Starting phenix.real_space_refine on Sun Aug 9 11:10:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gdc_51261/08_2026/9gdc_51261.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gdc_51261/08_2026/9gdc_51261.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gdc_51261/08_2026/9gdc_51261.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gdc_51261/08_2026/9gdc_51261.map" model { file = "/net/cci-nas-00/data/ceres_data/9gdc_51261/08_2026/9gdc_51261.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gdc_51261/08_2026/9gdc_51261.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.096 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 66 5.49 5 Mg 1 5.21 5 S 143 5.16 5 C 20555 2.51 5 N 5872 2.21 5 O 6473 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 294 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33115 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1803 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 223} Chain: "B" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1799 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 222} Chain: "C" Number of atoms: 10577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10577 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 54, 'TRANS': 1284} Chain: "D" Number of atoms: 10433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1342, 10433 Classifications: {'peptide': 1342} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1286} Chain breaks: 2 Chain: "E" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 709 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "F" Number of atoms: 6660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 840, 6660 Classifications: {'peptide': 840} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 795} Chain breaks: 1 Chain: "N" Number of atoms: 348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 348 Classifications: {'DNA': 28} Incomplete info: {'p_only': 12} Link IDs: {'rna3p': 27} Unresolved chain links: 12 Unresolved chain link angles: 48 Unresolved chain link dihedrals: 36 Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 367 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {' DT:plan': 7, ' DA:plan': 2, ' DA:plan2': 2, ' DC:plan': 2, ' DC:plan2': 2, ' DG:plan': 1, ' DG:plan2': 1} Unresolved non-hydrogen planarities: 132 Chain: "R" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 235 Classifications: {'RNA': 11} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna2p': 2, 'rna3p': 8} Chain: "T" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 545 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14644 SG CYS D 70 111.869 99.274 87.532 1.00295.71 S ATOM 14658 SG CYS D 72 111.568 103.158 89.401 1.00281.71 S ATOM 14766 SG CYS D 85 114.433 100.621 89.731 1.00276.02 S ATOM 14790 SG CYS D 88 110.672 99.961 90.718 1.00282.08 S ATOM 20478 SG CYS D 814 82.258 38.990 91.046 1.00173.19 S ATOM 21043 SG CYS D 888 81.551 42.598 90.968 1.00177.22 S ATOM 21094 SG CYS D 895 81.844 40.518 87.653 1.00169.34 S ATOM 21115 SG CYS D 898 78.831 40.075 89.785 1.00171.45 S ATOM 29893 SG CYS F 599 131.090 124.401 120.373 1.001027.4 S ATOM 29913 SG CYS F 602 134.110 126.665 120.223 1.001027.4 S ATOM 30033 SG CYS F 619 131.723 127.337 122.840 1.001027.4 S ATOM 30117 SG CYS F 630 130.483 128.063 119.393 1.001027.4 S ATOM 30367 SG CYS F 662 128.240 119.326 144.544 1.001027.4 S ATOM 30389 SG CYS F 665 126.292 120.798 147.455 1.001027.4 S ATOM 30530 SG CYS F 683 124.860 120.898 144.044 1.001027.4 S ATOM 30570 SG CYS F 689 127.722 123.218 144.976 1.001027.4 S ATOM 30746 SG CYS F 711 115.567 111.005 109.118 1.001027.4 S ATOM 30770 SG CYS F 714 117.490 108.836 110.986 1.001027.4 S ATOM 30902 SG CYS F 731 116.293 111.609 112.855 1.001027.4 S ATOM 30941 SG CYS F 736 118.843 112.168 109.905 1.001027.4 S Time building chain proxies: 7.02, per 1000 atoms: 0.21 Number of scatterers: 33115 At special positions: 0 Unit cell: (153.091, 169.642, 194.467, 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 66 15.00 Mg 1 11.99 O 6473 8.00 N 5872 7.00 C 20555 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: 2.25 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 619 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 602 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 599 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 630 " pdb=" ZN F1002 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 665 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 683 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 662 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 689 " pdb=" ZN F1003 " pdb="ZN ZN F1003 " - pdb=" SG CYS F 736 " pdb="ZN ZN F1003 " - pdb=" SG CYS F 714 " pdb="ZN ZN F1003 " - pdb=" SG CYS F 711 " pdb="ZN ZN F1003 " - pdb=" SG CYS F 731 " Number of angles added : 30 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7546 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 58 sheets defined 40.9% alpha, 18.6% beta 25 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 3.21 Creating SS restraints... Processing helix chain 'A' and resid 34 through 51 removed outlier: 4.011A pdb=" N MET A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 154 through 161 Processing helix chain 'A' and resid 191 through 195 Processing helix chain 'A' and resid 212 through 234 removed outlier: 3.772A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 51 removed outlier: 3.591A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N MET B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 212 through 229 Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.551A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 55 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.714A pdb=" N LEU C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG C 247 " --> pdb=" O PRO C 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 242 through 247' Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.578A pdb=" N ILE C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 391 Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 482 removed outlier: 3.705A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY C 482 " --> pdb=" O ARG C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 removed outlier: 3.682A pdb=" N MET C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 509 Processing helix chain 'C' and resid 519 through 529 Processing helix chain 'C' and resid 544 through 549 removed outlier: 3.681A pdb=" N ARG C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.676A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 569 removed outlier: 4.400A pdb=" N ASN C 568 " --> pdb=" O GLU C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 614 Processing helix chain 'C' and resid 656 through 661 removed outlier: 4.204A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 668 removed outlier: 4.293A pdb=" N ILE C 668 " --> pdb=" O GLY C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 removed outlier: 3.958A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 712 removed outlier: 4.446A pdb=" N ALA C 707 " --> pdb=" O GLY C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 865 removed outlier: 3.768A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU C 865 " --> pdb=" O ALA C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 Processing helix chain 'C' and resid 942 through 980 Processing helix chain 'C' and resid 985 through 991 Processing helix chain 'C' and resid 993 through 1000 Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1101 through 1107 removed outlier: 4.164A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1108 through 1134 removed outlier: 3.927A pdb=" N ILE C1112 " --> pdb=" O ASN C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.797A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1177 Processing helix chain 'C' and resid 1191 through 1203 Processing helix chain 'C' and resid 1238 through 1242 Processing helix chain 'C' and resid 1271 through 1281 Processing helix chain 'C' and resid 1283 through 1292 removed outlier: 3.622A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) Processing helix chain 'C' and resid 1299 through 1310 Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.667A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 95 through 101 removed outlier: 3.997A pdb=" N ARG D 99 " --> pdb=" O THR D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 119 removed outlier: 3.552A pdb=" N LEU D 117 " --> pdb=" O HIS D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 173 removed outlier: 3.905A pdb=" N GLU D 171 " --> pdb=" O ASP D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 191 Processing helix chain 'D' and resid 193 through 208 removed outlier: 4.052A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 256 through 258 No H-bonds generated for 'chain 'D' and resid 256 through 258' Processing helix chain 'D' and resid 263 through 285 Processing helix chain 'D' and resid 288 through 309 Processing helix chain 'D' and resid 327 through 331 Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 