Starting phenix.real_space_refine on Wed May 8 05:33:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woo_37694/05_2024/8woo_37694_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woo_37694/05_2024/8woo_37694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woo_37694/05_2024/8woo_37694.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woo_37694/05_2024/8woo_37694.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woo_37694/05_2024/8woo_37694_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woo_37694/05_2024/8woo_37694_neut_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.005 sd= 0.083 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 38 5.16 5 C 6007 2.51 5 N 1595 2.21 5 O 1764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 9412 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1217, 9314 Classifications: {'peptide': 1217} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 30, 'TRANS': 1186} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 98 Unusual residues: {' MG': 2, 'ANP': 2, 'BLD': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 5.77, per 1000 atoms: 0.61 Number of scatterers: 9412 At special positions: 0 Unit cell: (73.7, 108.9, 141.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 38 16.00 P 6 15.00 Mg 2 11.99 O 1764 8.00 N 1595 7.00 C 6007 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 - 3.50 Amino acid : False - 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: 3.64 Conformation dependent library (CDL) restraints added in 2.1 seconds 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2228 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 59 helices and 6 sheets defined 39.4% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.72 Creating SS restraints... Processing helix chain 'A' and resid 43 through 50 removed outlier: 4.398A pdb=" N ALA A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 65 removed outlier: 3.511A pdb=" N PHE A 59 " --> pdb=" O MET A 55 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU A 60 " --> pdb=" O PRO A 56 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY A 63 " --> pdb=" O PHE A 59 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 84 removed outlier: 4.044A pdb=" N VAL A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N HIS A 81 " --> pdb=" O HIS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 92 No H-bonds generated for 'chain 'A' and resid 89 through 92' Processing helix chain 'A' and resid 94 through 100 removed outlier: 4.172A pdb=" N PHE A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 128 Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 144 through 147 No H-bonds generated for 'chain 'A' and resid 144 through 147' Processing helix chain 'A' and resid 151 through 154 No H-bonds generated for 'chain 'A' and resid 151 through 154' Processing helix chain 'A' and resid 156 through 159 No H-bonds generated for 'chain 'A' and resid 156 through 159' Processing helix chain 'A' and resid 162 through 176 removed outlier: 3.687A pdb=" N HIS A 168 " --> pdb=" O GLY A 164 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 170 " --> pdb=" O PHE A 166 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE A 173 " --> pdb=" O TYR A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 183 Processing helix chain 'A' and resid 190 through 193 No H-bonds generated for 'chain 'A' and resid 190 through 193' Processing helix chain 'A' and resid 195 through 221 removed outlier: 4.082A pdb=" N ALA A 199 " --> pdb=" O PRO A 196 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N PHE A 200 " --> pdb=" O GLY A 197 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 204 " --> pdb=" O ALA A 201 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N TYR A 205 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 206 " --> pdb=" O GLY A 203 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR A 207 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU A 209 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE A 212 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N SER A 214 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG A 217 " --> pdb=" O SER A 214 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLU A 218 " --> pdb=" O LYS A 215 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER A 219 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR A 220 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 229 No H-bonds generated for 'chain 'A' and resid 226 through 229' Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 248 through 251 No H-bonds generated for 'chain 'A' and resid 248 through 251' Processing helix chain 'A' and resid 255 through 279 removed outlier: 3.764A pdb=" N LYS A 259 " --> pdb=" O GLN A 255 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LEU A 260 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N THR A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TYR