Starting phenix.real_space_refine (version: dev) on Tue Apr 5 05:34:52 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a91_6996/04_2022/6a91_6996_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a91_6996/04_2022/6a91_6996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a91_6996/04_2022/6a91_6996.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a91_6996/04_2022/6a91_6996.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a91_6996/04_2022/6a91_6996_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a91_6996/04_2022/6a91_6996_updated.pdb" } resolution = 3.2 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 ------------------------------------------------------------------------------- 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= 0.000 sd= 0.006 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 131": "NH1" <-> "NH2" Residue "A ARG 187": "NH1" <-> "NH2" Residue "A ARG 227": "NH1" <-> "NH2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A ARG 305": "NH1" <-> "NH2" Residue "A ARG 370": "NH1" <-> "NH2" Residue "A ARG 386": "NH1" <-> "NH2" Residue "A ARG 552": "NH1" <-> "NH2" Residue "A GLU 565": "OE1" <-> "OE2" Residue "A ARG 613": "NH1" <-> "NH2" Residue "A ARG 696": "NH1" <-> "NH2" Residue "A ARG 883": "NH1" <-> "NH2" Residue "A ARG 1074": "NH1" <-> "NH2" Residue "A ARG 1120": "NH1" <-> "NH2" Residue "A ARG 1131": "NH1" <-> "NH2" Residue "A ARG 1137": "NH1" <-> "NH2" Residue "A ARG 1138": "NH1" <-> "NH2" Residue "A ARG 1225": "NH1" <-> "NH2" Residue "A ARG 1274": "NH1" <-> "NH2" Residue "A ARG 1283": "NH1" <-> "NH2" Residue "A ARG 1297": "NH1" <-> "NH2" Residue "A ARG 1325": "NH1" <-> "NH2" Residue "A ARG 1369": "NH1" <-> "NH2" Residue "A ARG 1384": "NH1" <-> "NH2" Residue "B ARG 55": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 11182 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1323, 10537 Classifications: {'peptide': 1323} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 45, 'TRANS': 1275, 'PCIS': 2} Chain breaks: 2 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 296 Unresolved non-hydrogen angles: 375 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 10, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 7, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 171 Chain: "B" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 449 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "A" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 195 Unusual residues: {'PC1': 2, 'NAG': 7, '9SL': 1} Classifications: {'undetermined': 10, 'water': 2} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.93, per 1000 atoms: 0.62 Number of scatterers: 11182 At special positions: 0 Unit cell: (133.102, 133.102, 122.192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 74 16.00 P 2 15.00 O 1934 8.00 N 1788 7.00 C 7384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 337 " distance=1.56 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 343 " distance=2.03 Simple disulfide: pdb=" SG CYS A 709 " - pdb=" SG CYS A 717 " distance=2.05 Simple disulfide: pdb=" SG CYS A1011 " - pdb=" SG CYS A1030 " distance=2.03 Simple disulfide: pdb=" SG CYS A1368 " - pdb=" SG CYS A1381 " distance=2.04 Simple disulfide: pdb=" SG CYS B 13 " - pdb=" SG CYS B 26 " distance=2.02 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 40 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 54 " distance=2.04 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 52 " distance=2.03 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 Links applied BETA1-4 " NAG A1601 " - " NAG A1602 " " NAG A1603 " - " NAG A1604 " NAG-ASN " NAG A1601 " - " ASN A 330 " " NAG A1603 " - " ASN A1034 " " NAG A1605 " - " ASN A1015 " " NAG A1606 " - " ASN A 312 " " NAG A1607 " - " ASN A 308 " Time building additional restraints: 4.61 Conformation dependent library (CDL) restraints added in 1.8 seconds 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2618 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 4 sheets defined 57.4% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'A' and resid 48 through 55 Processing helix chain 'A' and resid 95 through 102 removed outlier: 3.845A pdb=" N PHE A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 137 removed outlier: 3.596A pdb=" N THR A 136 " --> pdb=" O ALA A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 153 removed outlier: 3.620A pdb=" N MET A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 158 No H-bonds generated for 'chain 'A' and resid 155 through 