Starting phenix.real_space_refine on Sat Feb 7 15:17:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gdc_51261/02_2026/9gdc_51261.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gdc_51261/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/9gdc_51261/02_2026/9gdc_51261.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gdc_51261/02_2026/9gdc_51261.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gdc_51261/02_2026/9gdc_51261.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gdc_51261/02_2026/9gdc_51261.map" } 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 8.29, per 1000 atoms: 0.25 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: 2.81 Conformation dependent library (CDL) restraints added in 1.4 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: 4.41 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: 9.40 Time building geometry restraints manager: 3.66 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=" 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=" N ASP F 675 " pdb=" CA ASP F 675 " ideal model delta sigma weight residual 1.455 1.500 -0.045 9.60e-03 1.09e+04 2.19e+01 bond pdb=" N VAL F 756 " pdb=" CA VAL F 756 " ideal model delta sigma weight residual 1.454 1.487 -0.032 7.70e-03 1.69e+04 1.77e+01 bond pdb=" SD MET F 320 " pdb=" CE MET F 320 " ideal model delta sigma weight residual 1.791 1.702 0.089 2.50e-02 1.60e+03 1.27e+01 ... (remaining 33728 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 44596 2.63 - 5.26: 1064 5.26 - 7.89: 103 7.89 - 10.52: 18 10.52 - 13.14: 7 Bond angle restraints: 45788 Sorted by residual: angle pdb=" C3' DC N 38 " pdb=" O3' DC N 38 " pdb=" P DG N 39 " ideal model delta sigma weight residual 120.20 107.06 13.14 1.50e+00 4.44e-01 7.68e+01 angle pdb=" O4' DC N 38 " pdb=" C1' DC N 38 " pdb=" N1 DC N 38 " ideal model delta sigma weight residual 108.40 96.35 12.05 1.50e+00 4.44e-01 6.46e+01 angle pdb=" N ARG F 793 " pdb=" CA ARG F 793 " pdb=" C ARG F 793 " ideal model delta sigma weight residual 108.76 120.43 -11.67 1.58e+00 4.01e-01 5.45e+01 angle pdb=" C3' DG T 16 " pdb=" O3' DG T 16 " pdb=" P DA T 17 " ideal model delta sigma weight residual 120.20 109.68 10.52 1.50e+00 4.44e-01 4.91e+01 angle pdb=" N THR F 792 " pdb=" CA THR F 792 " pdb=" C THR F 792 " ideal model delta sigma weight residual 108.34 119.81 -11.47 1.64e+00 3.72e-01 4.89e+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: 4872 0.109 - 0.218: 265 0.218 - 0.326: 21 0.326 - 0.435: 7 0.435 - 0.544: 7 Chirality restraints: 5172 Sorted by residual: 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=" P DG T 16 " pdb=" OP1 DG T 16 " pdb=" OP2 DG T 16 " pdb=" O5' DG T 16 " both_signs ideal model delta sigma weight residual True 2.35 -2.88 -0.53 2.00e-01 2.50e+01 7.13e+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: 0.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 40.670 Find NCS groups from input model: 0.250 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 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= 0.319 Angle : 0.932 23.203 45818 Z= 0.566 Chirality : 0.060 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 covalent geometry : bond 0.00575 (33733) covalent geometry : angle 0.91334 (45788) hydrogen bonds : bond 0.14860 ( 1510) hydrogen bonds : angle 6.83014 ( 4176) metal coordination : bond 0.03820 ( 20) metal coordination : angle 7.34725 ( 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 : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8458 (m-80) REVERT: C 561 ILE cc_start: 0.9752 (mm) cc_final: 0.9434 (mp) REVERT: C 684 ASN cc_start: 0.8797 (t0) cc_final: 0.8455 (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: 0.8400 (mtpt) REVERT: C 1078 LYS cc_start: 0.9252 (tptt) cc_final: 0.8954 (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: 0.8572 (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: 0.9079 (mt) REVERT: D 115 TRP cc_start: 0.9155 (m-10) cc_final: 0.8641 (m-10) REVERT: D 136 GLU cc_start: 0.9564 (pt0) cc_final: 0.9346 (pp20) REVERT: D 513 MET cc_start: 0.8844 (ttm) cc_final: 0.8547 (ttt) REVERT: D 625 MET cc_start: 0.9314 (tmm) cc_final: 0.9088 (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: 0.8617 (tp) REVERT: D 1348 LYS cc_start: 0.9687 (mtpp) cc_final: 0.9430 (mttt) REVERT: E 30 MET cc_start: 0.8991 (ttm) cc_final: 0.8781 (mtp) REVERT: F 104 ASP cc_start: 0.1281 (t0) cc_final: 0.0892 (m-30) REVERT: F 334 MET cc_start: 0.7387 (ttm) cc_final: 0.7114 (mtt) REVERT: F 538 MET cc_start: -0.1808 (mmm) cc_final: -0.3378 (mmt) REVERT: F 546 MET cc_start: -0.6444 (ttm) cc_final: -0.7202 (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: 0.6449 (mmm) REVERT: F 718 MET cc_start: 0.2798 (ttm) cc_final: 0.1280 (ttt) outliers start: 68 outliers final: 12 residues processed: 415 average time/residue: 0.2341 time to fit residues: 153.2333 Evaluate side-chains 214 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 201 time to evaluate : 1.238 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 513 GLN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS C 673 HIS C 688 GLN C 832 HIS ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1070 HIS C1244 HIS D 113 HIS D 157 GLN D 274 ASN D 335 GLN ** D 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN D 929 GLN D 951 GLN D1218 HIS ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN F 140 ASN F 152 ASN F 163 ASN F 242 ASN F 309 GLN F 353 ASN ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 533 ASN F 548 ASN F 574 GLN F 590 ASN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.067911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.049190 restraints weight = 362626.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.049771 restraints weight = 230030.