A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE A 278 " --> pdb=" O CYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 288 Processing helix chain 'A' and resid 290 through 293 No H-bonds generated for 'chain 'A' and resid 290 through 293' Processing helix chain 'A' and resid 303 through 318 removed outlier: 4.018A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER A 317 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LEU A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 341 removed outlier: 3.927A pdb=" N LYS A 330 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 338 " --> pdb=" O ALA A 334 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE A 341 " --> pdb=" O LYS A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 413 No H-bonds generated for 'chain 'A' and resid 410 through 413' Processing helix chain 'A' and resid 431 through 433 No H-bonds generated for 'chain 'A' and resid 431 through 433' Processing helix chain 'A' and resid 440 through 442 No H-bonds generated for 'chain 'A' and resid 440 through 442' Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'A' and resid 471 through 480 removed outlier: 3.797A pdb=" N ALA A 479 " --> pdb=" O ALA A 475 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA A 480 " --> pdb=" O ALA A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 519 Processing helix chain 'A' and resid 537 through 547 removed outlier: 3.564A pdb=" N ILE A 541 " --> pdb=" O SER A 537 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL A 542 " --> pdb=" O SER A 538 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 545 " --> pdb=" O ILE A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 603 Processing helix chain 'A' and resid 623 through 631 removed outlier: 3.668A pdb=" N SER A 628 " --> pdb=" O SER A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 679 removed outlier: 3.916A pdb=" N LEU A 677 " --> pdb=" O PHE A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 695 Proline residue: A 685 - end of helix removed outlier: 3.578A pdb=" N ILE A 688 " --> pdb=" O PRO A 685 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N MET A 689 " --> pdb=" O TYR A 686 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 690 " --> pdb=" O SER A 687 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL A 692 " --> pdb=" O MET A 689 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE A 695 " --> pdb=" O VAL A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 716 removed outlier: 3.876A pdb=" N GLY A 701 " --> pdb=" O GLY A 698 " (cutoff:3.500A) Proline residue: A 702 - end of helix removed outlier: 4.444A pdb=" N ILE A 706 " --> pdb=" O THR A 703 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 707 " --> pdb=" O PHE A 704 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N MET A 708 " --> pdb=" O ALA A 705 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER A 709 " --> pdb=" O ILE A 706 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET A 711 " --> pdb=" O MET A 708 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE A 712 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 714 " --> pdb=" O MET A 711 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE A 715 " --> pdb=" O ILE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 750 removed outlier: 4.761A pdb=" N ILE A 747 " --> pdb=" O GLY A 743 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN A 748 " --> pdb=" O ALA A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 771 removed outlier: 4.033A pdb=" N LEU A 768 " --> pdb=" O ARG A 764 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 769 " --> pdb=" O ARG A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 778 No H-bonds generated for 'chain 'A' and resid 776 through 778' Processing helix chain 'A' and resid 782 through 784 No H-bonds generated for 'chain 'A' and resid 782 through 784' Processing helix chain 'A' and resid 801 through 804 No H-bonds generated for 'chain 'A' and resid 801 through 804' Processing helix chain 'A' and resid 809 through 812 No H-bonds generated for 'chain 'A' and resid 809 through 812' Processing helix chain 'A' and resid 825 through 828 No H-bonds generated for 'chain 'A' and resid 825 through 828' Processing helix chain 'A' and resid 832 through 852 removed outlier: 3.918A pdb=" N LEU A 837 " --> pdb=" O SER A 833 " (cutoff:3.500A) Proline residue: A 841 - end of helix removed outlier: 4.070A pdb=" N LEU A 845 " --> pdb=" O PRO A 841 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 850 " --> pdb=" O ALA A 846 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLN A 851 " --> pdb=" O ASN A 847 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 852 " --> pdb=" O PHE A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 873 removed outlier: 4.056A pdb=" N HIS A 865 " --> pdb=" O THR A 861 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LYS A 867 " --> pdb=" O LYS A 863 