Starting phenix.real_space_refine on Mon Jul 6 09:55:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gdc_51261/07_2026/9gdc_51261.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gdc_51261/07_2026/9gdc_51261.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gdc_51261/07_2026/9gdc_51261.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gdc_51261/07_2026/9gdc_51261.map" model { file = "/net/cci-nas-00/data/ceres_data/9gdc_51261/07_2026/9gdc_51261.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gdc_51261/07_2026/9gdc_51261.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.096 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 5 6.06 5 P 66 5.49 5 Mg 1 5.21 5 S 143 5.16 5 C 20555 2.51 5 N 5872 2.21 5 O 6473 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 294 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33115 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1803 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 223} Chain: "B" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1799 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 222} Chain: "C" Number of atoms: 10577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10577 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 54, 'TRANS': 1284} Chain: "D" Number of atoms: 10433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1342, 10433 Classifications: {'peptide': 1342} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1286} Chain breaks: 2 Chain: "E" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 709 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "F" Number of atoms: 6660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 840, 6660 Classifications: {'peptide': 840} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 795} Chain breaks: 1 Chain: "N" Number of atoms: 348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 348 Classifications: {'DNA': 28} Incomplete info: {'p_only': 12} Link IDs: {'rna3p': 27} Unresolved chain links: 12 Unresolved chain link angles: 48 Unresolved chain link dihedrals: 36 Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 367 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {' DT:plan': 7, ' DA:plan': 2, ' DA:plan2': 2, ' DC:plan': 2, ' DC:plan2': 2, ' DG:plan': 1, ' DG:plan2': 1} Unresolved non-hydrogen planarities: 132 Chain: "R" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 235 Classifications: {'RNA': 11} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna2p': 2, 'rna3p': 8} Chain: "T" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 545 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14644 SG CYS D 70 111.869 99.274 87.532 1.00295.71 S ATOM 14658 SG CYS D 72 111.568 103.158 89.401 1.00281.71 S ATOM 14766 SG CYS D 85 114.433 100.621 89.731 1.00276.02 S ATOM 14790 SG CYS D 88 110.672 99.961 90.718 1.00282.08 S ATOM 20478 SG CYS D 814 82.258 38.990 91.046 1.00173.19 S ATOM 21043 SG CYS D 888 81.551 42.598 90.968 1.00177.22 S ATOM 21094 SG CYS D 895 81.844 40.518 87.653 1.00169.34 S ATOM 21115 SG CYS D 898 78.831 40.075 89.785 1.00171.45 S ATOM 29893 SG CYS F 599 131.090 124.401 120.373 1.001027.4 S ATOM 29913 SG CYS F 602 134.110 126.665 120.223 1.001027.4 S ATOM 30033 SG CYS F 619 131.723 127.337 122.840 1.001027.4 S ATOM 30117 SG CYS F 630 130.483 128.063 119.393 1.001027.4 S ATOM 30367 SG CYS F 662 128.240 119.326 144.544 1.001027.4 S ATOM 30389 SG CYS F 665 126.292 120.798 147.455 1.001027.4 S ATOM 30530 SG CYS F 683 124.860 120.898 144.044 1.001027.4 S ATOM 30570 SG CYS F 689 127.722 123.218 144.976 1.001027.4 S ATOM 30746 SG CYS F 711 115.567 111.005 109.118 1.001027.4 S ATOM 30770 SG CYS F 714 117.490 108.836 110.986 1.001027.4 S ATOM 30902 SG CYS F 731 116.293 111.609 112.855 1.001027.4 S ATOM 30941 SG CYS F 736 118.843 112.168 109.905 1.001027.4 S Time building chain proxies: 6.48, per 1000 atoms: 0.20 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: 2.95 Conformation dependent library (CDL) restraints added in 1.5 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: 4.43 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: 9.28 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6278 1.32 - 1.45: 8845 1.45 - 1.58: 18278 1.58 - 1.71: 89 1.71 - 1.84: 243 Bond restraints: 33733 Sorted by residual: bond pdb=" C PHE F 699 " pdb=" N ARG F 700 " ideal model delta sigma weight residual 1.328 1.230 0.099 1.42e-02 4.96e+03 4.81e+01 bond pdb=" C3' DG N 39 " pdb=" O3' DG N 39 " ideal model delta sigma weight residual 1.435 1.347 0.088 1.30e-02 5.92e+03 4.53e+01 bond pdb=" C ARG F 700 " pdb=" N ILE F 701 " ideal model delta sigma weight residual 1.330 1.256 0.074 1.35e-02 5.49e+03 3.04e+01 bond pdb=" P DG N 39 " pdb=" O5' DG N 39 " ideal model delta sigma weight residual 1.593 1.540 0.053 1.00e-02 1.00e+04 2.85e+01 bond pdb=" O4' DC N 38 " pdb=" C1' DC N 38 " ideal model delta sigma weight residual 1.420 1.365 0.055 1.10e-02 8.26e+03 2.51e+01 ... (remaining 33728 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 44566 2.63 - 5.26: 1095 5.26 - 7.89: 102 7.89 - 10.52: 18 10.52 - 13.14: 7 Bond angle restraints: 45788 Sorted by residual: angle pdb=" O4' DC N 38 " pdb=" C1' DC N 38 " pdb=" N1 DC N 38 " ideal model delta sigma weight residual 108.00 96.35 11.65 7.00e-01 2.04e+00 2.77e+02 angle pdb=" O4' DC N 38 " pdb=" C4' DC N 38 " pdb=" C3' DC N 38 " ideal model delta sigma weight residual 106.00 111.90 -5.90 6.00e-01 2.78e+00 9.67e+01 angle pdb=" C1' C R 11 " pdb=" N1 C R 11 " pdb=" C2 C R 11 " ideal model delta sigma weight residual 118.80 128.48 -9.68 1.10e+00 8.26e-01 7.74e+01 angle pdb=" C3' 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=" O5' DG N 39 " pdb=" C5' DG N 39 " pdb=" C4' DG N 39 " ideal model delta sigma weight residual 109.40 103.39 6.01 8.00e-01 1.56e+00 5.64e+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: 4858 0.109 - 0.218: 279 0.218 - 0.327: 21 0.327 - 0.435: 7 0.435 - 0.544: 7 Chirality restraints: 5172 Sorted by residual: chirality pdb=" P DG T 16 " pdb=" OP1 DG T 16 " pdb=" OP2 DG T 16 " pdb=" O5' DG T 16 " both_signs ideal model delta sigma weight residual True 2.34 -2.88 -0.54 2.00e-01 2.50e+01 7.41e+00 chirality pdb=" CA ARG F 793 " pdb=" N ARG F 793 " pdb=" C ARG F 793 " pdb=" CB ARG F 793 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.40e+00 chirality pdb=" CA ARG D 53 " pdb=" N ARG D 53 " pdb=" C ARG D 53 " pdb=" CB ARG D 53 