Starting phenix.real_space_refine on Sat Sep 12 23:33:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7qen_13934/09_2026/7qen_13934.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qen_13934/09_2026/7qen_13934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7qen_13934/09_2026/7qen_13934.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7qen_13934/09_2026/7qen_13934.cif" model { file = "/net/cci-nas-00/data/ceres_data/7qen_13934/09_2026/7qen_13934.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qen_13934/09_2026/7qen_13934.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qen_13934/09_2026/7qen_13934.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qen_13934/09_2026/7qen_13934.map" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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 76 5.49 5 Mg 2 5.21 5 S 91 5.16 5 C 11965 2.51 5 N 3245 2.21 5 O 3826 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 147 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19205 Number of models: 1 Model: "" Number of chains: 8 Chain: "F" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 735 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "G" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 700 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "B" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3318 Classifications: {'peptide': 419} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 11, 'TRANS': 407} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 3709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3709 Classifications: {'peptide': 465} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 452} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2345 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 1, 'TRANS': 289} Chain breaks: 5 Chain: "D" Number of atoms: 8334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1050, 8334 Classifications: {'peptide': 1050} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 1021} Chain breaks: 5 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.70, per 1000 atoms: 0.19 Number of scatterers: 19205 At special positions: 0 Unit cell: (135.2, 147.68, 166.4, 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 91 16.00 P 76 15.00 Mg 2 11.99 O 3826 8.00 N 3245 7.00 C 11965 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 734.7 milliseconds 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4264 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 8 sheets defined 65.2% alpha, 7.9% beta 35 base pairs and 68 stacking pairs defined. Time for finding SS restraints: 2.23 Creating SS restraints... Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.561A pdb=" N UNK B 138 " --> pdb=" O UNK B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 202 removed outlier: 3.850A pdb=" N VAL B 194 " --> pdb=" O GLY B 190 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 210 removed outlier: 3.746A pdb=" N ARG B 210 " --> pdb=" O ASN B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 217 Processing helix chain 'B' and resid 278 through 289 Processing helix chain 'B' and resid 322 through 331 removed outlier: 3.521A pdb=" N TYR B 326 " --> pdb=" O GLY B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 366 Processing helix chain 'B' and resid 1233 through 1286 removed outlier: 3.716A pdb=" N ARG B1237 " --> pdb=" O ALA B1233 " (cutoff:3.500A) Processing helix chain 'B' and resid 1300 through 1305 removed outlier: 4.657A pdb=" N GLU B1304 " --> pdb=" O ASP B1300 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY B1305 " --> pdb=" O PRO B1301 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1300 through 1305' Processing helix chain 'B' and resid 1321 through 1323 No H-bonds generated for 'chain 'B' and resid 1321 through 1323' Processing helix chain 'B' and resid 1324 through 1343 Processing helix chain 'B' and resid 1358 through 1371 Processing helix chain 'B' and resid 1384 through 1390 removed outlier: 3.925A pdb=" N PHE B1388 " --> pdb=" O ARG B1384 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU B1390 " --> pdb=" O ASN B1386 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 50 Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 123 through 132 removed outlier: 3.696A pdb=" N VAL A 127 " --> pdb=" O PRO A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 170 removed outlier: 3.618A