Starting phenix.real_space_refine on Mon Jul 6 10:07:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gdd_51262/07_2026/9gdd_51262.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gdd_51262/07_2026/9gdd_51262.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/9gdd_51262/07_2026/9gdd_51262.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gdd_51262/07_2026/9gdd_51262.map" model { file = "/net/cci-nas-00/data/ceres_data/9gdd_51262/07_2026/9gdd_51262.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gdd_51262/07_2026/9gdd_51262.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= 0.093 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 65 5.49 5 Mg 1 5.21 5 S 143 5.16 5 C 20587 2.51 5 N 5881 2.21 5 O 6491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 33173 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: 6700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 846, 6700 Classifications: {'peptide': 846} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 801} Chain breaks: 1 Chain: "N" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 366 Classifications: {'DNA': 27} Incomplete info: {'p_only': 10} Link IDs: {'rna3p': 26} Unresolved chain links: 10 Unresolved chain link angles: 43 Unresolved chain link dihedrals: 32 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {' DT:plan': 5, ' DA:plan': 2, ' DA:plan2': 2, ' DC:plan': 2, ' DC:plan2': 2, ' DG:plan': 1, ' DG:plan2': 1} Unresolved non-hydrogen planarities: 112 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 1.00258.03 S ATOM 14658 SG CYS D 72 111.568 103.158 89.401 1.00245.23 S ATOM 14766 SG CYS D 85 114.433 100.621 89.731 1.00257.23 S ATOM 14790 SG CYS D 88 110.672 99.961 90.718 1.00264.50 S ATOM 20478 SG CYS D 814 82.258 38.990 91.046 1.00162.89 S ATOM 21043 SG CYS D 888 81.551 42.598 90.968 1.00164.09 S ATOM 21094 SG CYS D 895 81.844 40.518 87.653 1.00155.31 S ATOM 21115 SG CYS D 898 78.831 40.075 89.785 1.00162.15 S ATOM 29933 SG CYS F 599 131.660 126.324 124.798 1.001019.3 S ATOM 29953 SG CYS F 602 134.651 128.593 125.208 1.001019.3 S ATOM 30073 SG CYS F 619 132.157 128.732 127.808 1.001019.3 S ATOM 30157 SG CYS F 630 131.040 130.103 124.518 1.001019.3 S ATOM 30407 SG CYS F 662 126.753 117.164 147.296 1.001019.3 S ATOM 30429 SG CYS F 665 124.835 118.346 150.356 1.001019.3 S ATOM 30570 SG CYS F 683 123.520 119.059 146.971 1.001019.3 S ATOM 30610 SG CYS F 689 126.520 120.981 148.290 1.001019.3 S ATOM 30786 SG CYS F 711 111.670 115.646 106.815 1.001019.3 S ATOM 30810 SG CYS F 714 114.533 113.404 107.859 1.001019.3 S ATOM 30942 SG CYS F 731 113.181 115.730 110.381 1.001019.3 S ATOM 30981 SG CYS F 736 114.985 117.191 107.364 1.001019.3 S Time building chain proxies: 6.63, per 1000 atoms: 0.20 Number of scatterers: 33173 At special positions: 0 Unit cell: (153.091, 169.642, 190.33, 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 65 15.00 Mg 1 11.99 O 6491 8.00 N 5881 7.00 C 20587 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 1.3 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 714 " pdb="ZN ZN F1003 " - pdb=" SG CYS F 736 " pdb="ZN ZN F1003 " - pdb=" SG CYS F 731 " pdb="ZN ZN F1003 " - pdb=" SG CYS F 711 " Number of angles added : 30 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7556 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 58 sheets defined 41.0% alpha, 18.0% beta 25 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 4.22 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) 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 22 removed outlier: 3.850A pdb=" N TYR F 20 " --> pdb=" O THR F 16 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY F 22 " --> pdb=" O ASN F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 72 Processing helix chain 'F' and resid 88 through 103 removed outlier: 4.486A pdb=" N VAL F 92 " --> pdb=" O GLY F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 128 Processing helix chain 'F' and resid 143 through 153 removed outlier: 3.919A pdb=" N LYS F 153 " --> pdb=" O GLN F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 187 Proline residue: F 181 - end of helix Processing helix chain 'F' and resid 194 through 214 removed outlier: 3.571A pdb=" N VAL F 199 " --> pdb=" O ARG F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 264 Processing helix chain 'F' and resid 285 through 298 Processing helix chain 'F' and resid 300 through 315 removed outlier: 3.659A pdb=" N THR F 304 " --> pdb=" O GLY F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 343 Processing helix chain 'F' and resid 344 through 348 Processing helix chain 'F' and resid 376 through 380 Processing helix chain 'F' and resid 384 through 402 removed outlier: 4.028A pdb=" N GLN F 402 " --> pdb=" O PHE F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 438 removed outlier: 3.700A pdb=" N VAL F 437 " --> pdb=" O GLY F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 478 through 490 Processing helix chain 'F' and resid 496 through 507 removed outlier: 3.866A pdb=" N GLN F 505 " --> pdb=" O ILE F 501 " (cutoff:3.500A) Processing helix chain 'F' and resid 520 through 534 Processing helix chain 'F' and resid 534 through 539 Processing helix chain 'F' and resid 539 through 556 Processing helix chain 'F' and resid 559 through 580 removed outlier: 4.169A pdb=" N LYS F 580 " --> pdb=" O ASP F 576 " (cutoff:3.500A) Processing helix chain 'F' and resid 621 through 624 Processing helix chain 'F' and resid 625 through 629 Processing helix chain 'F' and resid 644 through 648 Processing helix chain 'F' and resid 649 through 659 removed outlier: 4.198A pdb=" N THR F 653 " --> pdb=" O GLU F 649 " (cutoff:3.500A) Processing helix chain 'F' and resid 796 through 803 Processing helix chain 'F' and resid 811 through 817 removed outlier: 3.958A pdb=" N ALA F 815 " --> pdb=" O LEU F 811 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 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: 6.266A pdb=" N ALA F 4 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LYS F 28 " --> pdb=" O ALA F 4 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL F 6 " --> pdb=" O LYS F 28 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU F 5 " --> pdb=" O TYR F 107 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 244 through 245 removed outlier: 14.840A pdb=" N ALA F 233 " --> pdb=" O ARG F 427 " (cutoff:3.500A) removed outlier: 12.296A pdb=" N ARG F 427 " --> pdb=" O ALA F 233 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N ALA F 235 " --> pdb=" O ARG F 425 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ARG F 425 " --> pdb=" O ALA F 235 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ARG F 421 " --> pdb=" O THR F 239 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS F 407 " --> pdb=" O ARG F 430 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA F 406 " --> pdb=" O THR F 277 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR F 277 " --> pdb=" O ALA F 406 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N TYR F 408 " --> pdb=" O PRO F 275 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER F 410 " --> pdb=" O ASP F 273 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASP F 273 " --> pdb=" O SER F 410 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR F 412 " --> pdb=" O ARG F 271 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ARG F 271 " --> pdb=" O THR F 412 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR F 414 " --> pdb=" O LEU F 269 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 244 through 245 removed outlier: 4.626A pdb=" N VAL F 222 " --> pdb=" O VAL F 238 " (cutoff:3.500A) removed outlier: 9.357A