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.87e+00 ... (remaining 5169 not shown) Planarity restraints: 5825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 801 " -0.110 2.00e-02 2.50e+03 5.71e-02 6.52e+01 pdb=" CG TYR F 801 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR F 801 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 TYR F 801 " 0.043 2.00e-02 2.50e+03 pdb=" CE1 TYR F 801 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR F 801 " 0.022 2.00e-02 2.50e+03 pdb=" CZ TYR F 801 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 801 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 49 " 0.086 2.00e-02 2.50e+03 5.29e-02 4.90e+01 pdb=" CG PHE D 49 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 PHE D 49 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 PHE D 49 " -0.046 2.00e-02 2.50e+03 pdb=" CE1 PHE D 49 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE D 49 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE D 49 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 699 " -0.072 2.00e-02 2.50e+03 4.72e-02 3.89e+01 pdb=" CG PHE F 699 " 0.088 2.00e-02 2.50e+03 pdb=" CD1 PHE F 699 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 PHE F 699 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE F 699 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 PHE F 699 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE F 699 " -0.023 2.00e-02 2.50e+03 ... (remaining 5822 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 320 2.55 - 3.14: 27673 3.14 - 3.72: 53473 3.72 - 4.31: 71087 4.31 - 4.90: 116491 Nonbonded interactions: 269044 Sorted by model distance: nonbonded pdb=" OD2 ASP D 460 " pdb="MG MG D1500 " model vdw 1.961 2.170 nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D1500 " model vdw 2.025 2.170 nonbonded pdb=" OG1 THR D1169 " pdb=" OP1 DG N 51 " model vdw 2.054 3.040 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1500 " model vdw 2.156 2.170 nonbonded pdb=" OG1 THR A 111 " pdb=" O PRO A 126 " model vdw 2.171 3.040 ... (remaining 269039 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 4 through 235) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 38.650 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.134 33753 Z= 0.368 Angle : 0.936 23.203 45818 Z= 0.603 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/Z covalent geometry : bond 0.00589 / 0.37 (33733) covalent geometry : angle 0.91705 / 0.60 (45788) hydrogen bonds : bond 0.14860 / 9.80 ( 1510) hydrogen bonds : angle 6.83014 / 4.80 ( 4176) metal coordination : bond 0.03820 / 2.24 ( 20) metal coordination : angle 7.34725 / 4.71 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 351 time to evaluate : 1.154 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: 0.2355 time to fit residues: 154.8865 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 : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 7.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 HIS B 66 HIS ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 673 HIS C 688 GLN C 832 HIS ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1070 HIS C1175 ASN C1244 HIS D 157 GLN D 335 GLN D 435 GLN D 477 GLN D 875 ASN 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 197 GLN F 242 ASN F 309 GLN F 353 ASN ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 ASN ** F 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 590 ASN F 591 GLN F 681 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.068629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.048631 restraints weight = 360726.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.049194 restraints weight = 212648.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.049366 restraints weight = 152922.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.049887 restraints weight = 114137.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.050146 restraints weight = 91838.810| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 33753 Z= 0.187 Angle : 0.696 15.066 45818 Z= 0.363 Chirality : 0.045 0.215 5172 Planarity : 0.006 0.137 5825 Dihedral : 11.863 179.107 5127 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.36 % Favored : 97.56 % Rotamer: Outliers : 0.14 % Allowed : 2.88 % 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: 0.06 (0.13), residues: 4060 helix: 0.79 (0.13), residues: 1469 sheet: 0.03 (0.19), residues: 668 loop : -0.45 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 535 TYR 0.015 0.002 TYR D 46 PHE 0.020 0.002 PHE F 534 TRP 0.023 0.002 TRP F 560 HIS 0.018 0.002 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.19 (33733) covalent geometry : angle 0.68111 / 0.36 (45788) hydrogen bonds : bond 0.04989 / 3.43 ( 1510) hydrogen bonds : angle 5.44869 / 3.81 ( 4176) metal coordination : bond 0.01160 / 0.84 ( 20) metal coordination : angle 5.65557 / 3.55 ( 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 233 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 228 time to evaluate : 0.946 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: A 115 ILE cc_start: 0.9308 (OUTLIER) cc_final: 0.8932 (tp) REVERT: B 51 MET cc_start: 0.9325 (tpp) cc_final: 0.9007 (mmm) REVERT: C 459 MET cc_start: 0.9314 (mpp) cc_final: 0.9113 (mpp) REVERT: C 545 PHE cc_start: 0.8903 (m-80) cc_final: 0.8627 (m-80) REVERT: C 951 MET cc_start: 0.9334 (ppp) cc_final: 0.8959 (ppp) REVERT: C 1078 LYS cc_start: 0.9443 (tptt) cc_final: 0.8950 (tppp) REVERT: C 1085 MET cc_start: 0.9006 (mmm) cc_final: 0.8465 (mmm) REVERT: C 1107 MET cc_start: 0.9663 (mpp) cc_final: 0.9435 (mpp) REVERT: C 1131 MET cc_start: 0.8818 (ttm) cc_final: 0.8521 (mtp) REVERT: C 1230 MET cc_start: 0.8337 (tpt) cc_final: 0.7733 (tpp) REVERT: C 1235 LEU cc_start: 0.9453 (mm) cc_final: 0.9082 (mp) REVERT: C 1304 MET cc_start: 0.9384 (tpt) cc_final: 0.8922 (tpp) REVERT: C 1319 MET cc_start: 0.8548 (tpp) cc_final: 0.7967 (mmm) REVERT: C 1333 LEU cc_start: 0.9542 (tp) cc_final: 0.9198 (tt) REVERT: D 115 TRP cc_start: 0.9198 (m-10) cc_final: 0.8517 (m-10) REVERT: D 130 MET cc_start: 0.9198 (tpp) cc_final: 0.8841 (tpp) REVERT: D 180 MET cc_start: 0.8367 (tpt) cc_final: 0.8027 (tpt) REVERT: D 192 MET cc_start: 0.8386 (mtm) cc_final: 0.8129 (mtm) REVERT: D 278 ARG cc_start: 0.9628 (ttm110) cc_final: 0.8910 (ptp-110) REVERT: D 279 LEU cc_start: 0.9810 (tp) cc_final: 0.9523 (tp) REVERT: D 368 LEU cc_start: 0.9704 (tt) cc_final: 0.9313 (mp) REVERT: D 443 GLU cc_start: 0.9237 (tp30) cc_final: 0.8885 (tp30) REVERT: D 466 MET cc_start: 0.8677 (tpp) cc_final: 0.8405 (tmm) REVERT: D 485 MET cc_start: 0.8351 (mmp) cc_final: 0.7289 (mmm) REVERT: D 513 MET cc_start: 0.8879 (ttm) cc_final: 0.8118 (ttp) REVERT: D 581 MET cc_start: 0.8549 (tpp) cc_final: 0.8286 (tpp) REVERT: D 724 MET cc_start: 0.9271 (mmp) cc_final: 0.8950 (mmm) REVERT: D 747 MET cc_start: 0.7674 (ttt) cc_final: 0.7280 (ttt) REVERT: D 807 LEU cc_start: 0.8654 (tp) cc_final: 0.8343 (tp) REVERT: D 1025 MET cc_start: 0.8946 (tpt) cc_final: 0.8163 (tmm) REVERT: D 1145 PHE cc_start: 0.8925 (m-80) cc_final: 0.8104 (m-80) REVERT: F 376 MET cc_start: 0.0272 (mmp) cc_final: 0.0059 (mmp) REVERT: F 546 MET cc_start: -0.5651 (ttm) cc_final: -0.5852 (mmp) REVERT: F 590 ASN cc_start: -0.0343 (OUTLIER) cc_final: -0.0648 (t0) REVERT: F 669 MET cc_start: 0.6562 (mtm) cc_final: 0.6313 (mmm) outliers start: 5 outliers final: 1 residues processed: 232 average time/residue: 0.2089 time to fit residues: 78.6346 Evaluate side-chains 181 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 178 time to evaluate : 1.228 ------------------------------------------------------------------------------- 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: 9.9990 chunk 35 optimal weight: 20.0000 chunk 299 optimal weight: 7.9990 chunk 255 optimal weight: 3.9990 chunk 275 optimal weight: 8.9990 chunk 315 optimal weight: 8.9990 chunk 187 optimal weight: 7.9990 chunk 407 optimal weight: 50.0000 chunk 265 optimal weight: 10.0000 chunk 230 optimal weight: 20.0000 chunk 21 optimal weight: 2.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 ASN B 128 HIS C 31 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS C 760 ASN ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1264 GLN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1019 ASN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 533 ASN ** 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 = 0.3675 r_free = 0.3675 target = 0.066048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.046655 restraints weight = 365426.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.046511 restraints weight = 220813.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.047090 restraints weight = 145372.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.047576 restraints weight = 109365.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.047695 restraints weight = 91676.493| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 33753 Z= 0.218 Angle : 0.665 14.231 45818 Z= 0.346 Chirality : 0.043 0.238 5172 Planarity : 0.005 0.141 5825 Dihedral : 11.996 176.752 5127 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.46 % Favored : 97.46 % Rotamer: Outliers : 0.06 % Allowed : 3.55 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.13), residues: 4060 helix: 0.92 (0.13), residues: 1480 sheet: -0.21 (0.19), residues: 663 loop : -0.33 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 150 TYR 0.017 0.002 TYR D 457 PHE 0.025 0.002 PHE C 514 TRP 0.013 0.002 TRP D 33 HIS 0.010 0.001 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.22 (33733) covalent geometry : angle 0.65371 / 0.35 (45788) hydrogen bonds : bond 0.04808 / 3.33 ( 1510) hydrogen bonds : angle 5.23594 / 3.64 ( 4176) metal coordination : bond 0.01274 / 0.80 ( 20) metal coordination : angle 4.85380 / 2.99 ( 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 203 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 201 time to evaluate : 1.324 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: C 315 MET cc_start: 0.9263 (ptt) cc_final: 0.8960 (ptt) REVERT: C 403 MET cc_start: 0.9222 (ppp) cc_final: 0.8854 (ppp) REVERT: C 545 PHE cc_start: 0.8929 (m-80) cc_final: 0.8639 (m-80) REVERT: C 653 MET cc_start: 0.7830 (tpt) cc_final: 0.7446 (tpt) REVERT: C 681 MET cc_start: 0.9343 (mtm) cc_final: 0.8944 (ptp) REVERT: C 685 MET cc_start: 0.9165 (mtm) cc_final: 0.8917 (ptp) REVERT: C 768 MET cc_start: 0.8349 (ppp) cc_final: 0.8112 (ppp) REVERT: C 805 MET cc_start: 0.8644 (ppp) cc_final: 0.8350 (ppp) REVERT: C 814 ASP cc_start: 0.8355 (t0) cc_final: 0.8060 (t0) REVERT: C 1078 LYS cc_start: 0.9621 (tptt) cc_final: 0.9170 (tppp) REVERT: C 1085 MET cc_start: 0.9114 (mmm) cc_final: 0.8440 (mmp) REVERT: C 1107 MET cc_start: 0.9652 (mpp) cc_final: 0.9403 (mpp) REVERT: C 1131 MET cc_start: 0.8930 (ttm) cc_final: 0.8638 (mtp) REVERT: C 1304 MET cc_start: 0.9445 (tpt) cc_final: 0.9009 (tpp) REVERT: C 1319 MET cc_start: 0.9042 (tpp) cc_final: 0.8271 (tpp) REVERT: D 130 MET cc_start: 0.9194 (tpp) cc_final: 0.8845 (tpp) REVERT: D 180 MET cc_start: 0.8154 (tpt) cc_final: 0.7931 (tpt) REVERT: D 192 MET cc_start: 0.8420 (mtm) cc_final: 0.8089 (mtm) REVERT: D 278 ARG cc_start: 0.9679 (ttm110) cc_final: 0.9155 (ptp-110) REVERT: D 400 MET cc_start: 0.9255 (tpp) cc_final: 0.8992 (tpp) REVERT: D 443 GLU cc_start: 0.9296 (tp30) cc_final: 0.9047 (tp30) REVERT: D 485 MET cc_start: 0.8735 (mmp) cc_final: 0.7992 (mmm) REVERT: D 513 MET cc_start: 0.8662 (ttm) cc_final: 0.8110 (ttp) REVERT: D 581 MET cc_start: 0.8681 (tpp) cc_final: 0.8245 (tpp) REVERT: D 724 MET cc_start: 0.9290 (mmp) cc_final: 0.9006 (mmm) REVERT: D 725 MET cc_start: 0.9114 (mtp) cc_final: 0.8608 (mtp) REVERT: D 747 MET cc_start: 0.8065 (ttt) cc_final: 0.7791 (ttt) REVERT: D 807 LEU cc_start: 0.8737 (tp) cc_final: 0.8352 (tp) REVERT: D 1025 MET cc_start: 0.9155 (tpt) cc_final: 0.8324 (tmm) REVERT: D 1141 VAL cc_start: 0.9568 (m) cc_final: 0.8835 (p) REVERT: D 1145 PHE cc_start: 0.9179 (m-80) cc_final: 0.7879 (m-80) REVERT: F 171 MET cc_start: -0.0824 (tmm) cc_final: -0.1396 (ppp) REVERT: F 669 MET cc_start: 0.6474 (mtm) cc_final: 0.6200 (mtt) REVERT: F 729 MET cc_start: 0.3412 (ttp) cc_final: 0.2686 (tmm) outliers start: 2 outliers final: 0 residues processed: 203 average time/residue: 0.2182 time to fit residues: 73.1126 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 : 1.166 ------------------------------------------------------------------------------- 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: 10.0000 chunk 204 optimal weight: 5.9990 chunk 260 optimal weight: 8.9990 chunk 377 optimal weight: 5.9990 chunk 241 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 369 optimal weight: 0.0270 chunk 96 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 164 optimal weight: 20.0000 overall best weight: 6.