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N THR A 868 " --> pdb=" O ALA A 864 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N SER A 869 " --> pdb=" O HIS A 865 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N MET A 870 " --> pdb=" O ALA A 866 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE A 871 " --> pdb=" O LYS A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 886 removed outlier: 3.944A pdb=" N ALA A 884 " --> pdb=" O ARG A 880 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N PHE A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASN A 886 " --> pdb=" O VAL A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 904 No H-bonds generated for 'chain 'A' and resid 901 through 904' Processing helix chain 'A' and resid 908 through 918 removed outlier: 4.451A pdb=" N PHE A 917 " --> pdb=" O SER A 913 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY A 918 " --> pdb=" O GLY A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 925 No H-bonds generated for 'chain 'A' and resid 922 through 925' Processing helix chain 'A' and resid 931 through 938 removed outlier: 3.661A pdb=" N LEU A 938 " --> pdb=" O TYR A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 953 No H-bonds generated for 'chain 'A' and resid 950 through 953' Processing helix chain 'A' and resid 955 through 965 removed outlier: 4.761A pdb=" N ALA A 960 " --> pdb=" O LEU A 956 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER A 962 " --> pdb=" O ILE A 958 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A 964 " --> pdb=" O ALA A 960 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLU A 965 " --> pdb=" O ASN A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 974 removed outlier: 3.510A pdb=" N ALA A 970 " --> pdb=" O VAL A 967 " (cutoff:3.500A) Proline residue: A 971 - end of helix Processing helix chain 'A' and resid 1051 through 1053 No H-bonds generated for 'chain 'A' and resid 1051 through 1053' Processing helix chain 'A' and resid 1055 through 1057 No H-bonds generated for 'chain 'A' and resid 1055 through 1057' Processing helix chain 'A' and resid 1076 through 1078 No H-bonds generated for 'chain 'A' and resid 1076 through 1078' Processing helix chain 'A' and resid 1081 through 1087 removed outlier: 4.089A pdb=" N LEU A1086 " --> pdb=" O LYS A1082 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LYS A1087 " --> pdb=" O SER A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1122 removed outlier: 4.284A pdb=" N ASP A1120 " --> pdb=" O SER A1116 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA A1122 " --> pdb=" O VAL A1118 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1132 Processing helix chain 'A' and resid 1151 through 1165 removed outlier: 3.912A pdb=" N ARG A1156 " --> pdb=" O GLY A1152 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A1157 " --> pdb=" O GLN A1153 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A1159 " --> pdb=" O GLN A1155 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA A1160 " --> pdb=" O ARG A1156 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG A1161 " --> pdb=" O ILE A1157 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA A1162 " --> pdb=" O ALA A1158 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A1163 " --> pdb=" O ILE A1159 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A1164 " --> pdb=" O ALA A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1249 removed outlier: 3.888A pdb=" N GLN A1246 " --> pdb=" O SER A1242 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A1247 " --> pdb=" O ARG A1243 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN A1248 " --> pdb=" O LEU A1244 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N THR A1249 " --> pdb=" O LEU A1245 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1242 through 1249' Processing sheet with id= A, first strand: chain 'A' and resid 365 through 367 removed outlier: 3.673A pdb=" N GLU A 366 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU A 425 " --> pdb=" O GLU A 366 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 395 through 399 removed outlier: 7.118A pdb=" N THR A 555 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL A 398 " --> pdb=" O THR A 555 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL A 557 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY A 444 " --> pdb=" O ILE A 524 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 645 through 647 Processing sheet with id= D, first strand: chain 'A' and resid 1042 through 1044 removed outlier: 6.663A pdb=" N VAL A1202 " --> pdb=" O LEU A1043 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 1169 through 1171 removed outlier: 6.123A pdb=" N THR A1199 " --> pdb=" O LEU A1170 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 1217 through 1220 removed outlier: 3.825A pdb=" N VAL A1218 " --> pdb=" O GLU A1226 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU A1226 " --> pdb=" O VAL A1218 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N GLN A1220 " --> pdb=" O ILE A1224 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ILE A1224 " --> pdb=" O GLN A1220 " (cutoff:3.500A) No H-bonds generated for sheet with id= F 139 hydrogen bonds defined for protein. 