pdb=" N HIS F 240 " --> pdb=" O TRP F 220 " (cutoff:3.500A) removed outlier: 12.766A pdb=" N TRP F 220 " --> pdb=" O HIS F 240 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N SER F 225 " --> pdb=" O GLU F 463 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLU F 463 " --> pdb=" O SER F 225 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N THR F 227 " --> pdb=" O LEU F 461 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEU F 461 " --> pdb=" O THR F 227 " (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: 3.969A 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: 3.632A pdb=" N VAL F 637 " --> pdb=" O LEU F 673 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 709 through 710 Processing sheet with id=AG3, first strand: chain 'F' and resid 770 through 774 Processing sheet with id=AG4, first strand: chain 'F' and resid 827 through 832 removed outlier: 7.782A pdb=" N GLN F 838 " --> pdb=" O ALA F 853 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ALA F 853 " --> pdb=" O GLN F 838 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL F 840 " --> pdb=" O TRP F 851 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N TRP F 851 " --> pdb=" O VAL F 840 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N SER F 842 " --> pdb=" O THR F 849 " (cutoff:3.500A) 1452 hydrogen bonds defined for protein. 4071 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 9.32 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7290 1.33 - 1.45: 7265 1.45 - 1.57: 18894 1.57 - 1.70: 102 1.70 - 1.82: 244 Bond restraints: 33795 Sorted by residual: bond pdb=" P DC N 38 " pdb=" O5' DC N 38 " ideal model delta sigma weight residual 1.593 1.511 0.082 1.00e-02 1.00e+04 6.74e+01 bond pdb=" C3' DC N 38 " pdb=" O3' DC N 38 " ideal model delta sigma weight residual 1.435 1.335 0.100 1.30e-02 5.92e+03 5.89e+01 bond pdb=" C5' DC N 38 " pdb=" C4' DC N 38 " ideal model delta sigma weight residual 1.512 1.467 0.045 7.00e-03 2.04e+04 4.05e+01 bond pdb=" C3' DC N 38 " pdb=" C2' DC N 38 " ideal model delta sigma weight residual 1.516 1.560 -0.044 8.00e-03 1.56e+04 3.06e+01 bond pdb=" C3' DT T 12 " pdb=" O3' DT T 12 " ideal model delta sigma weight residual 1.435 1.374 0.061 1.30e-02 5.92e+03 2.22e+01 ... (remaining 33790 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 45700 3.67 - 7.34: 158 7.34 - 11.02: 11 11.02 - 14.69: 1 14.69 - 18.36: 2 Bond angle restraints: 45872 Sorted by residual: angle pdb=" O5' DC N 38 " pdb=" C5' DC N 38 " pdb=" C4' DC N 38 " ideal model delta sigma weight residual 109.40 91.69 17.71 8.00e-01 1.56e+00 4.90e+02 angle pdb=" O4' DC N 38 " pdb=" C1' DC N 38 " pdb=" N1 DC N 38 " ideal model delta sigma weight residual 108.00 98.72 9.28 7.00e-01 2.04e+00 1.76e+02 angle pdb=" O4' DA N 50 " pdb=" C1' DA N 50 " pdb=" N9 DA N 50 " ideal model delta sigma weight residual 108.00 101.98 6.02 7.00e-01 2.04e+00 7.41e+01 angle pdb=" C1' C R 11 " pdb=" N1 C R 11 " pdb=" C2 C R 11 " ideal model delta sigma weight residual 118.80 128.19 -9.39 1.10e+00 8.26e-01 7.29e+01 angle pdb=" P DC N 38 " pdb=" O5' DC N 38 " pdb=" C5' DC N 38 " ideal model delta sigma weight residual 120.90 133.89 -12.99 1.60e+00 3.91e-01 6.59e+01 ... (remaining 45867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.78: 20189 34.78 - 69.55: 509 69.55 - 104.33: 22 104.33 - 139.10: 0 139.10 - 173.88: 1 Dihedral angle restraints: 20721 sinusoidal: 8976 harmonic: 11745 Sorted by residual: dihedral pdb=" CA PHE F 284 " pdb=" C PHE F 284 " pdb=" N ILE F 285 " pdb=" CA ILE F 285 " ideal model delta harmonic sigma weight residual 180.00 150.85 29.15 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA GLU F 463 " pdb=" C GLU F 463 " pdb=" N LEU F 464 " pdb=" CA LEU F 464 " ideal model delta harmonic sigma weight residual -180.00 -151.12 -28.88 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA THR F 460 " pdb=" C THR F 460 " pdb=" N LEU F 461 " pdb=" CA LEU F 461 " ideal model delta harmonic sigma weight residual -180.00 -151.44 -28.56 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 20718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 5010 0.105 - 0.210: 168 0.210 - 0.314: 2 0.314 - 0.419: 0 0.419 - 0.524: 2 Chirality restraints: 5182 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 -2.86 -0.52 2.00e-01 2.50e+01 6.86e+00 chirality pdb=" P DA T 17 " pdb=" OP1 DA T 17 " pdb=" OP2 DA T 17 " pdb=" O5' DA T 17 " both_signs ideal model delta sigma weight residual True 2.34 -2.81 -0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" C3' DC N 38 " pdb=" C4' DC N 38 " pdb=" O3' DC N 38 " pdb=" C2' DC N 38 " both_signs ideal model delta sigma weight residual False -2.73 -2.48 -0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 5179 not shown) Planarity restraints: 5833 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 704 " -0.058 2.00e-02 2.50e+03 3.17e-02 2.01e+01 pdb=" CG TYR F 704 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR F 704 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR F 704 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR F 704 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR F 704 " 0.018 2.00e-02 2.50e+03 pdb=" CZ TYR F 704 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR F 704 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC N 38 " -0.052 2.00e-02 2.50e+03 2.91e-02 1.90e+01 pdb=" N1 DC N 38 " 0.068 2.00e-02 2.50e+03 pdb=" C2 DC N 38 " -0.002 2.00e-02 2.50e+03 pdb=" O2 DC N 38 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DC N 38 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DC N 38 " -0.008 2.00e-02 2.50e+03 pdb=" N4 DC N 38 " -0.013 2.00e-02 2.50e+03 pdb=" C5 DC N 38 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DC N 38 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC T 14 " 0.029 2.00e-02 2.50e+03 2.37e-02 1.27e+01 pdb=" N1 DC T 14 " -0.059 2.00e-02 2.50e+03 pdb=" C2 DC T 14 " 0.026 2.00e-02 2.50e+03 pdb=" O2 DC T 14 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DC T 14 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DC T 14 " 0.003 2.00e-02 2.50e+03 pdb=" N4 DC T 14 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DC T 14 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DC T 14 " 0.006 2.00e-02 2.50e+03 ... (remaining 5830 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 129 2.39 - 3.02: 20427 3.02 - 3.65: 51906 3.65 - 4.27: 74243 4.27 - 4.90: 121970 Nonbonded interactions: 268675 Sorted by model distance: nonbonded pdb=" O TYR D 46 " pdb=" CA ASP F 857 " model vdw 1.768 3.470 nonbonded pdb=" CB ARG F 744 " pdb=" OG1 THR F 792 " model vdw 1.843 3.440 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=" CZ PHE D 49 " pdb=" CG ASP F 857 " model vdw 2.069 3.570 ... (remaining 268670 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: 0.260 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: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 38.680 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: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 33815 Z= 0.302 Angle : 0.727 23.203 45902 Z= 0.460 Chirality : 0.046 0.524 5182 Planarity : 0.005 0.070 5833 Dihedral : 13.932 173.877 13165 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.93 % Favored : 96.90 % Rotamer: Outliers : 1.15 % Allowed : 6.42 % Favored : 92.