Starting phenix.real_space_refine on Tue Sep 15 01:41:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gde_51263/09_2026/9gde_51263.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gde_51263/09_2026/9gde_51263.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gde_51263/09_2026/9gde_51263.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gde_51263/09_2026/9gde_51263.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gde_51263/09_2026/9gde_51263.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gde_51263/09_2026/9gde_51263.map" } resolution = 4.0 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= 0.043 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 20696 2.51 5 N 5919 2.21 5 O 6557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33400 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: 6700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 846, 6700 Classifications: {'peptide': 846} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 801} Chain breaks: 1 Chain: "N" Number of atoms: 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': 1, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 9} 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 37.978 66.291 89.871 1.00241.61 S ATOM 14658 SG CYS D 72 37.163 62.339 90.321 1.00226.22 S ATOM 14766 SG CYS D 85 35.303 64.801 91.910 1.00237.41 S ATOM 14790 SG CYS D 88 38.932 64.875 92.735 1.00236.15 S ATOM 20478 SG CYS D 814 68.652 125.464 91.051 1.00186.27 S ATOM 21043 SG CYS D 888 69.715 121.737 90.708 1.00184.10 S ATOM 21094 SG CYS D 895 68.921 123.862 87.715 1.00179.10 S ATOM 21115 SG CYS D 898 72.065 124.403 89.368 1.00182.13 S ATOM 29933 SG CYS F 599 55.252 37.979 188.124 1.00489.61 S ATOM 29953 SG CYS F 602 55.605 36.650 191.226 1.00491.85 S ATOM 30073 SG CYS F 619 58.427 38.293 190.343 1.00456.19 S ATOM 30157 SG CYS F 630 57.921 35.223 188.276 1.00441.29 S ATOM 30407 SG CYS F 662 63.429 61.359 191.132 1.00437.98 S ATOM 30429 SG CYS F 665 66.781 63.115 190.789 1.00451.54 S ATOM 30570 SG CYS F 683 65.980 60.233 188.609 1.00439.14 S ATOM 30610 SG CYS F 689 66.815 59.672 192.273 1.00445.76 S ATOM 30786 SG CYS F 711 54.059 38.381 158.313 1.00704.02 S ATOM 30810 SG CYS F 714 50.619 39.836 158.360 1.00706.19 S ATOM 30942 SG CYS F 731 52.633 40.261 161.403 1.00721.64 S ATOM 30981 SG CYS F 736 51.540 36.757 160.603 1.00717.09 S Time building chain proxies: 6.96, per 1000 atoms: 0.21 Number of scatterers: 33400 At special positions: 0 Unit cell: (152.803, 160.792, 207.732, 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 6557 8.00 N 5919 7.00 C 20696 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.78 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 70 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 602 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 619 " 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 736 " pdb="ZN ZN F1003 " - pdb=" SG CYS F 711 " Number of angles added : 30 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7556 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 61 sheets defined 41.5% alpha, 18.2% beta 22 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 3.71 Creating SS restraints... Processing helix chain 'A' and resid 34 through 51 removed outlier: 3.688A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 88 Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.125A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 51 removed outlier: 4.048A pdb=" N MET B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.952A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 160 through 164 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: 3.802A pdb=" N ARG C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 4.136A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 165 through 169 removed outlier: 3.814A pdb=" N GLY C 168 " --> pdb=" O HIS C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.921A 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 293 removed outlier: 3.813A pdb=" N ILE C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 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 482 Processing helix chain 'C' and resid 488 through 493 removed outlier: 3.682A pdb=" N MET C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 509 removed outlier: 3.589A pdb=" N SER C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 539 through 543 removed outlier: 3.549A pdb=" N ALA C 543 " --> pdb=" O ARG C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 549 removed outlier: 3.675A pdb=" N ARG C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.605A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 614 removed outlier: 3.654A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 641 removed outlier: 3.622A pdb=" N GLY C 640 " --> pdb=" O ARG C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 650 removed outlier: 3.644A pdb=" N VAL C 650 " --> pdb=" O ARG C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 667 Processing helix chain 'C' and resid 670 through 674 removed outlier: 3.609A pdb=" N ASP C 674 " --> pdb=" O LEU C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 687 removed outlier: 4.160A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 865 removed outlier: 3.569A 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 Processing helix chain 'C' and resid 1101 through 1107 removed outlier: 4.169A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1108 through 1134 removed outlier: 4.101A pdb=" N ILE C1112 " --> pdb=" O ASN C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 Processing helix chain 'C' and resid 1160 through 1164 Processing helix chain 'C' and resid 1165 through 1177 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1283 through 1293 Processing helix chain 'C' and resid 1297 through 1311 Processing helix chain 'C' and resid 1320 through 1333 Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 96 through 101 removed outlier: 3.674A pdb=" N GLU D 100 " --> pdb=" O LYS D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 119 Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.693A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 174 through 176 No H-bonds generated for 'chain 'D' and resid 174 through 176' Processing helix chain 'D' and resid 180 through 190 removed outlier: 3.834A pdb=" N GLN D 186 " --> pdb=" O ALA D 182 " (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 285 removed outlier: 3.887A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 309 removed outlier: 3.585A pdb=" N VAL D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 332 removed outlier: 3.740A pdb=" N ILE D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 370 through 388 Proline residue: D 379 - end of helix Processing helix chain 'D' and resid 393 through 403 Processing helix chain 'D' and resid 405 through 416 removed outlier: 3.815A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) 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 451 through 455 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 515 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 580 Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.816A 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 648 through 670 removed outlier: 4.081A pdb=" N GLU D 652 " --> pdb=" O GLU D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 702 Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 removed outlier: 3.627A pdb=" N ILE D 737 " --> pdb=" O SER D 733 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA D 741 " --> pdb=" O ILE D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 805 removed outlier: 4.177A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 Processing helix chain 'D' and resid 865 through 876 Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 928 removed outlier: 3.570A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Proline residue: D 926 - end of helix Processing helix chain 'D' and resid 1136 through 1147 Processing helix chain 'D' and resid 1216 through 1245 removed outlier: 7.992A pdb=" N VAL D1226 " --> pdb=" O ARG D1222 " (cutoff:3.500A) removed outlier: 8.984A pdb=" N HIS D1227 " --> pdb=" O LEU D1223 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA D1228 " --> pdb=" O ARG D1224 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL D1234 " --> pdb=" O THR D1230 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.182A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1295 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 3.786A 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: 4.113A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG D1371 " --> pdb=" O GLN D1367 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG D1372 " --> pdb=" O ASP D1368 " (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 57 removed outlier: 3.714A pdb=" N ILE E 54 " --> pdb=" O ALA E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 91 Processing helix chain 'F' and resid 10 through 22 removed outlier: 4.061A pdb=" N TYR F 20 " --> pdb=" O THR F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 72 Processing helix chain 'F' and resid 88 through 103 removed outlier: 4.336A pdb=" N VAL F 92 " --> pdb=" O GLY F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 128 Processing helix chain 'F' and resid 129 through 133 Processing helix chain 'F' and resid 143 through 153 Processing helix chain 'F' and resid 158 through 187 Proline residue: F 181 - end of helix Processing helix chain 'F' and resid 194 through 213 removed outlier: 3.572A pdb=" N VAL F 199 " --> pdb=" O ARG F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 264 Processing helix chain 'F' and resid 285 through 298 Processing helix chain 'F' and resid 300 through 315 removed outlier: 3.659A pdb=" N THR F 304 " --> pdb=" O GLY F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 343 Processing helix chain 'F' and resid 344 through 348 Processing helix chain 'F' and resid 376 through 380 Processing helix chain 'F' and resid 384 through 403 removed outlier: 4.235A pdb=" N GLN F 402 " --> pdb=" O PHE F 398 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET F 403 " --> pdb=" O VAL F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 438 removed outlier: 3.700A pdb=" N VAL F 437 " --> pdb=" O GLY F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 478 through 490 Processing helix chain 'F' and resid 496 through 507 removed outlier: 3.867A pdb=" N GLN F 505 " --> pdb=" O ILE F 501 " (cutoff:3.500A) Processing helix chain 'F' and resid 520 through 534 Processing helix chain 'F' and resid 534 through 539 Processing helix chain 'F' and resid 539 through 556 Processing helix chain 'F' and resid 559 through 580 removed outlier: 4.170A pdb=" N LYS F 580 " --> pdb=" O ASP F 576 " (cutoff:3.500A) Processing helix chain 