pdb=" N ILE A 165 " --> pdb=" O ILE A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 203 removed outlier: 3.750A pdb=" N ARG A 177 " --> pdb=" O MET A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 240 removed outlier: 4.603A pdb=" N ARG A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 952 Processing helix chain 'A' and resid 960 through 982 removed outlier: 3.796A pdb=" N LYS A 974 " --> pdb=" O GLN A 970 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS A 980 " --> pdb=" O GLN A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1048 removed outlier: 3.632A pdb=" N MET A 989 " --> pdb=" O ASN A 985 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU A1023 " --> pdb=" O SER A1019 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N TYR A1024 " --> pdb=" O LYS A1020 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS A1035 " --> pdb=" O LYS A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1065 Processing helix chain 'A' and resid 1080 through 1084 removed outlier: 3.902A pdb=" N GLU A1083 " --> pdb=" O SER A1080 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU A1084 " --> pdb=" O LEU A1081 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1080 through 1084' Processing helix chain 'A' and resid 1085 through 1104 Processing helix chain 'A' and resid 1119 through 1132 removed outlier: 3.864A pdb=" N GLN A1124 " --> pdb=" O LEU A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1150 removed outlier: 3.823A pdb=" N PHE A1149 " --> pdb=" O LYS A1145 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 40 removed outlier: 3.633A pdb=" N ASP C 40 " --> pdb=" O LYS C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 58 Processing helix chain 'C' and resid 71 through 106 Processing helix chain 'C' and resid 185 through 197 removed outlier: 3.884A pdb=" N GLU C 197 " --> pdb=" O VAL C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 287 removed outlier: 3.638A pdb=" N LEU C 283 " --> pdb=" O GLU C 279 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.711A pdb=" N ALA C 294 " --> pdb=" O PHE C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 311 Processing helix chain 'C' and resid 314 through 318 removed outlier: 4.003A pdb=" N ASP C 317 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 672 Processing helix chain 'C' and resid 692 through 700 Processing helix chain 'C' and resid 712 through 727 Processing helix chain 'D' and resid 6 through 15 Processing helix chain 'D' and resid 26 through 39 removed outlier: 4.113A pdb=" N GLU D 30 " --> pdb=" O ASP D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 61 removed outlier: 3.701A pdb=" N HIS D 60 " --> pdb=" O ILE D 56 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP D 61 " --> pdb=" O ASP D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.871A pdb=" N LEU D 65 " --> pdb=" O PHE D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 66 through 94 removed outlier: 3.734A pdb=" N SER D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 136 removed outlier: 4.107A pdb=" N ILE D 101 " --> pdb=" O ASN D 97 " (cutoff:3.500A) Proline residue: D 106 - end of helix removed outlier: 4.038A pdb=" N GLN D 136 " --> pdb=" O LYS D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 175 removed outlier: 3.911A pdb=" N ALA D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 183 removed outlier: 3.641A pdb=" N ILE D 182 " --> pdb=" O ASN D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 204 Proline residue: D 199 - end of helix Processing helix chain 'D' and resid 213 through 229 removed outlier: 3.563A pdb=" N ASN D 229 " --> pdb=" O MET D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 247 removed outlier: 3.560A pdb=" N ILE D 236 " --> pdb=" O GLN D 232 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 264 Processing helix chain 'D' and resid 268 through 280 removed outlier: 3.537A pdb=" N GLU D 272 " --> pdb=" O PRO D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 305 Processing helix chain 'D' and resid 305 through 310 Processing helix chain 'D' and resid 312 through 317 Processing helix chain 'D' and resid 318 through 322 removed outlier: 3.634A pdb=" N ASN D 321 " --> pdb=" O THR D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 342 removed outlier: 3.710A pdb=" N ARG D 328 " --> pdb=" O SER D 324 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU D 342 " --> pdb=" O ILE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 348 removed outlier: 4.281A pdb=" N GLN D 347 " --> pdb=" O GLN D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 366 removed outlier: 3.511A pdb=" N ALA D 357 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU D 359 " --> pdb=" O GLN D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 369 No H-bonds generated for 'chain 'D' and resid 367 through 369' Processing helix chain 'D' and resid 371 through 386 removed outlier: 3.863A pdb=" N ARG D 375 " --> pdb=" O ASN D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 406 removed outlier: 4.010A pdb=" N LYS D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 409 No H-bonds generated for 'chain 'D' and resid 407 through 409' Processing helix chain 'D' and resid 411 through 428 removed outlier: 3.645A pdb=" N ARG D 415 " --> pdb=" O SER D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 450 Processing helix chain 'D' and resid 450 through 455 Processing helix chain 'D' and resid 523 through 551 removed outlier: 3.980A pdb=" N ILE D 527 " --> pdb=" O LEU D 523 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN D 549 " --> pdb=" O GLU D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 572 removed outlier: 3.563A pdb=" N VAL D 559 " --> pdb=" O ASN D 555 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 586 removed outlier: 3.968A pdb=" N HIS D 586 " --> pdb=" O LYS D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 589 No H-bonds generated for 'chain 'D' and resid 587 through 589' Processing helix chain 'D' and resid 599 through 613 removed outlier: 3.581A pdb=" N GLU D 606 " --> pdb=" O VAL D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 635 Processing helix chain 'D' and resid 640 through 657 removed outlier: 4.005A pdb=" N GLN D 649 " --> pdb=" O ALA D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 661 through 678 removed outlier: 3.692A pdb=" N ILE D 665 " --> pdb=" O ASP D 661 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA D 675 " --> pdb=" O ILE D 671 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER D 676 " --> pdb=" O TYR D 672 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA D 678 " --> pdb=" O SER D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 696 through 711 removed outlier: 3.531A pdb=" N ILE D 700 " --> pdb=" O SER D 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 715 through 720 removed outlier: 3.684A pdb=" N LEU D 719 " --> pdb=" O ASN D 715 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 729 removed outlier: 3.799A pdb=" N ASN D 727 " --> pdb=" O GLU D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 750 removed outlier: 3.732A pdb=" N ARG D 750 " --> pdb=" O LEU D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 764 through 780 removed outlier: 3.924A pdb=" N GLU D 768 " --> pdb=" O ASN D 764 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL D 770 " --> pdb=" O GLU D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 803 removed outlier: 3.600A pdb=" N MET D 791 " --> pdb=" O GLU D 787 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU D 793 " --> pdb=" O TYR D 789 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER D 797 " --> pdb=" O GLU D 793 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR D 801 " --> pdb=" O SER D 797 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER D 803 " --> pdb=" O LEU D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 805 through 823 removed outlier: 3.619A pdb=" N LEU D 809 " --> pdb=" O LYS D 805 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE D 822 " --> pdb=" O THR D 818 " (cutoff:3.500A) Processing helix chain 'D' and resid 838 through 880 removed outlier: 3.601A pdb=" N SER D 842 " --> pdb=" O SER D 838 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR D 877 " --> pdb=" O ILE D 873 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG D 878 " --> pdb=" O GLU D 874 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY D 880 " --> pdb=" O GLU D 876 " (cutoff:3.500A) Processing helix chain 'D' and resid 909 through 923 Processing helix chain 'D' and resid 932 through 944 removed outlier: 4.006A pdb=" N PHE D 936 " --> pdb=" O ILE D 932 " (cutoff:3.500A) Proline residue: D 938 - end of helix removed outlier: 3.714A pdb=" N GLU D 941 " --> pdb=" O CYS D 937 " (cutoff:3.500A) Processing