158' Processing helix chain 'A' and resid 169 through 176 removed outlier: 3.605A pdb=" N LEU A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 185 removed outlier: 3.779A pdb=" N VAL A 184 " --> pdb=" O VAL A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 214 removed outlier: 3.867A pdb=" N LEU A 207 " --> pdb=" O TRP A 203 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 240 removed outlier: 3.628A pdb=" N ARG A 227 " --> pdb=" O TYR A 224 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 228 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG A 230 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL A 231 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG A 233 " --> pdb=" O ARG A 230 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR A 237 " --> pdb=" O SER A 234 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 240 " --> pdb=" O THR A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 257 removed outlier: 4.211A pdb=" N ALA A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 280 removed outlier: 3.710A pdb=" N LEU A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A 264 " --> pdb=" O ASP A 260 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 352 through 354 No H-bonds generated for 'chain 'A' and resid 352 through 354' Processing helix chain 'A' and resid 361 through 373 removed outlier: 3.522A pdb=" N LEU A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE A 369 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 371 " --> pdb=" O SER A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 385 removed outlier: 3.586A pdb=" N LEU A 383 " --> pdb=" O ASP A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 404 removed outlier: 3.668A pdb=" N LEU A 394 " --> pdb=" O TRP A 391 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE A 397 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL A 399 " --> pdb=" O PHE A 396 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 400 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N TYR A 402 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A 403 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N THR A 404 " --> pdb=" O PHE A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 427 removed outlier: 3.626A pdb=" N MET A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A 426 " --> pdb=" O MET A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 433 No H-bonds generated for 'chain 'A' and resid 430 through 433' Processing helix chain 'A' and resid 503 through 515 removed outlier: 3.521A pdb=" N GLN A 509 " --> pdb=" O TRP A 505 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY A 510 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA A 511 " --> pdb=" O LYS A 507 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 514 " --> pdb=" O GLY A 510 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 536 removed outlier: 3.532A pdb=" N VAL A 530 " --> pdb=" O ALA A 526 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR A 534 " --> pdb=" O VAL A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 572 removed outlier: 3.875A pdb=" N LEU A 551 " --> pdb=" O PHE A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 597 removed outlier: 3.521A pdb=" N ILE A 589 " --> pdb=" O VAL A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 622 removed outlier: 3.510A pdb=" N PHE A 618 " --> pdb=" O LEU A 615 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS A 622 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 636 removed outlier: 3.858A pdb=" N VAL A 633 " --> pdb=" O ASN A 629 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET A 634 " --> pdb=" O PHE A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 663 removed outlier: 3.731A pdb=" N ASN A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A 653 " --> pdb=" O PHE A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 669 No H-bonds generated for 'chain 'A' and resid 666 through 669' Processing helix chain 'A' and resid 671 through 673 No H-bonds generated for 'chain 'A' and resid 671 through 673' Processing helix chain 'A' and resid 675 through 677 No H-bonds generated for 'chain 'A' and resid 675 through 677' Processing helix chain 'A' and resid 687 through 698 removed outlier: 3.504A pdb=" N MET A 692 " --> pdb=" O LEU A 688 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA A 697 " --> pdb=" O ILE A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 710 removed outlier: 3.854A pdb=" N ASP A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 728 