'F' and resid 621 through 624 Processing helix chain 'F' and resid 625 through 629 Processing helix chain 'F' and resid 644 through 648 Processing helix chain 'F' and resid 649 through 659 removed outlier: 4.198A 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 20 removed outlier: 5.303A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N HIS A 23 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU A 198 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ALA A 189 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LYS A 200 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL A 187 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL A 202 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TYR A 185 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLU A 204 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE A 183 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLU A 206 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 61 removed outlier: 4.962A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (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: 4.002A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 removed outlier: 3.686A pdb=" N ALA A 175 " --> pdb=" O VAL A 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 18 removed outlier: 3.796A pdb=" N GLU B 29 " --> pdb=" O ARG B 12 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B 14 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR B 27 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ILE B 16 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LYS B 25 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N GLN B 18 " --> pdb=" O HIS B 23 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N HIS B 23 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N THR B 196 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ARG B 191 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU B 198 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA B 189 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYS B 200 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL B 187 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B 202 " --> pdb=" O TYR B 185 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR B 185 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLU B 204 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE B 183 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU B 206 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 104 removed outlier: 7.482A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 111 Processing sheet with id=AB1, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.634A pdb=" N VAL B 153 " --> pdb=" O ALA B 175 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA B 175 " --> pdb=" O VAL B 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.512A 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: 6.486A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA C 94 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLY C 125 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU C 96 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N TYR C 123 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N VAL C 98 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU C 121 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU C 100 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU C 119 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU C 102 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE C 117 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.621A 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: 3.844A 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: 4.734A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 284 through 287 removed outlier: 4.006A pdb=" N LEU C 237 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU C 240 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AB9, first strand: chain 'C' and resid 301 through 303 Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 removed outlier: 6.531A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581 removed outlier: 7.792A pdb=" N ALA C 617 " --> pdb=" O ASP C 654 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 623 through 624 Processing sheet with id=AC4, first strand: chain 'C' and resid 634 through 636 removed outlier: 3.708A pdb=" N SER C 643 " --> pdb=" O CYS C 636 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.555A 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: 5.749A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (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 1066 through 1068 removed outlier: 4.302A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1066 through 1068 Processing sheet with id=AD2, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.828A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AD4, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.799A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1244 through 1245 Processing sheet with id=AD6, first strand: chain 'C' and resid 1244 through 1245 removed outlier: 7.675A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 1335 through 1339 Processing sheet with id=AD8, first strand: chain 'D' and resid 103 through 112 removed outlier: 10.926A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 11.010A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AE1, first strand: chain 'D' and resid 253 through 254 Processing sheet with id=AE2, first strand: chain 'D' and resid 367 through 369 removed outlier: 5.594A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AE4, first strand: chain 'D' and resid 703 through 707 Processing sheet with id=AE5, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE6, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE7, first strand: chain 'D' and resid 825 through 827 removed outlier: 6.950A pdb=" N VAL D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 848 through 849 removed outlier: 6.338A pdb=" N VAL D 848 " --> pdb=" O LEU D 857 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 949 through 952 removed outlier: 7.053A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 991 through 997 removed outlier: 6.462A pdb=" N LEU D 984 " --> pdb=" O LYS D 992 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER D 994 " --> pdb=" O LEU D 982 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU D 982 " --> pdb=" O SER D 994 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LYS D 996 " --> pdb=" O THR D 980 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N THR D 980 " --> pdb=" O LYS D 996 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1028 through 1029 Processing sheet with id=AF3, first strand: chain 'D' and resid 1098 through 1100 Processing sheet with id=AF4, first strand: chain 'D' and resid 1046 through 1050 Processing sheet with id=AF5, first strand: chain 'D' and resid 1186 through 1191 Processing sheet with id=AF6, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 6.730A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 25 through 29 removed outlier: 6.781A pdb=" N LEU F 5 " --> pdb=" O TYR F 107 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 35 through 36 Processing sheet with id=AF9, first strand: chain 'F' and resid 244 through 245 removed outlier: 14.960A pdb=" N ALA F 233 " --> pdb=" O ARG F 427 " (cutoff:3.500A) removed outlier: 12.436A pdb=" N ARG F 427 " --> pdb=" O ALA F 233 " (cutoff:3.500A) removed outlier: 8.984A pdb=" N ALA F 235 " --> pdb=" O ARG F 425 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ARG F 425 " --> pdb=" O ALA F 235 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ARG F 421 " --> pdb=" O THR F 239 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ARG F 421 " --> pdb=" O ALA F 417 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ALA F 417 " --> pdb=" O ARG F 421 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LYS F 423 " --> pdb=" O VAL F 415 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL F 415 " --> pdb=" O LYS F 423 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ARG F 425 " --> pdb=" O LEU F 413 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU F 413 " --> pdb=" O ARG F 425 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ARG F 427 " --> pdb=" O THR F 411 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N THR F 411 " --> pdb=" O ARG F 427 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU F 429 " --> pdb=" O ASP F 409 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ASP F 409 " --> pdb=" O LEU F 429 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY F 416 " --> pdb=" O VAL F 268 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N VAL F 268 " --> pdb=" O GLY F 416 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP F 457 " --> pdb=" O VAL F 268 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 244 through 245 removed outlier: 4.627A pdb=" N VAL F 222 " --> pdb=" O VAL F 238 " (cutoff:3.500A) removed outlier: 9.357A pdb=" N HIS F 240 " --> pdb=" O TRP F 220 " (cutoff:3.500A) removed outlier: 12.765A pdb=" N TRP F 220 " --> pdb=" O HIS F 240 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N PHE F 219 " --> pdb=" O GLN F 468 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLN F 468 " --> pdb=" O PHE F 219 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU F 221 " --> pdb=" O PRO F 466 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ASP F 223 " --> pdb=" O LEU F 464 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU F 464 " --> pdb=" O ASP F 223 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER F 225 " --> pdb=" O VAL F 462 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 510 through 513 Processing sheet with id=AG3, first strand: chain 'F' and resid 593 through 595 removed outlier: 3.605A pdb=" N VAL F 593 " --> pdb=" O ILE F 608 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 637 through 638 removed outlier: 3.516A pdb=" N VAL F 637 " --> pdb=" O LEU F 673 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 709 through 710 Processing sheet with id=AG6, first strand: chain 'F' and resid 756 through 762 removed outlier: 3.548A pdb=" N PHE F 770 " --> pdb=" O LEU F 758 " (cutoff:3.500A) Processing sheet with id=AG7, 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: 6.890A 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) 1449 hydrogen bonds defined for protein. 