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN D 419 HIS ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 HIS ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN F 166 GLN ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 533 ASN F 591 GLN ** F 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.065116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.044486 restraints weight = 369247.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.045029 restraints weight = 222095.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.045437 restraints weight = 155706.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.045921 restraints weight = 128453.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 67)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.046050 restraints weight = 110734.553| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 33753 Z= 0.205 Angle : 0.633 14.499 45818 Z= 0.333 Chirality : 0.043 0.215 5172 Planarity : 0.005 0.113 5825 Dihedral : 12.124 175.795 5127 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.64 % Favored : 97.32 % Rotamer: Outliers : 0.06 % Allowed : 3.20 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.13), residues: 4060 helix: 0.97 (0.13), residues: 1479 sheet: -0.35 (0.19), residues: 657 loop : -0.27 (0.14), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 378 TYR 0.024 0.002 TYR C 346 PHE 0.023 0.002 PHE F 567 TRP 0.012 0.001 TRP F 851 HIS 0.008 0.001 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.20 (33733) covalent geometry : angle 0.62276 / 0.33 (45788) hydrogen bonds : bond 0.04366 / 3.05 ( 1510) hydrogen bonds : angle 5.11210 / 3.56 ( 4176) metal coordination : bond 0.01846 / 1.16 ( 20) metal coordination : angle 4.39613 / 2.72 ( 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 188 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 186 time to evaluate : 1.350 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: C 315 MET cc_start: 0.9312 (ptt) cc_final: 0.9035 (ptt) REVERT: C 403 MET cc_start: 0.9298 (ppp) cc_final: 0.8916 (ppp) REVERT: C 459 MET cc_start: 0.9432 (mpp) cc_final: 0.9192 (mpp) REVERT: C 464 PHE cc_start: 0.8990 (t80) cc_final: 0.8659 (t80) REVERT: C 545 PHE cc_start: 0.8976 (m-80) cc_final: 0.8676 (m-80) REVERT: C 587 LEU cc_start: 0.9397 (mm) cc_final: 0.9120 (mt) REVERT: C 653 MET cc_start: 0.7684 (tpt) cc_final: 0.7374 (tpt) REVERT: C 681 MET cc_start: 0.9399 (mtm) cc_final: 0.8779 (mtt) REVERT: C 685 MET cc_start: 0.9289 (mtm) cc_final: 0.8694 (mtt) REVERT: C 805 MET cc_start: 0.8675 (ppp) cc_final: 0.8423 (ppp) REVERT: C 1078 LYS cc_start: 0.9620 (tptt) cc_final: 0.9271 (tppp) REVERT: C 1085 MET cc_start: 0.9159 (mmm) cc_final: 0.8434 (mmp) REVERT: C 1107 MET cc_start: 0.9592 (mpp) cc_final: 0.9365 (mpp) REVERT: C 1230 MET cc_start: 0.9011 (tpp) cc_final: 0.8140 (tpp) REVERT: C 1279 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8907 (mt-10) REVERT: C 1304 MET cc_start: 0.9474 (tpt) cc_final: 0.9100 (tpp) REVERT: C 1319 MET cc_start: 0.9109 (tpp) cc_final: 0.8207 (tpp) REVERT: D 102 MET cc_start: 0.7929 (ppp) cc_final: 0.7679 (ppp) REVERT: D 130 MET cc_start: 0.9188 (tpp) cc_final: 0.8882 (tpp) REVERT: D 192 MET cc_start: 0.8675 (mtm) cc_final: 0.8378 (mtm) REVERT: D 237 MET cc_start: 0.9032 (mtp) cc_final: 0.8806 (mtp) REVERT: D 278 ARG cc_start: 0.9607 (ttm110) cc_final: 0.9134 (ptp-110) REVERT: D 279 LEU cc_start: 0.9708 (tt) cc_final: 0.9412 (mm) REVERT: D 330 MET cc_start: 0.9397 (mmp) cc_final: 0.9187 (mmm) REVERT: D 400 MET cc_start: 0.9373 (tpp) cc_final: 0.9133 (tpp) REVERT: D 466 MET cc_start: 0.8735 (tpp) cc_final: 0.8530 (tpp) REVERT: D 485 MET cc_start: 0.8971 (mmp) cc_final: 0.8036 (mmm) REVERT: D 513 MET cc_start: 0.8600 (ttm) cc_final: 0.7807 (ttp) REVERT: D 581 MET cc_start: 0.8793 (tpp) cc_final: 0.8481 (tpp) REVERT: D 724 MET cc_start: 0.9306 (mmp) cc_final: 0.9065 (mmm) REVERT: D 725 MET cc_start: 0.8856 (mtp) cc_final: 0.8583 (mtp) REVERT: D 747 MET cc_start: 0.8066 (ttt) cc_final: 0.7795 (ttt) REVERT: D 1025 MET cc_start: 0.9021 (tpt) cc_final: 0.8099 (tmm) REVERT: D 1145 PHE cc_start: 0.9261 (m-80) cc_final: 0.8413 (m-80) REVERT: D 1307 LEU cc_start: 0.9638 (mp) cc_final: 0.9423 (mp) REVERT: F 376 MET cc_start: 0.1006 (mmp) cc_final: 0.0760 (mmp) REVERT: F 587 MET cc_start: 0.3512 (ttm) cc_final: 0.3291 (ttm) REVERT: F 669 MET cc_start: 0.6418 (mtm) cc_final: 0.6167 (mtt) REVERT: F 729 MET cc_start: 0.1192 (ttp) cc_final: 0.0886 (tmm) outliers start: 2 outliers final: 1 residues processed: 188 average time/residue: 0.2199 time to fit residues: 69.3039 Evaluate side-chains 160 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 1.307 ------------------------------------------------------------------------------- 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: 9.9990 chunk 292 optimal weight: 30.0000 chunk 7 optimal weight: 3.9990 chunk 344 optimal weight: 20.0000 chunk 227 optimal weight: 10.0000 chunk 410 optimal weight: 40.0000 chunk 269 optimal weight: 0.0040 chunk 40 optimal weight: 9.9990 chunk 126 optimal weight: 7.9990 chunk 179 optimal weight: 5.9990 chunk 204 optimal weight: 20.0000 overall best weight: 5.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 HIS C 86 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 518 ASN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 GLN C 760 ASN ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS ** C1080 ASN ** 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 591 GLN ** F 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.064768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.045267 restraints weight = 371880.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.045065 restraints weight = 224241.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.045648 restraints weight = 147526.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.045918 restraints weight = 109631.