370 through 388 Proline residue: D 379 - end of helix Processing helix chain 'D' and resid 393 through 403 Processing helix chain 'D' and resid 406 through 416 removed outlier: 3.545A pdb=" N ILE D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 457 removed outlier: 3.604A pdb=" N ALA D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 515 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 583 removed outlier: 4.085A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL D 583 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 613 through 636 removed outlier: 3.686A pdb=" N THR D 617 " --> pdb=" O GLY D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 670 removed outlier: 4.592A pdb=" N GLU D 652 " --> pdb=" O GLU D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 702 Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.902A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.576A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 876 Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 925 removed outlier: 4.150A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 929 Processing helix chain 'D' and resid 1069 through 1074 removed outlier: 4.246A pdb=" N ASP D1073 " --> pdb=" O ALA D1069 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU D1074 " --> pdb=" O GLY D1070 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1069 through 1074' Processing helix chain 'D' and resid 1136 through 1146 Processing helix chain 'D' and resid 1216 through 1245 removed outlier: 7.653A pdb=" N VAL D1226 " --> pdb=" O ARG D1222 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N HIS D1227 " --> pdb=" O LEU D1223 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA D1228 " --> pdb=" O ARG D1224 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 removed outlier: 3.870A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1295 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.964A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1376 removed outlier: 4.305A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 14 Processing helix chain 'E' and resid 15 through 32 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 91 Processing helix chain 'F' and resid 10 through 20 Processing helix chain 'F' and resid 64 through 72 Processing helix chain 'F' and resid 89 through 100 removed outlier: 3.506A pdb=" N GLN F 98 " --> pdb=" O SER F 94 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU F 99 " --> pdb=" O GLU F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 128 Processing helix chain 'F' and resid 130 through 132 No H-bonds generated for 'chain 'F' and resid 130 through 132' Processing helix chain 'F' and resid 143 through 153 removed outlier: 4.600A pdb=" N GLN F 149 " --> pdb=" O ASN F 145 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N PHE F 151 " --> pdb=" O ILE F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 187 removed outlier: 3.506A pdb=" N SER F 180 " --> pdb=" O GLY F 176 " (cutoff:3.500A) Proline residue: F 181 - end of helix Processing helix chain 'F' and resid 196 through 213 Processing helix chain 'F' and resid 250 through 264 removed outlier: 3.539A pdb=" N LEU F 260 " --> pdb=" O ALA F 256 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS F 263 " --> pdb=" O SER F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 298 Processing helix chain 'F' and resid 300 through 314 Processing helix chain 'F' and resid 328 through 343 Processing helix chain 'F' and resid 344 through 348 Processing helix chain 'F' and resid 376 through 380 Processing helix chain 'F' and resid 384 through 401 Processing helix chain 'F' and resid 432 through 437 Processing helix chain 'F' and resid 478 through 489 Processing helix chain 'F' and resid 496 through 507 removed outlier: 3.936A pdb=" N GLN F 505 " --> pdb=" O ILE F 501 " (cutoff:3.500A) Processing helix chain 'F' and resid 520 through 534 Processing helix chain 'F' and resid 541 through 555 Processing helix chain 'F' and resid 559 through 580 removed outlier: 3.593A pdb=" N LYS F 580 " --> pdb=" O ASP F 576 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 585 Processing helix chain 'F' and resid 621 through 624 Processing helix chain 'F' and resid 625 through 629 Processing helix chain 'F' and resid 644 through 648 Processing helix chain 'F' and resid 649 through 659 removed outlier: 4.196A 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: 3.907A pdb=" N ALA F 815 " --> pdb=" O LEU F 811 " (cutoff:3.500A) Processing helix chain 'F' and resid 833 through 836 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 18 removed outlier: 5.251A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.570A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.709A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 18 removed outlier: 5.677A pdb=" N LEU B 13 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N GLU B 29 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N HIS B 23 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N THR B 207 " --> pdb=" O HIS B 23 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LYS B 25 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N MET B 205 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR B 27 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ILE B 203 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N GLU B 29 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LEU B 201 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS B 200 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL B 187 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL B 202 " --> pdb=" O TYR B 185 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR B 185 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLU B 204 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE B 183 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLU B 206 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 104 removed outlier: 8.389A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 111 removed outlier: 6.291A pdb=" N GLY B 108 " --> pdb=" O HIS B 132 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N HIS B 132 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.139A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 61 removed outlier: 6.739A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA C 94 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLY C 125 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU C 96 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TYR C 123 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N VAL C 98 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU C 121 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU C 100 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLU C 119 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU C 102 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE C 117 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE C 104 " --> pdb=" O LYS C 115 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB4, first strand: chain 'C' and resid 451 through 454 removed outlier: 4.661A pdb=" N SER C 574 " --> pdb=" O CYS C 559 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 160 removed outlier: 3.624A pdb=" N LEU C 171 " --> pdb=" O ASP C 160 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 284 through 286 removed outlier: 4.449A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 250 through 251 removed outlier: 3.741A pdb=" N ARG C 267 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AB9, first strand: chain 'C' and resid 296 through 297 removed outlier: 3.699A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 301 through 303 removed outlier: 6.676A pdb=" N TYR C 301 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE C 310 " --> pdb=" O TYR C 301 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581 removed outlier: 6.536A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC4, first strand: chain 'C' and resid 716 through 717 removed outlier: 7.024A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.651A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.646A pdb=" N THR C 757 " --> pdb=" O ILE C 765 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE C 765 " --> pdb=" O THR C 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC8, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.430A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.650A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AD2, first strand: chain 'C' and resid 882 through 884 removed outlier: 7.185A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD4, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 7.631A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1335 through 1340 removed outlier: 4.015A pdb=" N ALA D 19 " --> pdb=" O GLU C1340 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 103 through 112 removed outlier: 3.531A pdb=" N LEU D 107 