Proline residue: A 719 - end of helix removed outlier: 4.066A pdb=" N VAL A 722 " --> pdb=" O PRO A 719 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL A 724 " --> pdb=" O PHE A 721 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE A 726 " --> pdb=" O ALA A 723 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL A 727 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY A 728 " --> pdb=" O PHE A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 743 removed outlier: 3.784A pdb=" N LEU A 740 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN A 742 " --> pdb=" O ALA A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 854 removed outlier: 4.505A pdb=" N ASN A 844 " --> pdb=" O ARG A 840 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 851 " --> pdb=" O ARG A 847 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA A 853 " --> pdb=" O CYS A 849 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 875 removed outlier: 3.701A pdb=" N THR A 863 " --> pdb=" O GLN A 859 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER A 870 " --> pdb=" O LEU A 866 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU A 873 " --> pdb=" O THR A 869 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A 875 " --> pdb=" O VAL A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 882 No H-bonds generated for 'chain 'A' and resid 880 through 882' Processing helix chain 'A' and resid 884 through 909 removed outlier: 3.775A pdb=" N ASN A 888 " --> pdb=" O PRO A 884 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASP A 894 " --> pdb=" O THR A 890 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A 895 " --> pdb=" O LEU A 891 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 896 " --> pdb=" O TYR A 892 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR A 898 " --> pdb=" O ASP A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 917 Processing helix chain 'A' and resid 921 through 941 removed outlier: 3.706A pdb=" N LEU A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 929 " --> pdb=" O LEU A 925 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN A 936 " --> pdb=" O ALA A 932 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A 937 " --> pdb=" O TYR A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 957 removed outlier: 3.796A pdb=" N ARG A 954 " --> pdb=" O ARG A 951 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL A 955 " --> pdb=" O LEU A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 977 removed outlier: 3.564A pdb=" N THR A 974 " --> pdb=" O VAL A 970 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 975 " --> pdb=" O VAL A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 1004 removed outlier: 3.751A pdb=" N PHE A 983 " --> pdb=" O VAL A 979 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN A 984 " --> pdb=" O PRO A 980 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 985 " --> pdb=" O HIS A 981 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE A 996 " --> pdb=" O PHE A 992 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLN A1002 " --> pdb=" O ILE A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1031 Processing helix chain 'A' and resid 1047 through 1056 removed outlier: 3.579A pdb=" N LEU A1052 " --> pdb=" O GLY A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1070 Processing helix chain 'A' and resid 1086 through 1099 removed outlier: 3.559A pdb=" N TYR A1089 " --> pdb=" O ILE A1086 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE A1093 " --> pdb=" O LEU A1090 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE A1094 " --> pdb=" O TYR A1091 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL A1097 " --> pdb=" O PHE A1094 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE A1098 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY A1099 " --> pdb=" O ILE A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1122 removed outlier: 3.502A pdb=" N LEU A1111 " --> pdb=" O PHE A1107 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN A1117 " --> pdb=" O ASP A1113 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG A1120 " --> pdb=" O ARG A1116 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS A1121 " --> pdb=" O GLN A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1140 removed outlier: 3.598A pdb=" N ALA A1139 " --> pdb=" O ILE A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1164 Processing helix chain 'A' and resid 1170 through 1175 Processing helix chain 'A' and resid 1178 through 1185 Processing helix chain 'A' and