351 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.66 Time building geometry restraints manager: 4.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1529 1.31 - 1.44: 2558 1.44 - 1.56: 5424 1.56 - 1.68: 8 1.68 - 1.81: 71 Bond restraints: 9590 Sorted by residual: bond pdb=" C ALA A 126 " pdb=" N VAL A 127 " ideal model delta sigma weight residual 1.334 1.267 0.068 1.25e-02 6.40e+03 2.94e+01 bond pdb=" O3A ANP A1303 " pdb=" PB ANP A1303 " ideal model delta sigma weight residual 1.700 1.592 0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" O3A ANP A1304 " pdb=" PB ANP A1304 " ideal model delta sigma weight residual 1.700 1.606 0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" C VAL A 127 " pdb=" O VAL A 127 " ideal model delta sigma weight residual 1.237 1.191 0.046 1.13e-02 7.83e+03 1.64e+01 bond pdb=" C4 ANP A1303 " pdb=" C5 ANP A1303 " ideal model delta sigma weight residual 1.387 1.464 -0.077 2.00e-02 2.50e+03 1.50e+01 ... (remaining 9585 not shown) Histogram of bond angle deviations from ideal: 88.12 - 97.75: 3 97.75 - 107.39: 307 107.39 - 117.03: 6244 117.03 - 126.67: 6353 126.67 - 136.31: 95 Bond angle restraints: 13002 Sorted by residual: angle pdb=" N GLN A 130 " pdb=" CA GLN A 130 " pdb=" C GLN A 130 " ideal model delta sigma weight residual 108.42 89.36 19.06 1.54e+00 4.22e-01 1.53e+02 angle pdb=" N GLN A 130 " pdb=" CA GLN A 130 " pdb=" CB GLN A 130 " ideal model delta sigma weight residual 111.56 129.54 -17.98 1.52e+00 4.33e-01 1.40e+02 angle pdb=" N ALA A1125 " pdb=" CA ALA A1125 " pdb=" C ALA A1125 " ideal model delta sigma weight residual 108.20 88.12 20.08 1.71e+00 3.42e-01 1.38e+02 angle pdb=" N TYR A 123 " pdb=" CA TYR A 123 " pdb=" C TYR A 123 " ideal model delta sigma weight residual 111.02 124.97 -13.95 1.22e+00 6.72e-01 1.31e+02 angle pdb=" C LYS A 122 " pdb=" CA LYS A 122 " pdb=" CB LYS A 122 " ideal model delta sigma weight residual 110.90 127.80 -16.90 1.58e+00 4.01e-01 1.14e+02 ... (remaining 12997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.77: 5660 31.77 - 63.55: 96 63.55 - 95.32: 22 95.32 - 127.09: 0 127.09 - 158.87: 2 Dihedral angle restraints: 5780 sinusoidal: 2292 harmonic: 3488 Sorted by residual: dihedral pdb=" C SER A 681 " pdb=" N SER A 681 " pdb=" CA SER A 681 " pdb=" CB SER A 681 " ideal model delta harmonic sigma weight residual -122.60 -162.82 40.22 0 2.50e+00 1.60e-01 2.59e+02 dihedral pdb=" N SER A 681 " pdb=" C SER A 681 " pdb=" CA SER A 681 " pdb=" CB SER A 681 " ideal model delta harmonic sigma weight residual 122.80 159.39 -36.59 0 2.50e+00 1.60e-01 2.14e+02 dihedral pdb=" C LYS A 122 " pdb=" N LYS A 122 " pdb=" CA LYS A 122 " pdb=" CB LYS A 122 " ideal model delta harmonic sigma weight residual -122.60 -148.01 25.41 0 2.50e+00 1.60e-01 1.03e+02 ... (remaining 5777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.339: 1491 0.339 - 0.677: 4 0.677 - 1.016: 4 1.016 - 1.355: 0 1.355 - 1.693: 1 Chirality restraints: 1500 Sorted by residual: chirality pdb=" CA SER A 681 " pdb=" N SER A 681 " pdb=" C SER A 681 " pdb=" CB SER A 681 " both_signs ideal model delta sigma weight residual False 2.51 0.82 1.69 2.00e-01 2.50e+01 7.17e+01 chirality pdb=" CA LYS A 122 " pdb=" N LYS A 122 " pdb=" C LYS A 122 " pdb=" CB LYS A 122 " both_signs ideal model delta sigma weight residual False 2.51 1.58 0.93 2.00e-01 2.50e+01 2.17e+01 chirality pdb=" CA ALA A 118 " pdb=" N ALA A 118 " pdb=" C ALA A 118 " pdb=" CB ALA A 118 " both_signs ideal model delta sigma weight residual False 2.48 1.74 0.74 2.00e-01 2.50e+01 1.39e+01 ... (remaining 1497 not shown) Planarity restraints: 1642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 55 " 0.050 5.00e-02 4.00e+02 7.39e-02 8.73e+00 pdb=" N PRO A 56 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 56 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 56 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 681 " 0.046 5.00e-02 4.00e+02 6.87e-02 7.55e+00 pdb=" N PRO A 682 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 682 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 682 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 377 " -0.043 5.00e-02 4.00e+02 6.49e-02 6.74e+00 pdb=" N PRO A 378 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 378 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 378 " -0.036 5.00e-02 4.00e+02 ... (remaining 1639 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 35 2.48 - 3.08: 5839 3.08 - 3.69: 13432 3.69 - 4.29: 19341 4.29 - 4.90: 31070 Nonbonded interactions: 69717 Sorted by model distance: nonbonded pdb=" NZ LYS A 406 " pdb=" CG1 VAL A 558 " model vdw 1.870 3.540 nonbonded pdb=" N GLN