.5906 (mtm) outliers start: 99 outliers final: 67 residues processed: 258 average time/residue: 0.1918 time to fit residues: 85.9759 Evaluate side-chains 239 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 163 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1059 ARG Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1138 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 535 ARG Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 629 PHE Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 656 GLU Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1019 ASN Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 472 LYS Chi-restraints excluded: chain F residue 507 ARG Chi-restraints excluded: chain F residue 539 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 36 optimal weight: 30.0000 chunk 409 optimal weight: 30.0000 chunk 355 optimal weight: 3.9990 chunk 388 optimal weight: 40.0000 chunk 224 optimal weight: 6.9990 chunk 71 optimal weight: 30.0000 chunk 363 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 chunk 236 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 392 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.051026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.033300 restraints weight = 269751.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.034351 restraints weight = 147813.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.035063 restraints weight = 99738.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.035504 restraints weight = 76599.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.035848 restraints weight = 64799.754| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 33922 Z= 0.223 Angle : 0.637 10.654 46096 Z= 0.327 Chirality : 0.042 0.258 5208 Planarity : 0.004 0.054 5815 Dihedral : 13.139 121.387 5275 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.51 % Favored : 96.46 % Rotamer: Outliers : 2.86 % Allowed : 14.27 % Favored : 82.87 % 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: 0.40 (0.13), residues: 4043 helix: 1.23 (0.13), residues: 1471 sheet: -0.15 (0.20), residues: 642 loop : -0.25 (0.15), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 700 TYR 0.019 0.001 TYR D 631 PHE 0.011 0.001 PHE C 230 TRP 0.011 0.001 TRP F 79 HIS 0.014 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.22 (33902) covalent geometry : angle 0.62814 / 0.33 (46066) hydrogen bonds : bond 0.04111 / 2.75 ( 1535) hydrogen bonds : angle 5.00470 / 3.44 ( 4247) metal coordination : bond 0.01197 / 0.75 ( 20) metal coordination : angle 4.19426 / 2.62 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 166 time to evaluate : 1.305 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 147 GLN cc_start: 0.8832 (pt0) cc_final: 0.8534 (pp30) REVERT: A 158 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7774 (ptt180) REVERT: A 160 HIS cc_start: 0.8869 (p90) cc_final: 0.8517 (p90) REVERT: B 46 ILE cc_start: 0.9708 (OUTLIER) cc_final: 0.9475 (tt) REVERT: C 395 TYR cc_start: 0.7510 (t80) cc_final: 0.7270 (t80) REVERT: C 429 MET cc_start: 0.9581 (mpp) cc_final: 0.9337 (mpp) REVERT: C 492 MET cc_start: 0.9397 (mmt) cc_final: 0.9100 (mmt) REVERT: C 538 LEU cc_start: 0.9592 (mp) cc_final: 0.9250 (tp) REVERT: C 611 GLU cc_start: 0.9040 (tt0) cc_final: 0.8776 (tm-30) REVERT: C 1094 VAL cc_start: 0.9364 (OUTLIER) cc_final: 0.9017 (p) REVERT: C 1131 MET cc_start: 0.9070 (ttt) cc_final: 0.8652 (ttt) REVERT: C 1170 MET cc_start: 0.9350 (mmm) cc_final: 0.8877 (mmp) REVERT: C 1304 MET cc_start: 0.9441 (tpp) cc_final: 0.9107 (tpp) REVERT: D 29 MET cc_start: 0.9377 (ptm) cc_final: 0.9163 (ptp) REVERT: D 180 MET cc_start: 0.7881 (mmt) cc_final: 0.7574 (mmp) REVERT: D 466 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7885 (tpt) REVERT: D 513 MET cc_start: 0.9107 (ttp) cc_final: 0.8888 (tpp) REVERT: D 535 ARG cc_start: 0.9533 (OUTLIER) cc_final: 0.8710 (ptp-170) REVERT: D 625 MET cc_start: 0.9170 (tpp) cc_final: 0.8788 (tpp) REVERT: D 724 MET cc_start: 0.9325 (ttm) cc_final: 0.8843 (mtp) REVERT: D 932 MET cc_start: 0.6333 (pmm) cc_final: 0.6055 (pmm) REVERT: E 8 ASP cc_start: 0.9486 (OUTLIER) cc_final: 0.9099 (p0) REVERT: E 30 MET cc_start: 0.8675 (mmm) cc_final: 0.8262 (tpp) REVERT: E 58 LEU cc_start: 0.8967 (mp) cc_final: 0.8454 (tt) REVERT: F 71 MET cc_start: 0.8674 (tmm) cc_final: 0.8370 (tmm) REVERT: F 145 ASN cc_start: 0.9130 (t0) cc_final: 0.8731 (p0) REVERT: F 171 MET cc_start: 0.8239 (mmt) cc_final: 0.8019 (mmm) REVERT: F 217 GLU cc_start: 0.9321 (mt-10) cc_final: 0.8935 (tm-30) REVERT: F 438 MET cc_start: 0.4552 (mtt) cc_final: 0.4124 (tpt) REVERT: F 507 ARG cc_start: 0.5217 (OUTLIER) cc_final: 0.4582 (mmm160) REVERT: F 539 ASN cc_start: 0.8878 (OUTLIER) cc_final: 0.8657 (p0) REVERT: F 556 HIS cc_start: 0.8671 (OUTLIER) cc_final: 0.8357 (m-70) REVERT: F 592 MET cc_start: 0.7392 (tpt) cc_final: 0.7078 (tpp) REVERT: F 606 MET cc_start: -0.0573 (OUTLIER) cc_final: -0.1223 (tpp) REVERT: F 669 MET cc_start: 0.6446 (mtm) cc_final: 0.6148 (mtm) outliers start: 99 outliers final: 70 residues processed: 254 average time/residue: 0.1903 time to fit residues: 83.2143 Evaluate side-chains 241 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 161 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1059 ARG Chi-restraints excluded: chain C residue 1072 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1138 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 535 ARG Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 656 GLU Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1019 ASN Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1280 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 472 LYS Chi-restraints excluded: chain F residue 507 ARG Chi-restraints excluded: chain F residue 539 ASN Chi-restraints excluded: chain F residue 556 HIS Chi-restraints excluded: chain F residue 606 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 125 optimal weight: 9.9990 chunk 393 optimal weight: 30.0000 chunk 50 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 266 optimal weight: 7.9990 chunk 181 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 389 optimal weight: 2.9990 chunk 281 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN C 932 GLN ** D 80 HIS ** 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 = 0.3484 r_free = 0.3484 target = 0.052048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.034178 restraints weight = 267632.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.035269 restraints weight = 144699.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.035990 restraints weight = 96688.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.036489 restraints weight = 74142.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.036828 restraints weight = 61991.615| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33922 Z= 0.125 Angle : 0.605 13.062 46096 Z= 0.306 Chirality : 0.042 0.264 5208 Planarity : 0.004 0.055 5815 Dihedral : 13.073 124.145 5273 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.60 % Favored : 97.38 % Rotamer: Outliers : 2.23 % Allowed : 15.31 % Favored : 82.47 % 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: 0.59 (0.13), residues: 4043 helix: 1.41 (0.13), residues: 1473 sheet: -0.02 (0.20), residues: 616 loop : -0.18 (0.14), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 169 TYR 0.016 0.001 TYR D 631 PHE 0.024 0.001 PHE D 629 TRP 0.010 0.001 TRP C 183 HIS 0.013 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (33902) covalent geometry : angle 0.59854 / 0.31 (46066) hydrogen bonds : bond 