resid 1198 through 1222 removed outlier: 3.622A pdb=" N ASP A1203 " --> pdb=" O SER A1199 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN A1206 " --> pdb=" O LEU A1202 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A1209 " --> pdb=" O LEU A1205 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE A1210 " --> pdb=" O ASN A1206 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE A1211 " --> pdb=" O LEU A1207 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE A1214 " --> pdb=" O ILE A1210 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL A1221 " --> pdb=" O CYS A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1228 through 1230 No H-bonds generated for 'chain 'A' and resid 1228 through 1230' Processing helix chain 'A' and resid 1232 through 1248 removed outlier: 3.586A pdb=" N ILE A1236 " --> pdb=" O PRO A1232 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP A1237 " --> pdb=" O TRP A1233 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A1241 " --> pdb=" O ASP A1237 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A1248 " --> pdb=" O ALA A1244 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1277 removed outlier: 3.569A pdb=" N LEU A1267 " --> pdb=" O LEU A1263 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A1269 " --> pdb=" O ARG A1265 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG A1271 " --> pdb=" O LEU A1267 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL A1272 " --> pdb=" O ARG A1268 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLY A1273 " --> pdb=" O ILE A1269 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ARG A1274 " --> pdb=" O LEU A1270 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LEU A1275 " --> pdb=" O ARG A1271 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU A1276 " --> pdb=" O VAL A1272 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG A1277 " --> pdb=" O GLY A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1293 removed outlier: 4.284A pdb=" N LEU A1288 " --> pdb=" O GLY A1284 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA A1291 " --> pdb=" O LEU A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1296 through 1320 removed outlier: 3.612A pdb=" N ASN A1301 " --> pdb=" O ARG A1297 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL A1302 " --> pdb=" O THR A1298 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A1303 " --> pdb=" O LEU A1299 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A1308 " --> pdb=" O PHE A1304 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1351 removed outlier: 3.556A pdb=" N LEU A1345 " --> pdb=" O GLN A1341 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN A1348 " --> pdb=" O ILE A1344 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR A1351 " --> pdb=" O PHE A1347 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1362 removed outlier: 3.804A pdb=" N ALA A1361 " --> pdb=" O GLY A1357 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1395 removed outlier: 3.632A pdb=" N SER A1393 " --> pdb=" O ALA A1389 " (cutoff:3.500A) Processing helix chain 'A' and resid 1398 through 1401 No H-bonds generated for 'chain 'A' and resid 1398 through 1401' Processing helix chain 'A' and resid 1403 through 1421 removed outlier: 4.286A pdb=" N ALA A1407 " --> pdb=" O ILE A1403 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA A1408 " --> pdb=" O ASN A1404 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP A1412 " --> pdb=" O ALA A1408 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A1415 " --> pdb=" O LEU A1411 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A1419 " --> pdb=" O LEU A1415 " (cutoff:3.500A) Processing helix chain 'A' and resid 1427 through 1437 removed outlier: 3.523A pdb=" N ASP A1431 " --> pdb=" O ASP A1427 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU A1435 " --> pdb=" O ASP A1431 " (cutoff:3.500A) Processing helix chain 'A' and resid 1450 through 1459 removed outlier: 3.696A pdb=" N LEU A1453 " --> pdb=" O TYR A1450 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER A1454 " --> pdb=" O ASP A1451 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU A1457 " --> pdb=" O SER A1454 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU A1458 " --> pdb=" O GLU A1455 " (cutoff:3.500A) Processing helix chain 'A' and resid 1471 through 1475 removed outlier: 3.599A pdb=" N LEU A1475 " --> pdb=" O LYS A1471 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1471 through 1475' Processing helix chain 'A' and resid 1490 through 1504 removed