4065 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 58 hydrogen bonds 116 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 10.22 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10822 1.34 - 1.46: 5344 1.46 - 1.58: 17508 1.58 - 1.70: 128 1.70 - 1.82: 244 Bond restraints: 34046 Sorted by residual: bond pdb=" O3' DT N 13 " pdb=" P DT N 14 " ideal model delta sigma weight residual 1.607 1.669 -0.062 1.20e-02 6.94e+03 2.66e+01 bond pdb=" N VAL F 215 " pdb=" CA VAL F 215 " ideal model delta sigma weight residual 1.456 1.495 -0.038 8.70e-03 1.32e+04 1.95e+01 bond pdb=" O3' DC T 14 " pdb=" P DC T 15 " ideal model delta sigma weight residual 1.607 1.655 -0.048 1.20e-02 6.94e+03 1.57e+01 bond pdb=" O3' DT N 18 " pdb=" P DT N 19 " ideal model delta sigma weight residual 1.607 1.654 -0.047 1.20e-02 6.94e+03 1.53e+01 bond pdb=" N ARG F 133 " pdb=" CA ARG F 133 " ideal model delta sigma weight residual 1.455 1.500 -0.045 1.25e-02 6.40e+03 1.28e+01 ... (remaining 34041 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.55: 45985 3.55 - 7.10: 257 7.10 - 10.64: 13 10.64 - 14.19: 1 14.19 - 17.74: 3 Bond angle restraints: 46259 Sorted by residual: angle pdb=" C3' DT N 15 " pdb=" O3' DT N 15 " pdb=" P DC N 16 " ideal model delta sigma weight residual 119.70 104.43 15.27 1.20e+00 6.94e-01 1.62e+02 angle pdb=" C3' U R 4 " pdb=" O3' U R 4 " pdb=" P C R 5 " ideal model delta sigma weight residual 119.70 128.42 -8.72 1.20e+00 6.94e-01 5.28e+01 angle pdb=" C3' DT N 13 " pdb=" O3' DT N 13 " pdb=" P DT N 14 " ideal model delta sigma weight residual 119.70 127.51 -7.81 1.20e+00 6.94e-01 4.23e+01 angle pdb=" N PRO F 755 " pdb=" CA PRO F 755 " pdb=" C PRO F 755 " ideal model delta sigma weight residual 110.80 101.65 9.15 1.51e+00 4.39e-01 3.67e+01 angle pdb=" C4' DT N 18 " pdb=" O4' DT N 18 " pdb=" C1' DT N 18 " ideal model delta sigma weight residual 110.10 104.13 5.97 1.00e+00 1.00e+00 3.57e+01 ... (remaining 46254 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.47: 19912 29.47 - 58.94: 848 58.94 - 88.41: 89 88.41 - 117.89: 0 117.89 - 147.36: 2 Dihedral angle restraints: 20851 sinusoidal: 9106 harmonic: 11745 Sorted by residual: dihedral pdb=" CA GLU F 463 " pdb=" C GLU F 463 " pdb=" N LEU F 464 " pdb=" CA LEU F 464 " ideal model delta harmonic sigma weight residual -180.00 -151.12 -28.88 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA THR F 460 " pdb=" C THR F 460 " pdb=" N LEU F 461 " pdb=" CA LEU F 461 " ideal model delta harmonic sigma weight residual -180.00 -151.43 -28.57 0 5.00e+00 4.00e-02 3.27e+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 -151.75 -28.25 0 5.00e+00 4.00e-02 3.19e+01 ... (remaining 20848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 5070 0.110 - 0.220: 144 0.220 - 0.329: 7 0.329 - 0.439: 3 0.439 - 0.549: 2 Chirality restraints: 5226 Sorted by residual: chirality pdb=" C3' DT N 13 " pdb=" C4' DT N 13 " pdb=" O3' DT N 13 " pdb=" C2' DT N 13 " both_signs ideal model delta sigma weight residual False -2.73 -2.18 -0.55 2.00e-01 2.50e+01 7.53e+00 chirality pdb=" C3' U R 4 " pdb=" C4' U R 4 " pdb=" O3' U R 4 " pdb=" C2' U R 4 " both_signs ideal model delta sigma weight residual False -2.48 -2.03 -0.44 2.00e-01 2.50e+01 4.91e+00 chirality pdb=" C4' DT N 18 " pdb=" C5' DT N 18 " pdb=" O4' DT N 18 " pdb=" C3' DT N 18 " both_signs ideal model delta sigma weight residual False -2.53 -2.10 -0.43 2.00e-01 2.50e+01 4.69e+00 ... (remaining 5223 not shown) Planarity restraints: 5844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA N 17 " 0.059 2.00e-02 2.50e+03 3.26e-02 2.92e+01 pdb=" N9 DA N 17 " -0.066 2.00e-02 2.50e+03 pdb=" C8 DA N 17 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DA N 17 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DA N 17 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA N 17 " 0.051 2.00e-02 2.50e+03 pdb=" N6 DA N 17 " 0.001 2.00e-02 2.50e+03 pdb=" N1 DA N 17 " -0.023 2.00e-02 2.50e+03 pdb=" C2 DA N 17 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DA N 17 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DA N 17 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 122 " -0.044 2.00e-02 2.50e+03 3.33e-02 1.66e+01 pdb=" CG HIS F 122 " 0.052 2.00e-02 2.50e+03 pdb=" ND1 HIS F 122 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 HIS F 122 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 HIS F 122 " -0.028 2.00e-02 2.50e+03 pdb=" NE2 HIS F 122 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG T 21 " 0.014 2.00e-02 2.50e+03 2.26e-02 1.54e+01 pdb=" N9 DG T 21 " 0.011 2.00e-02 2.50e+03 pdb=" C8 DG T 21 " -0.045 2.00e-02 2.50e+03 pdb=" N7 DG T 21 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DG T 21 " 0.023 2.00e-02 2.50e+03 pdb=" C6 DG T 21 " 0.038 2.00e-02 2.50e+03 pdb=" O6 DG T 21 " 0.001 2.00e-02 2.50e+03 pdb=" N1 DG T 21 " -0.043 2.00e-02 2.50e+03 pdb=" C2 DG T 21 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG T 21 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DG T 21 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DG T 21 " 0.001 2.00e-02 2.50e+03 ... (remaining 5841 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 148 2.42 - 3.04: 21643 3.04 - 3.66: 52734 3.66 - 4.28: 74447 4.28 - 4.90: 120730 Nonbonded interactions: 269702 Sorted by model distance: nonbonded pdb=" NH2 ARG F 507 " pdb=" OP2 DA N 17 " model vdw 1.802 3.120 nonbonded pdb=" NH2 ARG F 321 " pdb=" OP2 DT N 19 " model vdw 1.875 3.120 nonbonded pdb=" NH1 ARG D 133 " pdb=" O3' DG N 42 " model vdw 2.051 3.120 nonbonded pdb=" OH TYR D 679 " pdb=" O ILE D 754 " model vdw 2.102 3.040 nonbonded pdb=" NH2 ARG F 529 " pdb=" OE1 GLN F 591 " model vdw 2.118 3.120 ... (remaining 269697 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: 2.950 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: 0.090 Process input model: 39.910 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.208 34066 Z= 0.310 Angle : 0.792 18.775 46289 Z= 0.472 Chirality : 0.049 0.549 5226 Planarity : 0.006 0.078 5844 Dihedral : 15.506 147.357 13295 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.22 % Favored : 96.75 % Rotamer: Outliers : 0.63 % Allowed : 11.38 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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: -0.11 (0.13), residues: 4066 helix: 0.45 (0.13), residues: 1456 sheet: 0.11 (0.20), residues: 621 loop : -0.42 (0.14), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 833 TYR 0.020 0.002 TYR D 795 PHE 0.035 0.002 PHE F 139 TRP 0.020 0.002 TRP F 76 HIS 0.009 0.001 HIS F 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.31 (34046) covalent geometry : angle 0.77245 / 0.47 (46259) hydrogen bonds : bond 0.14934 / 10.24 ( 1499) hydrogen bonds : angle 6.90654 / 4.69 ( 4181) metal coordination : bond 0.06589 / 3.32 ( 20) metal coordination : angle 6.93954 / 4.34 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 350 time to evaluate : 1.267 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 142 MET cc_start: 0.8921 (mtt) cc_final: 0.8625 (mtp) REVERT: A 147 GLN cc_start: 0.9295 (mm-40) cc_final: 0.8657 (mp10) REVERT: B 33 ARG cc_start: 0.9239 (mmm-85) cc_final: 0.8914 (mmp80) REVERT: B 51 MET cc_start: 0.9341 (tpp) cc_final: 0.9135 (tpp) REVERT: B 200 LYS cc_start: 0.9566 (ttpp) cc_final: 0.9127 (ttpp) REVERT: C 146 VAL cc_start: 0.9407 (t) cc_final: 0.9173 (p) REVERT: C 378 ARG cc_start: 0.9087 (tpp-160) cc_final: 0.8680 (ttt180) REVERT: C 488 MET cc_start: 0.8843 (tmm) cc_final: 0.8613 (tmm) REVERT: C 565 GLU cc_start: 0.9168 (tm-30) cc_final: 0.8954 (tm-30) REVERT: C 685 MET cc_start: 0.9256 (ppp) cc_final: 0.9007 (ppp) REVERT: C 686 GLN cc_start: 0.9505 (tt0) cc_final: 0.8851 (mt0) REVERT: C 814 ASP cc_start: 0.8512 (m-30) cc_final: 0.7923 (t0) REVERT: C 1232 MET cc_start: 0.9532 (mmm) cc_final: 0.9276 (mmm) REVERT: C 1273 MET cc_start: 0.9379 (mmt) cc_final: 0.8982 (mmm) REVERT: C 1274 GLU cc_start: 0.9256 (mp0) cc_final: 0.8886 (mp0) REVERT: C 1290 MET cc_start: 0.9548 (tpp) cc_final: 0.9237 (mpp) REVERT: C 1304 MET cc_start: 0.9299 (tmm) cc_final: 0.9027 (tmm) REVERT: C 1329 GLU cc_start: 0.9432 (tp30) cc_final: 0.8879 (tp30) REVERT: D 151 MET cc_start: 0.9056 (mmm) cc_final: 0.8576 (mpp) REVERT: D 298 MET cc_start: 0.9051 (ttp) cc_final: 0.8643 (mtp) REVERT: D 304 ASP cc_start: 0.9356 (m-30) cc_final: 0.8947 (m-30) REVERT: D 330 MET cc_start: 0.9197 (ttm) cc_final: 0.8645 (tpp) REVERT: D 372 MET cc_start: 0.9099 (mtp) cc_final: 0.8893 (mtt) REVERT: D 458 ASN cc_start: 0.9630 (t0) cc_final: 0.9358 (t0) REVERT: D 484 MET cc_start: 0.9387 (mpp) cc_final: 0.8890 (mpp) REVERT: D 485 MET cc_start: 0.9168 (mmm) cc_final: 0.8829 (mmm) REVERT: D 513 MET cc_start: 0.9676 (ttp) cc_final: 0.9389 (ttp) REVERT: D 725 MET cc_start: 0.9418 (mtp) cc_final: 0.8879 (tmm) REVERT: D 822 MET cc_start: 0.9445 (mmm) cc_final: 0.9018 (mmm) REVERT: D 925 GLU cc_start: 0.9371 (tt0) cc_final: 0.9089 (tm-30) REVERT: D 932 MET cc_start: 0.8786 (ppp) cc_final: 0.8434 (ppp) REVERT: E 30 MET cc_start: 0.9204 (tpt) cc_final: 0.8872 (tpt) REVERT: F 276 THR cc_start: 0.8541 (OUTLIER) cc_final: 0.8335 (p) REVERT: F 305 MET cc_start: 0.9017 (mmm) cc_final: 0.8503 (mmm) REVERT: F 320 MET cc_start: 0.9144 (pmm) cc_final: 0.8554 (pmm) REVERT: F 329 GLN cc_start: 0.9744 (mm-40) cc_final: 0.9460 (tp-100) REVERT: F 403 MET cc_start: 0.9005 (mtp) cc_final: 0.8762 (mtp) REVERT: F 646 LEU cc_start: 0.8895 (tp) cc_final: 0.8619 (mt) REVERT: F 718 MET cc_start: 0.2731 (ttm) cc_final: 0.2230 (mtm) REVERT: F 722 MET cc_start: 0.0112 (mtp) cc_final: -0.0385 (ptt) outliers start: 22 outliers final: 5 residues processed: 368 average time/residue: 0.2174 time to fit residues: 128.6071 Evaluate side-chains 226 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 220 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain F residue 276 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.0370 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 50.0000 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 overall best weight: 5.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN A 23 HIS A 41 ASN A 75 GLN B 37 HIS ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN C 450 ASN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN C 659 GLN ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1256 GLN C1268 GLN C1288 GLN ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN D 606 ASN ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 921 GLN D 951 GLN D1244 GLN D1279 GLN E 29 GLN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN F 77 HIS F 149 GLN F 360 ASN F 681 HIS F 738 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.052666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.034926 restraints weight = 261106.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.036117 restraints weight = 146773.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.036909 restraints weight = 99371.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.037453 restraints weight = 75755.