0.03765 / 2.54 ( 1535) hydrogen bonds : angle 4.79740 / 3.29 ( 4247) metal coordination : bond 0.00692 / 0.42 ( 20) metal coordination : angle 3.61375 / 2.33 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 182 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.8913 (pmm) cc_final: 0.8307 (pmm) REVERT: A 147 GLN cc_start: 0.8771 (pt0) cc_final: 0.8500 (pp30) REVERT: A 158 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7700 (ptt180) REVERT: C 47 TYR cc_start: 0.8716 (m-80) cc_final: 0.8299 (m-80) REVERT: C 239 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.7829 (tmm) REVERT: C 429 MET cc_start: 0.9529 (mpp) cc_final: 0.9312 (mpp) REVERT: C 492 MET cc_start: 0.9369 (mmt) cc_final: 0.9071 (mmt) REVERT: C 538 LEU cc_start: 0.9554 (mp) cc_final: 0.9223 (tp) REVERT: C 611 GLU cc_start: 0.8999 (tt0) cc_final: 0.8693 (tm-30) REVERT: C 1131 MET cc_start: 0.9048 (ttt) cc_final: 0.8623 (ttt) REVERT: C 1170 MET cc_start: 0.9309 (mmm) cc_final: 0.8898 (mmm) REVERT: C 1304 MET cc_start: 0.9378 (tpp) cc_final: 0.9041 (tpp) REVERT: C 1315 MET cc_start: 0.8213 (tmm) cc_final: 0.7997 (tmm) REVERT: D 29 MET cc_start: 0.9311 (ptm) cc_final: 0.9110 (ptp) REVERT: D 180 MET cc_start: 0.7847 (mmt) cc_final: 0.7498 (mmp) REVERT: D 237 MET cc_start: 0.8872 (ttm) cc_final: 0.8510 (tmm) REVERT: D 400 MET cc_start: 0.9237 (mpp) cc_final: 0.9022 (pmm) REVERT: D 466 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7892 (tpt) REVERT: D 504 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8212 (mp10) REVERT: D 513 MET cc_start: 0.9041 (ttp) cc_final: 0.8757 (tpp) REVERT: D 724 MET cc_start: 0.9236 (ttm) cc_final: 0.8767 (mtp) REVERT: D 932 MET cc_start: 0.6220 (pmm) cc_final: 0.5927 (pmm) REVERT: D 1040 MET cc_start: 0.7976 (tmm) cc_final: 0.7626 (tpp) REVERT: D 1305 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.7737 (p0) REVERT: E 8 ASP cc_start: 0.9409 (OUTLIER) cc_final: 0.8928 (p0) REVERT: E 30 MET cc_start: 0.8557 (mmm) cc_final: 0.8155 (tpp) REVERT: E 58 LEU cc_start: 0.8887 (mp) cc_final: 0.8338 (tt) REVERT: F 71 MET cc_start: 0.8577 (tmm) cc_final: 0.8316 (tmm) REVERT: F 145 ASN cc_start: 0.9134 (t0) cc_final: 0.8717 (p0) REVERT: F 171 MET cc_start: 0.8244 (mmt) cc_final: 0.7951 (mmm) REVERT: F 217 GLU cc_start: 0.9318 (mt-10) cc_final: 0.8989 (tm-30) REVERT: F 438 MET cc_start: 0.4568 (mtt) cc_final: 0.4249 (tpt) REVERT: F 507 ARG cc_start: 0.5542 (OUTLIER) cc_final: 0.4981 (mmm160) REVERT: F 539 ASN cc_start: 0.8854 (OUTLIER) cc_final: 0.8636 (p0) REVERT: F 556 HIS cc_start: 0.8649 (OUTLIER) cc_final: 0.8344 (m-70) REVERT: F 592 MET cc_start: 0.7428 (tpt) cc_final: 0.7108 (tpp) REVERT: F 606 MET cc_start: -0.0771 (OUTLIER) cc_final: -0.1557 (tpp) REVERT: F 669 MET cc_start: 0.6257 (mtm) cc_final: 0.5937 (mtm) outliers start: 77 outliers final: 56 residues processed: 247 average time/residue: 0.1969 time to fit residues: 84.1120 Evaluate side-chains 234 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 168 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1019 ASN Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1305 ASP Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 472 LYS Chi-restraints excluded: chain F residue 507 ARG Chi-restraints excluded: chain F residue 539 ASN Chi-restraints excluded: chain F residue 556 HIS Chi-restraints excluded: chain F residue 606 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 47 optimal weight: 2.9990 chunk 369 optimal weight: 7.9990 chunk 169 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 233 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 392 optimal weight: 5.9990 chunk 351 optimal weight: 9.9990 chunk 267 optimal weight: 9.9990 chunk 95 optimal weight: 7.9990 chunk 336 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 ASN ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 690 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.051130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.033403 restraints weight = 271113.