outlier: 4.091A pdb=" N ALA A1495 " --> pdb=" O ASP A1491 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL A1500 " --> pdb=" O LEU A1496 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A1502 " --> pdb=" O LYS A1498 " (cutoff:3.500A) Processing helix chain 'A' and resid 1510 through 1520 removed outlier: 3.799A pdb=" N GLN A1514 " --> pdb=" O ALA A1510 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA A1515 " --> pdb=" O GLY A1511 " (cutoff:3.500A) Proline residue: A1516 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 1009 through 1012 removed outlier: 3.672A pdb=" N THR A1036 " --> pdb=" O VAL A1012 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1447 through 1449 removed outlier: 3.568A pdb=" N ILE A1487 " --> pdb=" O ILE A1448 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 6 through 8 removed outlier: 3.560A pdb=" N LYS B 28 " --> pdb=" O GLU B 8 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 38 through 42 394 hydrogen bonds defined for protein. 1080 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: 3.46 Time building geometry restraints manager: 4.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1703 1.30 - 1.43: 3332 1.43 - 1.56: 6310 1.56 - 1.69: 5 1.69 - 1.82: 119 Bond restraints: 11469 Sorted by residual: bond pdb=" C12 9SL A1610 " pdb=" N11 9SL A1610 " ideal model delta sigma weight residual 1.284 1.506 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C12 9SL A1610 " pdb=" N13 9SL A1610 " ideal model delta sigma weight residual 1.370 1.490 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" C CYS A 337 " pdb=" N PRO A 338 " ideal model delta sigma weight residual 1.329 1.390 -0.061 1.18e-02 7.18e+03 2.68e+01 bond pdb=" C02 9SL A1610 " pdb=" N21 9SL A1610 " ideal model delta sigma weight residual 1.345 1.445 -0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" C21 PC1 A1609 " pdb=" O21 PC1 A1609 " ideal model delta sigma weight residual 1.331 1.423 -0.092 2.00e-02 2.50e+03 2.14e+01 ... (remaining 11464 not shown) Histogram of bond angle deviations from ideal: 96.27 - 104.58: 165 104.58 - 112.89: 5869 112.89 - 121.20: 6783 121.20 - 129.52: 2674 129.52 - 137.83: 93 Bond angle restraints: 15584 Sorted by residual: angle pdb=" N VAL A1492 " pdb=" CA VAL A1492 " pdb=" C VAL A1492 " ideal model delta sigma weight residual 112.96 107.11 5.85 1.00e+00 1.00e+00 3.42e+01 angle pdb=" C CYS A 337 " pdb=" N PRO A 338 " pdb=" CA PRO A 338 " ideal model delta sigma weight residual 120.38 114.78 5.60 1.03e+00 9.43e-01 2.95e+01 angle pdb=" N LEU A1425 " pdb=" CA LEU A1425 " pdb=" C LEU A1425 " ideal model delta sigma weight residual 110.91 116.47 -5.56 1.17e+00 7.31e-01 2.26e+01 angle pdb=" O12 PC1 A1609 " pdb=" P PC1 A1609 " pdb=" O14 PC1 A1609 " ideal model delta sigma weight residual 123.67 109.46 14.21 3.00e+00 1.11e-01 2.24e+01 angle pdb=" O12 PC1 A1608 " pdb=" P PC1 A1608 " pdb=" O14 PC1 A1608 " ideal model delta sigma weight residual 123.67 109.46 14.21 3.00e+00 1.11e-01 2.24e+01 ... (remaining 15579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.07: 6164 16.07 - 32.14: 357 32.14 - 48.21: 102 48.21 - 64.28: 22 64.28 - 80.35: 15 Dihedral angle restraints: 6660 sinusoidal: 2602 harmonic: 4058 Sorted by residual: dihedral pdb=" CB CYS A 288 " pdb=" SG CYS A 288 " pdb=" SG CYS A 337 " pdb=" CB CYS A 337 " ideal model delta sinusoidal sigma weight residual 93.00 164.37 -71.37 1 1.00e+01 1.00e-02 6.53e+01 dihedral pdb=" CB CYS A 328 " pdb=" SG CYS A 328 " pdb=" SG CYS A 343 " pdb=" CB CYS A 343 " ideal model delta sinusoidal sigma weight residual -86.00 -156.97 70.97 1 1.00e+01 1.00e-02 6.47e+01 dihedral pdb=" CA PHE A 126 " pdb=" C PHE A 126 " pdb=" N THR A 127 " pdb=" CA THR A 127 " ideal model delta harmonic sigma weight residual 180.00 150.34 29.66 0 5.00e+00 4.00e-02 3.52e+01 ... (remaining 6657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.159: 1750 0.159 - 0.318: 27 0.318 - 0.477: 1 0.477 - 0.636: 1 0.636 - 0.795: 1 Chirality restraints: 1780 Sorted by residual: chirality pdb=" C1 NAG A1601 " pdb=" ND2 ASN A 330 " pdb=" C2 NAG A1601 " pdb=" O5 NAG A1601 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-01 2.50e+01 1.58e+01 chirality pdb=" C1 NAG A1605 " pdb=" ND2 ASN A1015 " pdb=" C2 NAG A1605 " pdb=" O5 NAG A1605 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.96e+00 chirality pdb=" C1 NAG A1603 " pdb=" ND2 ASN A1034 " pdb=" C2 NAG A1603 " pdb=" O5 NAG A1603 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.83e+00 ... (remaining 1777 not shown) Planarity