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.037810 restraints weight = 62910.785| |-----------------------------------------------------------------------------| r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 34066 Z= 0.225 Angle : 0.704 10.414 46289 Z= 0.366 Chirality : 0.044 0.213 5226 Planarity : 0.005 0.049 5844 Dihedral : 13.352 157.134 5279 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.30 % Allowed : 13.39 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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: 0.17 (0.13), residues: 4066 helix: 0.86 (0.13), residues: 1484 sheet: -0.05 (0.20), residues: 592 loop : -0.32 (0.14), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 371 TYR 0.024 0.002 TYR C1229 PHE 0.026 0.002 PHE D 719 TRP 0.012 0.001 TRP D 580 HIS 0.017 0.002 HIS F 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.23 (34046) covalent geometry : angle 0.69295 / 0.37 (46259) hydrogen bonds : bond 0.05075 / 3.42 ( 1499) hydrogen bonds : angle 5.58016 / 3.83 ( 4181) metal coordination : bond 0.01325 / 0.84 ( 20) metal coordination : angle 4.85989 / 3.24 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 230 time to evaluate : 1.018 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: 0.8893 (mtt) cc_final: 0.8623 (mtm) REVERT: A 147 GLN cc_start: 0.9171 (mm-40) cc_final: 0.8691 (mm110) REVERT: B 51 MET cc_start: 0.9400 (tpp) cc_final: 0.9157 (tpp) REVERT: B 142 MET cc_start: 0.9476 (pmm) cc_final: 0.9164 (pmm) REVERT: C 378 ARG cc_start: 0.8988 (tpp-160) cc_final: 0.8609 (ttt180) REVERT: C 429 MET cc_start: 0.9442 (mmm) cc_final: 0.9188 (mmm) REVERT: C 623 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8984 (mt) REVERT: C 653 MET cc_start: 0.9024 (tpp) cc_final: 0.8815 (tpt) REVERT: C 681 MET cc_start: 0.8958 (ptp) cc_final: 0.8740 (ptp) REVERT: C 685 MET cc_start: 0.9302 (ppp) cc_final: 0.9058 (ppp) REVERT: C 686 GLN cc_start: 0.9511 (tt0) cc_final: 0.8879 (mt0) REVERT: C 704 MET cc_start: 0.9039 (mmm) cc_final: 0.8653 (mmm) REVERT: C 814 ASP cc_start: 0.8663 (m-30) cc_final: 0.8053 (t0) REVERT: C 865 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9114 (mt) REVERT: C 1274 GLU cc_start: 0.9159 (mp0) cc_final: 0.8728 (mp0) REVERT: C 1290 MET cc_start: 0.9622 (tpp) cc_final: 0.9292 (mmm) REVERT: C 1304 MET cc_start: 0.9309 (tmm) cc_final: 0.9047 (tmm) REVERT: C 1329 GLU cc_start: 0.9409 (tp30) cc_final: 0.8779 (tp30) REVERT: D 151 MET cc_start: 0.9116 (mmm) cc_final: 0.8687 (mpp) REVERT: D 298 MET cc_start: 0.9053 (ttp) cc_final: 0.8599 (mtp) REVERT: D 304 ASP cc_start: 0.9253 (m-30) cc_final: 0.8876 (m-30) REVERT: D 330 MET cc_start: 0.9280 (OUTLIER) cc_final: 0.8879 (tpp) REVERT: D 366 CYS cc_start: 0.9292 (p) cc_final: 0.8603 (p) REVERT: D 458 ASN cc_start: 0.9624 (t0) cc_final: 0.9362 (t0) REVERT: D 484 MET cc_start: 0.9246 (mpp) cc_final: 0.9043 (mpp) REVERT: D 485 MET cc_start: 0.9189 (mmm) cc_final: 0.8843 (mmm) REVERT: D 606 ASN cc_start: 0.9496 (t0) cc_final: 0.9238 (t0) REVERT: D 743 MET cc_start: 0.8586 (mmm) cc_final: 0.7970 (mmm) REVERT: D 822 MET cc_start: 0.9435 (mmm) cc_final: 0.9141 (mmm) REVERT: D 915 ILE cc_start: 0.9798 (pt) cc_final: 0.9470 (mm) REVERT: D 925 GLU cc_start: 0.9371 (tt0) cc_final: 0.9039 (tm-30) REVERT: D 932 MET cc_start: 0.8912 (ppp) cc_final: 0.8444 (ppp) REVERT: D 1169 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8597 (p) REVERT: E 15 ASN cc_start: 0.8350 (t0) cc_final: 0.8011 (t0) REVERT: E 30 MET cc_start: 0.9199 (tpt) cc_final: 0.8898 (tpt) REVERT: F 305 MET cc_start: 0.9079 (mmm) cc_final: 0.8423 (mmm) REVERT: F 320 MET cc_start: 0.9091 (pmm) cc_final: 0.8340 (pmm) REVERT: F 329 GLN cc_start: 0.9763 (mm-40) cc_final: 0.9442 (tp-100) REVERT: F 403 MET cc_start: 0.8972 (mtp) cc_final: 0.8665 (mtp) REVERT: F 606 MET cc_start: 0.5983 (ttt) cc_final: 0.4561 (mmm) REVERT: F 646 LEU cc_start: 0.8891 (tp) cc_final: 0.8644 (mt) REVERT: F 718 MET cc_start: 0.3688 (ttm) cc_final: 0.3443 (ttp) REVERT: F 729 MET cc_start: 0.6790 (tpp) cc_final: 0.6266 (tpp) outliers start: 80 outliers final: 34 residues processed: 296 average time/residue: 0.1904 time to fit residues: 95.7209 Evaluate side-chains 242 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 204 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 1004 ASP Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 1093 THR Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1347 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain F residue 861 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 274 optimal weight: 20.0000 chunk 344 optimal weight: 8.9990 chunk 282 optimal weight: 2.9990 chunk 118 optimal weight: 20.0000 chunk 179 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 290 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 220 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS B 103 ASN B 227 GLN ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN D 951 GLN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN F 719 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.052555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.034691 restraints weight = 263951.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.035891 restraints weight = 147181.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.036693 restraints weight = 99373.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.037249 restraints weight = 75910.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.037581 restraints weight = 63129.579| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 34066 Z= 0.169 Angle : 0.625 10.206 46289 Z= 0.325 Chirality : 0.043 0.275 5226 Planarity : 0.004 0.053 5844 Dihedral : 13.214 154.879 5278 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.71 % Allowed : 13.48 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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: 0.30 (0.13), residues: 4066 helix: 1.04 (0.13), residues: 1481 sheet: -0.05 (0.20), residues: 589 loop : -0.28 (0.14), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 339 TYR 0.022 0.001 TYR F 408 PHE 0.012 0.001 PHE C 464 TRP 0.010 0.001 TRP D 115 HIS 0.007 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 (34046) covalent geometry : angle 0.61520 / 0.32 (46259) hydrogen bonds : bond 0.04295 / 2.91 ( 1499) hydrogen bonds : angle 5.26503 / 3.62 ( 4181) metal coordination : bond 0.00755 / 0.48 ( 20) metal coordination : angle 4.30151 / 2.84 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 210 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.8876 (mtt) cc_final: 0.8548 (mtm) REVERT: A 147 GLN cc_start: 0.9144 (mm-40) cc_final: 0.8866 (mm110) REVERT: A 205 MET cc_start: 0.8621 (pmm) cc_final: 0.8021 (pmm) REVERT: B 35 PHE cc_start: 0.9265 (m-80) cc_final: 0.9051 (m-80) REVERT: B 51 MET cc_start: 0.9421 (tpp) cc_final: 0.9180 (tpp) REVERT: C 378 ARG cc_start: 0.8996 (tpp-160) cc_final: 0.8677 (ttt180) REVERT: C 429 MET cc_start: 0.9474 (mmm) cc_final: 0.9179 (mmm) REVERT: C 623 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8971 (mt) REVERT: C 685 MET cc_start: 0.9309 (ppp) cc_final: 0.8941 (ppp) REVERT: C 686 GLN cc_start: 0.9486 (tt0) cc_final: 0.8971 (mt0) REVERT: C 814 ASP cc_start: 0.8716 (m-30) cc_final: 0.8021 (t0) REVERT: C 865 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9122 (mt) REVERT: C 1107 MET cc_start: 0.9533 (mpp) cc_final: 0.9317 (mpp) REVERT: C 1274 GLU cc_start: 0.9107 (mp0) cc_final: 0.8756 (mp0) REVERT: C 1290 MET cc_start: 0.9620 (tpp) cc_final: 0.9311 (mmm) REVERT: C 1304 MET cc_start: 0.9283 (tmm) cc_final: 0.9016 (tmm) REVERT: C 1329 GLU cc_start: 0.9385 (tp30) cc_final: 0.8686 (tp30) REVERT: C 1332 SER cc_start: 0.9722 (OUTLIER) cc_final: 0.9496 (p) REVERT: D 151 MET cc_start: 0.9117 (mmm) cc_final: 0.8697 (mpp) REVERT: D 298 MET cc_start: 0.9157 (ttp) cc_final: 0.8678 (mtp) REVERT: D 304 ASP cc_start: 0.9218 (m-30) cc_final: 0.8849 (m-30) REVERT: D 330 MET cc_start: 0.9225 (ttm) cc_final: 0.8880 (tpp) REVERT: D 366 CYS cc_start: 0.9227 (p) cc_final: 0.8832 (p) REVERT: D 400 MET cc_start: 0.9501 (mtm) cc_final: 0.9254 (mpp) REVERT: D 458 ASN cc_start: 0.9621 (t0) cc_final: 0.9379 (t0) REVERT: D 485 MET cc_start: 0.9175 (mmm) cc_final: 0.8801 (mmm) REVERT: D 513 MET cc_start: 0.9526 (OUTLIER) cc_final: 0.9302 (ttp) REVERT: D 606 ASN cc_start: 0.9451 (t0) cc_final: 0.9175 (t0) REVERT: D 743 MET cc_start: 0.8511 (mmm) cc_final: 0.8237 (tpp) REVERT: D 747 MET cc_start: 0.8931 (pmm) cc_final: 0.8222 (ppp) REVERT: D 915 ILE cc_start: 0.9796 (pt) cc_final: 0.9219 (mp) REVERT: D 925 GLU cc_start: 0.9345 (tt0) cc_final: 0.9003 (tm-30) REVERT: D 932 MET cc_start: 0.8789 (ppp) cc_final: 0.8318 (ppp) REVERT: D 1169 THR cc_start: 0.8904 (OUTLIER) cc_final: 0.8700 (p) REVERT: E 30 MET cc_start: 0.9214 (tpt) cc_final: 0.8988 (tpt) REVERT: F 305 MET cc_start: 0.9085 (mmm) cc_final: 0.8409 (mmm) REVERT: F 320 MET cc_start: 0.9081 (pmm) cc_final: 0.8303 (pmm) REVERT: F 329 GLN cc_start: 0.9771 (mm-40) cc_final: 0.9418 (tp-100) REVERT: F 383 MET cc_start: 0.5467 (mmm) cc_final: 0.5091 (mmm) REVERT: F 606 MET cc_start: 0.5555 (ttt) cc_final: 0.4477 (mmm) REVERT: F 646 LEU cc_start: 0.8871 (tp) cc_final: 0.8642 (mt) REVERT: F 718 MET cc_start: 0.4290 (ttm) cc_final: 0.3780 (ttp) REVERT: F 729 MET cc_start: 0.6929 (tpp) cc_final: 0.6424 (tpp) outliers start: 94 outliers final: 47 residues processed: 286 average time/residue: 0.1826 time to fit residues: 91.4871 Evaluate side-chains 247 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 195 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 1004 ASP Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1347 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 307 MET Chi-restraints excluded: chain F residue 472 LYS Chi-restraints excluded: chain F residue 861 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 218 optimal weight: 7.9990 chunk 43 optimal weight: 20.0000 chunk 186 optimal weight: 7.9990 chunk 242 optimal weight: 4.9990 chunk 208 optimal weight: 3.9990 chunk 258 optimal weight: 0.8980 chunk 268 optimal weight: 10.0000 chunk 308 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 264 optimal weight: 0.0270 chunk 248 optimal weight: 9.9990 overall best weight: 2.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.052601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.034837 restraints weight = 263322.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.036012 restraints weight = 148313.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.036796 restraints weight = 100773.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.037357 restraints weight = 77460.