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.046045 restraints weight = 92499.161| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 33753 Z= 0.190 Angle : 0.617 14.098 45818 Z= 0.321 Chirality : 0.042 0.216 5172 Planarity : 0.005 0.129 5825 Dihedral : 12.119 175.132 5127 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.71 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % 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: 0.23 (0.13), residues: 4060 helix: 1.05 (0.13), residues: 1486 sheet: -0.39 (0.19), residues: 670 loop : -0.25 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C1211 TYR 0.013 0.001 TYR D 537 PHE 0.019 0.002 PHE C 670 TRP 0.011 0.001 TRP F 560 HIS 0.011 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.19 (33733) covalent geometry : angle 0.60660 / 0.32 (45788) hydrogen bonds : bond 0.04233 / 2.95 ( 1510) hydrogen bonds : angle 5.07451 / 3.53 ( 4176) metal coordination : bond 0.00712 / 0.46 ( 20) metal coordination : angle 4.38996 / 2.69 ( 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 179 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.887 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: 0.9427 (mmp) cc_final: 0.9121 (mmm) REVERT: C 464 PHE cc_start: 0.8878 (t80) cc_final: 0.8572 (t80) REVERT: C 545 PHE cc_start: 0.8885 (m-80) cc_final: 0.8618 (m-80) REVERT: C 653 MET cc_start: 0.7798 (tpt) cc_final: 0.7452 (tpt) REVERT: C 681 MET cc_start: 0.9364 (mtm) cc_final: 0.8689 (mtt) REVERT: C 685 MET cc_start: 0.9140 (mtm) cc_final: 0.8586 (mtt) REVERT: C 805 MET cc_start: 0.8759 (ppp) cc_final: 0.8456 (ppp) REVERT: C 1078 LYS cc_start: 0.9744 (tptt) cc_final: 0.9415 (tppp) REVERT: C 1085 MET cc_start: 0.9097 (mmm) cc_final: 0.8463 (mmm) REVERT: C 1107 MET cc_start: 0.9610 (mpp) cc_final: 0.9368 (mpp) REVERT: C 1230 MET cc_start: 0.8837 (tpp) cc_final: 0.8145 (tpp) REVERT: C 1304 MET cc_start: 0.9430 (tpt) cc_final: 0.9047 (tpp) REVERT: C 1319 MET cc_start: 0.9187 (tpp) cc_final: 0.8272 (tpp) REVERT: D 130 MET cc_start: 0.8940 (tpp) cc_final: 0.8726 (tpp) REVERT: D 180 MET cc_start: 0.8357 (tpt) cc_final: 0.8143 (tpt) REVERT: D 279 LEU cc_start: 0.9751 (tt) cc_final: 0.9442 (mm) REVERT: D 466 MET cc_start: 0.8708 (tpp) cc_final: 0.8503 (tpp) REVERT: D 513 MET cc_start: 0.8618 (ttm) cc_final: 0.7755 (ttp) REVERT: D 581 MET cc_start: 0.8728 (tpp) cc_final: 0.8285 (tpp) REVERT: D 724 MET cc_start: 0.9249 (mmp) cc_final: 0.9001 (mmm) REVERT: D 725 MET cc_start: 0.8820 (mtp) cc_final: 0.8612 (mtp) REVERT: D 807 LEU cc_start: 0.8813 (tp) cc_final: 0.8280 (tp) REVERT: D 1025 MET cc_start: 0.9111 (tpt) cc_final: 0.8144 (tmm) REVERT: F 587 MET cc_start: 0.3549 (ttm) cc_final: 0.3007 (mtm) REVERT: F 729 MET cc_start: 0.2087 (ttp) cc_final: 0.1861 (tmm) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2144 time to fit residues: 64.5868 Evaluate side-chains 155 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.492 ------------------------------------------------------------------------------- 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: 9.9990 chunk 125 optimal weight: 10.0000 chunk 405 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 310 optimal weight: 0.0980 chunk 341 optimal weight: 50.0000 chunk 351 optimal weight: 7.9990 chunk 401 optimal weight: 20.0000 overall best weight: 5.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1324 ASN ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.061398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.039763 restraints weight = 346304.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.040427 restraints weight = 225830.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.040997 restraints weight = 165902.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.041249 restraints weight = 132100.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.041535 restraints weight = 115918.333| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 33753 Z= 0.197 Angle : 0.624 13.825 45818 Z= 0.324 Chirality : 0.042 0.216 5172 Planarity : 0.004 0.107 5825 Dihedral : 12.154 174.690 5127 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.76 % Favored : 97.19 % Rotamer: Outliers : 0.03 % Allowed : 2.02 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.13), residues: 4060 helix: 1.08 (0.13), residues: 1476 sheet: -0.47 (0.19), residues: 669 loop : -0.32 (0.14), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 88 TYR 0.014 0.001 TYR D 537 PHE 0.025 0.002 PHE C 514 TRP 0.012 0.001 TRP F 560 HIS 0.010 0.001 HIS D 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.20 (33733) covalent geometry : angle 0.61342 / 0.32 (45788) hydrogen bonds : bond 0.04224 / 2.96 ( 1510) hydrogen bonds : angle 5.07654 / 3.53 ( 4176) metal coordination : bond 0.01075 / 0.68 ( 20) metal coordination : angle 4.49095 / 2.87 ( 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 180 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 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: symmetry clash REVERT: B 51 MET cc_start: 0.9496 (mmp) cc_final: 0.9134 (mmm) REVERT: B 205 MET cc_start: 0.8725 (tmm) cc_final: 0.8396 (tmm) REVERT: C 403 MET cc_start: 0.9241 (ppp) cc_final: 0.8880 (ppp) REVERT: C 459 MET cc_start: 0.9436 (mpp) cc_final: 0.9188 (mpp) REVERT: C 464 PHE cc_start: 0.8955 (t80) cc_final: 0.8603 (t80) REVERT: C 545 PHE cc_start: 0.8459 (m-80) cc_final: 0.8256 (m-80) REVERT: C 653 MET cc_start: 0.7734 (tpt) cc_final: 0.7335 (tpt) REVERT: C 681 MET cc_start: 0.9429 (mtm) cc_final: 0.8756 (ptp) REVERT: C 685 MET cc_start: 0.9218 (mtm) cc_final: 0.8462 (mtt) REVERT: C 800 MET cc_start: 0.8929 (pmm) cc_final: 0.7677 (pmm) REVERT: C 805 MET cc_start: 0.8807 (ppp) cc_final: 0.8509 (ppp) REVERT: C 1078 LYS cc_start: 0.9676 (tptt) cc_final: 0.9404 (tppp) REVERT: C 1085 MET cc_start: 0.9058 (mmm) cc_final: 0.8480 (mmm) REVERT: C 1107 MET cc_start: 0.9611 (mpp) cc_final: 0.9382 (mpp) REVERT: C 1230 MET cc_start: 0.8769 (tpp) cc_final: 0.8197 (tpp) REVERT: C 1290 MET cc_start: 0.9431 (tpt) cc_final: 0.9218 (tpp) REVERT: C 1304 MET cc_start: 0.9472 (tpt) cc_final: 0.9097 (tpp) REVERT: C 1319 MET cc_start: 0.9276 (tpp) cc_final: 0.8462 (tpp) REVERT: D 130 MET cc_start: 0.8948 (tpp) cc_final: 0.8729 (tpp) REVERT: D 237 MET cc_start: 0.8997 (mtp) cc_final: 0.8784 (mtp) REVERT: D 279 LEU cc_start: 0.9766 (tt) cc_final: 0.9430 (mm) REVERT: D 466 MET cc_start: 0.8712 (tpp) cc_final: 0.8276 (mmt) REVERT: D 513 MET cc_start: 0.8630 (ttm) cc_final: 0.7836 (ttp) REVERT: D 724 MET cc_start: 0.9300 (mmp) cc_final: 0.9015 (mmm) REVERT: D 807 LEU cc_start: 0.8706 (tp) cc_final: 0.8403 (tp) REVERT: D 1025 MET cc_start: 0.8855 (tpt) cc_final: 0.8095 (tmm) REVERT: F 587 MET cc_start: 0.3745 (ttm) cc_final: 0.3269 (mtm) outliers start: 1 outliers final: 1 residues processed: 180 average time/residue: 0.2172 time to fit residues: 65.5289 Evaluate side-chains 149 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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: 2.9990 chunk 283 optimal weight: 8.9990 chunk 45 optimal weight: 0.6980 chunk 8 optimal weight: 10.0000 chunk 246 optimal weight: 8.9990 chunk 179 optimal weight: 1.9990 chunk 249 optimal weight: 6.9990 chunk 335 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 233 optimal weight: 5.9990 chunk 331 optimal weight: 40.