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.050071 restraints weight = 150954.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.050376 restraints weight = 119007.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.050418 restraints weight = 87768.753| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 33753 Z= 0.180 Angle : 0.657 13.850 45818 Z= 0.339 Chirality : 0.043 0.224 5172 Planarity : 0.005 0.131 5825 Dihedral : 11.721 176.590 5127 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.29 % Favored : 97.64 % Rotamer: Outliers : 0.06 % Allowed : 2.97 % Favored : 96.97 % 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: 0.20 (0.13), residues: 4060 helix: 0.99 (0.13), residues: 1470 sheet: 0.04 (0.19), residues: 672 loop : -0.41 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG F 535 TYR 0.017 0.001 TYR D 46 PHE 0.020 0.002 PHE C 15 TRP 0.021 0.002 TRP F 560 HIS 0.012 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00378 (33733) covalent geometry : angle 0.64340 (45788) hydrogen bonds : bond 0.04641 ( 1510) hydrogen bonds : angle 5.27120 ( 4176) metal coordination : bond 0.00873 ( 20) metal coordination : angle 5.28594 ( 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 230 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 228 time to evaluate : 1.162 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: C 545 PHE cc_start: 0.8960 (m-80) cc_final: 0.8678 (m-80) REVERT: C 653 MET cc_start: 0.7117 (tpt) cc_final: 0.6909 (tpt) REVERT: C 951 MET cc_start: 0.9376 (ppp) cc_final: 0.9001 (ppp) REVERT: C 1060 ILE cc_start: 0.9041 (mm) cc_final: 0.8829 (mp) REVERT: C 1078 LYS cc_start: 0.9507 (tptt) cc_final: 0.9034 (tppp) REVERT: C 1085 MET cc_start: 0.9062 (mmm) cc_final: 0.8388 (mmp) REVERT: C 1107 MET cc_start: 0.9668 (mpp) cc_final: 0.9413 (mpp) REVERT: C 1131 MET cc_start: 0.8886 (ttm) cc_final: 0.8586 (mtp) REVERT: C 1230 MET cc_start: 0.8187 (tpt) cc_final: 0.7880 (tpp) REVERT: C 1279 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8870 (mt-10) REVERT: C 1304 MET cc_start: 0.9390 (tpt) cc_final: 0.8948 (tpp) REVERT: C 1319 MET cc_start: 0.8639 (tpp) cc_final: 0.8015 (tpp) REVERT: C 1333 LEU cc_start: 0.9430 (tp) cc_final: 0.9051 (tt) REVERT: D 115 TRP cc_start: 0.9289 (m-10) cc_final: 0.8572 (m-10) REVERT: D 130 MET cc_start: 0.9231 (tpp) cc_final: 0.8887 (tpp) REVERT: D 180 MET cc_start: 0.8197 (tpt) cc_final: 0.7589 (tpt) REVERT: D 443 GLU cc_start: 0.9281 (tp30) cc_final: 0.8907 (tp30) REVERT: D 466 MET cc_start: 0.8841 (tpp) cc_final: 0.8450 (tmm) REVERT: D 485 MET cc_start: 0.8928 (mmp) cc_final: 0.7843 (mmm) REVERT: D 513 MET cc_start: 0.8660 (ttm) cc_final: 0.8033 (ttp) REVERT: D 581 MET cc_start: 0.8638 (tpp) cc_final: 0.8393 (tpp) REVERT: D 724 MET cc_start: 0.9238 (mmp) cc_final: 0.8986 (mmm) REVERT: D 747 MET cc_start: 0.8053 (ttt) cc_final: 0.7776 (ttt) REVERT: D 807 LEU cc_start: 0.8774 (tp) cc_final: 0.8437 (tp) REVERT: D 1025 MET cc_start: 0.9147 (tpt) cc_final: 0.8325 (tmm) REVERT: D 1145 PHE cc_start: 0.9074 (m-80) cc_final: 0.8221 (m-80) REVERT: F 376 MET cc_start: 0.0317 (mmp) cc_final: -0.0054 (mmp) REVERT: F 590 ASN cc_start: 0.0080 (OUTLIER) cc_final: -0.0177 (t0) REVERT: F 669 MET cc_start: 0.6547 (mtm) cc_final: 0.6309 (mmm) outliers start: 2 outliers final: 1 residues processed: 230 average time/residue: 0.2165 time to fit residues: 80.6429 Evaluate side-chains 173 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 171 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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: 20.0000 chunk 35 optimal weight: 30.0000 chunk 299 optimal weight: 6.9990 chunk 255 optimal weight: 6.9990 chunk 275 optimal weight: 10.0000 chunk 315 optimal weight: 9.9990 chunk 187 optimal weight: 6.9990 chunk 407 optimal weight: 50.0000 chunk 265 optimal weight: 9.9990 chunk 230 optimal weight: 20.0000 chunk 21 optimal weight: 7.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 ASN A 128 HIS ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN ** C 65 ASN ** 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 ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1264 GLN C1288 GLN D 164 GLN ** D 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 HIS ** D1019 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.063773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.042908 restraints weight = 373979.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.043310 restraints weight = 223346.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.043772 restraints weight = 159817.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 71)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.044132 restraints weight = 128247.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.044328 restraints weight = 107703.375| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 33753 Z= 0.266 Angle : 0.710 13.032 45818 Z= 0.368 Chirality : 0.044 0.223 5172 Planarity : 0.005 0.125 5825 Dihedral : 12.141 175.035 5127 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.88 % Favored : 97.04 % Rotamer: Outliers : 0.09 % Allowed : 4.36 % Favored : 95.56 % 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: 0.79 (0.13), residues: 1482 sheet: -0.19 (0.19), residues: 669 loop : -0.33 (0.14), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 827 TYR 0.020 0.002 TYR C 751 PHE 0.020 0.002 PHE C 15 TRP 0.016 0.002 TRP F 851 HIS 0.010 0.002 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00519 (33733) covalent geometry : angle 0.70013 (45788) hydrogen bonds : bond 0.05125 ( 1510) hydrogen bonds : angle 5.28736 ( 4176) metal coordination : bond 0.01037 ( 20) metal coordination : angle 4.72098 ( 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 190 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 187 time