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.13), residues: 4066 helix: 0.65 (0.13), residues: 1454 sheet: 0.32 (0.20), residues: 619 loop : -0.36 (0.14), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 136 TYR 0.058 0.002 TYR F 704 PHE 0.033 0.002 PHE F 699 TRP 0.020 0.002 TRP F 560 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.30 (33795) covalent geometry : angle 0.70803 / 0.46 (45872) hydrogen bonds : bond 0.13190 / 8.85 ( 1510) hydrogen bonds : angle 6.45111 / 4.41 ( 4203) metal coordination : bond 0.01639 / 1.06 ( 20) metal coordination : angle 6.56978 / 4.31 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 323 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.9203 (mmm) cc_final: 0.8515 (mmm) REVERT: B 51 MET cc_start: 0.9514 (tpp) cc_final: 0.8666 (mmm) REVERT: B 205 MET cc_start: 0.8680 (ttt) cc_final: 0.8361 (ttp) REVERT: B 231 PHE cc_start: 0.8635 (m-10) cc_final: 0.8374 (m-80) REVERT: C 239 MET cc_start: 0.9261 (ppp) cc_final: 0.8824 (ppp) REVERT: C 445 ILE cc_start: 0.9486 (pt) cc_final: 0.9188 (mm) REVERT: C 464 PHE cc_start: 0.8970 (t80) cc_final: 0.8574 (t80) REVERT: C 541 GLU cc_start: 0.9510 (mp0) cc_final: 0.8832 (tm-30) REVERT: C 681 MET cc_start: 0.9516 (mtt) cc_final: 0.9200 (mtt) REVERT: C 702 THR cc_start: 0.9173 (OUTLIER) cc_final: 0.8080 (p) REVERT: C 814 ASP cc_start: 0.8312 (m-30) cc_final: 0.7967 (t0) REVERT: C 1041 ASP cc_start: 0.9347 (p0) cc_final: 0.8961 (p0) REVERT: C 1073 LYS cc_start: 0.9208 (mtmt) cc_final: 0.8712 (mmtt) REVERT: C 1085 MET cc_start: 0.9112 (mmm) cc_final: 0.8868 (mmt) REVERT: C 1131 MET cc_start: 0.8966 (ttm) cc_final: 0.8647 (ttt) REVERT: C 1233 LEU cc_start: 0.9350 (mp) cc_final: 0.8387 (mm) REVERT: C 1273 MET cc_start: 0.9103 (mmm) cc_final: 0.8886 (mmp) REVERT: C 1279 GLU cc_start: 0.9300 (mt-10) cc_final: 0.8912 (mt-10) REVERT: C 1304 MET cc_start: 0.9328 (tpp) cc_final: 0.9112 (tpp) REVERT: C 1329 GLU cc_start: 0.9601 (mt-10) cc_final: 0.9199 (tt0) REVERT: D 298 MET cc_start: 0.9528 (mmp) cc_final: 0.9094 (mmm) REVERT: D 325 LYS cc_start: 0.9145 (mmmm) cc_final: 0.8880 (pttm) REVERT: D 342 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9084 (mm) REVERT: D 458 ASN cc_start: 0.9653 (t0) cc_final: 0.9450 (t0) REVERT: D 625 MET cc_start: 0.9224 (tmm) cc_final: 0.8859 (tmm) REVERT: D 697 MET cc_start: 0.9707 (ttp) cc_final: 0.9486 (tmm) REVERT: D 747 MET cc_start: 0.9168 (mtt) cc_final: 0.8860 (ttt) REVERT: D 802 ASP cc_start: 0.9355 (t70) cc_final: 0.8768 (t0) REVERT: D 822 MET cc_start: 0.9180 (mmt) cc_final: 0.8622 (tpp) REVERT: D 915 ILE cc_start: 0.9491 (pt) cc_final: 0.9246 (mt) REVERT: D 932 MET cc_start: 0.7386 (ttp) cc_final: 0.6619 (ptt) REVERT: D 1145 PHE cc_start: 0.9108 (m-10) cc_final: 0.8844 (m-80) REVERT: D 1253 ILE cc_start: 0.9710 (mm) cc_final: 0.9050 (tt) REVERT: E 64 LEU cc_start: 0.9753 (OUTLIER) cc_final: 0.9504 (mt) REVERT: F 305 MET cc_start: -0.1295 (mmm) cc_final: -0.2579 (mmt) REVERT: F 376 MET cc_start: 0.1127 (mmp) cc_final: 0.0322 (mmm) REVERT: F 438 MET cc_start: 0.3165 (tpt) cc_final: 0.2805 (mmm) REVERT: F 546 MET cc_start: -0.0566 (tpt) cc_final: -0.0852 (tpp) REVERT: F 606 MET cc_start: 0.5596 (mtp) cc_final: 0.5367 (mtp) outliers start: 40 outliers final: 8 residues processed: 361 average time/residue: 0.2134 time to fit residues: 123.0085 Evaluate side-chains 200 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 189 time to evaluate : 1.329 ------------------------------------------------------------------------------- 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: 8.9990 chunk 388 optimal weight: 40.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 9.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 0.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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** 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 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 HIS C 628 HIS C 673 HIS C 688 GLN C 832 HIS C1070 HIS C1244 HIS D 157 GLN D 335 GLN ** D 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 GLN D 875 ASN D 951 GLN D1019 ASN D1218 HIS ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN F 681 HIS F 719 HIS F 825 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.074522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.042001 restraints weight = 312960.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.040862 restraints weight = 212803.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.041203 restraints weight = 154067.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.041457 restraints weight = 131548.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.041485 restraints weight = 112340.182| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 33815 Z= 0.224 Angle : 0.682 16.384 45902 Z= 0.360 Chirality : 0.044 0.327 5182 Planarity : 0.005 0.075 5833 Dihedral : 12.055 176.634 5141 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.78 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.13), residues: 4066 helix: 1.01 (0.13), residues: 1481 sheet: 0.12 (0.20), residues: 669 loop : -0.38 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 182 TYR 0.032 0.002 TYR C1053 PHE 0.023 0.002 PHE D 116 TRP 0.017 0.002 TRP F 851 HIS 0.010 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.22 (33795) covalent geometry : angle 0.66827 / 0.36 (45872) hydrogen bonds : bond 0.05004 / 3.37 ( 1510) hydrogen bonds : angle 5.32831 / 3.65 ( 4203) metal coordination : bond 0.00886 / 0.60 ( 20) metal coordination : angle 5.32152 / 3.36 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 1.026 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: B 51 MET cc_start: 0.9424 (tpp) cc_final: 0.8553 (mmm) REVERT: B 231 PHE cc_start: 0.8592 (m-10) cc_final: 0.8329 (m-80) REVERT: C 239 MET cc_start: 0.9096 (ppp) cc_final: 0.8796 (ppp) REVERT: C 315 MET cc_start: 0.9642 (mmp) cc_final: 0.9416 (ptm) REVERT: C 464 PHE cc_start: 0.8935 (t80) cc_final: 0.8586 (t80) REVERT: C 541 GLU cc_start: 0.9438 (mp0) cc_final: 0.8805 (tm-30) REVERT: C 546 GLU cc_start: 0.9222 (mp0) cc_final: 0.8897 (pm20) REVERT: C 575 LEU cc_start: 0.9082 (tp) cc_final: 0.8869 (tp) REVERT: C 681 MET cc_start: 0.9273 (mtt) cc_final: 0.8883 (mtt) REVERT: C 800 MET cc_start: 0.8537 (mmp) cc_final: 0.8157 (mmm) REVERT: C 1041 ASP cc_start: 0.9335 (p0) cc_final: 0.8972 (p0) REVERT: C 1085 MET cc_start: 0.9397 (mmm) cc_final: 0.9013 (mmm) REVERT: C 1098 LEU cc_start: 0.9654 (tp) cc_final: 0.9347 (tt) REVERT: C 1131 MET cc_start: 0.9087 (ttm) cc_final: 0.8648 (ttt) REVERT: C 1170 MET cc_start: 0.9858 (mmp) cc_final: 0.9269 (mmm) REVERT: C 1241 ASP cc_start: 0.9451 (t70) cc_final: 0.9213 (m-30) REVERT: C 1243 MET cc_start: 0.9243 (tmm) cc_final: 0.8996 (tmm) REVERT: C 1273 MET cc_start: 0.9227 (mmm) cc_final: 0.8836 (mmp) REVERT: C 1279 GLU cc_start: 0.9439 (mt-10) cc_final: 0.8810 (mt-10) REVERT: C 1329 GLU cc_start: 0.9668 (mt-10) cc_final: 0.9301 (tt0) REVERT: D 29 MET cc_start: 0.9514 (tpt) cc_final: 0.9308 (tpp) REVERT: D 330 MET cc_start: 0.9393 (mmp) cc_final: 0.9119 (mmm) REVERT: D 372 MET cc_start: 0.9350 (mtt) cc_final: 0.9056 (mtt) REVERT: D 466 MET cc_start: 0.9570 (tpt) cc_final: 0.9120 (tpt) REVERT: D 485 MET cc_start: 0.9351 (mmp) cc_final: 0.8983 (mmm) REVERT: D 513 MET cc_start: 0.8318 (tpp) cc_final: 0.7391 (tpp) REVERT: D 604 MET cc_start: 0.8817 (mtm) cc_final: 0.8303 (mtt) REVERT: D 747 MET cc_start: 0.9098 (mtt) cc_final: 0.8700 (ttt) REVERT: D 932 MET cc_start: 0.7622 (ttp) cc_final: 0.6929 (ptt) REVERT: D 1040 MET cc_start: 0.5921 (ptm) cc_final: 0.5628 (ptm) REVERT: D 1145 PHE cc_start: 0.9182 (m-10) cc_final: 0.8888 (m-80) REVERT: D 1306 LEU cc_start: 0.9275 (tp) cc_final: 0.8193 (tp) REVERT: E 18 ASP cc_start: 0.9286 (t0) cc_final: 0.9079 (t0) REVERT: E 30 MET cc_start: 0.7930 (mtm) cc_final: 0.7386 (ptp) REVERT: F 305 MET cc_start: -0.2033 (mmm) cc_final: -0.2314 (mmt) REVERT: F 376 MET cc_start: 0.1224 (mmp) cc_final: 0.0977 (mmm) REVERT: F 438 MET cc_start: 0.2295 (tpt) cc_final: 0.1999 (mmm) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.2032 time to fit residues: 71.5198 Evaluate side-chains 164 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 68 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 237 optimal weight: 0.9980 chunk 175 optimal weight: 9.9990 chunk 376 optimal weight: 20.0000 chunk 24 optimal weight: 4.9990 chunk 179 optimal weight: 9.9990 chunk 221 optimal weight: 7.9990 chunk 390 optimal weight: 50.0000 chunk 107 optimal weight: 9.9990 chunk 313 optimal weight: 10.0000 overall best weight: 6.7988 ------------------------------------------------------------------------------- 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** B 41 ASN B 128 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 450 ASN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1264 GLN ** D 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** 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 = 0.3622 r_free = 0.3622 target = 0.072819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.040244 restraints weight = 313115.