A 130 " pdb=" O GLN A 130 " model vdw 2.237 2.496 nonbonded pdb=" O SER A 681 " pdb=" N GLU A 683 " model vdw 2.242 2.520 nonbonded pdb=" OH TYR A 644 " pdb=" O HIS A 865 " model vdw 2.280 2.440 nonbonded pdb=" OG SER A 697 " pdb=" O ALA A 744 " model vdw 2.290 2.440 ... (remaining 69712 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.390 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 29.940 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 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 0.108 9590 Z= 0.359 Angle : 1.136 20.084 13002 Z= 0.673 Chirality : 0.083 1.693 1500 Planarity : 0.007 0.074 1642 Dihedral : 13.301 158.867 3552 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.63 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.18 (0.16), residues: 1213 helix: -4.61 (0.09), residues: 623 sheet: -3.55 (0.48), residues: 89 loop : -3.26 (0.22), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 684 HIS 0.005 0.001 HIS A 51 PHE 0.024 0.002 PHE A1061 TYR 0.018 0.002 TYR A 463 ARG 0.006 0.001 ARG A 653 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLN cc_start: 0.8530 (mm110) cc_final: 0.8227 (mm110) REVERT: A 149 SER cc_start: 0.9054 (m) cc_final: 0.8751 (t) REVERT: A 157 ASP cc_start: 0.7757 (t0) cc_final: 0.7522 (t0) REVERT: A 266 MET cc_start: 0.8396 (ttp) cc_final: 0.8163 (ttm) REVERT: A 300 ASP cc_start: 0.7749 (p0) cc_final: 0.7061 (t0) REVERT: A 437 LYS cc_start: 0.8768 (mtpp) cc_final: 0.8550 (mmmm) REVERT: A 646 TYR cc_start: 0.8832 (m-80) cc_final: 0.8424 (m-80) REVERT: A 708 MET cc_start: 0.8782 (tmm) cc_final: 0.8516 (tmm) REVERT: A 819 LEU cc_start: 0.9338 (tp) cc_final: 0.8937 (tt) REVERT: A 905 ARG cc_start: 0.8136 (tmt170) cc_final: 0.7759 (tmt170) REVERT: A 908 TYR cc_start: 0.8373 (m-10) cc_final: 0.8085 (m-10) REVERT: A 1041 GLN cc_start: 0.8412 (tp-100) cc_final: 0.8155 (tp40) REVERT: A 1060 ARG cc_start: 0.7788 (mtm180) cc_final: 0.7480 (mtm-85) REVERT: A 1079 LEU cc_start: 0.9199 (mt) cc_final: 0.8994 (mm) REVERT: A 1083 SER cc_start: 0.8689 (t) cc_final: 0.8312 (t) REVERT: A 1148 GLN cc_start: 0.8677 (tp-100) cc_final: 0.8436 (tp40) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.2913 time to fit residues: 94.6588 Evaluate side-chains 128 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 70 optimal weight: 0.0870 chunk 109 optimal weight: 10.0000 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS A 483 HIS ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 HIS A 602 GLN ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 GLN A 758 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9590 Z= 0.202 Angle : 0.641 12.616 13002 Z= 0.330 Chirality : 0.043 0.180 1500 Planarity : 0.005 0.055 1642 Dihedral : 10.536 135.933 1471 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.25 % Favored : 92.66 % Rotamer: Outliers : 2.65 % Allowed : 11.62 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.25 (0.18), residues: 1213 helix: -3.91 (0.13), residues: 620 sheet: -2.84 (0.69), residues: 57 loop : -2.85 (0.23), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 684 HIS 0.002 0.001 HIS A 625 PHE 0.023 0.001 PHE A1031 TYR 0.024 0.001 TYR A1241 ARG 0.007 0.001 ARG A 992 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 143 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLN cc_start: 0.8622 (mm110) cc_final: 0.8277 (mm110) REVERT: A 149 SER cc_start: 0.9052 (m) cc_final: 0.8702 (t) REVERT: A 276 TYR cc_start: 0.7830 (m-80) cc_final: 0.7578 (m-80) REVERT: A 549 VAL cc_start: 0.8668 (p) cc_final: 0.8066 (m) REVERT: A 646 TYR cc_start: 0.8790 (m-80) cc_final: 0.8509 (m-80) REVERT: A 680 ASN cc_start: 0.8683 (t0) cc_final: 0.8265 (t0) REVERT: A 708 MET cc_start: 0.8675 (tmm) cc_final: 0.8442 (ttp) REVERT: A 799 ASP cc_start: 0.8410 (t0) cc_final: 0.8190 (t0) REVERT: A 975 ARG cc_start: 0.8027 (tmm-80) cc_final: 0.7614 (ttm170) REVERT: A 1041 GLN cc_start: 0.8021 (tp-100) cc_final: 0.7788 (tp40) REVERT: A 1063 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.8314 (t0) REVERT: A 1216 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7800 (mt) outliers start: 26 outliers final: 11 residues processed: 159 average time/residue: 0.2287 time to fit residues: 51.2928 Evaluate side-chains 123 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 110 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 796 ASP Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1063 ASP Chi-restraints excluded: chain A residue 1216 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 118 optimal weight: 20.0000 chunk 98 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 88 optimal weight: 0.4980 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 9590 Z= 0.451 Angle : 0.770 15.000 13002 Z= 0.394 Chirality : 0.047 0.171 1500 Planarity : 0.005 0.058 1642 Dihedral : 10.095 146.250 1471 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 3.57 % Allowed : 12.54 