to evaluate : 1.259 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: C 315 MET cc_start: 0.9332 (ptt) cc_final: 0.9065 (ptm) REVERT: C 403 MET cc_start: 0.9336 (ppp) cc_final: 0.8935 (ppp) REVERT: C 464 PHE cc_start: 0.8984 (t80) cc_final: 0.8636 (t80) REVERT: C 545 PHE cc_start: 0.8964 (m-80) cc_final: 0.8653 (m-80) REVERT: C 562 GLU cc_start: 0.8860 (tt0) cc_final: 0.8596 (mt-10) REVERT: C 653 MET cc_start: 0.8248 (tpt) cc_final: 0.8035 (tpt) REVERT: C 768 MET cc_start: 0.8610 (ppp) cc_final: 0.8359 (ppp) REVERT: C 794 LEU cc_start: 0.9255 (tp) cc_final: 0.8978 (tt) REVERT: C 805 MET cc_start: 0.8780 (ppp) cc_final: 0.8563 (ppp) REVERT: C 1078 LYS cc_start: 0.9671 (tptt) cc_final: 0.9345 (tppp) REVERT: C 1085 MET cc_start: 0.9089 (mmm) cc_final: 0.8348 (mmm) REVERT: C 1304 MET cc_start: 0.9468 (tpt) cc_final: 0.9092 (tpp) REVERT: C 1319 MET cc_start: 0.9286 (tpp) cc_final: 0.8450 (tpp) REVERT: D 130 MET cc_start: 0.8993 (tpp) cc_final: 0.8764 (tpp) REVERT: D 237 MET cc_start: 0.9276 (mtm) cc_final: 0.9052 (mtm) REVERT: D 330 MET cc_start: 0.9467 (mmp) cc_final: 0.9151 (mmm) REVERT: D 400 MET cc_start: 0.9398 (tpp) cc_final: 0.9138 (tpp) REVERT: D 466 MET cc_start: 0.9083 (tpp) cc_final: 0.8821 (tpt) REVERT: D 485 MET cc_start: 0.9099 (mmp) cc_final: 0.8394 (mmm) REVERT: D 513 MET cc_start: 0.8703 (ttm) cc_final: 0.8051 (ttp) REVERT: D 581 MET cc_start: 0.8829 (tpp) cc_final: 0.8560 (tpp) REVERT: D 644 MET cc_start: 0.8844 (mpp) cc_final: 0.8030 (tpp) REVERT: D 724 MET cc_start: 0.9286 (mmp) cc_final: 0.9037 (mmm) REVERT: D 725 MET cc_start: 0.9144 (mtp) cc_final: 0.8639 (mtp) REVERT: D 747 MET cc_start: 0.8140 (ttt) cc_final: 0.7938 (ttt) REVERT: D 1025 MET cc_start: 0.9161 (tpt) cc_final: 0.8291 (tmm) REVERT: E 67 ARG cc_start: 0.9755 (mtt-85) cc_final: 0.9525 (ptp-170) REVERT: F 669 MET cc_start: 0.6456 (mtm) cc_final: 0.6229 (mtt) REVERT: F 729 MET cc_start: 0.2346 (ttp) cc_final: 0.1661 (tmm) outliers start: 3 outliers final: 2 residues processed: 190 average time/residue: 0.1965 time to fit residues: 61.6350 Evaluate side-chains 158 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 156 time to evaluate : 1.289 ------------------------------------------------------------------------------- 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: 1.9990 chunk 204 optimal weight: 0.2980 chunk 260 optimal weight: 8.9990 chunk 377 optimal weight: 7.9990 chunk 241 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 369 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 164 optimal weight: 5.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS B 128 HIS C 86 GLN ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 518 ASN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS D 164 GLN D 419 HIS ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN D1019 ASN D1235 ASN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN F 681 HIS ** F 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.065411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.045870 restraints weight = 366783.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.045991 restraints weight = 220576.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 82)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.046362 restraints weight = 143080.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.046748 restraints weight = 108133.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.046946 restraints weight = 89529.119| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 33753 Z= 0.131 Angle : 0.576 14.117 45818 Z= 0.295 Chirality : 0.042 0.215 5172 Planarity : 0.004 0.122 5825 Dihedral : 12.003 174.517 5127 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.41 % Favored : 97.54 % Rotamer: Outliers : 0.03 % Allowed : 2.68 % Favored : 97.29 % 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: 0.36 (0.13), residues: 4060 helix: 1.15 (0.14), residues: 1477 sheet: -0.17 (0.20), residues: 650 loop : -0.23 (0.14), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 88 TYR 0.011 0.001 TYR D 537 PHE 0.016 0.001 PHE D1034 TRP 0.013 0.001 TRP F 560 HIS 0.011 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00272 (33733) covalent geometry : angle 0.56394 (45788) hydrogen bonds : bond 0.03578 ( 1510) hydrogen bonds : angle 4.92355 ( 4176) metal coordination : bond 0.00513 ( 20) metal coordination : angle 4.54636 ( 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 187 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 1.268 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: 0.9361 (mmp) cc_final: 0.9071 (mmm) REVERT: B 205 MET cc_start: 0.8369 (tmm) cc_final: 0.8164 (tmm) REVERT: C 459 MET cc_start: 0.9370 (mpp) cc_final: 0.9144 (mpp) REVERT: C 464 PHE cc_start: 0.8838 (t80) cc_final: 0.8536 (t80) REVERT: C 545 PHE cc_start: 0.8891 (m-80) cc_final: 0.8623 (m-80) REVERT: C 653 MET cc_start: 0.8219 (tpt) cc_final: 0.7887 (tpt) REVERT: C 805 MET cc_start: 0.8726 (ppp) cc_final: 0.8348 (ppp) REVERT: C 1066 MET cc_start: 0.7887 (pmm) cc_final: 0.7405 (pmm) REVERT: C 1078 LYS cc_start: 0.9697 (tptt) cc_final: 0.9385 (tppp) REVERT: C 1085 MET cc_start: 0.8950 (mmm) cc_final: 0.8349 (mmm) REVERT: C 1107 MET cc_start: 0.9598 (mpp) cc_final: 0.9379 (mpp) REVERT: C 1230 MET cc_start: 0.8872 (tpp) cc_final: 0.8068 (tpp) REVERT: C 1279 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8623 (mt-10) REVERT: C 1304 MET cc_start: 0.9409 (tpt) cc_final: 0.9048 (tpp) REVERT: C 1319 MET cc_start: 0.9304 (tpp) cc_final: 0.8501 (tpp) REVERT: D 278 ARG cc_start: 0.9610 (ttm110) cc_final: 0.9115 (ptp-110) REVERT: D 443 GLU cc_start: 0.9282 (tp30) cc_final: 0.8894 (tp30) REVERT: D 485 MET cc_start: 0.8706 (mmp) cc_final: 0.8115 (mmm) REVERT: D 513 MET cc_start: 0.8644 (ttm) cc_final: 0.7972 (ttp) REVERT: D 581 MET cc_start: 0.8772 (tpp) cc_final: 0.8486 (tpp) REVERT: D 604 MET cc_start: 0.8973 (mtm) cc_final: 0.8750 (ptp) REVERT: D 724 MET cc_start: 0.9209 (mmp) cc_final: 0.8976 (mmm) REVERT: D 747 MET cc_start: 0.8093 (ttt) cc_final: 0.7860 (ttt) REVERT: D 807 LEU cc_start: 0.8801 (tp) cc_final: 0.8289 (tp) REVERT: D 932 MET cc_start: 0.4423 (mmm) cc_final: 0.3570 (mmm) REVERT: D 1025 MET cc_start: 0.8937 (tpt) cc_final: 0.8287 (tmm) REVERT: D 1040 MET cc_start: 0.5832 (ttp) cc_final: 0.5575 (tmm) REVERT: D 1093 THR cc_start: 0.6796 (p) cc_final: 0.6560 (p) REVERT: F 587 MET cc_start: 0.3502 (ttm) cc_final: 0.2993 (mtm) REVERT: F 729 MET cc_start: 0.2047 (ttp) cc_final: 0.1630 (tmm) outliers start: 1 outliers final: 1 residues processed: 187 average time/residue: 0.1966 time to fit residues: 61.2409 Evaluate side-chains 156 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 1.302 ------------------------------------------------------------------------------- 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: 8.9990 chunk 292 optimal weight: 30.0000 chunk 7 optimal weight: 9.9990 chunk 344 optimal weight: 50.0000 chunk 227 optimal weight: 20.0000 chunk 410 optimal weight: 10.0000 chunk 269 optimal weight: 0.2980 chunk 40 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 179 optimal weight: 1.9990 chunk 204 optimal weight: 30.0000 overall best weight: 5.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN C 834 GLN ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1324 ASN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.063504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.042409 restraints weight = 373347.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.043375 restraints weight = 224806.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.043585 restraints weight = 161207.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.043895 restraints weight = 128349.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.044080 restraints weight = 112681.443| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 33753 Z= 0.202 Angle : 0.617 12.901 45818 Z= 0.317 Chirality : 0.042 0.222 5172 Planarity : 0.005 0.119 5825 Dihedral : 11.986 173.996 5127 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.78 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: 0.22 (0.13), residues: 4060 helix: 1.05 (0.13), residues: 1477 sheet: -0.31 (0.20), residues: 634 loop : -0.31 (0.14), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 88 TYR 0.018 0.002 TYR C1229 PHE 0.017 0.002 PHE F 567 TRP 0.015 0.002 TRP F 560 HIS 0.008 0.002 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00411 (33733) covalent geometry : angle 0.60667 (45788) hydrogen bonds : bond 0.04304 ( 1510) hydrogen bonds : angle 5.02155 ( 4176) metal coordination : bond 0.00580 ( 20) metal coordination : angle 4.38742 ( 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 176 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: 0.9521 (mmp) cc_final: 0.9177 (mmm) REVERT: C 403 MET cc_start: 0.9262 (ppp) cc_final: 0.8960 (ppp) REVERT: C 459 MET cc_start: 0.9499 (mpp) cc_final: 0.9264 (mpp) REVERT: C 464 PHE cc_start: 0.8983 (t80) cc_final: 0.8617 (t80) REVERT: C 653 MET cc_start: 0.8337 (tpt) cc_final: 0.8022 (tpt) REVERT: C 800 MET cc_start: 0.8894 (pmm) cc_final: 0.7240 (pmm) REVERT: C 805 MET cc_start: 0.8874 (ppp) cc_final: 0.8538 (ppp) REVERT: C 1066 MET cc_start: 0.7877 (pmm) cc_final: 0.7321 (pmm) REVERT: C 1078 LYS cc_start: 0.9695 (tptt) cc_final: 0.9378 (tppp) REVERT: C 1085 MET cc_start: 0.9033 (mmm) cc_final: 0.7710 (mmm) REVERT: C 1230 MET cc_start: 0.9277 (tpp) cc_final: 0.8591 (tpp) REVERT: C 1304 MET cc_start: 0.9437 (tpt) cc_final: 0.9046 (tpt) REVERT: C 1319 MET cc_start: 0.9377 (tpp) cc_final: 0.8540 (tpp) REVERT: D 130 MET cc_start: 0.9095 (tpt) cc_final: 0.8844 (tpp) REVERT: D 278 ARG cc_start: 0.9623 (ttm110) cc_final: 0.8850 (ptp-110) REVERT: D 400 MET cc_start: 0.9302 (tpp) cc_final: 0.8972 (tpp) REVERT: D 466 MET cc_start: 0.8757 (tpp) cc_final: 0.8372 (mmt) REVERT: D 513 MET cc_start: 0.8654 (ttm) cc_final: 0.8030 (ttp) REVERT: D 604 MET cc_start: 0.9229 (mtm) cc_final: 0.8800 (mtm) REVERT: D 625 MET cc_start: 0.9462 (ttt) cc_final: 0.9010 (tmm) REVERT: D 644 MET cc_start: 0.8828 (mpp) cc_final: 0.7990 (tpp) REVERT: D 724 MET cc_start: 0.9266 (mmp) cc_final: 0.8995 (mmm) REVERT: D 725 MET cc_start: 0.9379 (mtp) cc_final: 0.8933 (mtp) REVERT: D 747 MET cc_start: 0.8145 (ttt) cc_final: 0.7917 (ttt) REVERT: D 807 LEU cc_start: 0.8966 (tp) cc_final: 0.8391 (tp) REVERT: D 1025 MET cc_start: 0.9152 (tpt) cc_final: 0.8631 (tmm) REVERT: F 587 MET cc_start: 0.2833 (ttm) cc_final: 0.2434 (mtm) REVERT: F 729 MET cc_start: 0.2912 (ttp) cc_final: 0.2423 (tmm) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.2249 time to fit residues: 66.5250 Evaluate side-chains 144 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.404 ------------------------------------------------------------------------------- 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: 10.0000 chunk 350 optimal weight: 50.0000 chunk 385 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 405 optimal weight: 50.0000 chunk 91 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 310 optimal weight: 9.9990 chunk 341 optimal weight: 50.0000 chunk 351 optimal weight: 50.0000 chunk 401 optimal weight: 20.0000 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 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 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 623 GLN ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1244 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** F 825 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.063355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.043441 restraints weight = 372008.