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.037706 restraints weight = 64483.109| |-----------------------------------------------------------------------------| r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 34066 Z= 0.141 Angle : 0.606 9.780 46289 Z= 0.311 Chirality : 0.043 0.336 5226 Planarity : 0.004 0.064 5844 Dihedral : 13.123 156.168 5278 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.68 % Allowed : 14.49 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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: 0.37 (0.13), residues: 4066 helix: 1.14 (0.13), residues: 1481 sheet: -0.10 (0.20), residues: 596 loop : -0.24 (0.14), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 371 TYR 0.018 0.001 TYR F 408 PHE 0.012 0.001 PHE D 116 TRP 0.009 0.001 TRP D 580 HIS 0.024 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (34046) covalent geometry : angle 0.59847 / 0.31 (46259) hydrogen bonds : bond 0.03949 / 2.67 ( 1499) hydrogen bonds : angle 5.08036 / 3.48 ( 4181) metal coordination : bond 0.00619 / 0.40 ( 20) metal coordination : angle 3.84759 / 2.54 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 206 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.8797 (mtt) cc_final: 0.8497 (mtm) REVERT: A 147 GLN cc_start: 0.9112 (mm-40) cc_final: 0.8700 (mp10) REVERT: A 205 MET cc_start: 0.8617 (pmm) cc_final: 0.7954 (pmm) REVERT: B 35 PHE cc_start: 0.9268 (m-80) cc_final: 0.8897 (m-80) REVERT: B 37 HIS cc_start: 0.8871 (OUTLIER) cc_final: 0.8649 (t-90) REVERT: B 142 MET cc_start: 0.9358 (pmm) cc_final: 0.8974 (pmm) REVERT: C 378 ARG cc_start: 0.8890 (tpp-160) cc_final: 0.8672 (ttt180) REVERT: C 429 MET cc_start: 0.9473 (mmm) cc_final: 0.9155 (mmm) REVERT: C 623 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8950 (mt) REVERT: C 685 MET cc_start: 0.9161 (ppp) cc_final: 0.8861 (ppp) REVERT: C 686 GLN cc_start: 0.9449 (tt0) cc_final: 0.8979 (mt0) REVERT: C 697 LYS cc_start: 0.9513 (OUTLIER) cc_final: 0.9008 (ptmm) REVERT: C 865 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9135 (mt) REVERT: C 1066 MET cc_start: 0.8373 (tmm) cc_final: 0.7877 (tmm) REVERT: C 1107 MET cc_start: 0.9554 (mpp) cc_final: 0.9284 (mpp) REVERT: C 1170 MET cc_start: 0.9413 (mmp) cc_final: 0.8978 (mmm) REVERT: C 1230 MET cc_start: 0.8507 (tpt) cc_final: 0.7971 (tpt) REVERT: C 1274 GLU cc_start: 0.9091 (mp0) cc_final: 0.8732 (mp0) REVERT: C 1290 MET cc_start: 0.9612 (tpp) cc_final: 0.9185 (mmm) REVERT: C 1304 MET cc_start: 0.9223 (tmm) cc_final: 0.8959 (tmm) REVERT: C 1329 GLU cc_start: 0.9359 (tp30) cc_final: 0.8737 (tp30) REVERT: D 151 MET cc_start: 0.9116 (mmm) cc_final: 0.8701 (mpp) REVERT: D 298 MET cc_start: 0.9177 (ttp) cc_final: 0.8697 (mtp) REVERT: D 304 ASP cc_start: 0.9174 (m-30) cc_final: 0.8818 (m-30) REVERT: D 330 MET cc_start: 0.9241 (OUTLIER) cc_final: 0.8897 (tpp) REVERT: D 458 ASN cc_start: 0.9558 (t0) cc_final: 0.9310 (t0) REVERT: D 484 MET cc_start: 0.8929 (mpp) cc_final: 0.8663 (mpp) REVERT: D 541 LEU cc_start: 0.9536 (OUTLIER) cc_final: 0.9283 (tp) REVERT: D 606 ASN cc_start: 0.9376 (t0) cc_final: 0.9051 (t0) REVERT: D 743 MET cc_start: 0.8433 (mmm) cc_final: 0.7857 (mmm) REVERT: D 747 MET cc_start: 0.8833 (pmm) cc_final: 0.8170 (ppp) REVERT: D 915 ILE cc_start: 0.9838 (pt) cc_final: 0.9442 (mp) REVERT: D 925 GLU cc_start: 0.9304 (tt0) cc_final: 0.8996 (tm-30) REVERT: D 932 MET cc_start: 0.8728 (ppp) cc_final: 0.8226 (ppp) REVERT: D 1169 THR cc_start: 0.8840 (OUTLIER) cc_final: 0.8615 (p) REVERT: F 305 MET cc_start: 0.9075 (mmm) cc_final: 0.8413 (mmm) REVERT: F 320 MET cc_start: 0.9104 (pmm) cc_final: 0.8383 (pmm) REVERT: F 329 GLN cc_start: 0.9763 (mm-40) cc_final: 0.9409 (tp-100) REVERT: F 606 MET cc_start: 0.5583 (ttt) cc_final: 0.4621 (mmm) REVERT: F 646 LEU cc_start: 0.8834 (tp) cc_final: 0.8606 (mt) outliers start: 93 outliers final: 52 residues processed: 277 average time/residue: 0.1812 time to fit residues: 87.1963 Evaluate side-chains 259 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 200 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 1004 ASP Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain D residue 1347 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 307 MET Chi-restraints excluded: chain F residue 861 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 383 optimal weight: 0.5980 chunk 330 optimal weight: 20.0000 chunk 334 optimal weight: 10.0000 chunk 218 optimal weight: 7.9990 chunk 16 optimal weight: 30.0000 chunk 142 optimal weight: 8.9990 chunk 267 optimal weight: 4.9990 chunk 227 optimal weight: 20.0000 chunk 314 optimal weight: 0.7980 chunk 380 optimal weight: 9.9990 chunk 317 optimal weight: 4.9990 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN C 463 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN C1111 GLN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 HIS ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.051873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.034186 restraints weight = 265942.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.035349 restraints weight = 148664.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.036120 restraints weight = 100875.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.036669 restraints weight = 77291.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.036998 restraints weight = 64386.350| |-----------------------------------------------------------------------------| r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 34066 Z= 0.170 Angle : 0.614 13.333 46289 Z= 0.315 Chirality : 0.042 0.350 5226 Planarity : 0.004 0.051 5844 Dihedral : 13.104 157.690 5278 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.71 % Allowed : 15.21 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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: 0.37 (0.13), residues: 4066 helix: 1.17 (0.13), residues: 1481 sheet: -0.10 (0.20), residues: 604 loop : -0.27 (0.14), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 371 TYR 0.022 0.001 TYR D 631 PHE 0.019 0.001 PHE D 629 TRP 0.009 0.001 TRP D 580 HIS 0.014 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 (34046) covalent geometry : angle 0.60672 / 0.31 (46259) hydrogen bonds : bond 0.03901 / 2.65 ( 1499) hydrogen bonds : angle 5.03392 / 3.46 ( 4181) metal coordination : bond 0.00781 / 0.51 ( 20) metal coordination : angle 3.64010 / 2.41 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 202 time to evaluate : 1.372 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 75 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8710 (pp30) REVERT: A 142 MET cc_start: 0.8899 (mtt) cc_final: 0.8595 (mtm) REVERT: A 147 GLN cc_start: 0.9111 (mm-40) cc_final: 0.8789 (mm110) REVERT: B 35 PHE cc_start: 0.9228 (m-80) cc_final: 0.8933 (m-80) REVERT: C 429 MET cc_start: 0.9510 (mmm) cc_final: 0.9184 (mmm) REVERT: C 623 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8973 (mt) REVERT: C 685 MET cc_start: 0.9208 (ppp) cc_final: 0.8883 (ppp) REVERT: C 686 GLN cc_start: 0.9475 (tt0) cc_final: 0.9122 (mt0) REVERT: C 697 LYS cc_start: 0.9537 (OUTLIER) cc_final: 0.8989 (ptmm) REVERT: C 789 THR cc_start: 0.9641 (OUTLIER) cc_final: 0.9170 (p) REVERT: C 805 MET cc_start: 0.8637 (tmm) cc_final: 0.8372 (tmm) REVERT: C 865 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9114 (mt) REVERT: C 1107 MET cc_start: 0.9564 (mpp) cc_final: 0.9319 (mpp) REVERT: C 1230 MET cc_start: 0.8779 (tpt) cc_final: 0.8274 (tpt) REVERT: C 1243 MET cc_start: 0.9242 (tmm) cc_final: 0.8897 (tmm) REVERT: C 1274 GLU cc_start: 0.9124 (mp0) cc_final: 0.8754 (mp0) REVERT: C 1290 MET cc_start: 0.9602 (tpp) cc_final: 0.9254 (mpp) REVERT: C 1304 MET cc_start: 0.9281 (tmm) cc_final: 0.9012 (tmm) REVERT: C 1319 MET cc_start: 0.8971 (tpp) cc_final: 0.8728 (tpp) REVERT: C 1329 GLU cc_start: 0.9400 (tp30) cc_final: 0.8686 (tp30) REVERT: C 1332 SER cc_start: 0.9721 (OUTLIER) cc_final: 0.9478 (p) REVERT: D 151 MET cc_start: 0.9141 (mmm) cc_final: 0.8749 (mpp) REVERT: D 189 LEU cc_start: 0.9864 (OUTLIER) cc_final: 0.9659 (mt) REVERT: D 298 MET cc_start: 0.9216 (ttp) cc_final: 0.8750 (mtp) REVERT: D 304 ASP cc_start: 0.9175 (m-30) cc_final: 0.8822 (m-30) REVERT: D 330 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.8846 (tpp) REVERT: D 458 ASN cc_start: 0.9623 (t0) cc_final: 0.9290 (t0) REVERT: D 466 MET cc_start: 0.9169 (ptm) cc_final: 0.8835 (ptm) REVERT: D 484 MET cc_start: 0.9106 (mpp) cc_final: 0.8742 (mpp) REVERT: D 485 MET cc_start: 0.8852 (tpp) cc_final: 0.8440 (tpp) REVERT: D 541 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9313 (tp) REVERT: D 606 ASN cc_start: 0.9414 (t0) cc_final: 0.9112 (t0) REVERT: D 747 MET cc_start: 0.8888 (pmm) cc_final: 0.8588 (ppp) REVERT: D 772 TYR cc_start: 0.9353 (t80) cc_final: 0.9021 (t80) REVERT: D 821 MET cc_start: 0.9048 (tpp) cc_final: 0.8705 (tpp) REVERT: D 915 ILE cc_start: 0.9845 (pt) cc_final: 0.9430 (mp) REVERT: D 925 GLU cc_start: 0.9345 (tt0) cc_final: 0.8976 (tm-30) REVERT: D 932 MET cc_start: 0.8741 (ppp) cc_final: 0.8251 (ppp) REVERT: F 305 MET cc_start: 0.9091 (mmm) cc_final: 0.8367 (mmm) REVERT: F 320 MET cc_start: 0.9082 (pmm) cc_final: 0.8346 (pmm) REVERT: F 329 GLN cc_start: 0.9770 (mm-40) cc_final: 0.9403 (tp-100) REVERT: F 383 MET cc_start: 0.5516 (mmm) cc_final: 0.5001 (mmm) REVERT: F 606 MET cc_start: 0.5393 (ttt) cc_final: 0.4561 (mmm) REVERT: F 646 LEU cc_start: 0.8844 (tp) cc_final: 0.8615 (mt) REVERT: F 718 MET cc_start: 0.4362 (ttm) cc_final: 0.4118 (ttp) REVERT: F 729 MET cc_start: 0.6752 (tpp) cc_final: 0.6353 (tpp) outliers start: 94 outliers final: 54 residues processed: 277 average time/residue: 0.1940 time to fit residues: 93.3413 Evaluate side-chains 256 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 193 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 1004 ASP Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1347 LEU Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 861 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 38 optimal weight: 0.9990 chunk 94 optimal weight: 0.0970 chunk 315 optimal weight: 4.9990 chunk 313 optimal weight: 4.9990 chunk 165 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 344 optimal weight: 8.9990 chunk 230 optimal weight: 8.9990 chunk 278 optimal weight: 9.9990 chunk 251 optimal weight: 10.0000 chunk 287 optimal weight: 20.0000 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 GLN ** D 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.051565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.033958 restraints weight = 266089.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.035118 restraints weight = 149132.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.035880 restraints weight = 101428.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.036362 restraints weight = 77955.