helix chain 'D' and resid 952 through 968 removed outlier: 3.704A pdb=" N CYS D 968 " --> pdb=" O GLU D 964 " (cutoff:3.500A) Processing helix chain 'D' and resid 970 through 988 removed outlier: 3.865A pdb=" N LYS D 976 " --> pdb=" O LYS D 972 " (cutoff:3.500A) Proline residue: D 979 - end of helix Processing helix chain 'D' and resid 990 through 996 Processing helix chain 'D' and resid 997 through 1008 removed outlier: 3.729A pdb=" N VAL D1006 " --> pdb=" O GLY D1002 " (cutoff:3.500A) Processing helix chain 'D' and resid 1014 through 1016 No H-bonds generated for 'chain 'D' and resid 1014 through 1016' Processing helix chain 'D' and resid 1017 through 1022 Processing helix chain 'D' and resid 1027 through 1042 Processing helix chain 'D' and resid 1052 through 1058 Processing helix chain 'D' and resid 1059 through 1062 removed outlier: 3.570A pdb=" N ASN D1062 " --> pdb=" O CYS D1059 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1059 through 1062' Processing helix chain 'D' and resid 1064 through 1079 Processing helix chain 'D' and resid 1083 through 1097 removed outlier: 4.942A pdb=" N ILE D1090 " --> pdb=" O TYR D1086 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ASP D1091 " --> pdb=" O ASN D1087 " (cutoff:3.500A) Processing helix chain 'D' and resid 1103 through 1115 removed outlier: 4.118A pdb=" N LYS D1109 " --> pdb=" O GLU D1105 " (cutoff:3.500A) Processing helix chain 'D' and resid 1120 through 1136 removed outlier: 3.614A pdb=" N GLN D1124 " --> pdb=" O LYS D1120 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1153 removed outlier: 3.741A pdb=" N TRP D1144 " --> pdb=" O THR D1140 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN D1153 " --> pdb=" O PHE D1149 " (cutoff:3.500A) Processing helix chain 'D' and resid 1158 through 1167 Processing sheet with id=AA1, first strand: chain 'B' and resid 170 through 172 removed outlier: 5.668A pdb=" N LEU B 154 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL B 239 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ILE B 156 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLN B 237 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU B 158 " --> pdb=" O HIS B 235 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 170 through 172 removed outlier: 5.668A pdb=" N LEU B 154 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL B 239 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ILE B 156 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLN B 237 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU B 158 " --> pdb=" O HIS B 235 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N TYR B 270 " --> pdb=" O SER B 277 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 299 through 300 removed outlier: 6.721A pdb=" N ILE B 300 " --> pdb=" O ASP B1351 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N PHE B 180 " --> pdb=" O GLN B1393 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N VAL B1395 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA B 182 " --> pdb=" O VAL B1395 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL B1397 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL B 184 " --> pdb=" O VAL B1397 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N LYS B1399 " --> pdb=" O VAL B 184 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 1290 through 1295 Processing sheet with id=AA5, first strand: chain 'A' and resid 17 through 20 removed outlier: 6.024A pdb=" N VAL A 3 " --> pdb=" O ASP A 84 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ASP A 84 " --> pdb=" O VAL A 3 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 5 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR A 115 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 144 through 145 removed outlier: 6.626A pdb=" N ILE A 145 " --> pdb=" O ASP A1112 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TYR A1109 " --> pdb=" O ILE A1140 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N VAL A1142 " --> pdb=" O TYR A1109 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU A1111 " --> pdb=" O VAL A1142 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL A1155 " --> pdb=" O MET A1170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1051 through 1057 Processing sheet with id=AA8, first strand: chain 'C' and resid 689 through 691 1066 hydrogen bonds defined for protein. 