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.042954 restraints weight = 223671.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.043480 restraints weight = 156162.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.043930 restraints weight = 121594.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.044242 restraints weight = 105002.733| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 33753 Z= 0.186 Angle : 0.598 13.662 45818 Z= 0.308 Chirality : 0.042 0.218 5172 Planarity : 0.004 0.101 5825 Dihedral : 12.014 173.405 5127 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.91 % Favored : 97.04 % Rotamer: Outliers : 0.06 % Allowed : 2.02 % Favored : 97.92 % 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: 0.21 (0.13), residues: 4060 helix: 1.10 (0.13), residues: 1471 sheet: -0.40 (0.20), residues: 655 loop : -0.32 (0.14), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 88 TYR 0.041 0.001 TYR C1231 PHE 0.015 0.002 PHE C 57 TRP 0.014 0.001 TRP F 560 HIS 0.009 0.001 HIS F 566 Details of bonding type rmsd covalent geometry : bond 0.00376 (33733) covalent geometry : angle 0.58728 (45788) hydrogen bonds : bond 0.03855 ( 1510) hydrogen bonds : angle 4.98251 ( 4176) metal coordination : bond 0.00590 ( 20) metal coordination : angle 4.46875 ( 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 168 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 166 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: 0.9545 (mmp) cc_final: 0.9194 (mmm) REVERT: B 205 MET cc_start: 0.8601 (tmm) cc_final: 0.8219 (tmm) REVERT: C 403 MET cc_start: 0.9267 (ppp) cc_final: 0.8914 (ppp) REVERT: C 464 PHE cc_start: 0.8943 (t80) cc_final: 0.8646 (t80) REVERT: C 538 LEU cc_start: 0.8845 (tp) cc_final: 0.8586 (tp) REVERT: C 653 MET cc_start: 0.8329 (tpt) cc_final: 0.7986 (tpt) REVERT: C 805 MET cc_start: 0.8865 (ppp) cc_final: 0.8556 (ppp) REVERT: C 1066 MET cc_start: 0.7824 (pmm) cc_final: 0.7277 (pmm) REVERT: C 1078 LYS cc_start: 0.9728 (tptt) cc_final: 0.9388 (tppp) REVERT: C 1085 MET cc_start: 0.8948 (mmm) cc_final: 0.7688 (mmm) REVERT: C 1107 MET cc_start: 0.9640 (mpp) cc_final: 0.9432 (mpp) REVERT: C 1230 MET cc_start: 0.9268 (tpp) cc_final: 0.8525 (tpp) REVERT: C 1279 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8683 (mt-10) REVERT: C 1304 MET cc_start: 0.9457 (tpt) cc_final: 0.9073 (tpt) REVERT: C 1319 MET cc_start: 0.9362 (tpp) cc_final: 0.8531 (tpp) REVERT: D 130 MET cc_start: 0.9085 (tpt) cc_final: 0.8846 (tpp) REVERT: D 400 MET cc_start: 0.9257 (tpp) cc_final: 0.8970 (tpp) REVERT: D 466 MET cc_start: 0.8813 (tpp) cc_final: 0.8466 (mmt) REVERT: D 485 MET cc_start: 0.9052 (tpt) cc_final: 0.8847 (tpp) REVERT: D 513 MET cc_start: 0.8642 (ttm) cc_final: 0.7980 (ttp) REVERT: D 604 MET cc_start: 0.9141 (mtm) cc_final: 0.8723 (mtm) REVERT: D 625 MET cc_start: 0.9505 (ttt) cc_final: 0.9131 (tmm) REVERT: D 644 MET cc_start: 0.8805 (mpp) cc_final: 0.7959 (tpp) REVERT: D 724 MET cc_start: 0.9273 (mmp) cc_final: 0.9015 (mmm) REVERT: D 725 MET cc_start: 0.9370 (mtp) cc_final: 0.9033 (mtp) REVERT: D 807 LEU cc_start: 0.8946 (tp) cc_final: 0.8366 (tp) REVERT: D 1025 MET cc_start: 0.9441 (tpt) cc_final: 0.8779 (tmm) REVERT: F 587 MET cc_start: 0.2780 (ttm) cc_final: 0.2319 (mtm) REVERT: F 729 MET cc_start: 0.2703 (ttp) cc_final: 0.2304 (tmm) outliers start: 2 outliers final: 1 residues processed: 168 average time/residue: 0.2274 time to fit residues: 62.9996 Evaluate side-chains 147 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 1.309 ------------------------------------------------------------------------------- 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: 5.9990 chunk 283 optimal weight: 50.0000 chunk 45 optimal weight: 0.6980 chunk 8 optimal weight: 20.0000 chunk 246 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 chunk 249 optimal weight: 8.9990 chunk 335 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 233 optimal weight: 0.9990 chunk 331 optimal weight: 40.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** 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 760 ASN ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN ** D 274 ASN ** 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 = 0.3630 r_free = 0.3630 target = 0.063738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.043826 restraints weight = 373003.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.044507 restraints weight = 225416.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.044448 restraints weight = 152242.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.044617 restraints weight = 117171.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.044794 restraints weight = 95216.091| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33753 Z= 0.145 Angle : 0.577 12.664 45818 Z= 0.295 Chirality : 0.042 0.258 5172 Planarity : 0.004 0.126 5825 Dihedral : 11.931 172.983 5127 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.66 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % 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: 1.14 (0.14), residues: 1475 sheet: -0.31 (0.20), residues: 657 loop : -0.31 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 281 TYR 0.022 0.001 TYR C1231 PHE 0.018 0.001 PHE D 227 TRP 0.015 0.001 TRP F 560 HIS 0.007 0.001 HIS C 554 Details of bonding type rmsd covalent geometry : bond 0.00300 (33733) covalent geometry : angle 0.56573 (45788) hydrogen bonds : bond 0.03592 ( 1510) hydrogen bonds : angle 4.94512 ( 4176) metal coordination : bond 0.00692 ( 20) metal coordination : angle 4.37998 ( 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 166 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 1.347 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: 