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.458A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.179A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AD8, first strand: chain 'D' and resid 252 through 254 Processing sheet with id=AD9, first strand: chain 'D' and resid 367 through 369 Processing sheet with id=AE1, first strand: chain 'D' and resid 526 through 527 removed outlier: 7.226A pdb=" N LEU D 527 " --> pdb=" O ARG D 551 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N THR D 553 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 703 through 707 Processing sheet with id=AE3, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE4, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE5, first strand: chain 'D' and resid 825 through 827 removed outlier: 6.364A pdb=" N VAL D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 848 through 849 removed outlier: 6.453A pdb=" N VAL D 848 " --> pdb=" O LEU D 857 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 949 through 951 removed outlier: 4.165A pdb=" N ALA D1018 " --> pdb=" O ILE D 950 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 991 through 997 removed outlier: 6.342A pdb=" N LEU D 984 " --> pdb=" O LYS D 992 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER D 994 " --> pdb=" O LEU D 982 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU D 982 " --> pdb=" O SER D 994 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LYS D 996 " --> pdb=" O THR D 980 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N THR D 980 " --> pdb=" O LYS D 996 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1028 through 1029 Processing sheet with id=AF1, first strand: chain 'D' and resid 1098 through 1100 Processing sheet with id=AF2, first strand: chain 'D' and resid 1046 through 1050 removed outlier: 3.852A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 1186 through 1191 Processing sheet with id=AF4, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 6.741A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 25 through 29 removed outlier: 6.712A pdb=" N ALA F 4 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N LYS F 28 " --> pdb=" O ALA F 4 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL F 6 " --> pdb=" O LYS F 28 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N LYS F 3 " --> pdb=" O HIS F 105 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N TYR F 107 " --> pdb=" O LYS F 3 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU F 5 " --> pdb=" O TYR F 107 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 35 through 36 Processing sheet with id=AF7, first strand: chain 'F' and resid 244 through 245 removed outlier: 15.304A pdb=" N ALA F 233 " --> pdb=" O ARG F 427 " (cutoff:3.500A) removed outlier: 12.153A pdb=" N ARG F 427 " --> pdb=" O ALA F 233 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N ALA F 235 " --> pdb=" O ARG F 425 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ARG F 425 " --> pdb=" O ALA F 235 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG F 421 " --> pdb=" O THR F 239 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LYS F 407 " --> pdb=" O ARG F 430 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLY F 416 " --> pdb=" O VAL F 268 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N VAL F 268 " --> pdb=" O GLY F 416 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR F 266 " --> pdb=" O LEU F 459 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER F 225 " --> pdb=" O VAL F 462 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LEU F 464 " --> pdb=" O ASP F 223 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASP F 223 " --> pdb=" O LEU F 464 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLU F 221 " --> pdb=" O PRO F 466 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N GLN F 468 " --> pdb=" O PHE F 219 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N PHE F 219 " --> pdb=" O GLN F 468 " (cutoff:3.500A) removed outlier: 13.358A pdb=" N TRP F 220 " --> pdb=" O HIS F 240 " (cutoff:3.500A) removed outlier: 9.914A pdb=" N HIS F 240 " --> pdb=" O TRP F 220 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL F 222 " --> pdb=" O VAL F 238 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 510 through 513 Processing sheet with id=AF9, first strand: chain 'F' and resid 593 through 595 removed outlier: 3.785A pdb=" N VAL F 593 " --> pdb=" O ILE F 608 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 637 through 638 removed outlier: 3.670A pdb=" N VAL F 637 " --> pdb=" O LEU F 673 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 709 through 710 removed outlier: 7.688A pdb=" N LYS F 727 " --> pdb=" O ILE F 742 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE F 742 " --> pdb=" O LYS F 727 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LEU F 743 " --> pdb=" O GLU F 747 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N GLU F 747 " --> pdb=" O LEU F 743 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 756 through 762 removed outlier: 3.773A pdb=" N PHE F 770 " --> pdb=" O LEU F 758 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 826 through 832 removed outlier: 4.531A pdb=" N LYS F 826 " --> pdb=" O GLU F 843 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLN F 838 " --> pdb=" O TYR F 855 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N TYR F 855 " --> pdb=" O GLN F 838 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER F 842 " --> pdb=" O TRP F 851 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N TRP F 851 " --> pdb=" O SER F 842 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LYS F 844 " --> pdb=" O THR F 849 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N THR F 849 " --> pdb=" O LYS F 844 " (cutoff:3.500A) 1450 hydrogen bonds defined for protein. 4044 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 8.12 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6278 1.32 - 1.45: 8845 1.45 - 1.58: 18278 1.58 - 1.71: 89 1.71 - 1.84: 243 Bond restraints: 33733 Sorted by residual: bond pdb=" C PHE F 699 " pdb=" N ARG F 700 " ideal model delta sigma weight residual 1.328 1.230 0.099 1.42e-02 4.96e+03 4.81e+01 bond pdb=" C3' DG N 39 " pdb=" O3' DG N 39 " ideal model delta sigma weight residual 1.435 1.347 0.088 1.30e-02 5.92e+03 4.53e+01 bond pdb=" C ARG F 700 " pdb=" N ILE F 701 " ideal model delta sigma weight residual 1.330 1.256 0.074 1.35e-02 5.49e+03 3.04e+01 bond pdb=" P DG N 39 " pdb=" O5' DG N 39 " ideal model delta sigma weight residual 1.593 1.540 0.053 1.00e-02 1.00e+04 2.85e+01 bond pdb=" O4' DC N 38 " pdb=" C1' DC N 38 " ideal model delta sigma weight residual 1.420 1.365 0.055 1.10e-02 8.26e+03 2.51e+01 ... (remaining 33728 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 44475 2.53 - 5.06: 1163 5.06 - 7.59: 121 7.59 - 10.12: 23 10.12 - 12.64: 6 Bond angle restraints: 45788 Sorted by residual: angle pdb=" O4' DC N 38 " pdb=" C1' DC N 38 " pdb=" N1 DC N 38 " ideal model delta sigma weight residual 108.00 96.35 11.65 7.00e-01 2.04e+00 2.77e+02 angle pdb=" C3' DC N 38 " pdb=" O3' DC N 38 " pdb=" P DG N 39 " ideal model delta sigma weight residual 119.70 107.06 12.64 1.20e+00 6.94e-01 1.11e+02 angle pdb=" O4' DC N 38 " pdb=" C4' DC N 38 " pdb=" C3' DC N 38 " ideal model delta sigma weight residual 106.00 111.90 -5.90 6.00e-01 2.78e+00 9.67e+01 angle pdb=" C1' C R 11 " pdb=" N1 C R 11 " pdb=" C2 C R 11 " ideal model delta sigma weight residual 118.80 128.48 -9.68 1.10e+00 8.26e-01 7.74e+01 angle pdb=" C3' DG T 16 " pdb=" O3' DG T 16 " pdb=" P DA T 17 " ideal model delta sigma weight residual 119.70 109.68 10.02 1.20e+00 6.94e-01 6.97e+01 ... (remaining 45783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.75: 20097 34.75 - 69.50: 557 69.50 - 104.25: 33 104.25 - 139.01: 0 139.01 - 173.76: 1 Dihedral angle restraints: 20688 sinusoidal: 8959 harmonic: 11729 Sorted by residual: 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 -151.76 -28.24 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA SER A 49 " pdb=" C SER A 49 " pdb=" N SER A 50 " pdb=" CA SER A 50 " ideal model delta harmonic sigma weight residual -180.00 -152.38 -27.62 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" C ARG D 53 " pdb=" N ARG D 53 " pdb=" CA ARG D 53 " pdb=" CB ARG D 53 " ideal model delta harmonic sigma weight residual -122.60 -136.14 13.54 0 2.50e+00 1.60e-01 2.93e+01 ... (remaining 20685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 4848 0.109 - 0.218: 289 0.218 - 0.327: 21 0.327 - 0.435: 7 0.435 - 0.544: 7 Chirality restraints: 5172 Sorted by residual: chirality pdb=" P DG T 16 " pdb=" OP1 DG T 16 " pdb=" OP2 DG T 16 " pdb=" O5' DG T 16 " both_signs ideal model delta sigma weight residual True 2.34 -2.88 -0.54 2.00e-01 2.50e+01 7.41e+00 chirality pdb=" CA ARG F 793 " pdb=" N ARG F 793 " pdb=" C ARG F 793 " pdb=" CB ARG F 793 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.40e+00 chirality pdb=" CA ARG D 53 " pdb=" N ARG D 53 " pdb=" C ARG D 53 " pdb=" CB ARG D 53 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.87e+00 ... (remaining 5169 not shown) Planarity restraints: 