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.034461 restraints weight = 147955.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.035159 restraints weight = 99398.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.035644 restraints weight = 76362.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.035966 restraints weight = 64142.873| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 33922 Z= 0.211 Angle : 0.652 13.967 46096 Z= 0.329 Chirality : 0.042 0.276 5208 Planarity : 0.004 0.055 5815 Dihedral : 13.103 123.607 5272 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.54 % Favored : 96.44 % Rotamer: Outliers : 2.20 % Allowed : 15.57 % Favored : 82.23 % 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: 0.48 (0.13), residues: 4043 helix: 1.34 (0.13), residues: 1472 sheet: -0.20 (0.20), residues: 652 loop : -0.20 (0.15), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 169 TYR 0.042 0.001 TYR B 177 PHE 0.016 0.002 PHE C 514 TRP 0.011 0.001 TRP C 183 HIS 0.014 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.21 (33902) covalent geometry : angle 0.64593 / 0.33 (46066) hydrogen bonds : bond 0.04040 / 2.70 ( 1535) hydrogen bonds : angle 4.91670 / 3.38 ( 4247) metal coordination : bond 0.01044 / 0.66 ( 20) metal coordination : angle 3.56251 / 2.34 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 167 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.8936 (pmm) cc_final: 0.8306 (pmm) REVERT: A 147 GLN cc_start: 0.8822 (pt0) cc_final: 0.8526 (pp30) REVERT: A 158 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7710 (ptt180) REVERT: A 160 HIS cc_start: 0.8905 (p90) cc_final: 0.8537 (p90) REVERT: C 429 MET cc_start: 0.9584 (mpp) cc_final: 0.9338 (mpp) REVERT: C 492 MET cc_start: 0.9364 (mmt) cc_final: 0.9069 (mmt) REVERT: C 538 LEU cc_start: 0.9576 (mp) cc_final: 0.9242 (tp) REVERT: C 611 GLU cc_start: 0.9024 (tt0) cc_final: 0.8745 (tm-30) REVERT: C 704 MET cc_start: 0.8916 (mmp) cc_final: 0.8611 (mmt) REVERT: C 1094 VAL cc_start: 0.9386 (OUTLIER) cc_final: 0.9033 (p) REVERT: C 1131 MET cc_start: 0.9077 (ttt) cc_final: 0.8658 (ttt) REVERT: C 1170 MET cc_start: 0.9348 (mmm) cc_final: 0.8916 (mmm) REVERT: C 1243 MET cc_start: 0.9350 (tmm) cc_final: 0.9115 (tmm) REVERT: C 1304 MET cc_start: 0.9446 (tpp) cc_final: 0.9125 (tpp) REVERT: D 29 MET cc_start: 0.9376 (ptm) cc_final: 0.9162 (ptp) REVERT: D 400 MET cc_start: 0.9289 (mpp) cc_final: 0.9078 (pmm) REVERT: D 466 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7877 (tpt) REVERT: D 504 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8251 (mp10) REVERT: D 535 ARG cc_start: 0.9519 (OUTLIER) cc_final: 0.8764 (ptp-110) REVERT: D 625 MET cc_start: 0.9168 (tpp) cc_final: 0.8915 (tpp) REVERT: D 724 MET cc_start: 0.9319 (ttm) cc_final: 0.8824 (mtp) REVERT: D 743 MET cc_start: 0.8899 (mmm) cc_final: 0.8587 (mmm) REVERT: D 1040 MET cc_start: 0.8038 (tmm) cc_final: 0.7750 (tpp) REVERT: D 1305 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.7777 (p0) REVERT: E 8 ASP cc_start: 0.9476 (OUTLIER) cc_final: 0.9067 (p0) REVERT: E 30 MET cc_start: 0.8650 (mmm) cc_final: 0.8244 (tpp) REVERT: E 58 LEU cc_start: 0.8926 (mp) cc_final: 0.8381 (tt) REVERT: F 145 ASN cc_start: 0.9189 (t0) cc_final: 0.8777 (p0) REVERT: F 171 MET cc_start: 0.8266 (mmt) cc_final: 0.7992 (mmm) REVERT: F 438 MET cc_start: 0.4662 (mtt) cc_final: 0.4342 (tpt) REVERT: F 507 ARG cc_start: 0.5385 (OUTLIER) cc_final: 0.4842 (mmm160) REVERT: F 556 HIS cc_start: 0.8661 (OUTLIER) cc_final: 0.8354 (m-70) REVERT: F 592 MET cc_start: 0.7452 (tpt) cc_final: 0.7108 (tpp) REVERT: F 606 MET cc_start: -0.0529 (OUTLIER) cc_final: -0.0923 (tpp) REVERT: F 669 MET cc_start: 0.6591 (mtm) cc_final: 0.6013 (mtm) outliers start: 76 outliers final: 59 residues processed: 232 average time/residue: 0.1981 time to fit residues: 79.7293 Evaluate side-chains 233 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 164 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1244 HIS Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 535 ARG Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 656 GLU Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1019 ASN Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1280 VAL Chi-restraints excluded: chain D residue 1305 ASP Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 472 LYS Chi-restraints excluded: chain F residue 507 ARG Chi-restraints excluded: chain F residue 556 HIS Chi-restraints excluded: chain F residue 606 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 24 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 270 optimal weight: 2.9990 chunk 354 optimal weight: 1.9990 chunk 403 optimal weight: 10.0000 chunk 142 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 329 optimal weight: 5.9990 chunk 245 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.051621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.033826 restraints weight = 268568.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.034914 restraints weight = 145197.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.035621 restraints weight = 97200.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.036103 restraints weight = 74556.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.036404 restraints weight = 62413.240| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33922 Z= 0.152 Angle : 0.640 14.492 46096 Z= 0.317 Chirality : 0.042 0.259 5208 Planarity : 0.004 0.055 5815 Dihedral : 13.081 126.371 5270 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.84 % Favored : 97.13 % Rotamer: Outliers : 2.03 % Allowed : 15.97 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.13), residues: 4043 helix: 1.40 (0.13), residues: 1475 sheet: -0.09 (0.20), residues: 621 loop : -0.20 (0.15), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 169 TYR 0.031 0.001 TYR B 177 PHE 0.022 0.001 PHE D 629 TRP 0.012 0.001 TRP C 183 HIS 0.013 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (33902) covalent geometry : angle 0.63447 / 0.32 (46066) hydrogen bonds : bond 0.03775 / 2.54 ( 1535) hydrogen bonds : angle 4.80927 / 3.30 ( 4247) metal coordination : bond 0.00787 / 0.49 ( 20) metal coordination : angle 3.45088 / 2.28 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 168 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.8645 (mmm) cc_final: 0.8256 (mmm) REVERT: A 142 MET cc_start: 0.8917 (pmm) cc_final: 0.8253 (pmm) REVERT: A 147 GLN cc_start: 0.8790 (pt0) cc_final: 0.8477 (pp30) REVERT: A 158 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7643 (ptt180) REVERT: C 429 MET cc_start: 0.9573 (mpp) cc_final: 0.9326 (mpp) REVERT: C 492 MET cc_start: 0.9364 (mmt) cc_final: 0.9066 (mmt) REVERT: C 538 LEU cc_start: 0.9578 (mp) cc_final: 0.9233 (tp) REVERT: C 611 GLU cc_start: 0.9022 (tt0) cc_final: 0.8720 (tm-30) REVERT: C 1131 MET cc_start: 0.9090 (ttt) cc_final: 0.8658 (ttt) REVERT: C 1170 MET cc_start: 0.9342 (mmm) cc_final: 0.8912 (mmm) REVERT: C 1304 MET cc_start: 0.9422 (tpp) cc_final: 0.9085 (tpp) REVERT: D 29 MET cc_start: 0.9355 (ptm) cc_final: 0.9148 (ptp) REVERT: D 466 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7869 (tpt) REVERT: D 504 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8160 (mp10) REVERT: D 513 MET cc_start: 0.8773 (tpp) cc_final: 0.8285 (tpp) REVERT: D 625 MET cc_start: 0.9163 (tpp) cc_final: 0.8885 (tpp) REVERT: D 724 MET