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.040355 restraints weight = 215812.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.040615 restraints weight = 170548.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.040750 restraints weight = 153664.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.040804 restraints weight = 147561.668| |-----------------------------------------------------------------------------| r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 33815 Z= 0.237 Angle : 0.654 16.802 45902 Z= 0.345 Chirality : 0.043 0.482 5182 Planarity : 0.005 0.049 5833 Dihedral : 12.191 175.607 5141 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.56 % Favored : 97.37 % Rotamer: Outliers : 0.03 % Allowed : 4.23 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.13), residues: 4066 helix: 1.05 (0.13), residues: 1477 sheet: -0.19 (0.19), residues: 702 loop : -0.40 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 790 TYR 0.031 0.002 TYR C1231 PHE 0.026 0.002 PHE F 343 TRP 0.014 0.002 TRP D 580 HIS 0.011 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.24 (33795) covalent geometry : angle 0.64274 / 0.34 (45872) hydrogen bonds : bond 0.04685 / 3.16 ( 1510) hydrogen bonds : angle 5.11168 / 3.49 ( 4203) metal coordination : bond 0.01503 / 1.02 ( 20) metal coordination : angle 4.75199 / 2.88 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.958 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 239 MET cc_start: 0.9090 (ppp) cc_final: 0.8840 (ppp) REVERT: C 541 GLU cc_start: 0.9517 (mp0) cc_final: 0.8776 (tm-30) REVERT: C 546 GLU cc_start: 0.9209 (mp0) cc_final: 0.8985 (pm20) REVERT: C 671 LEU cc_start: 0.9712 (tp) cc_final: 0.9479 (pp) REVERT: C 681 MET cc_start: 0.9623 (mtt) cc_final: 0.9014 (mtt) REVERT: C 685 MET cc_start: 0.8795 (ppp) cc_final: 0.8567 (ppp) REVERT: C 800 MET cc_start: 0.8534 (mmp) cc_final: 0.8262 (mmm) REVERT: C 1041 ASP cc_start: 0.9323 (p0) cc_final: 0.8943 (p0) REVERT: C 1085 MET cc_start: 0.9455 (mmm) cc_final: 0.8933 (mmm) REVERT: C 1131 MET cc_start: 0.9100 (ttm) cc_final: 0.8633 (ttt) REVERT: C 1170 MET cc_start: 0.9780 (mmp) cc_final: 0.9276 (mmm) REVERT: C 1241 ASP cc_start: 0.9511 (t70) cc_final: 0.9190 (m-30) REVERT: C 1243 MET cc_start: 0.9243 (tmm) cc_final: 0.8734 (tmm) REVERT: C 1279 GLU cc_start: 0.9435 (mt-10) cc_final: 0.8662 (mt-10) REVERT: C 1290 MET cc_start: 0.9278 (mmp) cc_final: 0.9068 (mmp) REVERT: C 1304 MET cc_start: 0.9361 (tpt) cc_final: 0.9102 (tpt) REVERT: C 1329 GLU cc_start: 0.9753 (mt-10) cc_final: 0.9274 (tt0) REVERT: D 29 MET cc_start: 0.9372 (tpt) cc_final: 0.9160 (tpp) REVERT: D 180 MET cc_start: 0.6307 (mmm) cc_final: 0.6058 (mmm) REVERT: D 372 MET cc_start: 0.9353 (mtt) cc_final: 0.8754 (mmt) REVERT: D 429 LEU cc_start: 0.9754 (mp) cc_final: 0.8991 (tp) REVERT: D 466 MET cc_start: 0.9417 (tpt) cc_final: 0.8891 (tmm) REVERT: D 485 MET cc_start: 0.9488 (mmp) cc_final: 0.9156 (mmm) REVERT: D 604 MET cc_start: 0.8477 (mtm) cc_final: 0.7821 (mtt) REVERT: D 932 MET cc_start: 0.7571 (ttp) cc_final: 0.7142 (ptt) REVERT: D 1145 PHE cc_start: 0.9150 (m-10) cc_final: 0.8878 (m-80) REVERT: D 1332 LEU cc_start: 0.9753 (mm) cc_final: 0.9269 (tt) REVERT: E 18 ASP cc_start: 0.9276 (t0) cc_final: 0.9035 (t0) REVERT: F 305 MET cc_start: -0.1812 (mmm) cc_final: -0.2166 (mmt) REVERT: F 376 MET cc_start: 0.1713 (mmp) cc_final: 0.1139 (mmm) REVERT: F 383 MET cc_start: 0.7984 (mmt) cc_final: 0.7758 (mtp) REVERT: F 438 MET cc_start: 0.2297 (tpt) cc_final: 0.1952 (mmm) REVERT: F 522 MET cc_start: 0.1329 (tpt) cc_final: 0.1096 (tpt) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.1835 time to fit residues: 57.5391 Evaluate side-chains 153 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 86 optimal weight: 10.0000 chunk 227 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 302 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 chunk 338 optimal weight: 50.0000 chunk 207 optimal weight: 20.0000 chunk 154 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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** A 160 HIS ** 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 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1134 GLN D 419 HIS ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.073615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.041343 restraints weight = 308918.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.041741 restraints weight = 210696.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.042054 restraints weight = 184373.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.040306 restraints weight = 148242.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.040605 restraints weight = 119596.226| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33815 Z= 0.135 Angle : 0.584 16.252 45902 Z= 0.303 Chirality : 0.042 0.213 5182 Planarity : 0.004 0.049 5833 Dihedral : 12.093 175.153 5141 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.61 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.13), residues: 4066 helix: 1.20 (0.13), residues: 1485 sheet: -0.16 (0.19), residues: 675 loop : -0.32 (0.14), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 158 TYR 0.027 0.001 TYR C1231 PHE 0.017 0.001 PHE D1034 TRP 0.014 0.001 TRP F 851 HIS 0.008 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 (33795) covalent geometry : angle 0.57311 / 0.30 (45872) hydrogen bonds : bond 0.03773 / 2.56 ( 1510) hydrogen bonds : angle 4.83505 / 3.31 ( 4203) metal coordination : bond 0.00647 / 0.42 ( 20) metal coordination : angle 4.52395 / 2.82 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.184 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 515 MET cc_start: 0.8268 (tpt) cc_final: 0.7506 (tpt) REVERT: C 541 GLU cc_start: 0.9458 (mp0) cc_final: 0.8581 (tm-30) REVERT: C 671 LEU cc_start: 0.9704 (tp) cc_final: 0.9485 (pp) REVERT: C 681 MET cc_start: 0.9558 (mtt) cc_final: 0.8993 (mtt) REVERT: C 685 MET cc_start: 0.8608 (ppp) cc_final: 0.8351 (ppp) REVERT: C 1041 ASP cc_start: 0.9261 (p0) cc_final: 0.8875 (p0) REVERT: C 1066 MET cc_start: 0.8405 (pmm) cc_final: 0.7998 (pmm) REVERT: C 1085 MET cc_start: 0.9378 (mmm) cc_final: 0.8951 (mmm) REVERT: C 1131 MET cc_start: 0.9030 (ttm) cc_final: 0.8539 (ttt) REVERT: C 1170 MET cc_start: 0.9758 (mmp) cc_final: 0.9237 (mmm) REVERT: C 1241 ASP cc_start: 0.9354 (t70) cc_final: 0.9133 (m-30) REVERT: C 1243 MET cc_start: 0.9184 (tmm) cc_final: 0.8589 (tmm) REVERT: C 1279 GLU cc_start: 0.9348 (mt-10) cc_final: 0.8652 (mt-10) REVERT: C 1304 MET cc_start: 