5825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 801 " -0.110 2.00e-02 2.50e+03 5.71e-02 6.52e+01 pdb=" CG TYR F 801 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR F 801 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 TYR F 801 " 0.043 2.00e-02 2.50e+03 pdb=" CE1 TYR F 801 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR F 801 " 0.022 2.00e-02 2.50e+03 pdb=" CZ TYR F 801 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 801 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 49 " 0.086 2.00e-02 2.50e+03 5.29e-02 4.90e+01 pdb=" CG PHE D 49 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 PHE D 49 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 PHE D 49 " -0.046 2.00e-02 2.50e+03 pdb=" CE1 PHE D 49 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE D 49 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE D 49 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 699 " -0.072 2.00e-02 2.50e+03 4.72e-02 3.89e+01 pdb=" CG PHE F 699 " 0.088 2.00e-02 2.50e+03 pdb=" CD1 PHE F 699 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 PHE F 699 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE F 699 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 PHE F 699 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE F 699 " -0.023 2.00e-02 2.50e+03 ... (remaining 5822 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 320 2.55 - 3.14: 27673 3.14 - 3.72: 53473 3.72 - 4.31: 71087 4.31 - 4.90: 116491 Nonbonded interactions: 269044 Sorted by model distance: nonbonded pdb=" OD2 ASP D 460 " pdb="MG MG D1500 " model vdw 1.961 2.170 nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D1500 " model vdw 2.025 2.170 nonbonded pdb=" OG1 THR D1169 " pdb=" OP1 DG N 51 " model vdw 2.054 3.040 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1500 " model vdw 2.156 2.170 nonbonded pdb=" OG1 THR A 111 " pdb=" O PRO A 126 " model vdw 2.171 3.040 ... (remaining 269039 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: 0.240 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: 0.040 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 35.080 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 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 0.134 33753 Z= 0.368 Angle : 0.938 23.203 45818 Z= 0.610 Chirality : 0.061 0.544 5172 Planarity : 0.006 0.105 5825 Dihedral : 14.369 173.757 13142 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.08 % Favored : 96.65 % Rotamer: Outliers : 1.96 % Allowed : 6.69 % Favored : 91.35 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 3.43 % 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: 4060 helix: 0.27 (0.13), residues: 1448 sheet: 0.13 (0.21), residues: 597 loop : -0.57 (0.13), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 790 TYR 0.110 0.004 TYR F 801 PHE 0.088 0.004 PHE F 699 TRP 0.063 0.005 TRP F 79 HIS 0.005 0.001 HIS F 566 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.37 (33733) covalent geometry : angle 0.91919 / 0.61 (45788) hydrogen bonds : bond 0.14860 / 9.80 ( 1510) hydrogen bonds : angle 6.83014 / 4.80 ( 4176) metal coordination : bond 0.03820 / 2.24 ( 20) metal coordination : angle 7.34725 / 4.71 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 351 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 545 PHE cc_start: 0.8818 (m-80) cc_final: 0.8460 (m-80) REVERT: C 561 ILE cc_start: 0.9752 (mm) cc_final: 0.9435 (mp) REVERT: C 684 ASN cc_start: 0.8797 (t0) cc_final: 0.8396 (m110) REVERT: C 951 MET cc_start: 0.9306 (ppp) cc_final: 0.8861 (ppp) REVERT: C 1073 LYS cc_start: 0.8986 (mtmt) cc_final: 0.8551 (mtmt) REVERT: C 1078 LYS cc_start: 0.9252 (tptt) cc_final: 0.8953 (tppp) REVERT: C 1085 MET cc_start: 0.9022 (mmm) cc_final: 0.8779 (mmm) REVERT: C 1131 MET cc_start: 0.8750 (ttm) cc_final: 0.8467 (mtp) REVERT: C 1270 PHE cc_start: 0.9075 (t80) cc_final: 0.8571 (t80) REVERT: C 1286 THR cc_start: 0.9791 (t) cc_final: 0.9565 (p) REVERT: C 1319 MET cc_start: 0.8400 (tpp) cc_final: 0.7873 (mmm) REVERT: C 1333 LEU cc_start: 0.9577 (tp) cc_final: 0.9081 (mt) REVERT: D 115 TRP cc_start: 0.9155 (m-10) cc_final: 0.8646 (m-10) REVERT: D 136 GLU cc_start: 0.9564 (pt0) cc_final: 0.9338 (pp20) REVERT: D 513 MET cc_start: 0.8844 (ttm) cc_final: 0.8548 (ttt) REVERT: D 625 MET cc_start: 0.9314 (tmm) cc_final: 0.9089 (tmm) REVERT: D 725 MET cc_start: 0.8975 (mtp) cc_final: 0.8724 (mtp) REVERT: D 807 LEU cc_start: 0.8851 (tp) cc_final: 0.8616 (tp) REVERT: D 1348 LYS cc_start: 0.9687 (mtpp) cc_final: 0.9431 (mttt) REVERT: E 30 MET cc_start: 0.8991 (ttm) cc_final: 0.8780 (mtp) REVERT: F 104 ASP cc_start: 0.1281 (t0) cc_final: 0.0893 (m-30) REVERT: F 334 MET cc_start: 0.7387 (ttm) cc_final: 0.7113 (mtt) REVERT: F 538 MET cc_start: -0.1808 (mmm) cc_final: -0.3377 (mmt) REVERT: F 546 MET cc_start: -0.6444 (ttm) cc_final: -0.7203 (mmp) REVERT: F 587 MET cc_start: 0.2791 (ttm) cc_final: 0.2549 (ttm) REVERT: F 591 GLN cc_start: 0.6461 (OUTLIER) cc_final: 0.6128 (pt0) REVERT: F 669 MET cc_start: 0.6687 (mtm) cc_final: 0.6451 (mmm) REVERT: F 718 MET cc_start: 0.2798 (ttm) cc_final: 0.1279 (ttt) outliers start: 68 outliers final: 12 residues processed: 415 average time/residue: 0.2009 time to fit residues: 132.3774 Evaluate side-chains 212 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 199 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 7.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 HIS B 66 HIS ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 673 HIS C 688 GLN C 832 HIS ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1070 HIS C1175 ASN C1244 HIS D 113 HIS D 157 GLN D 335 GLN D 435 GLN D 477 GLN D 875 ASN D 951 GLN D1218 HIS D1235 ASN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN F 140 ASN F 152 ASN F 163 ASN F 197 GLN F 309 GLN F 353 ASN ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 ASN F 574 GLN F 590 ASN F 591 GLN F 681 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.068588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.049902 restraints weight = 360708.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.050499 restraints weight = 223908.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.050467 restraints weight = 154656.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.050972 restraints weight = 124943.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.051060 restraints weight = 93770.218| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 33753 Z= 0.187 Angle : 0.697 15.192 45818 Z= 0.363 Chirality : 0.045 0.407 5172 Planarity : 0.006 0.137 5825 Dihedral : 11.864 175.505 5127 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.36 % Favored : 97.56 % Rotamer: Outliers : 0.17 % Allowed : 3.03 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % 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: 0.05 (0.13), residues: 4060 helix: 0.77 (0.13), residues: 1471 sheet: 0.05 (0.19), residues: 662 loop : -0.46 (0.14), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG F 535 TYR 0.017 0.002 TYR C1231 PHE 0.023 0.002 PHE C1270 TRP 0.024 0.002 TRP F 560 HIS 0.016 0.002 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.19 (33733) covalent geometry : angle 0.68239 / 0.36 (45788) hydrogen bonds : bond 0.04921 / 3.38 ( 1510) hydrogen bonds : angle 5.43414 / 3.80 ( 4176) metal coordination : bond 0.01210 / 0.82 ( 20) metal coordination : angle 5.61822 / 3.52 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 230 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.8947 (tp) REVERT: B 51 MET cc_start: 0.9398 (tpp) cc_final: 0.9009 (mmm) REVERT: C 545 PHE cc_start: 0.8943 (m-80) cc_final: 0.8660 (m-80) REVERT: C 951 MET cc_start: 0.9353 (ppp) cc_final: 0.8977 (ppp) REVERT: C 1060 ILE cc_start: 0.9084 (mm) cc_final: 0.8882 (mp) REVERT: C 1078 LYS cc_start: 0.9428 (tptt) cc_final: 0.8933 (tppp) REVERT: C 1085 MET cc_start: 0.9007 (mmm) cc_final: 0.8471 (mmm) REVERT: C 1107 MET cc_start: 0.9679 (mpp) cc_final: 0.9470 (mpp) REVERT: C 1131 MET cc_start: 0.8872 (ttm) cc_final: 0.8552 (mtp) REVERT: C 1230 MET cc_start: 0.8351 (tpt) cc_final: 0.7735 (tpp) REVERT: C 1235 LEU cc_start: 0.9472 (mm) cc_final: 0.9100 (mp) REVERT: C 1304 MET cc_start: 0.9402 (tpt) cc_final: 0.8944 (tpp) REVERT: C 1319 MET cc_start: 0.8555 (tpp) cc_final: 0.7962 (mmm) REVERT: C 1333 LEU cc_start: 0.9443 (tp) cc_final: 0.9061 (tt) REVERT: D 115 TRP cc_start: 0.9251 (m-10) cc_final: 0.8562 (m-10) REVERT: D 130 MET cc_start: 0.9228 (tpp) cc_final: 0.8777 (tpp) REVERT: D 180 MET cc_start: 0.8391 (tpt) cc_final: 0.8061 (tpt) REVERT: D 192 MET cc_start: 0.8812 (mtm) cc_final: 0.8564 (mtm) REVERT: D 278 ARG cc_start: 0.9642 (ttm110) cc_final: 0.8918 (ptp-110) REVERT: D 279 LEU cc_start: 0.9821 (tp) cc_final: 0.9534 (tp) REVERT: D 400 MET cc_start: 0.9322 (tpp) cc_final: 0.9110 (tpp) REVERT: D 435 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7369 (mp10) REVERT: D 443 GLU cc_start: 0.9283 (tp30) cc_final: 0.8923 (tp30) REVERT: D 466 MET cc_start: 0.8691 (tpp) cc_final: 0.8317 (tmm) REVERT: D 485 MET cc_start: 0.8495 (mmp) cc_final: 0.7445 (mmm) REVERT: D 513 MET cc_start: 0.8998 (ttm) cc_final: 0.8335 (ttp) REVERT: D 581 MET cc_start: 0.8610 (tpp) cc_final: 0.8351 (tpp) REVERT: D 724 MET cc_start: 0.9321 (mmp) cc_final: 0.8987 (mmm) REVERT: D 747 MET cc_start: 0.7740 (ttt) cc_final: 0.7341 (ttt) REVERT: D 807 LEU cc_start: 0.8741 (tp) cc_final: 0.8431 (tp) REVERT: D 1025 MET cc_start: 0.9137 (tpt) cc_final: 0.8324 (tmm) REVERT: D 1145 PHE cc_start: 0.8973 (m-80) cc_final: 0.8144 (m-80) REVERT: F 104 ASP cc_start: 0.2420 (t0) cc_final: 0.2117 (m-30) REVERT: F 376 MET cc_start: 0.0298 (mmp) cc_final: 0.0088 (mmp) REVERT: F 590 ASN cc_start: -0.0327 (OUTLIER) cc_final: -0.0643 (t0) REVERT: F 669 MET cc_start: 0.6549 (mtm) cc_final: 0.6296 (mmm) outliers start: 6 outliers final: 1 residues processed: 235 average time/residue: 0.2015 time to fit residues: 76.5632 Evaluate side-chains 178 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 174 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 256 optimal weight: 8.9990 chunk 35 optimal weight: 20.0000 chunk 299 optimal weight: 5.9990 chunk 255 optimal weight: 4.9990 chunk 275 optimal weight: 9.9990 chunk 315 optimal weight: 8.9990 chunk 187 optimal weight: 20.0000 chunk 407 optimal weight: 50.0000 chunk 265 optimal weight: 9.9990 chunk 230 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 ASN A 128 HIS B 128 HIS C 31 GLN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 GLN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS C 834 GLN ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1264 GLN ** D 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1019 ASN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN F 242 ASN ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 533 ASN F 591 GLN ** F 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.065255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.045973 restraints weight = 368820.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.045919 restraints weight = 226254.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.046338 restraints weight = 148944.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.046634 restraints weight = 115848.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.046902 restraints weight = 97991.410| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 33753 Z= 0.237 Angle : 0.706 13.716 45818 Z= 0.365 Chirality : 0.044 0.428 5172 Planarity : 0.005 0.139 5825 Dihedral : 12.067 178.904 5127 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.56 % Favored : 97.36 % Rotamer: Outliers : 0.06 % Allowed : 4.12 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.13), residues: 4060 helix: 0.80 (0.13), residues: 1492 sheet: -0.28 (0.19), residues: 672 loop : -0.32 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 150 TYR 0.018 0.002 TYR F 855 PHE 0.028 0.002 PHE C 514 TRP 0.018 0.002 TRP F 851 HIS 0.011 0.002 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.24 (33733) covalent geometry : angle 0.69542 / 0.36 (45788) hydrogen bonds : bond 0.05136 / 3.56 ( 1510) hydrogen bonds : angle 5.27697 / 3.67 ( 4176) metal coordination : bond 0.00827 / 0.57 ( 20) metal coordination : angle 4.90518 / 3.00 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 197 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 315 MET cc_start: 0.9289 (ptt) cc_final: 0.9006 (ptt) REVERT: C 403 MET cc_start: 0.9231 (ppp) cc_final: 0.8858 (ppp) REVERT: C 459 MET cc_start: 0.9428 (mpp) cc_final: 0.9226 (mpp) REVERT: C 464 PHE cc_start: 0.8935 (t80) cc_final: 0.8679 (t80) REVERT: C 545 PHE cc_start: 0.8966 (m-80) cc_final: 0.8689 (m-80) REVERT: C 671 LEU cc_start: 0.9455 (mt) cc_final: 0.9253 (mt) REVERT: C 685 MET cc_start: 0.9294 (mtm) cc_final: 0.8993 (ptp) REVERT: C 805 MET cc_start: 0.8551 (ppp) cc_final: 0.8330 (ppp) REVERT: C 814 ASP cc_start: 0.8233 (t0) cc_final: 0.7988 (t0) REVERT: C 1078 LYS cc_start: 0.9654 (tptt) cc_final: 0.9212 (tppp) REVERT: C 1085 MET cc_start: 0.9140 (mmm) cc_final: 0.8433 (mmp) REVERT: C 1107 MET cc_start: 0.9628 (mpp) cc_final: 0.9376 (mpp) REVERT: C 1131 MET cc_start: 0.8956 (ttm) cc_final: 0.8676 (mtp) REVERT: C 1230 MET cc_start: 0.8011 (tpt) cc_final: 0.7703 (tpp) REVERT: C 1304 MET cc_start: 0.9453 (tpt) cc_final: 0.9027 (tpp) REVERT: C 1319 MET cc_start: 0.9096 (tpp) cc_final: 0.8223 (tpp) REVERT: D 102 MET cc_start: 0.8354 (ppp) cc_final: 0.8130 (ppp) REVERT: D 130 MET cc_start: 0.9174 (tpp) cc_final: 0.8846 (tpp) REVERT: D 136 GLU cc_start: 0.9516 (pt0) cc_final: 0.9258 (pp20) REVERT: D 278 ARG cc_start: 0.9678 (ttm110) cc_final: 0.9304 (ptp-110) REVERT: D 400 MET cc_start: 0.9317 (tpp) cc_final: 0.9117 (tpp) REVERT: D 466 MET cc_start: 0.9010 (tpp) cc_final: 0.8365 (tpt) REVERT: D 485 MET cc_start: 0.8984 (mmp) cc_final: 0.8195 (mmm) REVERT: D 513 MET cc_start: 0.8606 (ttm) cc_final: 0.8083 (ttp) REVERT: D 724 MET cc_start: 0.9316 (mmp) cc_final: 0.9015 (mmm) REVERT: D 725 MET cc_start: 0.9092 (mtp) cc_final: 0.8607 (mtp) REVERT: D 747 MET cc_start: 0.8138 (ttt) cc_final: 0.7850 (ttt) REVERT: D 807 LEU cc_start: 0.8767 (tp) cc_final: 0.8340 (tp) REVERT: D 1141 VAL cc_start: 0.9559 (m) cc_final: 0.8840 (p) REVERT: D 1145 PHE cc_start: 0.9239 (m-80) cc_final: 0.7969 (m-80) REVERT: D 1306 LEU cc_start: 0.8711 (mt) cc_final: 0.8326 (mp) REVERT: F 669 MET cc_start: 0.6462 (mtm) cc_final: 0.6188 (mtt) REVERT: F 729 MET cc_start: 0.3309 (ttp) cc_final: 0.2614 (tmm) outliers start: 2 outliers final: 0 residues processed: 198 average time/residue: 0.1763 time to fit residues: 58.0551 Evaluate side-chains 159 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 218 optimal weight: 9.9990 chunk 204 optimal weight: 8.9990 chunk 260 optimal weight: 7.9990 chunk 377 optimal weight: 6.9990 chunk 241 optimal weight: 4.9990 chunk 116 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 369 optimal weight: 20.0000 chunk 96 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 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 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 518 ASN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 GLN C 760 ASN ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 HIS ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 HIS ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN F 166 GLN ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN ** F 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.061548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.040298 restraints weight = 344359.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 81)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.040886 restraints weight = 219941.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.041287 restraints weight = 157366.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.041750 restraints weight = 127995.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.042202 restraints weight = 110078.425| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 33753 Z= 0.229 Angle : 0.655 14.525 45818 Z= 0.344 Chirality : 0.043 0.422 5172 Planarity : 0.005 0.111 5825 Dihedral : 12.229 179.863 5127 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.91 % Favored : 97.04 % Rotamer: Outliers : 0.06 % Allowed : 3.63 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % 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: 0.10 (0.13), residues: 4060 helix: 0.87 (0.13), residues: 1479 sheet: -0.44 (0.19), residues: 676 loop : -0.27 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 281 TYR 0.018 0.002 TYR C1229 PHE 0.016 0.002 PHE B 231 TRP 0.012 0.002 TRP F 560 HIS 0.010 0.002 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.23 (33733) covalent geometry : angle 0.64518 / 0.34 (45788) hydrogen bonds : bond 0.04512 / 3.15 ( 1510) hydrogen bonds : angle 5.22588 / 3.64 ( 4176) metal coordination : bond 0.01021 / 0.67 ( 20) metal coordination : angle 4.44220 / 2.77 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 178 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 403 MET cc_start: 0.9247 (ppp) cc_final: 0.8813 (ppp) REVERT: C 464 PHE cc_start: 0.8943 (t80) cc_final: 0.8705 (t80) REVERT: C 545 PHE cc_start: 0.8916 (m-80) cc_final: 0.8639 (m-80) REVERT: C 685 MET cc_start: 0.9308 (mtm) cc_final: 0.8962 (ptp) REVERT: C 760 ASN cc_start: 0.9011 (OUTLIER) cc_final: 0.8275 (t0) REVERT: C 768 MET cc_start: 0.7939 (ppp) cc_final: 0.7688 (ppp) REVERT: C 800 MET cc_start: 0.8517 (pmm) cc_final: 0.7173 (pmm) REVERT: C 805 MET cc_start: 0.8701 (ppp) cc_final: 0.8461 (ppp) REVERT: C 1078 LYS cc_start: 0.9679 (tptt) cc_final: 0.9356 (tppp) REVERT: C 1085 MET cc_start: 0.9033 (mmm) cc_final: 0.8439 (mmp) REVERT: C 1107 MET cc_start: 0.9726 (mpp) cc_final: 0.9415 (mpp) REVERT: C 1230 MET cc_start: 0.8061 (tpt) cc_final: 0.7771 (tpp) REVERT: C 1304 MET cc_start: 0.9400 (tpt) cc_final: 0.9023 (tpp) REVERT: C 1319 MET cc_start: 0.9169 (tpp) cc_final: 0.8254 (tpp) REVERT: D 130 MET cc_start: 0.8974 (tpp) cc_final: 0.8750 (tpp) REVERT: D 192 MET cc_start: 0.8492 (mtm) cc_final: 0.8226 (mtm) REVERT: D 237 MET cc_start: 