cc_start: 0.9286 (ttm) cc_final: 0.8767 (mtp) REVERT: D 747 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7335 (ttt) REVERT: D 822 MET cc_start: 0.8935 (tpp) cc_final: 0.8544 (tpp) REVERT: D 1040 MET cc_start: 0.8051 (tmm) cc_final: 0.7804 (tpp) REVERT: D 1305 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.7772 (p0) REVERT: D 1370 MET cc_start: 0.9172 (mmp) cc_final: 0.8902 (mmp) REVERT: E 8 ASP cc_start: 0.9447 (OUTLIER) cc_final: 0.9025 (p0) REVERT: E 30 MET cc_start: 0.8621 (mmm) cc_final: 0.8222 (tpp) REVERT: E 58 LEU cc_start: 0.8896 (mp) cc_final: 0.8335 (tt) REVERT: F 145 ASN cc_start: 0.9153 (t0) cc_final: 0.8719 (p0) REVERT: F 171 MET cc_start: 0.8266 (mmt) cc_final: 0.8002 (mmm) REVERT: F 438 MET cc_start: 0.4807 (mtt) cc_final: 0.4444 (tpt) REVERT: F 507 ARG cc_start: 0.5547 (OUTLIER) cc_final: 0.5012 (mmm160) REVERT: F 538 MET cc_start: 0.4660 (ttt) cc_final: 0.3032 (ppp) REVERT: F 556 HIS cc_start: 0.8648 (OUTLIER) cc_final: 0.8340 (m-70) REVERT: F 592 MET cc_start: 0.7425 (tpt) cc_final: 0.7072 (tpp) REVERT: F 606 MET cc_start: -0.0594 (OUTLIER) cc_final: -0.0889 (tpp) REVERT: F 669 MET cc_start: 0.6501 (mtm) cc_final: 0.6192 (mtm) outliers start: 70 outliers final: 53 residues processed: 226 average time/residue: 0.2006 time to fit residues: 78.6160 Evaluate side-chains 227 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 165 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1244 HIS Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1019 ASN Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1280 VAL Chi-restraints excluded: chain D residue 1305 ASP Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 472 LYS Chi-restraints excluded: chain F residue 507 ARG Chi-restraints excluded: chain F residue 556 HIS Chi-restraints excluded: chain F residue 606 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 298 optimal weight: 5.9990 chunk 190 optimal weight: 0.3980 chunk 66 optimal weight: 5.9990 chunk 170 optimal weight: 5.9990 chunk 375 optimal weight: 8.9990 chunk 179 optimal weight: 6.9990 chunk 289 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 chunk 368 optimal weight: 7.9990 chunk 110 optimal weight: 10.0000 chunk 132 optimal weight: 20.0000 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.051355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.033627 restraints weight = 269822.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.034709 restraints weight = 146029.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.035412 restraints weight = 97520.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.035893 restraints weight = 74823.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.036212 restraints weight = 62803.740| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 33922 Z= 0.176 Angle : 0.641 14.791 46096 Z= 0.319 Chirality : 0.042 0.246 5208 Planarity : 0.004 0.054 5815 Dihedral : 13.073 127.003 5270 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.31 % Favored : 96.66 % Rotamer: Outliers : 2.11 % Allowed : 15.86 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.13), residues: 4043 helix: 1.40 (0.13), residues: 1476 sheet: -0.16 (0.20), residues: 632 loop : -0.21 (0.15), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 169 TYR 0.050 0.001 TYR B 177 PHE 0.019 0.001 PHE D 629 TRP 0.012 0.001 TRP C 183 HIS 0.013 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.18 (33902) covalent geometry : angle 0.63549 / 0.32 (46066) hydrogen bonds : bond 0.03813 / 2.56 ( 1535) hydrogen bonds : angle 4.81945 / 3.31 ( 4247) metal coordination : bond 0.00879 / 0.56 ( 20) metal coordination : angle 3.31749 / 2.21 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8753.36 seconds wall clock time: 150 minutes 45.35 seconds (9045.35 seconds total)