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.82 (0.20), residues: 1213 helix: -3.54 (0.15), residues: 626 sheet: -2.90 (0.62), residues: 66 loop : -2.59 (0.25), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 778 HIS 0.005 0.001 HIS A 560 PHE 0.020 0.002 PHE A 946 TYR 0.018 0.002 TYR A 595 ARG 0.015 0.001 ARG A1223 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 123 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 SER cc_start: 0.9199 (m) cc_final: 0.8866 (t) REVERT: A 276 TYR cc_start: 0.8001 (m-80) cc_final: 0.7671 (m-80) REVERT: A 286 VAL cc_start: 0.9574 (m) cc_final: 0.9330 (p) REVERT: A 549 VAL cc_start: 0.8394 (p) cc_final: 0.8100 (m) REVERT: A 646 TYR cc_start: 0.8911 (m-80) cc_final: 0.8524 (m-80) REVERT: A 827 ILE cc_start: 0.9202 (mm) cc_final: 0.8893 (mt) REVERT: A 975 ARG cc_start: 0.8257 (tmm-80) cc_final: 0.7578 (ttm170) REVERT: A 1041 GLN cc_start: 0.8344 (tp-100) cc_final: 0.7812 (tm-30) REVERT: A 1063 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8356 (t0) REVERT: A 1123 ARG cc_start: 0.7105 (ptp-170) cc_final: 0.6046 (ptp-170) REVERT: A 1148 GLN cc_start: 0.8306 (tp40) cc_final: 0.8021 (tp40) outliers start: 35 outliers final: 28 residues processed: 149 average time/residue: 0.2346 time to fit residues: 48.7535 Evaluate side-chains 136 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 107 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 796 ASP Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 847 ASN Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1063 ASP Chi-restraints excluded: chain A residue 1070 MET Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1168 THR Chi-restraints excluded: chain A residue 1210 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.0970 chunk 82 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 97 optimal weight: 10.0000 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9590 Z= 0.151 Angle : 0.585 13.882 13002 Z= 0.299 Chirality : 0.041 0.163 1500 Planarity : 0.004 0.050 1642 Dihedral : 9.170 143.355 1471 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.65 % Allowed : 15.29 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.43 (0.21), residues: 1213 helix: -3.16 (0.16), residues: 629 sheet: -2.80 (0.62), residues: 66 loop : -2.46 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 933 HIS 0.002 0.001 HIS A 51 PHE 0.019 0.001 PHE A 386 TYR 0.019 0.001 TYR A1241 ARG 0.004 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 SER cc_start: 0.9174 (m) cc_final: 0.8867 (t) REVERT: A 381 MET cc_start: 0.8175 (mmp) cc_final: 0.7973 (mmp) REVERT: A 549 VAL cc_start: 0.8305 (p) cc_final: 0.8029 (m) REVERT: A 646 TYR cc_start: 0.8847 (m-80) cc_final: 0.8525 (m-80) REVERT: A 799 ASP cc_start: 0.8435 (t0) cc_final: 0.8172 (t0) REVERT: A 975 ARG cc_start: 0.8178 (tmm-80) cc_final: 0.7604 (ttm170) REVERT: A 1028 PHE cc_start: 0.8663 (m-80) cc_final: 0.8232 (m-80) REVERT: A 1041 GLN cc_start: 0.8192 (tp-100) cc_final: 0.7657 (tm-30) REVERT: A 1063 ASP cc_start: 0.8624 (OUTLIER) cc_final: 0.8356 (t0) REVERT: A 1148 GLN cc_start: 0.8328 (tp40) cc_final: 0.8030 (tp40) outliers start: 26 outliers final: 15 residues processed: 143 average time/residue: 0.2203 time to fit residues: 44.3126 Evaluate side-chains 126 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 684 TRP Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1063 ASP Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1210 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 0.4980 chunk 1 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 chunk 80 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9590 Z= 0.151 Angle : 0.564 14.382 13002 Z= 0.287 Chirality : 0.040 0.172 1500 Planarity : 0.003 0.042 1642 Dihedral : 8.645 143.116 1471 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.45 % Allowed : 14.98 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.07 (0.21), residues: 1213 helix: -2.83 (0.18), residues: 623 sheet: -2.63 (0.62), residues: 70 loop : -2.36 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 933 HIS 0.002 0.000 HIS A 51 PHE 0.015 0.001 PHE A 287 TYR 0.012 0.001 TYR A 595 ARG 0.006 0.000 ARG A1060 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 117 time to evaluate : 1.055 Fit side-chains revert: symmetry clash REVERT: A 149 SER cc_start: 0.9163 (m) cc_final: 0.8829 (p) REVERT: A 549 VAL cc_start: 0.8235 (p) cc_final: 0.8009 (m) REVERT: A 815 MET cc_start: 0.7862 (mmt) cc_final: 0.7543 (mmt) REVERT: A 975 ARG cc_start: 0.8165 (tmm-80) cc_final: 0.7636 (ttm170) REVERT: A 1028 PHE cc_start: 0.8579 (m-80) cc_final: 0.8253 (m-80) REVERT: A 1041 GLN cc_start: 0.8345 (tp-100) cc_final: 0.7720 (tm-30) REVERT: A 1123 ARG cc_start: 0.7006 (ptp-170) cc_final: 0.5877 (ptp-170) REVERT: A 1148 GLN cc_start: 0.8387 (tp40) cc_final: 0.8089 (tp40) outliers start: 24 outliers final: 17 residues processed: 135 average time/residue: 0.2073 time to fit residues: 40.3294 