restraints: 1920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 308 " 0.079 2.00e-02 2.50e+03 3.18e-01 1.26e+03 pdb=" CG ASN A 308 " -0.097 2.00e-02 2.50e+03 pdb=" OD1 ASN A 308 " 0.201 2.00e-02 2.50e+03 pdb=" ND2 ASN A 308 " -0.556 2.00e-02 2.50e+03 pdb=" C1 NAG A1607 " 0.374 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 330 " -0.174 2.00e-02 2.50e+03 1.93e-01 4.64e+02 pdb=" CG ASN A 330 " 0.078 2.00e-02 2.50e+03 pdb=" OD1 ASN A 330 " 0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN A 330 " 0.304 2.00e-02 2.50e+03 pdb=" C1 NAG A1601 " -0.237 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1605 " 0.207 2.00e-02 2.50e+03 1.76e-01 3.88e+02 pdb=" C7 NAG A1605 " -0.044 2.00e-02 2.50e+03 pdb=" C8 NAG A1605 " -0.039 2.00e-02 2.50e+03 pdb=" N2 NAG A1605 " -0.287 2.00e-02 2.50e+03 pdb=" O7 NAG A1605 " 0.162 2.00e-02 2.50e+03 ... (remaining 1917 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2517 2.77 - 3.30: 9895 3.30 - 3.84: 17336 3.84 - 4.37: 20570 4.37 - 4.90: 35221 Nonbonded interactions: 85539 Sorted by model distance: nonbonded pdb=" O TYR A 341 " pdb=" OG1 THR A 342 " model vdw 2.238 2.440 nonbonded pdb=" NH2 ARG A 370 " pdb=" O TYR A 376 " model vdw 2.332 2.520 nonbonded pdb=" OE2 GLU A 701 " pdb=" C04 9SL A1610 " model vdw 2.332 3.440 nonbonded pdb=" O LEU A1460 " pdb=" NE2 GLN A1465 " model vdw 2.346 2.520 nonbonded pdb=" OD1 ASP A1441 " pdb=" OG1 THR A1445 " model vdw 2.349 2.440 ... (remaining 85534 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 74 5.16 5 C 7384 2.51 5 N 1788 2.21 5 O 1934 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 individual isotropic 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: 1.230 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: 0.010 Extract box with map and model: 7.950 Check model and map are aligned: 0.160 Convert atoms to be neutral: 0.080 Process input model: 32.340 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 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 : 0.009 0.222 11469 Z= 0.563 Angle : 1.138 14.211 15584 Z= 0.590 Chirality : 0.064 0.795 1780 Planarity : 0.008 0.176 1915 Dihedral : 12.439 80.351 4015 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.80 % Favored : 91.62 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -6.38 (0.14), residues: 1372 helix: -4.45 (0.08), residues: 821 sheet: -3.47 (1.12), residues: 20 loop : -3.61 (0.22), residues: 531 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 256 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 2 residues processed: 266 average time/residue: 0.2650 time to fit residues: 97.2872 Evaluate side-chains 158 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 156 time to evaluate : 1.221 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0993 time to fit residues: 2.0548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS A 291 HIS A 532 ASN A1056 GLN A1118 GLN A1169 ASN ** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1194 GLN A1280 GLN A1470 ASN A1478 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 11469 Z= 0.208 Angle : 0.647 7.308 15584 Z= 0.343 Chirality : 0.047 0.600 1780 Planarity : 0.005 0.075 1915 Dihedral : 8.059 66.739 1596 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.07 % Favored : 92.78 % Rotamer Outliers : 3.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -4.72 (0.17), residues: 1372 helix: -2.92 (0.13), residues: 824 sheet: -3.73 (0.95), residues: 20 loop : -3.24 (0.23), residues: 528 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 177 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 20 residues processed: 208 average time/residue: 0.2204 time to fit residues: 67.7393 Evaluate side-chains 162 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 142 time to evaluate : 1.250 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 20 outliers final: 1 residues processed: 20 average time/residue: 0.1010 time to fit residues: 5.4824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN A 540 HIS ** A1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1194 GLN A1465 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 11469 Z= 0.288 Angle : 0.638 7.787 15584 Z= 0.333 Chirality : 0.046 0.527 1780 Planarity : 0.004 0.053 1915 Dihedral : 7.627 67.784 1596 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.38 % Favored : 91.47 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -3.62 (0.20), residues: 1372 helix: -1.93 (0.16), residues: 823 sheet: -3.63 (1.00), residues: 20 loop : -3.00 (0.24), residues: 