0.9294 (tpt) cc_final: 0.9019 (tpt) REVERT: C 1329 GLU cc_start: 0.9734 (mt-10) cc_final: 0.9252 (tt0) REVERT: D 102 MET cc_start: 0.8520 (pmm) cc_final: 0.8297 (ptt) REVERT: D 372 MET cc_start: 0.9298 (mtt) cc_final: 0.8753 (mmt) REVERT: D 429 LEU cc_start: 0.9687 (mp) cc_final: 0.8849 (tp) REVERT: D 466 MET cc_start: 0.9437 (tpt) cc_final: 0.8899 (tpt) REVERT: D 485 MET cc_start: 0.9465 (mmp) cc_final: 0.9144 (mmm) REVERT: D 513 MET cc_start: 0.8912 (ttt) cc_final: 0.8140 (tpp) REVERT: D 604 MET cc_start: 0.8294 (mtm) cc_final: 0.8033 (mtt) REVERT: D 802 ASP cc_start: 0.9110 (t0) cc_final: 0.8886 (t0) REVERT: D 932 MET cc_start: 0.7656 (ttp) cc_final: 0.7186 (ptt) REVERT: D 1145 PHE cc_start: 0.9069 (m-10) cc_final: 0.8672 (m-80) REVERT: D 1189 MET cc_start: 0.9306 (tpt) cc_final: 0.9077 (tpt) REVERT: D 1306 LEU cc_start: 0.9453 (tp) cc_final: 0.9111 (tp) REVERT: D 1332 LEU cc_start: 0.9726 (mm) cc_final: 0.9288 (tt) REVERT: E 18 ASP cc_start: 0.9199 (t0) cc_final: 0.8948 (t0) REVERT: F 171 MET cc_start: -0.3017 (ptt) cc_final: -0.3368 (ptt) REVERT: F 305 MET cc_start: -0.1788 (mmm) cc_final: -0.2292 (mmm) REVERT: F 376 MET cc_start: 0.1570 (mmp) cc_final: 0.1295 (mmm) REVERT: F 383 MET cc_start: 0.8048 (mmt) cc_final: 0.7815 (mtp) REVERT: F 438 MET cc_start: 0.3450 (tpt) cc_final: 0.3036 (mmm) REVERT: F 606 MET cc_start: 0.4041 (ptp) cc_final: 0.3473 (ptp) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1942 time to fit residues: 61.4053 Evaluate side-chains 152 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 201 optimal weight: 7.9990 chunk 311 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 357 optimal weight: 0.0770 chunk 38 optimal weight: 0.0050 chunk 178 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 56 optimal weight: 0.3980 chunk 202 optimal weight: 9.9990 overall best weight: 2.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 ASN ** A 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 HIS ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 469 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.075933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.043377 restraints weight = 330788.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 87)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.041354 restraints weight = 203976.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.041547 restraints weight = 146144.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.041653 restraints weight = 134857.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.041761 restraints weight = 129666.432| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33815 Z= 0.127 Angle : 0.575 14.840 45902 Z= 0.298 Chirality : 0.042 0.213 5182 Planarity : 0.004 0.048 5833 Dihedral : 12.021 174.742 5141 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.41 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.13), residues: 4066 helix: 1.22 (0.13), residues: 1503 sheet: -0.07 (0.20), residues: 662 loop : -0.34 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 245 TYR 0.029 0.001 TYR C1231 PHE 0.024 0.001 PHE C 514 TRP 0.012 0.001 TRP F 851 HIS 0.012 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 (33795) covalent geometry : angle 0.56495 / 0.30 (45872) hydrogen bonds : bond 0.03620 / 2.47 ( 1510) hydrogen bonds : angle 4.72666 / 3.23 ( 4203) metal coordination : bond 0.00561 / 0.37 ( 20) metal coordination : angle 4.13110 / 2.59 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: 0.9674 (mmp) cc_final: 0.8848 (mmm) REVERT: C 239 MET cc_start: 0.8983 (ppp) cc_final: 0.8662 (ppp) REVERT: C 403 MET cc_start: 0.9537 (tmm) cc_final: 0.9310 (tmm) REVERT: C 541 GLU cc_start: 0.9466 (mp0) cc_final: 0.8770 (tm-30) REVERT: C 671 LEU cc_start: 0.9721 (tp) cc_final: 0.9460 (pp) REVERT: C 681 MET cc_start: 0.9473 (mtt) cc_final: 0.9047 (mtt) REVERT: C 685 MET cc_start: 0.8683 (ppp) cc_final: 0.8442 (ppp) REVERT: C 1041 ASP cc_start: 0.9290 (p0) cc_final: 0.8938 (p0) REVERT: C 1085 MET cc_start: 0.9398 (mmm) cc_final: 0.8943 (mmm) REVERT: C 1119 MET cc_start: 0.9429 (mmm) cc_final: 0.9184 (mmp) REVERT: C 1131 MET cc_start: 0.9060 (ttm) cc_final: 0.8716 (ttt) REVERT: C 1170 MET cc_start: 0.9775 (mmp) cc_final: 0.9246 (mmm) REVERT: C 1241 ASP cc_start: 0.9438 (t70) cc_final: 0.9136 (m-30) REVERT: C 1243 MET cc_start: 0.9282 (tmm) cc_final: 0.8762 (tmm) REVERT: C 1279 GLU cc_start: 0.9407 (mt-10) cc_final: 0.8714 (mt-10) REVERT: C 1290 MET cc_start: 0.9417 (mmp) cc_final: 0.9149 (mmm) REVERT: C 1304 MET cc_start: 0.9393 (tpt) cc_final: 0.9126 (tpt) REVERT: C 1319 MET cc_start: 0.9386 (tmm) cc_final: 0.8667 (tmm) REVERT: C 1329 GLU cc_start: 0.9725 (mt-10) cc_final: 0.9172 (tt0) REVERT: D 372 MET cc_start: 0.9303 (mtt) cc_final: 0.8585 (mtt) REVERT: D 429 LEU cc_start: 0.9728 (mp) cc_final: 0.8870 (tp) REVERT: D 466 MET cc_start: 0.9453 (tpt) cc_final: 0.8940 (tpt) REVERT: D 485 MET cc_start: 0.9571 (mmp) cc_final: 0.9157 (mmm) REVERT: D 513 MET cc_start: 0.9179 (ttt) cc_final: 0.8974 (ttt) REVERT: D 604 MET cc_start: 0.8333 (mtm) cc_final: 0.8037 (mtt) REVERT: D 747 MET cc_start: 0.7393 (ttt) cc_final: 0.7072 (ttp) REVERT: D 932 MET cc_start: 0.7557 (ttp) cc_final: 0.7163 (ptt) REVERT: D 1145 PHE cc_start: 0.9168 (m-10) cc_final: 0.8814 (m-80) REVERT: D 1332 LEU cc_start: 0.9740 (mm) cc_final: 0.9277 (tt) REVERT: E 18 ASP cc_start: 0.9200 (t0) cc_final: 0.8899 (t0) REVERT: F 171 MET cc_start: -0.3079 (ptt) cc_final: -0.3432 (ptt) REVERT: F 305 MET cc_start: -0.1985 (mmm) cc_final: -0.2279 (mmm) REVERT: F 383 MET cc_start: 0.8064 (mmt) cc_final: 0.7843 (mtp) REVERT: F 438 MET cc_start: 0.3452 (tpt) cc_final: 0.3129 (mmm) REVERT: F 606 MET cc_start: 0.4015 (ptp) cc_final: 0.3686 (ptp) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.1998 time to fit residues: 62.7203 Evaluate side-chains 151 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 209 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 356 optimal weight: 4.9990 chunk 225 optimal weight: 0.0050 chunk 183 optimal weight: 5.9990 chunk 264 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 150 optimal weight: 20.0000 overall best weight: 2.9400 ------------------------------------------------------------------------------- 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** A 160 HIS ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 HIS C 554 HIS C 649 GLN C 760 ASN C1023 HIS C1080 ASN C1134 GLN D 771 GLN D 777 HIS D 951 GLN ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.075612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.047663 restraints weight = 331016.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 76)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.044710 restraints weight = 204836.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.044905 restraints weight = 137410.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.044854 restraints weight = 105537.