Evaluate side-chains 125 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 108 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 684 TRP Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1210 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 0.0570 chunk 23 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 117 optimal weight: 0.0770 chunk 97 optimal weight: 10.0000 chunk 54 optimal weight: 0.0470 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 0.1980 chunk 61 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 overall best weight: 0.1954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9590 Z= 0.118 Angle : 0.544 11.063 13002 Z= 0.278 Chirality : 0.039 0.166 1500 Planarity : 0.004 0.052 1642 Dihedral : 8.162 139.725 1471 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.83 % Allowed : 16.62 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.78 (0.22), residues: 1213 helix: -2.55 (0.18), residues: 625 sheet: -2.21 (0.64), residues: 70 loop : -2.32 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 933 HIS 0.002 0.000 HIS A 937 PHE 0.013 0.001 PHE A 386 TYR 0.020 0.001 TYR A1241 ARG 0.005 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 125 time to evaluate : 1.086 Fit side-chains REVERT: A 149 SER cc_start: 0.9137 (m) cc_final: 0.8804 (p) REVERT: A 518 MET cc_start: 0.8587 (mmm) cc_final: 0.7953 (mmm) REVERT: A 815 MET cc_start: 0.7899 (mmt) cc_final: 0.7565 (mmt) REVERT: A 975 ARG cc_start: 0.8153 (tmm-80) cc_final: 0.7483 (tpp-160) REVERT: A 1123 ARG cc_start: 0.7076 (ptp-170) cc_final: 0.5936 (ptp-170) outliers start: 18 outliers final: 14 residues processed: 136 average time/residue: 0.2074 time to fit residues: 40.9344 Evaluate side-chains 122 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 108 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 684 TRP Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1210 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 0.9980 chunk 66 optimal weight: 0.0980 chunk 85 optimal weight: 0.9980 chunk 98 optimal weight: 0.0020 chunk 65 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 ASN ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1105 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9590 Z= 0.136 Angle : 0.552 9.254 13002 Z= 0.281 Chirality : 0.040 0.165 1500 Planarity : 0.003 0.036 1642 Dihedral : 7.917 138.920 1471 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 1.83 % Allowed : 17.74 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.22), residues: 1213 helix: -2.34 (0.19), residues: 616 sheet: -2.00 (0.65), residues: 70 loop : -2.29 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 684 HIS 0.002 0.000 HIS A 937 PHE 0.011 0.001 PHE A1031 TYR 0.010 0.001 TYR A 646 ARG 0.005 0.000 ARG A1193 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 0.999 Fit side-chains REVERT: A 149 SER cc_start: 0.9137 (m) cc_final: 0.8814 (p) REVERT: A 449 GLU cc_start: 0.7032 (pt0) cc_final: 0.5856 (pp20) REVERT: A 815 MET cc_start: 0.7902 (mmt) cc_final: 0.7615 (mmt) REVERT: A 975 ARG cc_start: 0.8151 (tmm-80) cc_final: 0.7491 (tpp-160) REVERT: A 1123 ARG cc_start: 0.7001 (ptp-170) cc_final: 0.5860 (ptp-170) outliers start: 18 outliers final: 14 residues processed: 117 average time/residue: 0.2063 time to fit residues: 35.8069 Evaluate side-chains 117 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 103 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 684 TRP Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1210 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 111 optimal weight: 8.9990 chunk 101 optimal weight: 20.0000 chunk 108 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9590 Z= 0.190 Angle : 0.573 8.825 13002 Z= 0.293 Chirality : 0.041 0.162 1500 Planarity : 0.004 0.034 1642 Dihedral : 7.919 141.262 1471 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.14 % Allowed : 18.04 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.23), residues: 1213 helix: -2.13 (0.20), residues: 608 sheet: -2.11 (0.70), residues: 59 loop : -2.23 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 684 HIS 0.002 0.001 HIS A 749 PHE 0.013 0.001 PHE A1031 TYR 0.011 0.001 TYR A 207 ARG 0.007 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 104 time to evaluate : 1.042 Fit side-chains REVERT: A 149 SER cc_start: 0.9181 (m) cc_final: 0.8873 (p) REVERT: A 815 MET cc_start: 0.7875 (mmt) cc_final: 0.7565 (mmt) REVERT: A 870 MET cc_start: 0.8367 (mmt) cc_final: 0.7603 (mmt) REVERT: A 975 ARG cc_start: 0.8208 (tmm-80) cc_final: 0.7543 (tpp-160) REVERT: A 1011 GLU cc_start: 0.6859 (tp30) cc_final: 0.6463 (tp30) REVERT: A 1123 ARG cc_start: 0.6967 (ptp-170) cc_final: 0.5810 (ptp-170) outliers start: 21 outliers final: 18 residues processed: 117 average time/residue: 0.2153 time to fit residues: 36.3183 Evaluate side-chains 118 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 684 TRP Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain A residue 1210 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 9.9990 chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 102 optimal weight: 0.0370 chunk 108 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 114 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 ASN A 748 GLN ** A1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9590 Z= 0.169 Angle : 0.571 9.433 13002 Z= 0.289 Chirality : 0.041 0.162 1500 Planarity : 0.003 0.035 1642 Dihedral : 7.813 142.077 1471 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.65 % Allowed : 18.04 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.23), residues: 1213 helix: -2.00 (0.20), residues: 612 sheet: -1.99 (0.65), residues: 69 loop : -2.22 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 933 HIS 0.002 0.000 HIS A 749 PHE 0.011 0.001 PHE A 287 TYR 0.012 0.001 TYR A 646 ARG 0.004 0.000 ARG A1193 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 106 time to evaluate : 1.015 Fit side-chains REVERT: A 149 SER cc_start: 0.9201 (m) cc_final: 0.8924 (p) REVERT: A 489 LEU cc_start: 0.7580 (pp) cc_final: 0.7051 (mm) REVERT: A 595 TYR cc_start: 0.8324 (t80) cc_final: 0.7985 (m-80) REVERT: A 815 MET cc_start: 0.7834 (mmt) cc_final: 0.7528 (mmt) REVERT: A 870 MET cc_start: 0.8379 (mmt) cc_final: 0.7582 (mmt) REVERT: A 898 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8493 (tm-30) REVERT: A 975 ARG cc_start: 0.8192 (tmm-80) cc_final: 0.7548 (tpp-160) REVERT: A 993 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.8048 (mt) REVERT: A 1011 GLU cc_start: 0.6891 (tp30) cc_final: 0.6397 (tp30) REVERT: A 1123 ARG cc_start: 0.6966 (ptp-170) cc_final: 0.5788 (ptp-170) outliers start: 26 outliers final: 21 residues processed: 122 average time/residue: 0.2346 time to fit residues: 42.1648 Evaluate side-chains 126 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 684 TRP Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1210 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 0.0030 chunk 79 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 overall best weight: 1.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9590 Z= 0.195 Angle : 0.585 9.341 13002 Z= 0.297 Chirality : 0.041 0.164 1500 Planarity : 0.003 0.036 1642 Dihedral : 7.831 144.156 1471 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 2.34 % Allowed : 18.76 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.23), residues: 1213 helix: -1.92 (0.20), residues: 606 sheet: -1.94 (0.67), residues: 66 loop : -2.25 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 684 HIS 0.002 0.001 HIS A 749 PHE 0.012 0.001 PHE A 287 TYR 0.012 0.001 TYR A 646 ARG 0.008 0.000 ARG A 600 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 107 time to evaluate : 1.127 Fit side-chains REVERT: A 149 SER cc_start: 0.9240 (m) cc_final: 0.8952 (p) REVERT: A 449 GLU cc_start: 0.6969 (pt0) cc_final: 0.5850 (pp20) REVERT: A 489 LEU cc_start: 0.7538 (pp) cc_final: 0.6993 (mm) REVERT: A 655 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7153 (mm-30) REVERT: A 815 MET cc_start: 0.7899 (mmt) cc_final: 0.7579 (mmt) REVERT: A 870 MET cc_start: 0.8374 (mmt) cc_final: 0.7533 (mmt) REVERT: A 898 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8657 (tm-30) REVERT: A 975 ARG cc_start: 0.8194 (tmm-80) cc_final: 0.7533 (tpp-160) REVERT: A 1011 GLU cc_start: 0.6854 (tp30) cc_final: 0.6352 (tp30) REVERT: A 1123 ARG cc_start: 0.6911 (ptp-170) cc_final: 0.5679 (ptp-170) outliers start: 23 outliers final: 22 residues processed: 121 average time/residue: 0.2018 time to fit residues: 35.9468 Evaluate side-chains 126 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 684 TRP Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1210 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 96 optimal weight: 0.0010 chunk 40 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 HIS ** A1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.166022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.120905 restraints weight = 15458.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.123245 restraints weight = 9304.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.124073 restraints weight = 6057.705| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9590 Z= 0.144 Angle : 0.564 10.499 13002 Z= 0.283 Chirality : 0.040 0.165 1500 Planarity : 0.003 0.035 1642 Dihedral : 7.637 142.714 1471 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.55 % Allowed : 19.06 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.23), residues: 1213 helix: -1.74 (0.20), residues: 612 sheet: -1.86 (0.64), residues: 70 loop : -2.27 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 684 HIS 0.002 0.000 HIS A 937 PHE 0.009 0.001 PHE A 287 TYR 0.012 0.001 TYR A 646 ARG 0.007 0.000 ARG A 600 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1999.40 seconds wall clock time: 37 minutes 43.95 seconds (2263.95 seconds total)