529 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 147 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 7 residues processed: 162 average time/residue: 0.2081 time to fit residues: 51.0327 Evaluate side-chains 143 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 136 time to evaluate : 1.360 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.1090 time to fit residues: 3.1879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 123 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 13 optimal weight: 0.0470 chunk 59 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 125 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1465 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 11469 Z= 0.171 Angle : 0.552 6.897 15584 Z= 0.288 Chirality : 0.043 0.435 1780 Planarity : 0.003 0.041 1915 Dihedral : 7.257 65.998 1596 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.56 % Favored : 93.29 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -2.84 (0.21), residues: 1372 helix: -1.22 (0.17), residues: 824 sheet: -3.27 (0.80), residues: 29 loop : -2.80 (0.25), residues: 519 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 158 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 173 average time/residue: 0.2122 time to fit residues: 55.3011 Evaluate side-chains 153 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 143 time to evaluate : 1.460 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1410 time to fit residues: 4.1717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 110 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 1 optimal weight: 30.0000 chunk 98 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 113 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 0 optimal weight: 40.0000 chunk 67 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 11469 Z= 0.192 Angle : 0.557 8.482 15584 Z= 0.290 Chirality : 0.043 0.402 1780 Planarity : 0.003 0.062 1915 Dihedral : 7.057 66.651 1596 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.58 % Favored : 92.27 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -2.38 (0.22), residues: 1372 helix: -0.81 (0.18), residues: 829 sheet: -3.04 (0.87), residues: 29 loop : -2.72 (0.26), residues: 514 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 142 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 153 average time/residue: 0.2129 time to fit residues: 49.5676 Evaluate side-chains 144 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 133 time to evaluate : 1.319 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1118 time to fit residues: 4.0838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 44 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 11 optimal weight: 0.0050 chunk 43 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 11469 Z= 0.194 Angle : 0.557 8.865 15584 Z= 0.287 Chirality : 0.043 0.366 1780 Planarity : 0.003 0.038 1915 Dihedral : 6.913 67.302 1596 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.29 % Favored : 92.57 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -1.97 (0.22), residues: 1372 helix: -0.43 (0.18), residues: 825 sheet: -3.01 (0.86), residues: 29 loop : -2.61 (0.26), residues: 518 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 141 time to evaluate : 2.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 154 average time/residue: 0.2079 time to fit residues: 48.3401 Evaluate side-chains 143 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 135 time to evaluate : 1.288 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.1673 time to fit residues: 3.7552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 127 optimal weight: 0.1980 chunk 14 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 11469 Z= 0.175 Angle : 0.541 6.581 15584 Z= 0.280 Chirality : 0.042 0.345 1780 Planarity : 0.003 0.029 1915 Dihedral : 6.715 66.649 1596 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.14 % Favored : 92.71 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -1.71 (0.23), residues: 1372 helix: -0.20 (0.18), residues: 825 sheet: -3.02 (0.86), residues: 29 loop : -2.54 (0.26), residues: 518 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 139 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 146 average time/residue: 0.2211 time to fit residues: 48.3313 Evaluate side-chains 137 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 134 time to evaluate : 1.316 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1167 time to fit residues: 2.4133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 