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.061768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.040043 restraints weight = 345851.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.040668 restraints weight = 228144.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.041029 restraints weight = 167696.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.041373 restraints weight = 140719.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 69)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.041795 restraints weight = 126251.251| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33753 Z= 0.148 Angle : 0.601 13.527 45818 Z= 0.307 Chirality : 0.042 0.216 5172 Planarity : 0.005 0.133 5825 Dihedral : 12.096 174.237 5127 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.49 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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: 0.26 (0.13), residues: 4060 helix: 1.20 (0.13), residues: 1484 sheet: -0.46 (0.20), residues: 668 loop : -0.31 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 47 TYR 0.039 0.001 TYR F 855 PHE 0.018 0.001 PHE C 186 TRP 0.012 0.001 TRP F 560 HIS 0.009 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 (33733) covalent geometry : angle 0.58774 / 0.31 (45788) hydrogen bonds : bond 0.03856 / 2.70 ( 1510) hydrogen bonds : angle 4.97367 / 3.46 ( 4176) metal coordination : bond 0.00863 / 0.61 ( 20) metal coordination : angle 4.91074 / 3.16 ( 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 172 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.948 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: 0.9503 (mmp) cc_final: 0.9138 (mmm) REVERT: C 403 MET cc_start: 0.9372 (ppp) cc_final: 0.9084 (ppp) REVERT: C 459 MET cc_start: 0.9428 (mpp) cc_final: 0.9187 (mpp) REVERT: C 464 PHE cc_start: 0.8876 (t80) cc_final: 0.8459 (t80) REVERT: C 545 PHE cc_start: 0.8431 (m-80) cc_final: 0.8218 (m-80) REVERT: C 653 MET cc_start: 0.8494 (tpt) cc_final: 0.8168 (tpt) REVERT: C 681 MET cc_start: 0.9440 (mtm) cc_final: 0.8769 (ptp) REVERT: C 685 MET cc_start: 0.9286 (mtm) cc_final: 0.8477 (mtt) REVERT: C 800 MET cc_start: 0.8931 (pmm) cc_final: 0.7408 (pmm) REVERT: C 805 MET cc_start: 0.8797 (ppp) cc_final: 0.8472 (ppp) REVERT: C 1078 LYS cc_start: 0.9718 (tptt) cc_final: 0.9418 (tppp) REVERT: C 1085 MET cc_start: 0.8999 (mmm) cc_final: 0.8487 (mmm) REVERT: C 1107 MET cc_start: 0.9677 (mpp) cc_final: 0.9419 (mpp) REVERT: C 1230 MET cc_start: 0.8997 (tpp) cc_final: 0.8237 (tpp) REVERT: C 1279 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8739 (mt-10) REVERT: C 1304 MET cc_start: 0.9443 (tpt) cc_final: 0.9094 (tpp) REVERT: C 1319 MET cc_start: 0.9281 (tpp) cc_final: 0.8461 (tpp) REVERT: D 192 MET cc_start: 0.8470 (mtm) cc_final: 0.8229 (mtm) REVERT: D 237 MET cc_start: 0.8946 (mtp) cc_final: 0.8723 (mtp) REVERT: D 278 ARG cc_start: 0.9638 (ttm110) cc_final: 0.9142 (ptp-110) REVERT: D 279 LEU cc_start: 0.9764 (tt) cc_final: 0.9368 (mm) REVERT: D 372 MET cc_start: 0.9415 (mmt) cc_final: 0.8693 (mmm) REVERT: D 466 MET cc_start: 0.8738 (tpp) cc_final: 0.8315 (mmt) REVERT: D 513 MET cc_start: 0.8652 (ttm) cc_final: 0.7910 (ttp) REVERT: D 724 MET cc_start: 0.9269 (mmp) cc_final: 0.8998 (mmm) REVERT: D 725 MET cc_start: 0.9365 (mtp) cc_final: 0.8944 (mtp) REVERT: D 807 LEU cc_start: 0.8729 (tp) cc_final: 0.8434 (tp) REVERT: D 1025 MET cc_start: 0.9256 (tpt) cc_final: 0.8401 (tmm) REVERT: D 1306 LEU cc_start: 0.9005 (mt) cc_final: 0.8698 (mt) REVERT: F 587 MET cc_start: 0.3614 (ttm) cc_final: 0.3253 (mtm) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.2128 time to fit residues: 61.4208 Evaluate side-chains 150 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.325 ------------------------------------------------------------------------------- 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: 6.9990 chunk 67 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 296 optimal weight: 7.9990 chunk 396 optimal weight: 0.9990 chunk 311 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 301 optimal weight: 9.9990 chunk 216 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN ** F 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 825 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.061698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.040200 restraints weight = 342438.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.040707 restraints weight = 220230.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.041186 restraints weight = 158768.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.041686 restraints weight = 126011.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.041782 restraints weight = 108686.397| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33753 Z= 0.144 Angle : 0.596 12.843 45818 Z= 0.306 Chirality : 0.042 0.216 5172 Planarity : 0.004 0.113 5825 Dihedral : 12.048 173.893 5127 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.54 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % 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: 0.26 (0.13), residues: 4060 helix: 1.20 (0.13), residues: 1485 sheet: -0.42 (0.20), residues: 663 loop : -0.33 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG D 47 TYR 0.029 0.001 TYR F 855 PHE 0.017 0.001 PHE C 514 TRP 0.015 0.001 TRP F 560 HIS 0.007 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (33733) covalent geometry : angle 0.58509 / 0.31 (45788) hydrogen bonds : bond 0.03795 / 2.66 ( 1510) hydrogen bonds : angle 4.97177 / 3.46 ( 4176) metal coordination : bond 0.00726 / 0.49 ( 20) metal coordination : angle 4.51100 / 2.96 ( 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 167 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.327 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: 0.9516 (mmp) cc_final: 0.9143 (mmm) REVERT: C 403 MET cc_start: 0.9379 (ppp) cc_final: 0.9077 (ppp) REVERT: C 459 MET cc_start: 0.9426 (mpp) cc_final: 0.9197 (mpp) REVERT: C 464 PHE cc_start: 0.8845 (t80) cc_final: 0.8409 (t80) REVERT: C 545 PHE cc_start: 0.8444 (m-80) cc_final: 0.8227 (m-80) REVERT: C 653 MET cc_start: 0.8493 (tpt) cc_final: 0.8182 (tpt) REVERT: C 681 MET cc_start: 0.9448 (mtm) cc_final: 0.8780 (ptp) REVERT: C 685 MET cc_start: 0.9293 (mtm) cc_final: 0.8472 (mtt) REVERT: C 800 MET cc_start: 0.8887 (pmm) cc_final: 0.7511 (pmm) REVERT: C 805 MET cc_start: 0.8820 (ppp) cc_final: 0.8469 (ppp) REVERT: C 1078 LYS cc_start: 0.9733 (tptt) cc_final: 0.9414 (tppp) REVERT: C 1085 MET cc_start: 0.9098 (mmm) cc_final: 0.8189 (mmm) REVERT: C 1107 MET cc_start: 0.9583 (mpp) cc_final: 0.9369 (mpp) REVERT: C 1230 MET cc_start: 0.9015 (tpp) cc_final: 0.8236 (tpp) REVERT: C 1279 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8750 (mt-10) REVERT: C 1290 MET cc_start: 0.9429 (tpt) cc_final: 0.9221 (tpp) REVERT: C 1304 MET cc_start: 0.9454 (tpt) cc_final: 0.9134 (tpp) REVERT: C 1319 MET cc_start: 0.9117 (tpp) cc_final: 0.8351 (tpp) REVERT: D 130 MET cc_start: 0.9095 (tpt) cc_final: 0.8885 (tpp) REVERT: D 192 MET cc_start: 0.8531 (mtm) cc_final: 0.8226 (mtm) REVERT: D 237 MET cc_start: 0.8979 (mtp) cc_final: 0.8757 (mtp) REVERT: D 278 ARG cc_start: 0.9642 (ttm110) cc_final: 0.9151 (ptp-110) REVERT: D 279 LEU cc_start: 0.9771 (tt) cc_final: 0.9368 (mm) REVERT: D 372 MET cc_start: 0.9202 (mmm) cc_final: 0.8668 (mmm) REVERT: D 466 MET cc_start: 0.8769 (tpp) cc_final: 0.8346 (mmt) REVERT: D 485 MET cc_start: 0.8950 (mmp) cc_final: 0.7969 (mmm) REVERT: D 513 MET cc_start: 0.8660 (ttm) cc_final: 0.7881 (ttp) REVERT: D 581 MET cc_start: 0.8410 (mmt) cc_final: 0.8156 (mmm) REVERT: D 724 MET cc_start: 0.9260 (mmp) cc_final: 0.8984 (mmm) REVERT: D 725 MET cc_start: 0.9348 (mtp) cc_final: 0.8969 (mtp) REVERT: D 807 LEU cc_start: 0.8867 (tp) cc_final: 0.8593 (tp) REVERT: D 1025 MET cc_start: 0.9294 (tpt) cc_final: 0.8544 (tmm) REVERT: D 1260 MET cc_start: 0.9006 (tpp) cc_final: 0.8789 (tpp) REVERT: F 587 MET cc_start: 0.2806 (ttm) cc_final: 0.2260 (mtm) REVERT: F 669 MET cc_start: 0.5979 (mmt) cc_final: 0.5734 (mmp) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2111 time to fit residues: 59.1889 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 : 1.273 ------------------------------------------------------------------------------- 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: 4.9990 chunk 58 optimal weight: 20.0000 chunk 4 optimal weight: 8.9990 chunk 331 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 391 optimal weight: 8.9990 chunk 361 optimal weight: 50.0000 chunk 204 optimal weight: 9.9990 chunk 153 optimal weight: 2.9990 chunk 263 optimal weight: 0.0050 overall best weight: 4.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN C1008 GLN ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN D1244 GLN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN ** F 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.064080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.045096 restraints weight = 371057.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.044885 restraints weight = 238049.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.045123 restraints weight = 160801.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.045494 restraints weight = 127500.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.045483 restraints weight = 102371.585| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33753 Z= 0.164 Angle : 0.596 12.503 45818 Z= 0.308 Chirality : 0.042 0.217 5172 Planarity : 0.004 0.104 5825 Dihedral : 12.043 173.622 5127 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.64 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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: 0.22 (0.13), residues: 4060 helix: 1.16 (0.13), residues: 1487 sheet: -0.52 (0.20), residues: 661 loop : -0.32 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 47 TYR 0.023 0.001 TYR C1231 PHE 0.015 0.001 PHE C 514 TRP 0.019 0.001 TRP F 560 HIS 0.007 0.001 HIS C 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 (33733) covalent geometry : angle 0.58628 / 0.31 (45788) hydrogen bonds : bond 0.03900 / 2.72 ( 1510) hydrogen bonds : angle 4.95549 / 3.45 ( 4176) metal coordination : bond 0.00676 / 0.46 ( 20) metal coordination : angle 4.23369 / 2.79 ( 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 170 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: 0.9536 (mmp) cc_final: 0.9157 (mmm) REVERT: C 403 MET cc_start: 0.9363 (ppp) cc_final: 0.9048 (ppp) REVERT: C 464 PHE cc_start: 0.8791 (t80) cc_final: 0.8446 (t80) REVERT: C 653 MET cc_start: 0.8612 (tpt) cc_final: 0.8343 (tpt) REVERT: C 681 MET cc_start: 0.9388 (mtm) cc_final: 0.8943 (ptp) REVERT: C 684 ASN cc_start: 0.8453 (m110) cc_final: 0.8042 (m110) REVERT: C 685 MET cc_start: 0.9249 (mtm) cc_final: 0.8454 (mtt) REVERT: C 800 MET cc_start: 0.8899 (pmm) cc_final: 0.7530 (pmm) REVERT: C 805 MET cc_start: 0.8822 (ppp) cc_final: 0.8452 (ppp) REVERT: C 1078 LYS cc_start: 0.9750 (tptt) cc_final: 0.9407 (tppp) REVERT: C 1085 MET cc_start: 0.9053 (mmm) cc_final: 0.7851 (mmm) REVERT: C 1107 MET cc_start: 0.9576 (mpp) cc_final: 0.9356 (mpp) REVERT: C 1230 MET cc_start: 0.9007 (tpp) cc_final: 0.8172 (tpp) REVERT: C 1279 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8737 (mt-10) REVERT: C 1290 MET cc_start: 0.9417 (tpt) cc_final: 0.9205 (tpp) REVERT: C 1304 MET cc_start: 0.9409 (tpt) cc_final: 0.9112 (tpp) REVERT: C 1319 MET cc_start: 0.9292 (tpp) cc_final: 0.8450 (tpp) REVERT: D 192 MET cc_start: 0.8474 (mtm) cc_final: 0.8247 (mtm) REVERT: D 252 LEU cc_start: 0.8813 (tp) cc_final: 0.8564 (tp) REVERT: D 278 ARG cc_start: 0.9632 (ttm110) cc_final: 0.9142 (ptp-110) REVERT: D 279 LEU cc_start: 0.9783 (tt) cc_final: 0.9384 (mm) REVERT: D 466 MET cc_start: 0.8705 (tpp) cc_final: 0.8229 (mmt) REVERT: D 485 MET cc_start: 0.9168 (mmp) cc_final: 0.8112 (mmm) REVERT: D 724 MET cc_start: 0.9207 (mmp) cc_final: 0.8977 (mmm) REVERT: D 725 MET cc_start: 0.9300 (mtp) cc_final: 0.8953 (mtp) REVERT: D 807 LEU cc_start: 0.8898 (tp) cc_final: 0.8612 (tp) REVERT: D 1025 MET cc_start: 0.9370 (tpt) cc_final: 0.8628 (tmm) REVERT: D 1260 MET cc_start: 0.9001 (tpp) cc_final: 0.8741 (tpp) REVERT: F 587 MET cc_start: 0.2790 (ttm) cc_final: 0.2388 (mtm) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1986 time to fit residues: 56.8317 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 : 1.311 ------------------------------------------------------------------------------- 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: 0.9990 chunk 313 optimal weight: 5.9990 chunk 363 optimal weight: 50.0000 chunk 252 optimal weight: 6.9990 chunk 208 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 222 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 336 optimal weight: 40.0000 chunk 357 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 HIS ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN ** F 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.061252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.039623 restraints weight = 343645.