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.045103 restraints weight = 94151.007| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33815 Z= 0.131 Angle : 0.562 14.052 45902 Z= 0.289 Chirality : 0.041 0.261 5182 Planarity : 0.004 0.051 5833 Dihedral : 11.986 174.443 5141 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.53 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.13), residues: 4066 helix: 1.19 (0.13), residues: 1518 sheet: -0.10 (0.20), residues: 667 loop : -0.33 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 88 TYR 0.027 0.001 TYR C1231 PHE 0.016 0.001 PHE C 514 TRP 0.011 0.001 TRP F 851 HIS 0.012 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (33795) covalent geometry : angle 0.55172 / 0.29 (45872) hydrogen bonds : bond 0.03548 / 2.43 ( 1510) hydrogen bonds : angle 4.67747 / 3.20 ( 4203) metal coordination : bond 0.00813 / 0.59 ( 20) metal coordination : angle 4.24299 / 2.77 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.308 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: 0.9617 (mmp) cc_final: 0.8854 (mmm) REVERT: C 130 MET cc_start: 0.8788 (ttt) cc_final: 0.8518 (tmm) REVERT: C 239 MET cc_start: 0.8818 (ppp) cc_final: 0.8580 (ppp) REVERT: C 403 MET cc_start: 0.9481 (tmm) cc_final: 0.9273 (tmm) REVERT: C 429 MET cc_start: 0.9060 (mtm) cc_final: 0.8855 (mtp) REVERT: C 541 GLU cc_start: 0.9459 (mp0) cc_final: 0.8748 (tm-30) REVERT: C 671 LEU cc_start: 0.9700 (tp) cc_final: 0.9497 (pp) REVERT: C 681 MET cc_start: 0.9452 (mtt) cc_final: 0.9062 (mtt) REVERT: C 685 MET cc_start: 0.8757 (ppp) cc_final: 0.8554 (ppp) REVERT: C 1041 ASP cc_start: 0.9230 (p0) cc_final: 0.8840 (p0) REVERT: C 1066 MET cc_start: 0.8352 (pmm) cc_final: 0.8018 (pmm) REVERT: C 1080 ASN cc_start: 0.8659 (m110) cc_final: 0.8449 (t0) REVERT: C 1085 MET cc_start: 0.9283 (mmm) cc_final: 0.8299 (mmm) REVERT: C 1131 MET cc_start: 0.9014 (ttm) cc_final: 0.8680 (ttt) REVERT: C 1170 MET cc_start: 0.9731 (mmp) cc_final: 0.9221 (mmm) REVERT: C 1230 MET cc_start: 0.8242 (ppp) cc_final: 0.7629 (ppp) REVERT: C 1241 ASP cc_start: 0.9366 (t70) cc_final: 0.9102 (m-30) REVERT: C 1243 MET cc_start: 0.9243 (tmm) cc_final: 0.8902 (tmm) REVERT: C 1273 MET cc_start: 0.9367 (mpp) cc_final: 0.9095 (mtm) REVERT: C 1279 GLU cc_start: 0.9402 (mt-10) cc_final: 0.8695 (mt-10) REVERT: C 1290 MET cc_start: 0.9369 (mmp) cc_final: 0.9155 (mmp) REVERT: C 1304 MET cc_start: 0.9339 (tpt) cc_final: 0.9041 (tpt) REVERT: C 1319 MET cc_start: 0.9337 (tmm) cc_final: 0.8624 (tmm) REVERT: C 1329 GLU cc_start: 0.9669 (mt-10) cc_final: 0.9092 (tt0) REVERT: D 29 MET cc_start: 0.9366 (tpt) cc_final: 0.9135 (tpp) REVERT: D 130 MET cc_start: 0.9189 (mmp) cc_final: 0.8975 (mmm) REVERT: D 372 MET cc_start: 0.9210 (mtt) cc_final: 0.8888 (mtt) REVERT: D 429 LEU cc_start: 0.9724 (mp) cc_final: 0.8882 (tp) REVERT: D 466 MET cc_start: 0.9439 (tpt) cc_final: 0.8900 (tpt) REVERT: D 485 MET cc_start: 0.9572 (mmp) cc_final: 0.9119 (mmm) REVERT: D 581 MET cc_start: 0.9092 (mmp) cc_final: 0.8376 (mmm) REVERT: D 604 MET cc_start: 0.8312 (mtm) cc_final: 0.8008 (mtt) REVERT: D 747 MET cc_start: 0.7411 (ttt) cc_final: 0.7049 (ttp) REVERT: D 932 MET cc_start: 0.7753 (ttp) cc_final: 0.7293 (ptt) REVERT: D 1040 MET cc_start: 0.4152 (ptm) cc_final: 0.3860 (ptm) REVERT: D 1260 MET cc_start: 0.9100 (tpp) cc_final: 0.8694 (tpt) REVERT: D 1332 LEU cc_start: 0.9740 (mm) cc_final: 0.9454 (mt) REVERT: E 18 ASP cc_start: 0.9200 (t0) cc_final: 0.8905 (t0) REVERT: F 171 MET cc_start: -0.3017 (ptt) cc_final: -0.3344 (ptt) REVERT: F 376 MET cc_start: 0.0526 (mmm) cc_final: 0.0077 (tpt) REVERT: F 383 MET cc_start: 0.7808 (mmt) cc_final: 0.7481 (mtp) REVERT: F 403 MET cc_start: 0.2012 (ptm) cc_final: 0.1723 (ptt) REVERT: F 592 MET cc_start: 0.0849 (mmt) cc_final: 0.0533 (tpp) REVERT: F 606 MET cc_start: 0.4040 (ptp) cc_final: 0.3687 (ptp) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1953 time to fit residues: 59.4502 Evaluate side-chains 148 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 216 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 170 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 chunk 344 optimal weight: 50.0000 chunk 206 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 chunk 325 optimal weight: 50.0000 chunk 304 optimal weight: 9.9990 chunk 223 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN C1134 GLN C1220 GLN ** D 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN ** F 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.073875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.041322 restraints weight = 338611.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.039898 restraints weight = 212866.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.039296 restraints weight = 153085.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.039553 restraints weight = 114993.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.039694 restraints weight = 97790.467| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 33815 Z= 0.231 Angle : 0.625 15.304 45902 Z= 0.326 Chirality : 0.042 0.211 5182 Planarity : 0.004 0.052 5833 Dihedral : 12.107 174.000 5141 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.98 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.13), residues: 4066 helix: 1.07 (0.13), residues: 1517 sheet: -0.18 (0.20), residues: 648 loop : -0.40 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 143 TYR 0.042 0.002 TYR C1231 PHE 0.018 0.002 PHE C 390 TRP 0.027 0.002 TRP D 236 HIS 0.015 0.002 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.23 (33795) covalent geometry : angle 0.61528 / 0.33 (45872) hydrogen bonds : bond 0.04232 / 2.88 ( 1510) hydrogen bonds : angle 4.79257 / 3.28 ( 4203) metal coordination : bond 0.01112 / 0.74 ( 20) metal coordination : angle 4.42505 / 2.81 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.309 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: 0.9378 (mmp) cc_final: 0.8783 (mmm) REVERT: C 239 MET cc_start: 0.8922 (ppp) cc_final: 0.8625 (ppp) REVERT: C 429 MET cc_start: 0.9096 (mtm) cc_final: 0.8807 (mtp) REVERT: C 541 GLU cc_start: 0.9480 (mp0) cc_final: 0.8599 (tm-30) REVERT: C 681 MET cc_start: 0.9404 (mtt) cc_final: 0.9086 (mtt) REVERT: C 1066 MET cc_start: 0.8320 (pmm) cc_final: 0.8064 (pmm) REVERT: C 1085 MET cc_start: 0.9333 (mmm) cc_final: 0.8403 (mmm) REVERT: C 1131 MET cc_start: 0.9039 (ttm) cc_final: 0.8730 (ttt) REVERT: C 1170 MET cc_start: 0.9721 (mmp) cc_final: 0.9211 (mmm) REVERT: C 1241 ASP cc_start: 0.9339 (t70) cc_final: 0.8975 (m-30) REVERT: C 1243 MET cc_start: 0.9166 (tmm) cc_final: 0.8803 (tmm) REVERT: C 1276 TRP cc_start: 0.9260 (m-10) cc_final: 0.8874 (m-10) REVERT: C 1279 GLU cc_start: 0.9337 (mt-10) cc_final: 0.8745 (mt-10) REVERT: C 1304 MET cc_start: 0.9332 (tpt) cc_final: 0.9049 (tpt) REVERT: D 29 MET cc_start: 0.9388 (tpt) cc_final: 0.9174 (tpp) REVERT: D 130 MET cc_start: 0.9192 (mmp) cc_final: 0.8977 (mmm) REVERT: D 165 TYR cc_start: 0.9132 (t80) cc_final: 0.8904 (t80) REVERT: D 180 MET cc_start: 0.5787 (mmm) cc_final: 0.5566 (mmm) REVERT: D 330 MET cc_start: 0.9272 (mmp) cc_final: 0.9067 (mmm) REVERT: D 372 MET cc_start: 0.9059 (mtt) cc_final: 0.8643 (mtt) REVERT: D 429 LEU cc_start: 0.9726 (mp) cc_final: 0.8920 (tp) REVERT: D 485 MET cc_start: 0.9614 (mmp) cc_final: 0.9176 (mmm) REVERT: D 581 MET cc_start: 0.9091 (mmp) cc_final: 0.8687 (mmm) REVERT: D 604 MET cc_start: 0.8399 (mtm) cc_final: 0.8032 (mtt) REVERT: D 747 MET cc_start: 0.7515 (ttt) cc_final: 0.7109 (ttp) REVERT: D 932 MET cc_start: 0.7841 (ttp) cc_final: 0.7485 (ptt) REVERT: D 1145 PHE cc_start: 0.9063 (m-80) cc_final: 0.8641 (m-80) REVERT: D 1332 LEU cc_start: 0.9758 (mm) cc_final: 0.9469 (mt) REVERT: E 18 ASP cc_start: 0.9190 (t0) cc_final: 0.8940 (t0) REVERT: F 171 MET cc_start: -0.3007 (ptt) cc_final: -0.3344 (ptt) REVERT: F 383 MET cc_start: 0.7768 (mmt) cc_final: 0.7189 (mtp) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1985 time to fit residues: 58.1694 Evaluate side-chains 142 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 137 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 210 optimal weight: 10.0000 chunk 243 optimal weight: 3.9990 chunk 391 optimal weight: 0.0870 chunk 55 optimal weight: 5.