0.9532 (mmp) cc_final: 0.9191 (mmm) REVERT: B 205 MET cc_start: 0.8478 (tmm) cc_final: 0.8088 (tmm) REVERT: C 403 MET cc_start: 0.9385 (ppp) cc_final: 0.9048 (ppp) REVERT: C 459 MET cc_start: 0.9490 (mpp) cc_final: 0.9256 (mpp) REVERT: C 464 PHE cc_start: 0.8861 (t80) cc_final: 0.8596 (t80) REVERT: C 492 MET cc_start: 0.8102 (mtm) cc_final: 0.7862 (ptp) REVERT: C 538 LEU cc_start: 0.8870 (tp) cc_final: 0.8599 (tp) REVERT: C 545 PHE cc_start: 0.8689 (m-80) cc_final: 0.8462 (m-80) REVERT: C 653 MET cc_start: 0.8427 (tpt) cc_final: 0.8133 (tpt) REVERT: C 681 MET cc_start: 0.8672 (ptp) cc_final: 0.8449 (ptp) REVERT: C 800 MET cc_start: 0.9167 (pmm) cc_final: 0.8475 (pmm) REVERT: C 1066 MET cc_start: 0.7865 (pmm) cc_final: 0.7342 (pmm) REVERT: C 1078 LYS cc_start: 0.9762 (tptt) cc_final: 0.9393 (tppp) REVERT: C 1085 MET cc_start: 0.8834 (mmm) cc_final: 0.7651 (mmm) REVERT: C 1107 MET cc_start: 0.9620 (mpp) cc_final: 0.9405 (mpp) REVERT: C 1230 MET cc_start: 0.9288 (tpp) cc_final: 0.8509 (tpp) REVERT: C 1304 MET cc_start: 0.9378 (tpt) cc_final: 0.9090 (tpp) REVERT: C 1319 MET cc_start: 0.9228 (tpp) cc_final: 0.8621 (tpp) REVERT: D 400 MET cc_start: 0.9181 (tpp) cc_final: 0.8921 (tpp) REVERT: D 466 MET cc_start: 0.8659 (tpp) cc_final: 0.8109 (mmt) REVERT: D 513 MET cc_start: 0.8574 (ttm) cc_final: 0.7869 (ttp) REVERT: D 604 MET cc_start: 0.9049 (mtm) cc_final: 0.8633 (mtm) REVERT: D 724 MET cc_start: 0.9211 (mmp) cc_final: 0.8926 (mmm) REVERT: D 725 MET cc_start: 0.9250 (mtp) cc_final: 0.9035 (mtp) REVERT: D 747 MET cc_start: 0.8070 (ttt) cc_final: 0.7765 (ttt) REVERT: D 807 LEU cc_start: 0.8800 (tp) cc_final: 0.8534 (tp) REVERT: D 1025 MET cc_start: 0.9169 (tpt) cc_final: 0.8410 (tmm) REVERT: D 1093 THR cc_start: 0.7116 (p) cc_final: 0.6893 (p) REVERT: F 307 MET cc_start: 0.6328 (ptm) cc_final: 0.6126 (tmm) REVERT: F 587 MET cc_start: 0.2887 (ttm) cc_final: 0.2264 (mtm) REVERT: F 729 MET cc_start: 0.2661 (ttp) cc_final: 0.2440 (tmm) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2188 time to fit residues: 59.9501 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 : 1.385 ------------------------------------------------------------------------------- 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: 0.6980 chunk 67 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 296 optimal weight: 8.9990 chunk 396 optimal weight: 8.9990 chunk 311 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 160 optimal weight: 5.9990 chunk 301 optimal weight: 10.0000 chunk 216 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** 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 760 ASN ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 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 197 GLN ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN F 681 HIS ** 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 = 0.3626 r_free = 0.3626 target = 0.063604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.043697 restraints weight = 372893.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.043681 restraints weight = 226797.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.044093 restraints weight = 149211.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.044508 restraints weight = 113691.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 73)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.044719 restraints weight = 95032.351| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.4909 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= 0.148 Angle : 0.579 12.489 45818 Z= 0.295 Chirality : 0.042 0.216 5172 Planarity : 0.004 0.108 5825 Dihedral : 11.889 172.547 5127 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.64 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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: 0.28 (0.13), residues: 4060 helix: 1.18 (0.14), residues: 1480 sheet: -0.31 (0.20), residues: 657 loop : -0.32 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 158 TYR 0.028 0.001 TYR D 269 PHE 0.017 0.001 PHE C 186 TRP 0.017 0.001 TRP F 560 HIS 0.007 0.001 HIS C 554 Details of bonding type rmsd covalent geometry : bond 0.00306 (33733) covalent geometry : angle 0.56801 (45788) hydrogen bonds : bond 0.03627 ( 1510) hydrogen bonds : angle 4.91826 ( 4176) metal coordination : bond 0.00637 ( 20) metal coordination : angle 4.38797 ( 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 164 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.387 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: 0.9507 (mmp) cc_final: 0.9146 (mmm) REVERT: B 205 MET cc_start: 0.8781 (tmm) cc_final: 0.8494 (tmm) REVERT: C 403 MET cc_start: 0.9410 (ppp) cc_final: 0.9060 (ppp) REVERT: C 459 MET cc_start: 0.9444 (mpp) cc_final: 0.9206 (mpp) REVERT: C 464 PHE cc_start: 0.8876 (t80) cc_final: 0.8590 (t80) REVERT: C 538 LEU cc_start: 0.8908 (tp) cc_final: 0.8604 (tp) REVERT: C 545 PHE cc_start: 0.8651 (m-80) cc_final: 0.8438 (m-80) REVERT: C 653 MET cc_start: 0.8460 (tpt) cc_final: 0.8182 (tpt) REVERT: C 800 MET cc_start: 0.9178 (pmm) cc_final: 0.8496 (pmm) REVERT: C 805 MET cc_start: 0.8975 (ppp) cc_final: 0.8603 (ppp) REVERT: C 1066 MET cc_start: 0.7811 (pmm) cc_final: 0.7288 (pmm) REVERT: C 1085 MET cc_start: 0.8763 (mmm) cc_final: 0.7770 (mmm) REVERT: C 1107 MET cc_start: 0.9654 (mpp) cc_final: 0.9440 (mpp) REVERT: C 1230 MET cc_start: 0.9249 (tpp) cc_final: 0.8505 (tpp) REVERT: C 1304 MET cc_start: 0.9470 (tpt) cc_final: 0.9205 (tpp) REVERT: C 1319 MET cc_start: 0.9070 (tpp) cc_final: 0.8588 (tpp) REVERT: D 252 LEU cc_start: 0.8857 (tp) cc_final: 0.8611 (tp) REVERT: D 330 MET cc_start: 0.9405 (mmp) cc_final: 0.8992 (mmp) REVERT: D 400 MET cc_start: 0.9210 (tpp) cc_final: 0.8976 (tpp) REVERT: D 466 MET cc_start: 0.8687 (tpp) cc_final: 