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.036751 restraints weight = 65453.293| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 34066 Z= 0.172 Angle : 0.609 12.701 46289 Z= 0.312 Chirality : 0.042 0.345 5226 Planarity : 0.004 0.051 5844 Dihedral : 13.098 158.614 5278 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.65 % Allowed : 15.87 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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: 0.39 (0.13), residues: 4066 helix: 1.22 (0.13), residues: 1476 sheet: -0.12 (0.20), residues: 604 loop : -0.27 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 535 TYR 0.020 0.001 TYR D 631 PHE 0.031 0.001 PHE D 629 TRP 0.008 0.001 TRP D 580 HIS 0.019 0.001 HIS A 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (34046) covalent geometry : angle 0.60247 / 0.31 (46259) hydrogen bonds : bond 0.03772 / 2.57 ( 1499) hydrogen bonds : angle 4.97680 / 3.42 ( 4181) metal coordination : bond 0.00768 / 0.50 ( 20) metal coordination : angle 3.57820 / 2.38 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 192 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.8840 (mtt) cc_final: 0.8559 (mtm) REVERT: A 147 GLN cc_start: 0.9088 (mm-40) cc_final: 0.8795 (mm110) REVERT: A 205 MET cc_start: 0.8651 (pmm) cc_final: 0.8235 (pmm) REVERT: B 35 PHE cc_start: 0.9231 (m-80) cc_final: 0.8935 (m-80) REVERT: B 37 HIS cc_start: 0.8303 (OUTLIER) cc_final: 0.7955 (t-90) REVERT: C 211 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8293 (ttm170) REVERT: C 322 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9182 (pp) REVERT: C 369 MET cc_start: 0.9309 (tmm) cc_final: 0.9030 (tmm) REVERT: C 429 MET cc_start: 0.9498 (mmm) cc_final: 0.9174 (mmm) REVERT: C 623 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8973 (mt) REVERT: C 685 MET cc_start: 0.9203 (ppp) cc_final: 0.8887 (ppp) REVERT: C 686 GLN cc_start: 0.9453 (tt0) cc_final: 0.8851 (mt0) REVERT: C 697 LYS cc_start: 0.9559 (OUTLIER) cc_final: 0.8982 (ptmm) REVERT: C 704 MET cc_start: 0.8963 (mmm) cc_final: 0.8631 (mmm) REVERT: C 805 MET cc_start: 0.8698 (tmm) cc_final: 0.8486 (tmm) REVERT: C 814 ASP cc_start: 0.8661 (m-30) cc_final: 0.7901 (t0) REVERT: C 865 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9127 (mt) REVERT: C 1107 MET cc_start: 0.9589 (mpp) cc_final: 0.9107 (mpp) REVERT: C 1170 MET cc_start: 0.9432 (mmp) cc_final: 0.8986 (mmm) REVERT: C 1243 MET cc_start: 0.9051 (tmm) cc_final: 0.8746 (tmm) REVERT: C 1268 GLN cc_start: 0.8837 (mm-40) cc_final: 0.8579 (mm-40) REVERT: C 1274 GLU cc_start: 0.9092 (mp0) cc_final: 0.8725 (mp0) REVERT: C 1290 MET cc_start: 0.9547 (tpp) cc_final: 0.9191 (mpp) REVERT: C 1304 MET cc_start: 0.9244 (tmm) cc_final: 0.8988 (tmm) REVERT: C 1329 GLU cc_start: 0.9342 (tp30) cc_final: 0.8676 (tp30) REVERT: C 1332 SER cc_start: 0.9733 (OUTLIER) cc_final: 0.9515 (p) REVERT: D 151 MET cc_start: 0.9158 (mmm) cc_final: 0.8808 (mpp) REVERT: D 298 MET cc_start: 0.9200 (ttp) cc_final: 0.8738 (mtp) REVERT: D 304 ASP cc_start: 0.9163 (m-30) cc_final: 0.8830 (m-30) REVERT: D 330 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8832 (tpp) REVERT: D 372 MET cc_start: 0.9382 (OUTLIER) cc_final: 0.8835 (mmt) REVERT: D 400 MET cc_start: 0.9498 (mtm) cc_final: 0.9180 (mpp) REVERT: D 458 ASN cc_start: 0.9594 (t0) cc_final: 0.9266 (t0) REVERT: D 466 MET cc_start: 0.9163 (ptm) cc_final: 0.8900 (ptm) REVERT: D 484 MET cc_start: 0.9085 (mpp) cc_final: 0.8738 (mpp) REVERT: D 485 MET cc_start: 0.8905 (tpp) cc_final: 0.8512 (tpp) REVERT: D 541 LEU cc_start: 0.9564 (OUTLIER) cc_final: 0.9315 (tp) REVERT: D 606 ASN cc_start: 0.9385 (t0) cc_final: 0.9078 (t0) REVERT: D 747 MET cc_start: 0.8757 (pmm) cc_final: 0.8527 (ppp) REVERT: D 772 TYR cc_start: 0.9312 (t80) cc_final: 0.9054 (t80) REVERT: D 915 ILE cc_start: 0.9836 (pt) cc_final: 0.9402 (mp) REVERT: D 925 GLU cc_start: 0.9318 (tt0) cc_final: 0.8956 (tm-30) REVERT: D 932 MET cc_start: 0.8745 (ppp) cc_final: 0.8222 (ppp) REVERT: E 46 THR cc_start: 0.9536 (OUTLIER) cc_final: 0.9329 (t) REVERT: F 305 MET cc_start: 0.9089 (mmm) cc_final: 0.8338 (mmm) REVERT: F 320 MET cc_start: 0.9076 (pmm) cc_final: 0.8354 (pmm) REVERT: F 329 GLN cc_start: 0.9762 (mm-40) cc_final: 0.9391 (tp-100) REVERT: F 538 MET cc_start: 0.6294 (ptt) cc_final: 0.6088 (ptt) REVERT: F 606 MET cc_start: 0.5471 (ttt) cc_final: 0.4676 (mmm) REVERT: F 646 LEU cc_start: 0.8853 (tp) cc_final: 0.8611 (mt) REVERT: F 718 MET cc_start: 0.4308 (ttm) cc_final: 0.3877 (ttp) REVERT: F 722 MET cc_start: -0.2262 (ttp) cc_final: -0.2852 (ptt) REVERT: F 729 MET cc_start: 0.6549 (tpp) cc_final: 0.6092 (tpp) outliers start: 92 outliers final: 60 residues processed: 267 average time/residue: 0.1918 time to fit residues: 89.2864 Evaluate side-chains 259 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 188 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 211 ARG Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 818 VAL Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 1004 ASP Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1299 ASN Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1347 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 669 MET Chi-restraints excluded: chain F residue 861 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 7 optimal weight: 9.9990 chunk 184 optimal weight: 10.0000 chunk 360 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 301 optimal weight: 4.9990 chunk 216 optimal weight: 0.8980 chunk 306 optimal weight: 20.0000 chunk 64 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 194 optimal weight: 9.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1070 HIS ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.050844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.033395 restraints weight = 269945.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.034515 restraints weight = 153335.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.035259 restraints weight = 104487.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.035778 restraints weight = 80379.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.036101 restraints weight = 67228.323| |-----------------------------------------------------------------------------| r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 34066 Z= 0.220 Angle : 0.642 10.586 46289 Z= 0.328 Chirality : 0.042 0.338 5226 Planarity : 0.004 0.052 5844 Dihedral : 13.125 159.631 5277 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.44 % Favored : 96.53 % Rotamer: Outliers : 2.51 % Allowed : 16.07 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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: 0.36 (0.13), residues: 4066 helix: 1.20 (0.13), residues: 1474 sheet: -0.15 (0.20), residues: 613 loop : -0.29 (0.14), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 431 TYR 0.017 0.001 TYR C1229 PHE 0.026 0.001 PHE D 629 TRP 0.009 0.001 TRP C1276 HIS 0.007 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.22 (34046) covalent geometry : angle 0.63534 / 0.33 (46259) hydrogen bonds : bond 0.03915 / 2.66 ( 1499) hydrogen bonds : angle 5.03590 / 3.46 ( 4181) metal coordination : bond 0.01003 / 0.66 ( 20) metal coordination : angle 3.80525 / 2.55 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 189 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.8901 (mtt) cc_final: 0.8585 (mtm) REVERT: A 147 GLN cc_start: 0.9092 (mm-40) cc_final: 0.8772 (mm110) REVERT: B 37 HIS cc_start: 0.8521 (OUTLIER) cc_final: 0.8163 (t-90) REVERT: C 211 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8335 (ttm170) REVERT: C 322 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9182 (pp) REVERT: C 429 MET cc_start: 0.9516 (mmm) cc_final: 0.9201 (mmm) REVERT: C 623 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8964 (mt) REVERT: C 681 MET cc_start: 0.9418 (ptp) cc_final: 0.9006 (ppp) REVERT: C 685 MET cc_start: 0.9242 (ppp) cc_final: 0.8991 (ppp) REVERT: C 686 GLN cc_start: 0.9468 (tt0) cc_final: 0.8867 (mt0) REVERT: C 697 LYS cc_start: 0.9570 (OUTLIER) cc_final: 0.8976 (ptmm) REVERT: C 704 MET cc_start: 0.9009 (mmm) cc_final: 0.8667 (mmm) REVERT: C 789 THR cc_start: 0.9603 (OUTLIER) cc_final: 0.9091 (p) REVERT: C 805 MET cc_start: 0.8748 (tmm) cc_final: 0.8444 (tmm) REVERT: C 814 ASP cc_start: 0.8793 (m-30) cc_final: 0.7950 (t0) REVERT: C 865 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9115 (mt) REVERT: C 1064 ASP cc_start: 0.9122 (t70) cc_final: 0.8898 (t70) REVERT: C 1107 MET cc_start: 0.9573 (mpp) cc_final: 0.9350 (mpp) REVERT: C 1170 MET cc_start: 0.9454 (mmp) cc_final: 0.9000 (mmm) REVERT: C 1243 MET cc_start: 0.9098 (tmm) cc_final: 0.8792 (tmm) REVERT: C 1268 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8598 (mm-40) REVERT: C 1273 MET cc_start: 0.9412 (mmm) cc_final: 0.8861 (mtm) REVERT: C 1274 GLU cc_start: 0.9122 (mp0) cc_final: 0.8889 (mp0) REVERT: C 1290 MET cc_start: 0.9560 (tpp) cc_final: 0.9135 (mpp) REVERT: C 1304 MET cc_start: 0.9284 (tmm) cc_final: 0.9048 (tmm) REVERT: C 1319 MET cc_start: 0.8677 (tpp) cc_final: 0.8263 (tpp) REVERT: C 1329 GLU cc_start: 0.9384 (tp30) cc_final: 0.8743 (tp30) REVERT: C 1332 SER cc_start: 0.9734 (OUTLIER) cc_final: 0.9496 (p) REVERT: D 151 MET cc_start: 0.9163 (mmm) cc_final: 0.8871 (mpp) REVERT: D 298 MET cc_start: 0.9204 (ttp) cc_final: 0.8751 (mtp) REVERT: D 304 ASP cc_start: 0.9193 (m-30) cc_final: 0.8881 (m-30) REVERT: D 330 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.8851 (tpp) REVERT: D 372 MET cc_start: 0.9434 (OUTLIER) cc_final: 0.9064 (mmt) REVERT: D 400 MET cc_start: 0.9484 (mtm) cc_final: 0.9172 (mpp) REVERT: D 458 ASN cc_start: 0.9643 (t0) cc_final: 0.9393 (t0) REVERT: D 466 MET cc_start: 0.9199 (ptm) cc_final: 0.8915 (ptm) REVERT: D 484 MET cc_start: 0.9157 (mpp) cc_final: 0.8747 (mpp) REVERT: D 485 MET cc_start: 0.9011 (tpp) cc_final: 0.8483 (tpp) REVERT: D 541 LEU cc_start: 0.9587 (OUTLIER) cc_final: 0.9236 (tp) REVERT: D 606 ASN cc_start: 0.9444 (t0) cc_final: 0.9194 (t0) REVERT: D 625 MET cc_start: 0.9415 (mmm) cc_final: 0.8774 (tpp) REVERT: D 664 ILE cc_start: 0.9409 (OUTLIER) cc_final: 0.9161 (mt) REVERT: D 725 MET cc_start: 0.9405 (mtp) cc_final: 0.8714 (tmm) REVERT: D 747 MET cc_start: 0.8829 (pmm) cc_final: 0.8596 (ppp) REVERT: D 772 TYR cc_start: 0.9348 (t80) cc_final: 0.9125 (t80) REVERT: D 821 MET cc_start: 0.9169 (tpp) cc_final: 0.8643 (tpp) REVERT: D 915 ILE cc_start: 0.9848 (pt) cc_final: 0.9397 (mp) REVERT: D 925 GLU cc_start: 0.9364 (tt0) cc_final: 0.8946 (tm-30) REVERT: D 932 MET cc_start: 0.8830 (ppp) cc_final: 0.8360 (ppp) REVERT: D 1186 TYR cc_start: 0.8601 (OUTLIER) cc_final: 0.8269 (t80) REVERT: E 46 THR cc_start: 0.9549 (OUTLIER) cc_final: 0.9346 (t) REVERT: F 305 MET cc_start: 0.9112 (mmm) cc_final: 0.8364 (mmm) REVERT: F 320 MET cc_start: 0.9088 (pmm) cc_final: 0.8358 (pmm) REVERT: F 329 GLN cc_start: 0.9762 (mm-40) cc_final: 0.9445 (tp-100) REVERT: F 438 MET cc_start: 0.9332 (tpp) cc_final: 0.9101 (tmm) REVERT: F 606 MET cc_start: 0.5540 (ttt) cc_final: 0.4744 (mmm) REVERT: F 646 LEU cc_start: 0.8816 (tp) cc_final: 0.8550 (mt) REVERT: F 718 MET cc_start: 0.4339 (ttm) cc_final: 0.3911 (ttp) REVERT: F 722 MET cc_start: -0.2056 (ttp) cc_final: -0.2666 (ptt) REVERT: F 729 MET cc_start: 0.6451 (tpp) cc_final: 0.5990 (tpp) outliers start: 87 outliers final: 63 residues processed: 262 average time/residue: 0.1893 time to fit residues: 86.4904 Evaluate side-chains 262 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 185 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 211 ARG Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 770 CYS Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 1004 ASP Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1299 ASN Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1186 TYR Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1260 MET Chi-restraints excluded: chain D residue 1347 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 472 LYS Chi-restraints excluded: chain F residue 861 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 17 optimal weight: 9.9990 chunk 159 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 406 optimal weight: 40.0000 chunk 149 optimal weight: 6.9990 chunk 374 optimal weight: 30.0000 chunk 9 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.050299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.032939 restraints weight = 275502.