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.040344 restraints weight = 221947.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.040789 restraints weight = 160533.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.041272 restraints weight = 130259.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 67)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.041656 restraints weight = 113943.445| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.131 33753 Z= 0.157 Angle : 0.600 12.727 45818 Z= 0.308 Chirality : 0.042 0.217 5172 Planarity : 0.004 0.099 5825 Dihedral : 12.026 173.242 5127 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.56 % Favored : 97.39 % 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: 0.22 (0.13), residues: 4060 helix: 1.16 (0.13), residues: 1486 sheet: -0.53 (0.20), residues: 657 loop : -0.32 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 515 TYR 0.024 0.001 TYR C1231 PHE 0.015 0.001 PHE C 514 TRP 0.021 0.001 TRP F 560 HIS 0.007 0.001 HIS C 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 (33733) covalent geometry : angle 0.58801 / 0.31 (45788) hydrogen bonds : bond 0.03833 / 2.68 ( 1510) hydrogen bonds : angle 4.95799 / 3.45 ( 4176) metal coordination : bond 0.00671 / 0.45 ( 20) metal coordination : angle 4.66785 / 3.07 ( 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 164 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.332 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: 0.9542 (mmp) cc_final: 0.9177 (mmm) REVERT: C 403 MET cc_start: 0.9360 (ppp) cc_final: 0.9040 (ppp) REVERT: C 459 MET cc_start: 0.9444 (mpp) cc_final: 0.9233 (mpp) REVERT: C 464 PHE cc_start: 0.8798 (t80) cc_final: 0.8457 (t80) REVERT: C 515 MET cc_start: 0.8291 (tpt) cc_final: 0.8023 (tpp) REVERT: C 538 LEU cc_start: 0.8793 (tp) cc_final: 0.8565 (tp) REVERT: C 653 MET cc_start: 0.8548 (tpt) cc_final: 0.8309 (tpt) REVERT: C 684 ASN cc_start: 0.8437 (m110) cc_final: 0.8000 (m110) REVERT: C 685 MET cc_start: 0.9273 (mtm) cc_final: 0.8654 (mtt) REVERT: C 800 MET cc_start: 0.8877 (pmm) cc_final: 0.7610 (pmm) REVERT: C 805 MET cc_start: 0.8826 (ppp) cc_final: 0.8432 (ppp) REVERT: C 1085 MET cc_start: 0.8998 (mmm) cc_final: 0.7855 (mmm) REVERT: C 1107 MET cc_start: 0.9578 (mpp) cc_final: 0.9289 (mpp) REVERT: C 1230 MET cc_start: 0.9044 (tpp) cc_final: 0.8190 (tpp) REVERT: C 1279 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8703 (mt-10) REVERT: C 1304 MET cc_start: 0.9432 (tpt) cc_final: 0.9122 (tpp) REVERT: C 1319 MET cc_start: 0.9034 (tpp) cc_final: 0.8556 (tpp) REVERT: D 180 MET cc_start: 0.8543 (tpt) cc_final: 0.8114 (tpt) REVERT: D 192 MET cc_start: 0.8510 (mtm) cc_final: 0.8267 (mtm) REVERT: D 237 MET cc_start: 0.8917 (mtp) cc_final: 0.8646 (mtp) REVERT: D 252 LEU cc_start: 0.8775 (tp) cc_final: 0.8561 (tp) REVERT: D 278 ARG cc_start: 0.9640 (ttm110) cc_final: 0.9165 (ptp-110) REVERT: D 279 LEU cc_start: 0.9778 (tt) cc_final: 0.9378 (mm) REVERT: D 372 MET cc_start: 0.9255 (mmt) cc_final: 0.8450 (mmm) REVERT: D 466 MET cc_start: 0.8802 (tpp) cc_final: 0.8346 (mmt) REVERT: D 485 MET cc_start: 0.9199 (mmp) cc_final: 0.8163 (mmm) REVERT: D 724 MET cc_start: 0.9217 (mmp) cc_final: 0.8956 (mmm) REVERT: D 725 MET cc_start: 0.9274 (mtp) cc_final: 0.8980 (mtp) REVERT: D 807 LEU cc_start: 0.8830 (tp) cc_final: 0.8556 (tp) REVERT: D 1025 MET cc_start: 0.9297 (tpt) cc_final: 0.8519 (tmm) REVERT: D 1260 MET cc_start: 0.8943 (tpp) cc_final: 0.8681 (tpp) REVERT: F 71 MET cc_start: -0.1726 (mpp) cc_final: -0.2354 (mpp) REVERT: F 587 MET cc_start: 0.2676 (ttm) cc_final: 0.2051 (mtm) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2084 time to fit residues: 57.7822 Evaluate side-chains 145 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.328 ------------------------------------------------------------------------------- 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: 10.0000 chunk 110 optimal weight: 7.9990 chunk 351 optimal weight: 30.0000 chunk 209 optimal weight: 5.9990 chunk 324 optimal weight: 9.9990 chunk 145 optimal weight: 0.0470 chunk 178 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 216 optimal weight: 5.9990 chunk 211 optimal weight: 1.9990 chunk 262 optimal weight: 6.9990 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1134 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.064434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.045293 restraints weight = 370030.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.045192 restraints weight = 226934.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 74)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.045335 restraints weight = 148105.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.045630 restraints weight = 112361.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.045876 restraints weight = 92506.685| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33753 Z= 0.125 Angle : 0.581 12.249 45818 Z= 0.297 Chirality : 0.042 0.216 5172 Planarity : 0.004 0.095 5825 Dihedral : 11.948 172.892 5127 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.39 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: 0.26 (0.13), residues: 4060 helix: 1.24 (0.14), residues: 1480 sheet: -0.57 (0.20), residues: 660 loop : -0.31 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 47 TYR 0.022 0.001 TYR C1231 PHE 0.016 0.001 PHE D 629 TRP 0.021 0.001 TRP F 560 HIS 0.007 0.001 HIS C 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 (33733) covalent geometry : angle 0.57046 / 0.30 (45788) hydrogen bonds : bond 0.03560 / 2.49 ( 1510) hydrogen bonds : angle 4.85783 / 3.38 ( 4176) metal coordination : bond 0.00662 / 0.45 ( 20) metal coordination : angle 4.33131 / 2.85 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10509.19 seconds wall clock time: 180 minutes 16.76 seconds (10816.76 seconds total)