0.8165 (mmt) REVERT: D 485 MET cc_start: 0.9224 (mmp) cc_final: 0.8241 (mmm) REVERT: D 513 MET cc_start: 0.8440 (ttm) cc_final: 0.7710 (ttp) REVERT: D 604 MET cc_start: 0.9203 (mtm) cc_final: 0.8833 (mtm) REVERT: D 724 MET cc_start: 0.9254 (mmp) cc_final: 0.8939 (mmm) REVERT: D 747 MET cc_start: 0.8132 (ttt) cc_final: 0.7801 (ttt) REVERT: D 807 LEU cc_start: 0.8867 (tp) cc_final: 0.8600 (tp) REVERT: D 1025 MET cc_start: 0.9221 (tpt) cc_final: 0.8457 (tmm) REVERT: F 587 MET cc_start: 0.3131 (ttm) cc_final: 0.2629 (mtm) REVERT: F 729 MET cc_start: 0.2715 (ttp) cc_final: 0.2425 (tmm) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2193 time to fit residues: 59.7765 Evaluate side-chains 144 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.369 ------------------------------------------------------------------------------- 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: 1.9990 chunk 58 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 331 optimal weight: 50.0000 chunk 129 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 391 optimal weight: 20.0000 chunk 361 optimal weight: 50.0000 chunk 204 optimal weight: 20.0000 chunk 153 optimal weight: 6.9990 chunk 263 optimal weight: 0.0570 overall best weight: 4.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** 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 760 ASN C1008 GLN C1080 ASN D 164 GLN ** D 274 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 Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.063123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.044252 restraints weight = 370818.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.043934 restraints weight = 222264.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.044541 restraints weight = 144800.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.044955 restraints weight = 111489.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.044928 restraints weight = 91991.926| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.5157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33753 Z= 0.158 Angle : 0.583 12.178 45818 Z= 0.298 Chirality : 0.042 0.215 5172 Planarity : 0.004 0.098 5825 Dihedral : 11.901 172.127 5127 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.78 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: 0.25 (0.13), residues: 4060 helix: 1.14 (0.14), residues: 1491 sheet: -0.38 (0.20), residues: 656 loop : -0.32 (0.14), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 158 TYR 0.021 0.001 TYR C1231 PHE 0.018 0.001 PHE D 141 TRP 0.020 0.001 TRP F 560 HIS 0.007 0.001 HIS C 554 Details of bonding type rmsd covalent geometry : bond 0.00325 (33733) covalent geometry : angle 0.57247 (45788) hydrogen bonds : bond 0.03675 ( 1510) hydrogen bonds : angle 4.90283 ( 4176) metal coordination : bond 0.00623 ( 20) metal coordination : angle 4.26892 ( 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 163 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.275 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: 0.9478 (mmp) cc_final: 0.9165 (mmm) REVERT: C 403 MET cc_start: 0.9388 (ppp) cc_final: 0.9025 (ppp) REVERT: C 459 MET cc_start: 0.9448 (mpp) cc_final: 0.9215 (mpp) REVERT: C 464 PHE cc_start: 0.8806 (t80) cc_final: 0.8536 (t80) REVERT: C 538 LEU cc_start: 0.9077 (tp) cc_final: 0.8773 (tp) REVERT: C 545 PHE cc_start: 0.8789 (m-80) cc_final: 0.8546 (m-80) REVERT: C 653 MET cc_start: 0.8418 (tpt) cc_final: 0.8134 (tpt) REVERT: C 681 MET cc_start: 0.8907 (ptp) cc_final: 0.8441 (ptp) REVERT: C 684 ASN cc_start: 0.8725 (m110) cc_final: 0.8027 (m110) REVERT: C 685 MET cc_start: 0.9262 (ptp) cc_final: 0.8277 (mpp) REVERT: C 800 MET cc_start: 0.9059 (pmm) cc_final: 0.8199 (pmm) REVERT: C 805 MET cc_start: 0.8914 (ppp) cc_final: 0.8620 (ppp) REVERT: C 1066 MET cc_start: 0.7793 (pmm) cc_final: 0.7309 (pmm) REVERT: C 1085 MET cc_start: 0.8715 (mmm) cc_final: 0.7797 (mmm) REVERT: C 1107 MET cc_start: 0.9661 (mpp) cc_final: 0.9433 (mpp) REVERT: C 1230 MET cc_start: 0.9316 (tpp) cc_final: 0.8937 (tpp) REVERT: C 1304 MET cc_start: 0.9430 (tpt) cc_final: 0.9148 (tpp) REVERT: C 1319 MET cc_start: 0.9213 (tpp) cc_final: 0.8672 (tpp) REVERT: D 252 LEU cc_start: 0.8811 (tp) cc_final: 0.8606 (tp) REVERT: D 278 ARG cc_start: 0.9652 (ttm110) cc_final: 0.9386 (ttp-110) REVERT: D 466 MET cc_start: 0.8673 (tpp) cc_final: 0.8170 (mmt) REVERT: D 485 MET cc_start: 0.9224 (mmp) cc_final: 0.8266 (mmm) REVERT: D 513 MET cc_start: 0.8296 (ttm) cc_final: 0.7503 (ttp) REVERT: D 604 MET cc_start: 0.9155 (mtm) cc_final: 0.8802 (mtm) REVERT: D 724 MET cc_start: 0.9202 (mmp) cc_final: 0.8863 (mmm) REVERT: D 747 MET cc_start: 0.8131 (ttt) cc_final: 0.7807 (ttt) REVERT: D 807 LEU cc_start: 0.8803 (tp) cc_final: 0.8538 (tp) REVERT: D 1025 MET cc_start: 0.9236 (tpt) cc_final: 0.8477 (tmm) REVERT: F 587 MET cc_start: 0.1854 (ttm) cc_final: 0.1455 (mtm) REVERT: F 729 MET cc_start: 0.2717 (ttp) cc_final: 0.2456 (tmm) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2095 time to fit residues: 57.6844 Evaluate side-chains 148 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.375 ------------------------------------------------------------------------------- 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: 2.9990 chunk 313 optimal weight: 10.0000 chunk 363 optimal weight: 50.0000 chunk 252 optimal weight: 0.9990 chunk 208 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 84 optimal weight: 0.6980 chunk 222 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 chunk 336 optimal weight: 6.9990 chunk 357 optimal weight: 9.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** 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 760 ASN D 164 GLN D 274 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.063249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.042610 restraints weight = 375671.