52 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 83 optimal weight: 0.0970 chunk 89 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 11469 Z= 0.159 Angle : 0.529 6.953 15584 Z= 0.273 Chirality : 0.041 0.316 1780 Planarity : 0.003 0.028 1915 Dihedral : 6.528 65.301 1596 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.00 % Favored : 92.86 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -1.44 (0.23), residues: 1372 helix: 0.05 (0.19), residues: 824 sheet: -2.99 (0.86), residues: 29 loop : -2.49 (0.26), residues: 519 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 140 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 147 average time/residue: 0.2355 time to fit residues: 51.3054 Evaluate side-chains 143 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 136 time to evaluate : 1.272 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.1117 time to fit residues: 3.1768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 126 optimal weight: 0.0170 chunk 74 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.8822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.110 11469 Z= 0.207 Angle : 0.564 10.462 15584 Z= 0.294 Chirality : 0.042 0.318 1780 Planarity : 0.004 0.110 1915 Dihedral : 6.498 66.386 1596 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.29 % Favored : 92.57 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -1.37 (0.23), residues: 1372 helix: 0.11 (0.19), residues: 824 sheet: -2.96 (0.84), residues: 29 loop : -2.48 (0.26), residues: 519 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 138 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 143 average time/residue: 0.2297 time to fit residues: 48.3700 Evaluate side-chains 139 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 133 time to evaluate : 1.370 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.1904 time to fit residues: 3.4907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 130 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 11 optimal weight: 0.0770 chunk 83 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 86 optimal weight: 0.3980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.087 11469 Z= 0.156 Angle : 0.537 8.115 15584 Z= 0.279 Chirality : 0.041 0.296 1780 Planarity : 0.003 0.087 1915 Dihedral : 6.527 65.077 1596 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.78 % Favored : 93.08 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -1.17 (0.23), residues: 1372 helix: 0.30 (0.19), residues: 820 sheet: -2.98 (0.84), residues: 29 loop : -2.42 (0.26), residues: 523 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 141 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 143 average time/residue: 0.2419 time to fit residues: 51.3314 Evaluate side-chains 136 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 1.339 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1115 time to fit residues: 1.9913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 100 optimal weight: 0.0670 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 HIS A1021 HIS ** A1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.139546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.104937 restraints weight = 16132.423| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.13 r_work: 0.3160 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 1.90 restraints_weight: 0.2500 r_work: 0.3131 rms_B_bonded: 1.95 restraints_weight: 0.1250 r_work: 0.3114 rms_B_bonded: 2.06 restraints_weight: 0.0625 r_work: 0.3095 rms_B_bonded: 2.23 restraints_weight: 0.0312 r_work: 0.3074 rms_B_bonded: 2.48 restraints_weight: 0.0156 r_work: 0.3049 rms_B_bonded: 2.81 restraints_weight: 0.0078 r_work: 0.3019 rms_B_bonded: 3.25 restraints_weight: 0.0039 r_work: 0.2985 rms_B_bonded: 3.82 restraints_weight: 0.0020 r_work: 0.2945 rms_B_bonded: 4.55 restraints_weight: 0.0010 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.125 11469 Z= 0.184 Angle : 0.543 8.526 15584 Z= 0.284 Chirality : 0.042 0.288 1780 Planarity : 0.004 0.107 1915 Dihedral : 6.477 64.676 1596 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.07 % Favored : 92.78 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -1.10 (0.23), residues: 1372 helix: 0.37 (0.19), residues: 825 sheet: -2.97 (0.84), residues: 29 loop : -2.42 (0.27), residues: 518 =============================================================================== Job complete usr+sys time: 2153.99 seconds wall clock time: 39 minutes 48.09 seconds (2388.09 seconds total)