0.8995 (mtp) cc_final: 0.8794 (mtp) REVERT: D 485 MET cc_start: 0.8985 (mmp) cc_final: 0.8058 (mmm) REVERT: D 513 MET cc_start: 0.8576 (ttm) cc_final: 0.7888 (ttp) REVERT: D 724 MET cc_start: 0.9312 (mmp) cc_final: 0.9036 (mmm) REVERT: D 725 MET cc_start: 0.8851 (mtp) cc_final: 0.8564 (mtp) REVERT: D 1025 MET cc_start: 0.9187 (tpt) cc_final: 0.8231 (tmm) REVERT: D 1306 LEU cc_start: 0.8918 (mt) cc_final: 0.8652 (mt) REVERT: F 587 MET cc_start: 0.3327 (ttm) cc_final: 0.3071 (ttm) REVERT: F 669 MET cc_start: 0.6437 (mtm) cc_final: 0.6211 (mtt) REVERT: F 729 MET cc_start: 0.1150 (ttp) cc_final: 0.0878 (tmm) outliers start: 2 outliers final: 1 residues processed: 180 average time/residue: 0.1835 time to fit residues: 55.6200 Evaluate side-chains 153 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 151 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 92 optimal weight: 3.9990 chunk 292 optimal weight: 30.0000 chunk 7 optimal weight: 4.9990 chunk 344 optimal weight: 10.0000 chunk 227 optimal weight: 5.9990 chunk 410 optimal weight: 40.0000 chunk 269 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 chunk 204 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1324 ASN ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN ** F 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.064667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.043947 restraints weight = 371140.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 74)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.044237 restraints weight = 221358.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.044876 restraints weight = 151702.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 81)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.045515 restraints weight = 115875.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.045788 restraints weight = 96229.448| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33753 Z= 0.170 Angle : 0.611 14.308 45818 Z= 0.315 Chirality : 0.043 0.425 5172 Planarity : 0.005 0.131 5825 Dihedral : 12.176 179.430 5127 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.64 % Favored : 97.32 % Rotamer: Outliers : 0.03 % Allowed : 2.22 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % 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: 0.18 (0.13), residues: 4060 helix: 1.01 (0.13), residues: 1481 sheet: -0.44 (0.19), residues: 681 loop : -0.27 (0.15), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D1048 TYR 0.017 0.001 TYR C1229 PHE 0.017 0.001 PHE D1034 TRP 0.011 0.001 TRP F 560 HIS 0.011 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.17 (33733) covalent geometry : angle 0.60066 / 0.31 (45788) hydrogen bonds : bond 0.04085 / 2.86 ( 1510) hydrogen bonds : angle 5.06662 / 3.52 ( 4176) metal coordination : bond 0.00643 / 0.43 ( 20) metal coordination : angle 4.40731 / 2.72 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: 0.9643 (mmp) cc_final: 0.9217 (mmm) REVERT: C 403 MET cc_start: 0.9378 (ppp) cc_final: 0.9035 (ppp) REVERT: C 459 MET cc_start: 0.9401 (mpp) cc_final: 0.9182 (mpp) REVERT: C 464 PHE cc_start: 0.8897 (t80) cc_final: 0.8638 (t80) REVERT: C 768 MET cc_start: 0.8048 (ppp) cc_final: 0.7729 (ppp) REVERT: C 800 MET cc_start: 0.8835 (pmm) cc_final: 0.7299 (pmm) REVERT: C 805 MET cc_start: 0.8776 (ppp) cc_final: 0.8448 (ppp) REVERT: C 1078 LYS cc_start: 0.9752 (tptt) cc_final: 0.9448 (tppp) REVERT: C 1085 MET cc_start: 0.9055 (mmm) cc_final: 0.8437 (mmm) REVERT: C 1107 MET cc_start: 0.9599 (mpp) cc_final: 0.9362 (mpp) REVERT: C 1230 MET cc_start: 0.8043 (tpt) cc_final: 0.7705 (tpp) REVERT: C 1304 MET cc_start: 0.9456 (tpt) cc_final: 0.9074 (tpp) REVERT: C 1319 MET cc_start: 0.9250 (tpp) cc_final: 0.8442 (tpp) REVERT: D 400 MET cc_start: 0.9233 (tpp) cc_final: 0.8870 (tpp) REVERT: D 466 MET cc_start: 0.8675 (tpt) cc_final: 0.7555 (tpt) REVERT: D 513 MET cc_start: 0.8589 (ttm) cc_final: 0.7810 (ttp) REVERT: D 581 MET cc_start: 0.8565 (mmt) cc_final: 0.8068 (mmm) REVERT: D 724 MET cc_start: 0.9254 (mmp) cc_final: 0.8990 (mmm) REVERT: D 807 LEU cc_start: 0.8828 (tp) cc_final: 0.8281 (tp) REVERT: D 1025 MET cc_start: 0.9159 (tpt) cc_final: 0.8189 (tmm) REVERT: D 1306 LEU cc_start: 0.9002 (mt) cc_final: 0.8706 (mt) REVERT: F 376 MET cc_start: 0.0805 (mmp) cc_final: 0.0603 (mmp) REVERT: F 587 MET cc_start: 0.3628 (ttm) cc_final: 0.3273 (mtm) REVERT: F 669 MET cc_start: 0.6751 (mtm) cc_final: 0.6548 (mtt) REVERT: F 729 MET cc_start: 0.2605 (ttp) cc_final: 0.2286 (tmm) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.1947 time to fit residues: 60.5154 Evaluate side-chains 153 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 37 optimal weight: 9.9990 chunk 350 optimal weight: 30.0000 chunk 385 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 chunk 405 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 310 optimal weight: 8.9990 chunk 341 optimal weight: 50.0000 chunk 351 optimal weight: 10.0000 chunk 401 optimal weight: 20.0000 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN ** F 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.060953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.039663 restraints weight = 341289.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.040495 restraints weight = 220074.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.041053 restraints weight = 159146.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.041275 restraints weight = 126786.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.041535 restraints weight = 112527.321| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 33753 Z= 0.214 Angle : 0.634 13.760 45818 Z= 0.330 Chirality : 0.042 0.425 5172 Planarity : 0.005 0.106 5825 Dihedral : 12.202 178.820 5127 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.98 % Favored : 96.97 % Rotamer: Outliers : 0.03 % Allowed : 2.42 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % 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: 0.10 (0.13), residues: 4060 helix: 0.97 (0.13), residues: 1481 sheet: -0.52 (0.19), residues: 675 loop : -0.33 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 88 TYR 0.030 0.002 TYR F 855 PHE 0.025 0.002 PHE C 514 TRP 0.012 0.001 TRP F 560 HIS 0.008 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.21 (33733) covalent geometry : angle 0.62391 / 0.33 (45788) hydrogen bonds : bond 0.04390 / 3.07 ( 1510) hydrogen bonds : angle 5.11582 / 3.56 ( 4176) metal coordination : bond 0.00749 / 0.48 ( 20) metal coordination : angle 4.54560 / 2.93 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 1.004 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: B 51 MET cc_start: 0.9476 (mmp) cc_final: 0.9140 (mmm) REVERT: C 459 MET cc_start: 0.9474 (mpp) cc_final: 0.9268 (mpp) REVERT: C 464 PHE cc_start: 0.8916 (t80) cc_final: 0.8653 (t80) REVERT: C 681 MET cc_start: 0.9382 (mtm) cc_final: 0.9098 (mtt) REVERT: C 768 MET cc_start: 0.8124 (ppp) cc_final: 0.7862 (ppp) REVERT: C 800 MET cc_start: 0.8911 (pmm) cc_final: 0.7605 (pmm) REVERT: C 805 MET cc_start: 0.8811 (ppp) cc_final: 0.8531 (ppp) REVERT: C 1078 LYS cc_start: 0.9706 (tptt) cc_final: 0.9436 (tppp) REVERT: C 1085 MET cc_start: 0.9000 (mmm) cc_final: 0.8475 (mmm) REVERT: C 1107 MET cc_start: 0.9680 (mpp) cc_final: 0.9427 (mpp) REVERT: C 1290 MET cc_start: 0.9423 (tpt) cc_final: 0.9198 (tpp) REVERT: C 1304 MET cc_start: 0.9389 (tpt) cc_final: 0.9061 (tpp) REVERT: C 1319 MET cc_start: 0.9283 (tpp) cc_final: 0.8478 (tpp) REVERT: D 130 MET cc_start: 0.9153 (tpt) cc_final: 0.8850 (tpp) REVERT: D 180 MET cc_start: 0.8285 (tpt) cc_final: 0.8064 (tpt) REVERT: D 192 MET cc_start: 0.8490 (mtm) cc_final: 0.8278 (mtm) REVERT: D 278 ARG cc_start: 0.9628 (ttm110) cc_final: 0.9132 (ptp-110) REVERT: D 400 MET cc_start: 0.9217 (tpp) cc_final: 0.8890 (tpp) REVERT: D 513 MET cc_start: 0.8483 (ttm) cc_final: 0.7710 (ttp) REVERT: D 581 MET cc_start: 0.8609 (mmt) cc_final: 0.8178 (mmm) REVERT: D 724 MET cc_start: 0.9277 (mmp) cc_final: 0.9008 (mmm) REVERT: D 725 MET cc_start: 0.9393 (mtp) cc_final: 0.9011 (mtp) REVERT: D 807 LEU cc_start: 0.8638 (tp) cc_final: 0.8368 (tp) REVERT: D 1025 MET cc_start: 0.8858 (tpt) cc_final: 0.8094 (tmm) REVERT: D 1306 LEU cc_start: 0.9093 (mt) cc_final: 0.8816 (mt) REVERT: F 587 MET cc_start: 0.3721 (ttm) cc_final: 0.3257 (mtm) REVERT: F 729 MET cc_start: 0.2330 (ttp) cc_final: 0.1852 (tmm) outliers start: 1 outliers final: 1 residues processed: 177 average time/residue: 0.1860 time to fit residues: 54.5138 Evaluate side-chains 148 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 153 optimal weight: 0.5980 chunk 283 optimal weight: 50.0000 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 246 optimal weight: 0.7980 chunk 179 optimal weight: 3.9990 chunk 249 optimal weight: 20.0000 chunk 335 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 233 optimal weight: 5.9990 chunk 331 optimal weight: 50.0000 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** 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 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 518 ASN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN ** F 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 825 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.061633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.040189 restraints weight = 340299.