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.043432 restraints weight = 225553.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.043390 restraints weight = 174906.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.043316 restraints weight = 160394.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.043614 restraints weight = 124727.700| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33753 Z= 0.146 Angle : 0.593 13.480 45818 Z= 0.300 Chirality : 0.042 0.215 5172 Planarity : 0.004 0.094 5825 Dihedral : 11.908 171.916 5127 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.86 % Favored : 97.09 % 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: 0.25 (0.13), residues: 4060 helix: 1.17 (0.14), residues: 1484 sheet: -0.41 (0.20), residues: 650 loop : -0.33 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 12 TYR 0.018 0.001 TYR C1231 PHE 0.014 0.001 PHE D1034 TRP 0.020 0.001 TRP F 560 HIS 0.007 0.001 HIS C 554 Details of bonding type rmsd covalent geometry : bond 0.00304 (33733) covalent geometry : angle 0.58303 (45788) hydrogen bonds : bond 0.03555 ( 1510) hydrogen bonds : angle 4.91726 ( 4176) metal coordination : bond 0.00744 ( 20) metal coordination : angle 4.32581 ( 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 162 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.410 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: 0.9567 (mmp) cc_final: 0.9212 (mmm) REVERT: C 403 MET cc_start: 0.9395 (ppp) cc_final: 0.9035 (ppp) REVERT: C 459 MET cc_start: 0.9468 (mpp) cc_final: 0.9223 (mpp) REVERT: C 464 PHE cc_start: 0.8850 (t80) cc_final: 0.8558 (t80) REVERT: C 492 MET cc_start: 0.8587 (mpp) cc_final: 0.8371 (mpp) REVERT: C 538 LEU cc_start: 0.9130 (tp) cc_final: 0.8837 (tp) REVERT: C 545 PHE cc_start: 0.8873 (m-80) cc_final: 0.8591 (m-80) REVERT: C 653 MET cc_start: 0.8622 (tpt) cc_final: 0.8422 (tpt) REVERT: C 681 MET cc_start: 0.8768 (ptp) cc_final: 0.8047 (ptp) REVERT: C 685 MET cc_start: 0.9310 (ptp) cc_final: 0.8347 (mpp) REVERT: C 800 MET cc_start: 0.9159 (pmm) cc_final: 0.8535 (pmm) REVERT: C 805 MET cc_start: 0.9043 (ppp) cc_final: 0.8636 (ppp) REVERT: C 1066 MET cc_start: 0.7753 (pmm) cc_final: 0.7223 (pmm) REVERT: C 1085 MET cc_start: 0.8647 (mmm) cc_final: 0.7691 (mmm) REVERT: C 1107 MET cc_start: 0.9665 (mpp) cc_final: 0.9441 (mpp) REVERT: C 1230 MET cc_start: 0.9319 (tpp) cc_final: 0.9020 (tpp) REVERT: C 1304 MET cc_start: 0.9323 (tpt) cc_final: 0.9122 (tpp) REVERT: C 1319 MET cc_start: 0.9247 (tpp) cc_final: 0.8632 (tpp) REVERT: D 278 ARG cc_start: 0.9669 (ttm110) cc_final: 0.9410 (ttp-110) REVERT: D 330 MET cc_start: 0.9415 (mmp) cc_final: 0.8973 (mmp) REVERT: D 466 MET cc_start: 0.8775 (tpp) cc_final: 0.8239 (mmt) REVERT: D 485 MET cc_start: 0.9372 (mmp) cc_final: 0.8398 (mmm) REVERT: D 513 MET cc_start: 0.8430 (ttm) cc_final: 0.7712 (ttp) REVERT: D 604 MET cc_start: 0.9237 (mtm) cc_final: 0.8890 (mtm) REVERT: D 724 MET cc_start: 0.9273 (mmp) cc_final: 0.8893 (mmm) REVERT: D 747 MET cc_start: 0.8360 (ttt) cc_final: 0.8034 (ttt) REVERT: D 1025 MET cc_start: 0.9244 (tpt) cc_final: 0.8721 (tmm) REVERT: E 30 MET cc_start: 0.8024 (ptt) cc_final: 0.7823 (ppp) REVERT: F 320 MET cc_start: 0.5256 (tpp) cc_final: 0.5015 (tpp) REVERT: F 587 MET cc_start: 0.1830 (ttm) cc_final: 0.1573 (mtm) REVERT: F 729 MET cc_start: 0.2763 (ttp) cc_final: 0.2516 (tmm) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2158 time to fit residues: 59.1692 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 : 1.285 ------------------------------------------------------------------------------- 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: 6.9990 chunk 351 optimal weight: 10.0000 chunk 209 optimal weight: 20.0000 chunk 324 optimal weight: 0.3980 chunk 145 optimal weight: 30.0000 chunk 178 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 216 optimal weight: 9.9990 chunk 211 optimal weight: 4.9990 chunk 262 optimal weight: 8.9990 overall best weight: 6.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN ** C 65 ASN ** 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 760 ASN C 952 GLN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 590 ASN F 591 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.061801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.042270 restraints weight = 379224.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.042382 restraints weight = 238571.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.042451 restraints weight = 172012.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.042576 restraints weight = 127930.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.042782 restraints weight = 106855.897| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.5689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 33753 Z= 0.209 Angle : 0.636 13.518 45818 Z= 0.327 Chirality : 0.042 0.249 5172 Planarity : 0.005 0.090 5825 Dihedral : 12.066 171.459 5127 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.45 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: 0.09 (0.13), residues: 4060 helix: 0.99 (0.13), residues: 1489 sheet: -0.39 (0.20), residues: 653 loop : -0.42 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 933 TYR 0.020 0.002 TYR C1229 PHE 0.023 0.002 PHE D 141 TRP 0.019 0.002 TRP F 560 HIS 0.008 0.002 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00424 (33733) covalent geometry : angle 0.62554 (45788) hydrogen bonds : bond 0.04257 ( 1510) hydrogen bonds : angle 5.07984 ( 4176) metal coordination : bond 0.00910 ( 20) metal coordination : angle 4.44551 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10750.27 seconds wall clock time: 184 minutes 23.31 seconds (11063.31 seconds total)