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.034063 restraints weight = 154561.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.034788 restraints weight = 104902.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.035301 restraints weight = 81052.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.035655 restraints weight = 67973.443| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 34066 Z= 0.249 Angle : 0.679 16.545 46289 Z= 0.344 Chirality : 0.043 0.329 5226 Planarity : 0.004 0.049 5844 Dihedral : 13.177 160.565 5277 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.71 % Allowed : 16.33 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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: 0.24 (0.13), residues: 4066 helix: 1.09 (0.13), residues: 1476 sheet: -0.27 (0.20), residues: 606 loop : -0.33 (0.14), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 661 TYR 0.019 0.002 TYR D 631 PHE 0.024 0.002 PHE D 629 TRP 0.011 0.002 TRP C1276 HIS 0.011 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.25 (34046) covalent geometry : angle 0.67084 / 0.34 (46259) hydrogen bonds : bond 0.04044 / 2.74 ( 1499) hydrogen bonds : angle 5.11118 / 3.51 ( 4181) metal coordination : bond 0.01106 / 0.73 ( 20) metal coordination : angle 4.05589 / 2.69 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 184 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.8955 (mtt) cc_final: 0.8634 (mtm) REVERT: A 147 GLN cc_start: 0.9109 (mm-40) cc_final: 0.8799 (mm110) REVERT: B 35 PHE cc_start: 0.9239 (m-80) cc_final: 0.8573 (m-80) REVERT: B 37 HIS cc_start: 0.8599 (OUTLIER) cc_final: 0.8218 (t-90) REVERT: C 211 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.8336 (ttm170) REVERT: C 322 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9160 (pp) REVERT: C 429 MET cc_start: 0.9503 (mmm) cc_final: 0.9192 (mmm) REVERT: C 508 SER cc_start: 0.9123 (t) cc_final: 0.8807 (m) REVERT: C 562 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8044 (tm-30) REVERT: C 623 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8964 (mt) REVERT: C 685 MET cc_start: 0.9250 (ppp) cc_final: 0.8963 (ppp) REVERT: C 686 GLN cc_start: 0.9475 (tt0) cc_final: 0.8844 (mt0) REVERT: C 697 LYS cc_start: 0.9573 (OUTLIER) cc_final: 0.8953 (ptmm) REVERT: C 789 THR cc_start: 0.9586 (OUTLIER) cc_final: 0.9058 (p) REVERT: C 805 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8423 (tmm) REVERT: C 814 ASP cc_start: 0.8855 (m-30) cc_final: 0.7994 (t0) REVERT: C 865 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9116 (mt) REVERT: C 1107 MET cc_start: 0.9584 (mpp) cc_final: 0.9349 (mpp) REVERT: C 1170 MET cc_start: 0.9460 (mmp) cc_final: 0.9021 (mmm) REVERT: C 1230 MET cc_start: 0.8590 (tpt) cc_final: 0.8076 (tpt) REVERT: C 1243 MET cc_start: 0.9144 (tmm) cc_final: 0.8854 (tmm) REVERT: C 1273 MET cc_start: 0.9392 (mmm) cc_final: 0.8921 (mtm) REVERT: C 1274 GLU cc_start: 0.9103 (mp0) cc_final: 0.8865 (mp0) REVERT: C 1290 MET cc_start: 0.9534 (tpp) cc_final: 0.9313 (tpp) REVERT: C 1304 MET cc_start: 0.9302 (tmm) cc_final: 0.9078 (tmm) REVERT: C 1319 MET cc_start: 0.8765 (tpp) cc_final: 0.8318 (tpp) REVERT: C 1329 GLU cc_start: 0.9375 (tp30) cc_final: 0.8735 (tp30) REVERT: C 1332 SER cc_start: 0.9733 (OUTLIER) cc_final: 0.9486 (p) REVERT: D 151 MET cc_start: 0.9188 (mmm) cc_final: 0.8922 (mpp) REVERT: D 298 MET cc_start: 0.9186 (ttp) cc_final: 0.8757 (mtp) REVERT: D 304 ASP cc_start: 0.9138 (m-30) cc_final: 0.8829 (m-30) REVERT: D 330 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8867 (tpp) REVERT: D 372 MET cc_start: 0.9446 (OUTLIER) cc_final: 0.9128 (mmt) REVERT: D 466 MET cc_start: 0.9231 (ptm) cc_final: 0.8959 (ptm) REVERT: D 484 MET cc_start: 0.9180 (mpp) cc_final: 0.8769 (mpp) REVERT: D 485 MET cc_start: 0.9080 (tpp) cc_final: 0.8491 (tpp) REVERT: D 541 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9250 (tp) REVERT: D 606 ASN cc_start: 0.9394 (t0) cc_final: 0.9113 (t0) REVERT: D 664 ILE cc_start: 0.9416 (OUTLIER) cc_final: 0.9161 (mt) REVERT: D 747 MET cc_start: 0.8810 (pmm) cc_final: 0.8587 (ppp) REVERT: D 895 CYS cc_start: 0.8511 (OUTLIER) cc_final: 0.7632 (p) REVERT: D 915 ILE cc_start: 0.9842 (pt) cc_final: 0.9399 (mp) REVERT: D 925 GLU cc_start: 0.9362 (tt0) cc_final: 0.8918 (tm-30) REVERT: D 932 MET cc_start: 0.8913 (ppp) cc_final: 0.8384 (ppp) REVERT: D 1186 TYR cc_start: 0.8626 (OUTLIER) cc_final: 0.8290 (t80) REVERT: D 1189 MET cc_start: 0.9310 (mmm) cc_final: 0.9031 (mmm) REVERT: E 46 THR cc_start: 0.9561 (OUTLIER) cc_final: 0.9346 (t) REVERT: F 171 MET cc_start: 0.8991 (mpp) cc_final: 0.8718 (mpp) REVERT: F 305 MET cc_start: 0.9108 (mmm) cc_final: 0.8328 (mmm) REVERT: F 320 MET cc_start: 0.9085 (pmm) cc_final: 0.8325 (pmm) REVERT: F 329 GLN cc_start: 0.9768 (mm-40) cc_final: 0.9408 (tp-100) REVERT: F 438 MET cc_start: 0.9344 (tpp) cc_final: 0.9107 (tmm) REVERT: F 538 MET cc_start: 0.6293 (OUTLIER) cc_final: 0.6012 (ptt) REVERT: F 606 MET cc_start: 0.5506 (ttt) cc_final: 0.4743 (mmm) REVERT: F 646 LEU cc_start: 0.8784 (tp) cc_final: 0.8509 (mt) REVERT: F 718 MET cc_start: 0.4140 (ttm) cc_final: 0.3724 (ttp) REVERT: F 722 MET cc_start: -0.1885 (ttp) cc_final: -0.2453 (ptt) REVERT: F 729 MET cc_start: 0.6495 (tpp) cc_final: 0.6066 (tpp) outliers start: 94 outliers final: 66 residues processed: 262 average time/residue: 0.1855 time to fit residues: 85.1642 Evaluate side-chains 263 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 180 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 211 ARG Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 770 CYS Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 1004 ASP Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1299 ASN Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1162 ILE Chi-restraints excluded: chain D residue 1186 TYR Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1347 LEU Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 472 LYS Chi-restraints excluded: chain F residue 538 MET Chi-restraints excluded: chain F residue 861 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 326 optimal weight: 20.0000 chunk 200 optimal weight: 7.9990 chunk 168 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 404 optimal weight: 6.9990 chunk 141 optimal weight: 9.9990 chunk 256 optimal weight: 5.9990 chunk 288 optimal weight: 9.9990 chunk 353 optimal weight: 10.0000 chunk 282 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 ASN D 365 GLN ** D 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 685 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.049330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.032037 restraints weight = 277778.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.033147 restraints weight = 157267.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.033864 restraints weight = 106974.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.034360 restraints weight = 82515.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.034728 restraints weight = 69378.058| |-----------------------------------------------------------------------------| r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 34066 Z= 0.285 Angle : 0.731 13.060 46289 Z= 0.372 Chirality : 0.044 0.312 5226 Planarity : 0.005 0.054 5844 Dihedral : 13.287 161.774 5277 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.68 % Allowed : 16.62 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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: -0.01 (0.13), residues: 4066 helix: 0.91 (0.13), residues: 1475 sheet: -0.47 (0.20), residues: 615 loop : -0.47 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 661 TYR 0.025 0.002 TYR A 68 PHE 0.021 0.002 PHE D 629 TRP 0.019 0.002 TRP F 184 HIS 0.008 0.002 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.29 (34046) covalent geometry : angle 0.72263 / 0.37 (46259) hydrogen bonds : bond 0.04343 / 2.95 ( 1499) hydrogen bonds : angle 5.30901 / 3.66 ( 4181) metal coordination : bond 0.01361 / 0.90 ( 20) metal coordination : angle 4.51426 / 2.99 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 183 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.9033 (mtt) cc_final: 0.8749 (mtm) REVERT: A 147 GLN cc_start: 0.9125 (mm-40) cc_final: 0.8844 (mm110) REVERT: B 37 HIS cc_start: 0.8654 (OUTLIER) cc_final: 0.8246 (t-90) REVERT: C 369 MET cc_start: 0.9334 (tmm) cc_final: 0.9116 (tmm) REVERT: C 429 MET cc_start: 0.9493 (mmm) cc_final: 0.9175 (mmm) REVERT: C 562 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8039 (tm-30) REVERT: C 623 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8960 (mt) REVERT: C 674 ASP cc_start: 0.9042 (p0) cc_final: 0.8798 (p0) REVERT: C 681 MET cc_start: 0.9510 (ptp) cc_final: 0.9210 (ppp) REVERT: C 686 GLN cc_start: 0.9457 (tt0) cc_final: 0.8813 (mt0) REVERT: C 697 LYS cc_start: 0.9573 (OUTLIER) cc_final: 0.8791 (ptpp) REVERT: C 704 MET cc_start: 0.8995 (mmm) cc_final: 0.8685 (mmm) REVERT: C 789 THR cc_start: 0.9552 (OUTLIER) cc_final: 0.8998 (p) REVERT: C 805 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8406 (ppp) REVERT: C 814 ASP cc_start: 0.9038 (m-30) cc_final: 0.8138 (t0) REVERT: C 1107 MET cc_start: 0.9568 (mpp) cc_final: 0.9353 (mpp) REVERT: C 1170 MET cc_start: 0.9476 (mmp) cc_final: 0.9048 (mmm) REVERT: C 1243 MET cc_start: 0.9238 (tmm) cc_final: 0.8931 (tmm) REVERT: C 1273 MET cc_start: 0.9400 (mmm) cc_final: 0.8953 (mtm) REVERT: C 1279 GLU cc_start: 0.9396 (mt-10) cc_final: 0.9130 (mt-10) REVERT: C 1290 MET cc_start: 0.9562 (tpp) cc_final: 0.9083 (mpp) REVERT: C 1304 MET cc_start: 0.9343 (tmm) cc_final: 0.9129 (tmm) REVERT: C 1319 MET cc_start: 0.8887 (tpp) cc_final: 0.8376 (tpp) REVERT: C 1329 GLU cc_start: 