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.041034 restraints weight = 217715.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.041510 restraints weight = 155176.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.042009 restraints weight = 124677.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.042203 restraints weight = 107410.647| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33753 Z= 0.142 Angle : 0.604 13.726 45818 Z= 0.307 Chirality : 0.043 0.423 5172 Planarity : 0.004 0.131 5825 Dihedral : 12.145 178.400 5127 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.71 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % 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: 4060 helix: 1.06 (0.13), residues: 1487 sheet: -0.47 (0.19), residues: 671 loop : -0.33 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 47 TYR 0.025 0.001 TYR F 855 PHE 0.019 0.001 PHE C 186 TRP 0.011 0.001 TRP F 560 HIS 0.008 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (33733) covalent geometry : angle 0.59038 / 0.31 (45788) hydrogen bonds : bond 0.03859 / 2.70 ( 1510) hydrogen bonds : angle 4.98691 / 3.47 ( 4176) metal coordination : bond 0.00784 / 0.54 ( 20) metal coordination : angle 4.94819 / 3.20 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: 0.9457 (mmp) cc_final: 0.9111 (mmm) REVERT: C 403 MET cc_start: 0.9316 (ppp) cc_final: 0.9065 (ppp) REVERT: C 459 MET cc_start: 0.9439 (mpp) cc_final: 0.9231 (mpp) REVERT: C 464 PHE cc_start: 0.8932 (t80) cc_final: 0.8677 (t80) REVERT: C 768 MET cc_start: 0.8125 (ppp) cc_final: 0.7839 (ppp) REVERT: C 800 MET cc_start: 0.8969 (pmm) cc_final: 0.7539 (pmm) REVERT: C 805 MET cc_start: 0.8844 (ppp) cc_final: 0.8513 (ppp) REVERT: C 1078 LYS cc_start: 0.9729 (tptt) cc_final: 0.9437 (tppp) REVERT: C 1085 MET cc_start: 0.9068 (mmm) cc_final: 0.8191 (mmm) REVERT: C 1107 MET cc_start: 0.9665 (mpp) cc_final: 0.9346 (mpp) REVERT: C 1230 MET cc_start: 0.9104 (tpp) cc_final: 0.8169 (tpp) REVERT: C 1304 MET cc_start: 0.9408 (tpt) cc_final: 0.9042 (tpp) REVERT: C 1319 MET cc_start: 0.9268 (tpp) cc_final: 0.8461 (tpp) REVERT: D 130 MET cc_start: 0.9102 (tpt) cc_final: 0.8820 (tpp) REVERT: D 192 MET cc_start: 0.8453 (mtm) cc_final: 0.8231 (mtm) REVERT: D 237 MET cc_start: 0.8936 (mtp) cc_final: 0.8705 (mtp) REVERT: D 278 ARG cc_start: 0.9632 (ttm110) cc_final: 0.9173 (ptp-110) REVERT: D 400 MET cc_start: 0.9197 (tpp) cc_final: 0.8881 (tpp) REVERT: D 449 LEU cc_start: 0.9138 (tp) cc_final: 0.8860 (tt) REVERT: D 466 MET cc_start: 0.8498 (tpt) cc_final: 0.7837 (tpt) REVERT: D 485 MET cc_start: 0.9007 (mmp) cc_final: 0.7966 (mmm) REVERT: D 513 MET cc_start: 0.8482 (ttm) cc_final: 0.7654 (ttp) REVERT: D 581 MET cc_start: 0.8482 (mmt) cc_final: 0.8094 (mmm) REVERT: D 724 MET cc_start: 0.9233 (mmp) cc_final: 0.8955 (mmm) REVERT: D 725 MET cc_start: 0.9048 (mtp) cc_final: 0.8806 (mtp) REVERT: D 807 LEU cc_start: 0.8652 (tp) cc_final: 0.8373 (tp) REVERT: D 1025 MET cc_start: 0.8994 (tpt) cc_final: 0.8330 (tmm) REVERT: D 1306 LEU cc_start: 0.9092 (mt) cc_final: 0.8778 (mt) REVERT: F 587 MET cc_start: 0.3658 (ttm) cc_final: 0.3317 (mtm) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1895 time to fit residues: 54.4443 Evaluate side-chains 147 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 295 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 296 optimal weight: 7.9990 chunk 396 optimal weight: 2.9990 chunk 311 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 160 optimal weight: 10.0000 chunk 301 optimal weight: 4.9990 chunk 216 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** 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 447 HIS C 450 ASN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN C1008 GLN ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN D1244 GLN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN ** F 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.064631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.043914 restraints weight = 370162.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.044185 restraints weight = 220651.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.044723 restraints weight = 149416.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.045015 restraints weight = 116723.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.045297 restraints weight = 101067.597| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33753 Z= 0.132 Angle : 0.580 12.657 45818 Z= 0.297 Chirality : 0.042 0.422 5172 Planarity : 0.004 0.113 5825 Dihedral : 12.028 177.729 5127 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.54 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % 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: 4060 helix: 1.16 (0.14), residues: 1485 sheet: -0.40 (0.20), residues: 652 loop : -0.29 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 47 TYR 0.016 0.001 TYR D 46 PHE 0.017 0.001 PHE C 514 TRP 0.017 0.001 TRP F 560 HIS 0.007 0.001 HIS C 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (33733) covalent geometry : angle 0.56904 / 0.30 (45788) hydrogen bonds : bond 0.03683 / 2.57 ( 1510) hydrogen bonds : angle 4.89179 / 3.40 ( 4176) metal coordination : bond 0.00736 / 0.50 ( 20) metal coordination : angle 4.35362 / 2.84 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.458 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: B 51 MET cc_start: 0.9540 (mmp) cc_final: 0.9127 (mmm) REVERT: C 403 MET cc_start: 0.9371 (ppp) cc_final: 0.9120 (ppp) REVERT: C 459 MET cc_start: 0.9463 (mpp) cc_final: 0.9242 (mpp) REVERT: C 464 PHE cc_start: 0.8870 (t80) cc_final: 0.8523 (t80) REVERT: C 768 MET cc_start: 0.8165 (ppp) cc_final: 0.7869 (ppp) REVERT: C 800 MET cc_start: 0.9287 (pmm) cc_final: 0.8079 (pmm) REVERT: C 805 MET cc_start: 0.8905 (ppp) cc_final: 0.8508 (ppp) REVERT: C 1078 LYS cc_start: 0.9739 (tptt) cc_final: 0.9421 (tppp) REVERT: C 1085 MET cc_start: 0.9035 (mmm) cc_final: 0.7761 (mmm) REVERT: C 1107 MET cc_start: 0.9583 (mpp) cc_final: 0.9299 (mpp) REVERT: C 1230 MET cc_start: 0.9100 (tpp) cc_final: 0.8268 (tpp) REVERT: C 1304 MET cc_start: 0.9486 (tpt) cc_final: 0.9167 (tpp) REVERT: C 1319 MET cc_start: 0.9128 (tpp) cc_final: 0.8358 (tpp) REVERT: D 130 MET cc_start: 0.9060 (tpt) cc_final: 0.8804 (tpp) REVERT: D 180 MET cc_start: 0.8086 (tpt) cc_final: 0.7858 (tpt) REVERT: D 192 MET cc_start: 0.8477 (mtm) cc_final: 0.8240 (mtm) REVERT: D 237 MET cc_start: 0.8936 (mtp) cc_final: 0.8712 (mtp) REVERT: D 252 LEU cc_start: 0.8604 (tp) cc_final: 0.8392 (tp) REVERT: D 278 ARG cc_start: 0.9655 (ttm110) cc_final: 0.9133 (ptp-110) REVERT: D 400 MET cc_start: 0.9275 (tpp) cc_final: 0.8944 (tpp) REVERT: D 449 LEU cc_start: 0.9137 (tp) cc_final: 0.8883 (tt) REVERT: D 466 MET cc_start: 0.8537 (tpt) cc_final: 0.7880 (tpt) REVERT: D 485 MET cc_start: 0.9219 (mmp) cc_final: 0.7991 (mmm) REVERT: D 581 MET cc_start: 0.8516 (mmt) cc_final: 0.8136 (mmt) REVERT: D 724 MET cc_start: 0.9277 (mmp) cc_final: 0.8978 (mmm) REVERT: D 807 LEU cc_start: 0.8725 (tp) cc_final: 0.8434 (tp) REVERT: D 1025 MET cc_start: 0.9297 (tpt) cc_final: 0.8552 (tmm) REVERT: D 1306 LEU cc_start: 0.9159 (mt) cc_final: 0.8830 (mt) REVERT: F 587 MET cc_start: 0.3036 (ttm) cc_final: 0.2383 (mtm) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1904 time to fit residues: 53.0864 Evaluate side-chains 146 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 200 optimal weight: 6.9990 chunk 58 optimal weight: 20.0000 chunk 4 optimal weight: 9.9990 chunk 331 optimal weight: 20.0000 chunk 129 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 391 optimal weight: 7.9990 chunk 361 optimal weight: 50.0000 chunk 204 optimal weight: 7.9990 chunk 153 optimal weight: 2.9990 chunk 263 optimal weight: 0.0050 overall best weight: 5.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 573 GLN F 574 GLN F 591 GLN ** F 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.063822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.044213 restraints weight = 371269.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.043857 restraints weight = 225176.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.044351 restraints weight = 149611.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.044642 restraints weight = 114450.