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 HIS ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 HIS ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN C1070 HIS C1134 GLN D1098 GLN D1235 ASN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 533 ASN ** F 838 GLN ** 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 = 0.3641 r_free = 0.3641 target = 0.073430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.041117 restraints weight = 308782.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.041284 restraints weight = 211531.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.040307 restraints weight = 161269.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.040294 restraints weight = 137434.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.040393 restraints weight = 117694.776| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 33815 Z= 0.122 Angle : 0.574 15.533 45902 Z= 0.293 Chirality : 0.042 0.212 5182 Planarity : 0.004 0.049 5833 Dihedral : 12.054 174.039 5141 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.63 % Favored : 97.32 % Rotamer: Outliers : 0.03 % Allowed : 1.01 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.13), residues: 4066 helix: 1.23 (0.13), residues: 1515 sheet: -0.10 (0.21), residues: 644 loop : -0.33 (0.14), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 12 TYR 0.023 0.001 TYR C1231 PHE 0.019 0.001 PHE C 514 TRP 0.012 0.001 TRP D 236 HIS 0.008 0.001 HIS F 719 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (33795) covalent geometry : angle 0.56163 / 0.29 (45872) hydrogen bonds : bond 0.03401 / 2.33 ( 1510) hydrogen bonds : angle 4.62490 / 3.17 ( 4203) metal coordination : bond 0.00773 / 0.50 ( 20) metal coordination : angle 4.62095 / 2.91 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 HIS cc_start: 0.9287 (m90) cc_final: 0.9048 (m90) REVERT: B 51 MET cc_start: 0.9405 (mmp) cc_final: 0.8746 (mmm) REVERT: C 239 MET cc_start: 0.8871 (ppp) cc_final: 0.8600 (ppp) REVERT: C 429 MET cc_start: 0.9035 (mtm) cc_final: 0.8556 (ptp) REVERT: C 541 GLU cc_start: 0.9489 (mp0) cc_final: 0.8594 (tm-30) REVERT: C 575 LEU cc_start: 0.9066 (tp) cc_final: 0.8841 (tp) REVERT: C 681 MET cc_start: 0.9370 (mtt) cc_final: 0.9093 (mtt) REVERT: C 1041 ASP cc_start: 0.9009 (p0) cc_final: 0.8538 (p0) REVERT: C 1085 MET cc_start: 0.9240 (mmm) cc_final: 0.8721 (mmm) REVERT: C 1131 MET cc_start: 0.9063 (ttm) cc_final: 0.8699 (ttt) REVERT: C 1170 MET cc_start: 0.9715 (mmp) cc_final: 0.9185 (mmm) REVERT: C 1241 ASP cc_start: 0.9345 (t70) cc_final: 0.9001 (m-30) REVERT: C 1243 MET cc_start: 0.9160 (tmm) cc_final: 0.8803 (tmm) REVERT: C 1276 TRP cc_start: 0.9299 (m-10) cc_final: 0.8978 (m-10) REVERT: C 1279 GLU cc_start: 0.9313 (mt-10) cc_final: 0.8716 (mt-10) REVERT: C 1290 MET cc_start: 0.9360 (mmp) cc_final: 0.9087 (mmm) REVERT: C 1304 MET cc_start: 0.9331 (tpt) cc_final: 0.9043 (tpt) REVERT: C 1329 GLU cc_start: 0.9576 (mt-10) cc_final: 0.9179 (mt-10) REVERT: D 29 MET cc_start: 0.9390 (tpt) cc_final: 0.9068 (tpp) REVERT: D 102 MET cc_start: 0.8662 (pmm) cc_final: 0.8111 (ptt) REVERT: D 130 MET cc_start: 0.9177 (mmp) cc_final: 0.8950 (mmm) REVERT: D 180 MET cc_start: 0.5606 (mmm) cc_final: 0.5394 (mmm) REVERT: D 372 MET cc_start: 0.9140 (mtt) cc_final: 0.8716 (mtt) REVERT: D 429 LEU cc_start: 0.9687 (mp) cc_final: 0.8818 (tp) REVERT: D 466 MET cc_start: 0.9212 (tpt) cc_final: 0.8668 (tpt) REVERT: D 485 MET cc_start: 0.9587 (mmp) cc_final: 0.9124 (mmm) REVERT: D 513 MET cc_start: 0.8945 (ttt) cc_final: 0.8152 (tpp) REVERT: D 604 MET cc_start: 0.8321 (mtm) cc_final: 0.7944 (mtt) REVERT: D 747 MET cc_start: 0.7733 (ttt) cc_final: 0.7153 (ttp) REVERT: D 802 ASP cc_start: 0.9013 (t0) cc_final: 0.8790 (t0) REVERT: D 932 MET cc_start: 0.7688 (ttp) cc_final: 0.7204 (ptt) REVERT: D 1145 PHE cc_start: 0.9027 (m-80) cc_final: 0.8592 (m-80) REVERT: D 1307 LEU cc_start: 0.9691 (mp) cc_final: 0.9175 (tp) REVERT: D 1332 LEU cc_start: 0.9742 (mm) cc_final: 0.9459 (mt) REVERT: E 18 ASP cc_start: 0.9233 (t0) cc_final: 0.8923 (t0) REVERT: F 171 MET cc_start: -0.3020 (ptt) cc_final: -0.3309 (ptt) REVERT: F 383 MET cc_start: 0.7999 (mmt) cc_final: 0.7638 (mtp) REVERT: F 403 MET cc_start: 0.2219 (ptm) cc_final: 0.1872 (ptt) REVERT: F 592 MET cc_start: 0.0931 (mmt) cc_final: 0.0389 (tpp) outliers start: 1 outliers final: 0 residues processed: 175 average time/residue: 0.1907 time to fit residues: 57.6238 Evaluate side-chains 148 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 317 optimal weight: 0.9980 chunk 378 optimal weight: 20.0000 chunk 154 optimal weight: 2.9990 chunk 326 optimal weight: 9.9990 chunk 166 optimal weight: 8.9990 chunk 365 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 291 optimal weight: 8.9990 chunk 294 optimal weight: 6.9990 chunk 290 optimal weight: 5.9990 chunk 330 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN A 66 HIS B 37 HIS ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN C 832 HIS C1134 GLN D 951 GLN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 838 GLN ** 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 = 0.3670 r_free = 0.3670 target = 0.074271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.046727 restraints weight = 332552.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 114)---------------| | r_work = 0.3043 r_free = 0.3043 target = 0.044278 restraints weight = 203300.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.043665 restraints weight = 141652.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.043860 restraints weight = 114882.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.044042 restraints weight = 100134.914| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33815 Z= 0.174 Angle : 0.589 14.962 45902 Z= 0.305 Chirality : 0.041 0.211 5182 Planarity : 0.004 0.060 5833 Dihedral : 12.081 173.585 5141 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.78 % Favored : 97.17 % Rotamer: Outliers : 0.03 % Allowed : 0.75 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.13), residues: 4066 helix: 1.21 (0.13), residues: 1512 sheet: -0.21 (0.21), residues: 633 loop : -0.38 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 378 TYR 0.029 0.001 TYR C1231 PHE 0.015 0.001 PHE B 231 TRP 0.011 0.001 TRP D 115 HIS 0.010 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (33795) covalent geometry : angle 0.57787 / 0.30 (45872) hydrogen bonds : bond 0.03778 / 2.59 ( 1510) hydrogen bonds : angle 4.69640 / 3.23 ( 4203) metal coordination : bond 0.01011 / 0.67 ( 20) metal coordination : angle 4.52233 / 2.83 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 HIS cc_start: 0.9133 (m90) cc_final: 0.8922 (m-70) REVERT: B 51 MET cc_start: 0.9432 (mmp) cc_final: 0.8792 (mmm) REVERT: C 239 MET cc_start: 0.8864 (ppp) cc_final: 0.8605 (ppp) REVERT: C 429 MET cc_start: 0.9017 (mtm) cc_final: 0.8752 (mtp) REVERT: C 488 MET cc_start: 0.8152 (tpt) cc_final: 0.7842 (tmm) REVERT: C 541 GLU cc_start: 0.9494 (mp0) cc_final: 0.8598 (tm-30) REVERT: C 575 LEU cc_start: 0.9141 (tp) cc_final: 0.8929 (tp) REVERT: C 681 MET cc_start: 0.9388 (mtt) cc_final: 0.9156 (mtt) REVERT: C 1066 MET cc_start: 0.8507 (pmm) cc_final: 0.8194 (pmm) REVERT: C 1085 MET cc_start: 0.9318 (mmm) cc_final: 0.8704 (mmm) REVERT: C 1131 MET cc_start: 0.9070 (ttm) cc_final: 0.8730 (ttt) REVERT: C 1170 MET cc_start: 0.9708 (mmp) cc_final: 0.9197 (mmm) REVERT: C 1241 ASP cc_start: 0.9336 (t70) cc_final: 0.8955 (m-30) REVERT: C 1276 TRP cc_start: 0.9246 (m-10) cc_final: 0.8879 (m-10) REVERT: C 1279 GLU cc_start: 0.9331 (mt-10) cc_final: 0.8760 (mt-10) REVERT: C 1290 MET cc_start: 0.9427 (mmp) cc_final: 0.9168 (mmm) REVERT: C 1304 MET cc_start: 0.9376 (tpt) cc_final: 0.9087 (tpt) REVERT: C 1329 GLU cc_start: 0.9536 (mt-10) cc_final: 0.9144 (mt-10) REVERT: D 130 MET cc_start: 0.9167 (mmp) cc_final: 0.8949 (mmm) REVERT: D 429 LEU cc_start: 0.9703 (mp) cc_final: 0.8787 (tp) REVERT: D 466 MET cc_start: 0.9066 (tpt) cc_final: 0.8460 (tpt) REVERT: D 485 MET cc_start: 0.9616 (mmp) cc_final: 0.9137 (mmm) REVERT: D 513 MET cc_start: 0.9078 (ttt) cc_final: 0.8340 (tpp) REVERT: D 581 MET cc_start: 0.9207 (mmp) cc_final: 0.8882 (mmm) REVERT: D 604 MET cc_start: 0.8407 (mtm) cc_final: 0.7990 (mtt) REVERT: D 747 MET cc_start: 0.7732 (ttt) cc_final: 0.7121 (ttp) REVERT: D 802 ASP cc_start: 0.9088 (t0) cc_final: 0.8876 (t0) REVERT: D 932 MET cc_start: 0.7763 (ttp) cc_final: 0.7337 (ptt) REVERT: D 1145 PHE cc_start: 0.9091 (m-80) cc_final: 0.8609 (m-80) REVERT: D 1260 MET cc_start: 0.9165 (tpp) cc_final: 0.8800 (tpt) REVERT: E 18 ASP cc_start: 0.9223 (t0) cc_final: 0.8968 (t0) REVERT: F 171 MET cc_start: -0.3038 (ptt) cc_final: -0.3339 (ptt) REVERT: F 376 MET cc_start: 0.0510 (mmm) cc_final: 0.0157 (mmm) REVERT: F 383 MET cc_start: 0.7980 (mmt) cc_final: 0.7607 (mtp) REVERT: F 438 MET cc_start: 0.3614 (tpt) cc_final: 0.3177 (mmm) REVERT: F 592 MET cc_start: 0.1042 (mmt) cc_final: 0.0125 (mmp) REVERT: F 729 MET cc_start: -0.0258 (mmm) cc_final: -0.0555 (mmm) outliers start: 1 outliers final: 0 residues processed: 169 average time/residue: 0.1950 time to fit residues: 57.0114 Evaluate side-chains 142 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 42 optimal weight: 20.0000 chunk 394 optimal weight: 40.0000 chunk 279 optimal weight: 20.0000 chunk 307 optimal weight: 10.0000 chunk 178 optimal weight: 10.0000 chunk 222 optimal weight: 9.9990 chunk 172 optimal weight: 10.0000 chunk 230 optimal weight: 5.9990 chunk 244 optimal weight: 9.9990 chunk 389 optimal weight: 10.0000 chunk 407 optimal weight: 50.0000 overall best weight: 9.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN C 952 GLN C1134 GLN ** D 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 GLN D1235 ASN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 719 HIS ** F 838 GLN ** 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 = 0.3579 r_free = 0.3579 target = 0.070521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.042210 restraints weight = 320029.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.039691 restraints weight = 219759.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.039953 restraints weight = 161309.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.040085 restraints weight = 141486.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.040187 restraints weight = 115098.106| |-----------------------------------------------------------------------------| r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 33815 Z= 0.301 Angle : 0.733 18.240 45902 Z= 0.380 Chirality : 0.044 0.236 5182 Planarity : 0.006 0.102 5833 Dihedral : 12.395 173.155 5141 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.66 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.13), residues: 4066 helix: 0.77 (0.13), residues: 1511 sheet: -0.38 (0.20), residues: 633 loop : -0.58 (0.14), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG C1246 TYR 0.029 0.002 TYR D 631 PHE 0.030 0.002 PHE B 231 TRP 0.019 0.002 TRP C1276 HIS 0.014 0.002 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.30 (33795) covalent geometry : angle 0.71990 / 0.38 (45872) hydrogen bonds : bond 0.04967 / 3.37 ( 1510) hydrogen bonds : angle 5.06327 / 3.49 ( 4203) metal coordination : bond 0.01477 / 0.96 ( 20) metal coordination : angle 5.37065 / 3.25 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.207 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: 0.9440 (mmp) cc_final: 0.8926 (mmm) REVERT: C 239 MET cc_start: 0.9005 (ppp) cc_final: 0.8655 (ppp) REVERT: C 541 GLU cc_start: 0.9508 (mp0) cc_final: 0.8735 (tm-30) REVERT: C 681 MET cc_start: 0.9414 (mtt) cc_final: 0.9204 (mtt) REVERT: C 1131 MET cc_start: 0.9095 (ttm) cc_final: 0.8717 (ttt) REVERT: C 1170 MET cc_start: 0.9694 (mmp) cc_final: 0.9179 (mmm) REVERT: C 1230 MET cc_start: 0.8881 (ppp) cc_final: 0.7645 (ppp) REVERT: C 1241 ASP cc_start: 0.9301 (t70) cc_final: 0.8885 (m-30) REVERT: C 1276 TRP cc_start: 0.9387 (m-10) cc_final: 0.8945 (m-10) REVERT: C 1279 GLU cc_start: 0.9348 (mt-10) cc_final: 0.8879 (mt-10) REVERT: C 1304 MET cc_start: 0.9390 (tpt) cc_final: 0.9129 (tpt) REVERT: C 1329 GLU cc_start: 0.9559 (mt-10) cc_final: 0.9320 (tm-30) REVERT: D 130 MET cc_start: 0.9193 (mmp) cc_final: 0.8931 (mmm) REVERT: D 513 MET cc_start: 0.8947 (ttt) cc_final: 0.8041 (tpp) REVERT: D 581 MET cc_start: 0.9304 (mmp) cc_final: 0.8941 (mmm) REVERT: D 604 MET cc_start: 0.8458 (mtm) cc_final: 0.7979 (mtt) REVERT: D 725 MET cc_start: 0.9198 (mpp) cc_final: 0.8966 (ptp) REVERT: D 747 MET cc_start: 0.7866 (ttt) cc_final: 0.7291 (ttp) REVERT: D 822 MET cc_start: 0.8872 (mmm) cc_final: 0.8647 (tpp) REVERT: D 1145 PHE cc_start: 0.9177 (m-80) cc_final: 0.8654 (m-80) REVERT: D 1260 MET cc_start: 0.9143 (tpp) cc_final: 0.8824 (tpt) REVERT: D 1307 LEU cc_start: 0.9686 (mp) cc_final: 0.9092 (tp) REVERT: E 18 ASP cc_start: 0.9285 (t0) cc_final: 0.9024 (t0) REVERT: F 171 MET cc_start: -0.3112 (ptt) cc_final: -0.3393 (ptt) REVERT: F 376 MET cc_start: 0.0463 (mmm) cc_final: 0.0139 (mmm) REVERT: F 438 MET cc_start: 0.3534 (tpt) cc_final: 0.3110 (mmm) REVERT: F 592 MET cc_start: 0.1277 (mmt) cc_final: 0.0433 (mmp) REVERT: F 729 MET cc_start: -0.0370 (mmm) cc_final: -0.0626 (mmm) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1924 time to fit residues: 56.0932 Evaluate side-chains 141 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 145 optimal weight: 0.0570 chunk 142 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 193 optimal weight: 5.9990 chunk 358 optimal weight: 9.9990 chunk 146 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 111 optimal weight: 8.9990 chunk 161 optimal weight: 20.0000 chunk 205 optimal weight: 0.9990 chunk 310 optimal weight: 6.9990 overall best weight: 4.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN C 832 HIS C1008 GLN C1134 GLN D 951 GLN D1235 ASN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 838 GLN ** 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 = 0.3604 r_free = 0.3604 target = 0.071786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.042001 restraints weight = 313176.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.040271 restraints weight = 204290.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.040483 restraints weight = 153928.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.040532 restraints weight = 139906.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.040577 restraints weight = 137018.802| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 33815 Z= 0.160 Angle : 0.613 18.632 45902 Z= 0.313 Chirality : 0.042 0.211 5182 Planarity : 0.004 0.071 5833 Dihedral : 12.341 173.338 5141 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.95 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.13), residues: 4066 helix: 1.02 (0.13), residues: 1511 sheet: -0.32 (0.21), residues: 622 loop : -0.56 (0.14), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 821 TYR 0.033 0.001 TYR D 795 PHE 0.019 0.001 PHE D 141 TRP 0.014 0.002 TRP C1276 HIS 0.017 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.16 (33795) covalent geometry : angle 0.59792 / 0.31 (45872) hydrogen bonds : bond 0.03764 / 2.58 ( 1510) hydrogen bonds : angle 4.84576 / 3.33 ( 4203) metal coordination : bond 0.00911 / 0.58 ( 20) metal coordination : angle 5.29516 / 3.22 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12834.18 seconds wall clock time: 219 minutes 21.40 seconds (13161.40 seconds total)