0.9380 (tp30) cc_final: 0.8779 (tp30) REVERT: C 1332 SER cc_start: 0.9725 (OUTLIER) cc_final: 0.9458 (p) REVERT: D 298 MET cc_start: 0.9172 (ttp) cc_final: 0.8759 (mtp) REVERT: D 304 ASP cc_start: 0.9086 (m-30) cc_final: 0.8739 (m-30) REVERT: D 330 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8876 (tpp) REVERT: D 366 CYS cc_start: 0.9313 (p) cc_final: 0.8684 (p) REVERT: D 372 MET cc_start: 0.9450 (OUTLIER) cc_final: 0.9064 (mmt) REVERT: D 466 MET cc_start: 0.9250 (ptm) cc_final: 0.8920 (ptm) REVERT: D 484 MET cc_start: 0.9180 (mpp) cc_final: 0.8790 (mpp) REVERT: D 485 MET cc_start: 0.9156 (tpp) cc_final: 0.8638 (tpp) REVERT: D 541 LEU cc_start: 0.9600 (OUTLIER) cc_final: 0.9248 (tp) REVERT: D 606 ASN cc_start: 0.9432 (t0) cc_final: 0.9171 (t0) REVERT: D 625 MET cc_start: 0.9443 (mmm) cc_final: 0.8778 (tpt) REVERT: D 664 ILE cc_start: 0.9430 (OUTLIER) cc_final: 0.9181 (mt) REVERT: D 747 MET cc_start: 0.8805 (pmm) cc_final: 0.8409 (ppp) REVERT: D 895 CYS cc_start: 0.8489 (OUTLIER) cc_final: 0.7664 (p) REVERT: D 915 ILE cc_start: 0.9850 (OUTLIER) cc_final: 0.9395 (mp) REVERT: D 925 GLU cc_start: 0.9341 (tt0) cc_final: 0.8887 (tm-30) REVERT: D 932 MET cc_start: 0.9055 (ppp) cc_final: 0.8562 (ppp) REVERT: D 1186 TYR cc_start: 0.8697 (OUTLIER) cc_final: 0.8362 (t80) REVERT: E 46 THR cc_start: 0.9597 (OUTLIER) cc_final: 0.9390 (t) REVERT: F 305 MET cc_start: 0.9136 (mmm) cc_final: 0.8403 (mmm) REVERT: F 320 MET cc_start: 0.9067 (pmm) cc_final: 0.8324 (pmm) REVERT: F 329 GLN cc_start: 0.9774 (mm-40) cc_final: 0.9399 (tp-100) REVERT: F 438 MET cc_start: 0.9378 (tpp) cc_final: 0.9164 (tmm) REVERT: F 538 MET cc_start: 0.6203 (OUTLIER) cc_final: 0.5917 (ptt) REVERT: F 546 MET cc_start: 0.8489 (tpp) cc_final: 0.8240 (tmm) REVERT: F 646 LEU cc_start: 0.8847 (tp) cc_final: 0.8591 (mt) REVERT: F 718 MET cc_start: 0.4289 (ttm) cc_final: 0.3967 (ttp) REVERT: F 722 MET cc_start: -0.1482 (ttp) cc_final: -0.1953 (ptt) REVERT: F 729 MET cc_start: 0.6731 (tpp) cc_final: 0.6401 (tpp) outliers start: 93 outliers final: 67 residues processed: 260 average time/residue: 0.1889 time to fit residues: 86.3528 Evaluate side-chains 262 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 180 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 770 CYS Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 1004 ASP Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1299 ASN Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 840 LEU 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 1162 ILE Chi-restraints excluded: chain D residue 1186 TYR Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1347 LEU Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 472 LYS Chi-restraints excluded: chain F residue 538 MET Chi-restraints excluded: chain F residue 861 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 210 optimal weight: 8.9990 chunk 259 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 206 optimal weight: 4.9990 chunk 174 optimal weight: 0.3980 chunk 241 optimal weight: 0.9990 chunk 284 optimal weight: 6.9990 chunk 205 optimal weight: 1.9990 chunk 315 optimal weight: 6.9990 chunk 295 optimal weight: 6.9990 chunk 251 optimal weight: 4.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1244 HIS ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.050827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.033283 restraints weight = 270545.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.034438 restraints weight = 151483.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.035197 restraints weight = 102620.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.035724 restraints weight = 78978.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.036088 restraints weight = 66094.878| |-----------------------------------------------------------------------------| r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34066 Z= 0.128 Angle : 0.666 20.779 46289 Z= 0.330 Chirality : 0.044 0.560 5226 Planarity : 0.004 0.050 5844 Dihedral : 13.174 160.722 5277 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.16 % Allowed : 17.14 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.13), residues: 4066 helix: 1.16 (0.13), residues: 1479 sheet: -0.41 (0.20), residues: 639 loop : -0.29 (0.14), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 310 TYR 0.016 0.001 TYR C1229 PHE 0.026 0.001 PHE C 188 TRP 0.017 0.002 TRP D 580 HIS 0.006 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (34046) covalent geometry : angle 0.65927 / 0.33 (46259) hydrogen bonds : bond 0.03616 / 2.48 ( 1499) hydrogen bonds : angle 4.97324 / 3.41 ( 4181) metal coordination : bond 0.00607 / 0.38 ( 20) metal coordination : angle 3.78674 / 2.48 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 202 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.8989 (mtt) cc_final: 0.8689 (mtm) REVERT: A 147 GLN cc_start: 0.9097 (mm-40) cc_final: 0.8775 (mm110) REVERT: B 35 PHE cc_start: 0.9119 (m-80) cc_final: 0.8552 (m-80) REVERT: B 37 HIS cc_start: 0.8466 (OUTLIER) cc_final: 0.8048 (t-90) REVERT: C 369 MET cc_start: 0.9250 (tmm) cc_final: 0.8949 (tmm) REVERT: C 429 MET cc_start: 0.9563 (mmm) cc_final: 0.9263 (mmm) REVERT: C 508 SER cc_start: 0.9175 (t) cc_final: 0.8850 (m) REVERT: C 562 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8014 (tm-30) REVERT: C 623 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8933 (mt) REVERT: C 681 MET cc_start: 0.9454 (ptp) cc_final: 0.8880 (ppp) REVERT: C 685 MET cc_start: 0.9285 (ppp) cc_final: 0.8933 (ppp) REVERT: C 686 GLN cc_start: 0.9423 (tt0) cc_final: 0.8645 (mt0) REVERT: C 697 LYS cc_start: 0.9601 (OUTLIER) cc_final: 0.8811 (ptpp) REVERT: C 789 THR cc_start: 0.9601 (OUTLIER) cc_final: 0.9111 (p) REVERT: C 805 MET cc_start: 0.8727 (tmm) cc_final: 0.8387 (tmm) REVERT: C 1065 LYS cc_start: 0.9400 (OUTLIER) cc_final: 0.8903 (tppp) REVERT: C 1107 MET cc_start: 0.9591 (mpp) cc_final: 0.9095 (mpp) REVERT: C 1170 MET cc_start: 0.9451 (mmp) cc_final: 0.9085 (mmm) REVERT: C 1232 MET cc_start: 0.9223 (mmp) cc_final: 0.8571 (mmm) REVERT: C 1243 MET cc_start: 0.9167 (tmm) cc_final: 0.8942 (tmm) REVERT: C 1273 MET cc_start: 0.9345 (mmm) cc_final: 0.8981 (mtm) REVERT: C 1290 MET cc_start: 0.9510 (tpp) cc_final: 0.9272 (tpp) REVERT: C 1304 MET cc_start: 0.9257 (tmm) cc_final: 0.8998 (tmm) REVERT: C 1319 MET cc_start: 0.8802 (tpp) cc_final: 0.8307 (tpp) REVERT: C 1329 GLU cc_start: 0.9339 (tp30) cc_final: 0.8856 (tp30) REVERT: D 298 MET cc_start: 0.9222 (ttp) cc_final: 0.8815 (mtp) REVERT: D 304 ASP cc_start: 0.9141 (m-30) cc_final: 0.8833 (m-30) REVERT: D 329 ASP cc_start: 0.9518 (OUTLIER) cc_final: 0.9273 (m-30) REVERT: D 330 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8840 (tpp) REVERT: D 372 MET cc_start: 0.9411 (OUTLIER) cc_final: 0.9105 (mmt) REVERT: D 466 MET cc_start: 0.9255 (ptm) cc_final: 0.8887 (ptm) REVERT: D 484 MET cc_start: 0.9099 (mpp) cc_final: 0.8685 (mpp) REVERT: D 485 MET cc_start: 0.9039 (tpp) cc_final: 0.8450 (tpp) REVERT: D 541 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9248 (tp) REVERT: D 606 ASN cc_start: 0.9395 (t0) cc_final: 0.9087 (t0) REVERT: D 724 MET cc_start: 0.9567 (ptp) cc_final: 0.8772 (mpp) REVERT: D 736 GLN cc_start: 0.9524 (mp10) cc_final: 0.9199 (mp10) REVERT: D 915 ILE cc_start: 0.9835 (pt) cc_final: 0.9364 (mp) REVERT: D 925 GLU cc_start: 0.9337 (tt0) cc_final: 0.8905 (tm-30) REVERT: D 932 MET cc_start: 0.9048 (ppp) cc_final: 0.8483 (ppp) REVERT: D 1186 TYR cc_start: 0.8668 (OUTLIER) cc_final: 0.8344 (t80) REVERT: F 171 MET cc_start: 0.8979 (mpp) cc_final: 0.8608 (mpp) REVERT: F 305 MET cc_start: 0.9165 (mmm) cc_final: 0.8510 (mmm) REVERT: F 320 MET cc_start: 0.9056 (pmm) cc_final: 0.8352 (pmm) REVERT: F 329 GLN cc_start: 0.9771 (mm-40) cc_final: 0.9386 (tp-100) REVERT: F 438 MET cc_start: 0.9370 (tpp) cc_final: 0.9158 (tmm) REVERT: F 538 MET cc_start: 0.6026 (OUTLIER) cc_final: 0.5728 (ptt) REVERT: F 646 LEU cc_start: 0.8869 (tp) cc_final: 0.8609 (mt) REVERT: F 718 MET cc_start: 0.3953 (ttm) cc_final: 0.3692 (ttp) REVERT: F 722 MET cc_start: -0.1556 (ttp) cc_final: -0.2067 (ptt) REVERT: F 729 MET cc_start: 0.6637 (tpp) cc_final: 0.6381 (tpp) outliers start: 75 outliers final: 57 residues processed: 264 average time/residue: 0.1908 time to fit residues: 87.3526 Evaluate side-chains 266 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 198 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 1004 ASP Chi-restraints excluded: chain C residue 1065 LYS Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1299 ASN Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1186 TYR Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain D residue 1260 MET Chi-restraints excluded: chain D residue 1347 LEU Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 472 LYS Chi-restraints excluded: chain F residue 538 MET Chi-restraints excluded: chain F residue 861 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 133 optimal weight: 5.9990 chunk 145 optimal weight: 20.0000 chunk 290 optimal weight: 8.9990 chunk 311 optimal weight: 5.9990 chunk 197 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 338 optimal weight: 10.0000 chunk 384 optimal weight: 30.0000 chunk 392 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 348 optimal weight: 0.0670 overall best weight: 4.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.050751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.033247 restraints weight = 269779.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.034398 restraints weight = 151490.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.035145 restraints weight = 103296.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.035631 restraints weight = 79397.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.036021 restraints weight = 66652.665| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.165 34066 Z= 0.167 Angle : 0.751 59.180 46289 Z= 0.394 Chirality : 0.044 0.523 5226 Planarity : 0.004 0.051 5844 Dihedral : 13.168 160.670 5277 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.07 % Allowed : 17.22 % Favored : 80.70 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.13), residues: 4066 helix: 1.15 (0.13), residues: 1479 sheet: -0.42 (0.20), residues: 640 loop : -0.27 (0.14), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 310 TYR 0.016 0.001 TYR F 408 PHE 0.028 0.001 PHE C 136 TRP 0.015 0.001 TRP D 580 HIS 0.006 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 (34046) covalent geometry : angle 0.74478 / 0.39 (46259) hydrogen bonds : bond 0.03654 / 2.51 ( 1499) hydrogen bonds : angle 4.99244 / 3.43 ( 4181) metal coordination : bond 0.00640 / 0.41 ( 20) metal coordination : angle 3.77038 / 2.47 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9278.11 seconds wall clock time: 159 minutes 34.65 seconds (9574.65 seconds total)