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.045072 restraints weight = 98761.597| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.125 33753 Z= 0.174 Angle : 0.603 12.782 45818 Z= 0.311 Chirality : 0.042 0.422 5172 Planarity : 0.004 0.106 5825 Dihedral : 12.049 177.399 5127 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.81 % Favored : 97.14 % Rotamer: Outliers : 0.03 % Allowed : 0.58 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % 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: 0.18 (0.13), residues: 4060 helix: 1.08 (0.13), residues: 1487 sheet: -0.51 (0.19), residues: 674 loop : -0.31 (0.15), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 515 TYR 0.013 0.001 TYR D 46 PHE 0.014 0.001 PHE C 514 TRP 0.016 0.001 TRP F 560 HIS 0.007 0.001 HIS C 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 (33733) covalent geometry : angle 0.59373 / 0.31 (45788) hydrogen bonds : bond 0.04017 / 2.81 ( 1510) hydrogen bonds : angle 4.99005 / 3.46 ( 4176) metal coordination : bond 0.00698 / 0.47 ( 20) metal coordination : angle 4.11375 / 2.70 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: 0.9483 (mmp) cc_final: 0.9133 (mmm) REVERT: C 403 MET cc_start: 0.9353 (ppp) cc_final: 0.9081 (ppp) REVERT: C 459 MET cc_start: 0.9454 (mpp) cc_final: 0.9240 (mpp) REVERT: C 464 PHE cc_start: 0.8767 (t80) cc_final: 0.8411 (t80) REVERT: C 538 LEU cc_start: 0.8772 (tp) cc_final: 0.8570 (tp) REVERT: C 768 MET cc_start: 0.8225 (ppp) cc_final: 0.7967 (ppp) REVERT: C 800 MET cc_start: 0.9175 (pmm) cc_final: 0.8226 (pmm) REVERT: C 805 MET cc_start: 0.8902 (ppp) cc_final: 0.8545 (ppp) REVERT: C 1078 LYS cc_start: 0.9774 (tptt) cc_final: 0.9432 (tppp) REVERT: C 1085 MET cc_start: 0.9018 (mmm) cc_final: 0.7825 (mmm) REVERT: C 1107 MET cc_start: 0.9565 (mpp) cc_final: 0.9301 (mpp) REVERT: C 1230 MET cc_start: 0.9060 (tpp) cc_final: 0.8186 (tpp) REVERT: C 1304 MET cc_start: 0.9427 (tpt) cc_final: 0.9124 (tpp) REVERT: C 1319 MET cc_start: 0.9153 (tpp) cc_final: 0.8388 (tpp) REVERT: D 130 MET cc_start: 0.9035 (tpt) cc_final: 0.8815 (tpp) REVERT: D 237 MET cc_start: 0.8908 (mtp) cc_final: 0.8698 (mtp) REVERT: D 252 LEU cc_start: 0.8723 (tp) cc_final: 0.8514 (tp) REVERT: D 400 MET cc_start: 0.9209 (tpp) cc_final: 0.8938 (tpp) REVERT: D 466 MET cc_start: 0.8526 (tpt) cc_final: 0.7866 (tpt) REVERT: D 485 MET cc_start: 0.9259 (mmp) cc_final: 0.8099 (mmm) REVERT: D 581 MET cc_start: 0.8544 (mmt) cc_final: 0.8343 (mmt) REVERT: D 604 MET cc_start: 0.9051 (mmt) cc_final: 0.8609 (mmp) REVERT: D 724 MET cc_start: 0.9238 (mmp) cc_final: 0.8997 (mmm) REVERT: D 807 LEU cc_start: 0.8672 (tp) cc_final: 0.8379 (tp) REVERT: D 1025 MET cc_start: 0.9257 (tpt) cc_final: 0.8501 (tmm) REVERT: D 1306 LEU cc_start: 0.9159 (mt) cc_final: 0.8862 (mt) REVERT: F 71 MET cc_start: -0.1695 (mpp) cc_final: -0.2070 (mpp) REVERT: F 587 MET cc_start: 0.2787 (ttm) cc_final: 0.2248 (mtm) outliers start: 1 outliers final: 0 residues processed: 166 average time/residue: 0.1923 time to fit residues: 53.7913 Evaluate side-chains 146 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 164 optimal weight: 20.0000 chunk 313 optimal weight: 9.9990 chunk 363 optimal weight: 5.9990 chunk 252 optimal weight: 1.9990 chunk 208 optimal weight: 9.9990 chunk 71 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 chunk 222 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 336 optimal weight: 9.9990 chunk 357 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** 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 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN D 951 GLN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN ** F 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.062831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.043186 restraints weight = 378054.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.042883 restraints weight = 230010.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.043364 restraints weight = 152643.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 76)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.043870 restraints weight = 116580.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.043946 restraints weight = 94625.622| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 33753 Z= 0.205 Angle : 0.635 13.150 45818 Z= 0.328 Chirality : 0.043 0.425 5172 Planarity : 0.005 0.102 5825 Dihedral : 12.148 176.945 5127 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.93 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % 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: 0.03 (0.13), residues: 4060 helix: 0.95 (0.13), residues: 1482 sheet: -0.55 (0.20), residues: 646 loop : -0.41 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 47 TYR 0.025 0.002 TYR C1229 PHE 0.015 0.002 PHE C 57 TRP 0.022 0.002 TRP C1276 HIS 0.011 0.002 HIS F 681 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.20 (33733) covalent geometry : angle 0.62440 / 0.33 (45788) hydrogen bonds : bond 0.04325 / 3.02 ( 1510) hydrogen bonds : angle 5.07021 / 3.51 ( 4176) metal coordination : bond 0.00920 / 0.63 ( 20) metal coordination : angle 4.55520 / 2.89 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.913 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: B 51 MET cc_start: 0.9547 (mmp) cc_final: 0.9199 (mmm) REVERT: C 403 MET cc_start: 0.9380 (ppp) cc_final: 0.9107 (ppp) REVERT: C 459 MET cc_start: 0.9502 (mpp) cc_final: 0.9246 (mpp) REVERT: C 464 PHE cc_start: 0.8765 (t80) cc_final: 0.8394 (t80) REVERT: C 538 LEU cc_start: 0.8854 (tp) cc_final: 0.8586 (tp) REVERT: C 685 MET cc_start: 0.9457 (ptp) cc_final: 0.8593 (mpp) REVERT: C 768 MET cc_start: 0.8308 (ppp) cc_final: 0.8037 (ppp) REVERT: C 800 MET cc_start: 0.9244 (pmm) cc_final: 0.8284 (pmm) REVERT: C 805 MET cc_start: 0.8917 (ppp) cc_final: 0.8517 (ppp) REVERT: C 1085 MET cc_start: 0.9022 (mmm) cc_final: 0.7858 (mmm) REVERT: C 1107 MET cc_start: 0.9609 (mpp) cc_final: 0.9275 (mpp) REVERT: C 1230 MET cc_start: 0.9021 (tpp) cc_final: 0.8180 (tpp) REVERT: C 1290 MET cc_start: 0.9390 (tpt) cc_final: 0.9171 (tpp) REVERT: C 1304 MET cc_start: 0.9425 (tpt) cc_final: 0.9139 (tpp) REVERT: C 1319 MET cc_start: 0.9090 (tpp) cc_final: 0.8588 (tpp) REVERT: D 130 MET cc_start: 0.9034 (tpt) cc_final: 0.8817 (tpp) REVERT: D 252 LEU cc_start: 0.8768 (tp) cc_final: 0.8562 (tp) REVERT: D 278 ARG cc_start: 0.9641 (ttm110) cc_final: 0.9441 (ttm110) REVERT: D 330 MET cc_start: 0.9475 (mmp) cc_final: 0.9047 (mmp) REVERT: D 400 MET cc_start: 0.9211 (tpp) cc_final: 0.8962 (tpp) REVERT: D 466 MET cc_start: 0.8702 (tpt) cc_final: 0.7891 (tpt) REVERT: D 485 MET cc_start: 0.9318 (mmp) cc_final: 0.8282 (mmm) REVERT: D 581 MET cc_start: 0.8716 (mmt) cc_final: 0.8339 (mmt) REVERT: D 604 MET cc_start: 0.9058 (mmt) cc_final: 0.8626 (mmp) REVERT: D 807 LEU cc_start: 0.8683 (tp) cc_final: 0.8380 (tp) REVERT: D 1025 MET cc_start: 0.9270 (tpt) cc_final: 0.8530 (tmm) REVERT: D 1095 MET cc_start: 0.7472 (tmm) cc_final: 0.7233 (tmm) REVERT: D 1306 LEU cc_start: 0.9175 (mt) cc_final: 0.8910 (mt) REVERT: F 71 MET cc_start: -0.1698 (mpp) cc_final: -0.2029 (mpp) REVERT: F 587 MET cc_start: 0.2974 (ttm) cc_final: 0.2332 (mtm) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1816 time to fit residues: 48.0142 Evaluate side-chains 143 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 186 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 351 optimal weight: 40.0000 chunk 209 optimal weight: 8.9990 chunk 324 optimal weight: 6.9990 chunk 145 optimal weight: 0.4980 chunk 178 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 216 optimal weight: 5.9990 chunk 211 optimal weight: 10.0000 chunk 262 optimal weight: 10.0000 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** 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 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN ** F 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.062792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.043559 restraints weight = 375184.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.043336 restraints weight = 238871.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 73)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.043635 restraints weight = 157301.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.044028 restraints weight = 116968.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 72)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.044192 restraints weight = 95333.912| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 33753 Z= 0.185 Angle : 0.619 13.713 45818 Z= 0.318 Chirality : 0.043 0.422 5172 Planarity : 0.004 0.098 5825 Dihedral : 12.155 176.453 5127 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.98 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % 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: 0.03 (0.13), residues: 4060 helix: 0.96 (0.13), residues: 1489 sheet: -0.59 (0.20), residues: 647 loop : -0.41 (0.14), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 515 TYR 0.033 0.002 TYR D 631 PHE 0.016 0.002 PHE C 57 TRP 0.019 0.002 TRP F 560 HIS 0.007 0.001 HIS C 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.19 (33733) covalent geometry : angle 0.60752 / 0.32 (45788) hydrogen bonds : bond 0.04092 / 2.86 ( 1510) hydrogen bonds : angle 5.07264 / 3.52 ( 4176) metal coordination : bond 0.00793 / 0.54 ( 20) metal coordination : angle 4.77497 / 3.12 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8941.51 seconds wall clock time: 153 minutes 28.84 seconds (9208.84 seconds total)