3135 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 68 stacking parallelities Total time for adding SS restraints: 4.21 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5472 1.34 - 1.46: 3450 1.46 - 1.57: 10420 1.57 - 1.69: 132 1.69 - 1.81: 152 Bond restraints: 19626 Sorted by residual: bond pdb=" C4 ATP B2000 " pdb=" C5 ATP B2000 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.02e+01 bond pdb=" C4 ATP A2000 " pdb=" C5 ATP A2000 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.68e+01 bond pdb=" C5 ATP B2000 " pdb=" C6 ATP B2000 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.31e+01 bond pdb=" C5 ATP A2000 " pdb=" C6 ATP A2000 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 4.03e+01 bond pdb=" C5 ATP A2000 " pdb=" N7 ATP A2000 " ideal model delta sigma weight residual 1.387 1.340 0.047 1.00e-02 1.00e+04 2.19e+01 ... (remaining 19621 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.79: 26490 3.79 - 7.58: 225 7.58 - 11.36: 20 11.36 - 15.15: 1 15.15 - 18.94: 4 Bond angle restraints: 26740 Sorted by residual: angle pdb=" PB ATP B2000 " pdb=" O3B ATP B2000 " pdb=" PG ATP B2000 " ideal model delta sigma weight residual 139.87 120.93 18.94 1.00e+00 1.00e+00 3.59e+02 angle pdb=" PB ATP A2000 " pdb=" O3B ATP A2000 " pdb=" PG ATP A2000 " ideal model delta sigma weight residual 139.87 122.06 17.81 1.00e+00 1.00e+00 3.17e+02 angle pdb=" PA ATP B2000 " pdb=" O3A ATP B2000 " pdb=" PB ATP B2000 " ideal model delta sigma weight residual 136.83 120.98 15.85 1.00e+00 1.00e+00 2.51e+02 angle pdb=" PA ATP A2000 " pdb=" O3A ATP A2000 " pdb=" PB ATP A2000 " ideal model delta sigma weight residual 136.83 121.64 15.19 1.00e+00 1.00e+00 2.31e+02 angle pdb=" C5 ATP B2000 " pdb=" C4 ATP B2000 " pdb=" N3 ATP B2000 " ideal model delta sigma weight residual 126.80 118.82 7.98 1.00e+00 1.00e+00 6.37e+01 ... (remaining 26735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 10013 17.99 - 35.98: 1317 35.98 - 53.98: 419 53.98 - 71.97: 177 71.97 - 89.96: 19 Dihedral angle restraints: 11945 sinusoidal: 5418 harmonic: 6527 Sorted by residual: dihedral pdb=" CA ASP D 345 " pdb=" C ASP D 345 " pdb=" N PRO D 346 " pdb=" CA PRO D 346 " ideal model delta harmonic sigma weight residual 180.00 -150.12 -29.88 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA GLN D 344 " pdb=" C GLN D 344 " pdb=" N ASP D 345 " pdb=" CA ASP D 345 " ideal model delta harmonic sigma weight residual 180.00 -152.56 -27.44 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA VAL B 173 " pdb=" C VAL B 173 " pdb=" N GLY B 174 " pdb=" CA GLY B 174 " ideal model delta harmonic sigma weight residual 180.00 155.34 24.66 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 11942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2645 0.072 - 0.143: 413 0.143 - 0.215: 35 0.215 - 0.286: 7 0.286 - 0.358: 1 Chirality restraints: 3101 Sorted by residual: chirality pdb=" CB VAL D1049 " pdb=" CA VAL D1049 " pdb=" CG1 VAL D1049 " pdb=" CG2 VAL D1049 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" CA THR D 186 " pdb=" N THR D 186 " pdb=" C THR D 186 " pdb=" CB THR D 186 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA ASN D 266 " pdb=" N ASN D 266 " pdb=" C ASN D 266 " pdb=" CB ASN D 266 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 3098 not shown) Planarity restraints: 3141 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 290 " -0.062 5.00e-02 4.00e+02 9.31e-02 1.39e+01 pdb=" N PRO D 291 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO D 291 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO D 291 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 66 " -0.046 5.00e-02 4.00e+02 6.94e-02 7.70e+00 pdb=" N PRO D 67 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO D 67 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 67 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 186 " 0.044 5.00e-02 4.00e+02 6.53e-02 6.82e+00 pdb=" N PRO D 187 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 187 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 187 " 0.037 5.00e-02 4.00e+02 ... (remaining 3138 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 196 2.63 - 3.20: 16211 3.20 - 3.77: 31055 3.77 - 4.33: 41733 4.33 - 4.90: 65904 Nonbonded interactions: 155099 Sorted by model distance: nonbonded pdb=" OE1 GLN A 147 " pdb="MG MG A2001 " model vdw 2.068 2.170 nonbonded pdb=" O2B ATP A2000 " pdb="MG MG A2001 " model vdw 2.080 2.170 nonbonded pdb=" OE1 GLN B 302 " pdb="MG MG B2001 " model vdw 2.085 2.170 nonbonded pdb=" O2B ATP B2000 " pdb="MG MG B2001 " model vdw 2.089 2.170 nonbonded pdb=" OG SER B 192 " pdb="MG MG B2001 " model vdw 2.139 2.170 ... (remaining 155094 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 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: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.570 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 19626 Z= 0.386 Angle : 0.981 18.938 26740 Z= 0.664 Chirality : 0.053 0.358 3101 Planarity : 0.007 0.093 3141 Dihedral : 18.872 89.959 7681 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.20 % Allowed : 6.39 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.65 (0.14), residues: 2177 helix: -2.38 (0.10), residues: 1295 sheet: -0.38 (0.40), residues: 166 loop : -2.66 (0.19), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 965 TYR 0.024 0.002 TYR D 529 PHE 0.032 0.002 PHE A 27 TRP 0.017 0.002 TRP D 669 HIS 0.009 0.001 HIS D 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.39 (19626) covalent geometry : angle 0.98061 / 0.66 (26740) hydrogen bonds : bond 0.13518 / 14.81 ( 1129) hydrogen bonds : angle 6.19740 / 7.20 ( 3275) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 590 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 252 GLU cc_start: 0.7172 (pm20) cc_final: 0.6939 (pm20) REVERT: B 263 PHE cc_start: 0.8544 (m-80) cc_final: 0.8105 (m-80) REVERT: B 264 LYS cc_start: 0.8761 (mmtt) cc_final: 0.8289 (tppt) REVERT: B 269 LYS cc_start: 0.8015 (mtpt) cc_final: 0.7710 (mtpt) REVERT: B 288 ASN cc_start: 0.8162 (t0) cc_final: 0.7746 (t0) REVERT: B 289 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7830 (mm-30) REVERT: B 307 ASN cc_start: 0.8136 (m-40) cc_final: 0.7934 (m110) REVERT: B 312 LYS cc_start: 0.8404 (mptt) cc_final: 0.8082 (mptt) REVERT: B 325 GLU cc_start: 0.7679 (mp0) cc_final: 0.7327 (mp0) REVERT: B 336 TYR cc_start: 0.8548 (m-80) cc_final: 0.8312 (m-10) REVERT: B 1260 LYS cc_start: 0.7892 (mttt) cc_final: 0.7572 (mtpp) REVERT: B 1265 ASP cc_start: 0.7792 (t0) cc_final: 0.7588 (t0) REVERT: B 1267 PHE cc_start: 0.8130 (t80) cc_final: 0.7919 (t80) REVERT: B 1271 PHE cc_start: 0.8171 (t80) cc_final: 0.7927 (t80) REVERT: B 1343 LYS cc_start: 0.8084 (tttt) cc_final: 0.7829 (ttmt) REVERT: B 1405 LYS cc_start: 0.8633 (mttt) cc_final: 0.8267 (mttm) REVERT: B 1412 ILE cc_start: 0.8289 (pt) cc_final: 0.8059 (pt) REVERT: A 19 VAL cc_start: 0.8581 (t) cc_final: 0.8274 (p) REVERT: A 28 ASN cc_start: 0.7403 (m-40) cc_final: 0.7181 (m-40) REVERT: A 54 MET cc_start: 0.7482 (mmt) cc_final: 0.7125 (mmt) REVERT: A 81 ILE cc_start: 0.7845 (tt) cc_final: 0.7592 (tt) REVERT: A 109 LEU cc_start: 0.8640 (mt) cc_final: 0.8406 (mp) REVERT: A 129 GLN cc_start: 0.7396 (tm-30) cc_final: 0.6866 (tm-30) REVERT: A 135 GLN cc_start: 0.8065 (pt0) cc_final: 0.7784 (pt0) REVERT: A 157 LYS cc_start: 0.7749 (mptt) cc_final: 0.7495 (mptt) REVERT: A 160 GLU cc_start: 0.6971 (mp0) cc_final: 0.6546 (mp0) REVERT: A 178 ARG cc_start: 0.7242 (tmm160) cc_final: 0.6734 (ttp-110) REVERT: A 187 LYS cc_start: 0.8521 (tppt) cc_final: 0.8203 (tppt) REVERT: A 188 LYS cc_start: 0.8565 (mmtt) cc_final: 0.8328 (mmtm) REVERT: A 189 GLU cc_start: 0.7881 (tp30) cc_final: 0.7666 (tp30) REVERT: A 198 LEU cc_start: 0.8304 (tt) cc_final: 0.8056 (tp) REVERT: A 217 PHE cc_start: 0.7205 (t80) cc_final: 0.6759 (t80) REVERT: A 985 ASN cc_start: 0.7891 (p0) cc_final: 0.7442 (p0) REVERT: A 994 GLU cc_start: 0.7450 (mm-30) cc_final: 0.6993 (mm-30) REVERT: A 997 GLU cc_start: 0.6888 (tp30) cc_final: 0.6601 (tp30) REVERT: A 1005 LYS cc_start: 0.8047 (mttt) cc_final: 0.7662 (mttp) REVERT: A 1009 LYS cc_start: 0.7790 (tttt) cc_final: 0.7396 (ttmm) REVERT: A 1016 GLU cc_start: 0.7310 (tt0) cc_final: 0.6934 (tt0) REVERT: A 1018 ILE cc_start: 0.8128 (pt) cc_final: 0.7841 (mt) REVERT: A 1023 GLU cc_start: 0.6961 (tp30) cc_final: 0.6639 (tp30) REVERT: A 1029 LEU cc_start: 0.7455 (tp) cc_final: 0.7015 (mm) REVERT: A 1082 ILE cc_start: 0.8646 (tp) cc_final: 0.8008 (pt) REVERT: A 1146 GLU cc_start: 0.7326 (tt0) cc_final: 0.6903 (tt0) REVERT: C 32 GLU cc_start: 0.7973 (tp30) cc_final: 0.7703 (mm-30) REVERT: C 42 LYS cc_start: 0.7501 (mmmt) cc_final: 0.7184 (mmmt) REVERT: C 64 LYS cc_start: 0.8324 (mtmt) cc_final: 0.7827 (mmmm) REVERT: C 84 LYS cc_start: 0.7987 (mmtp) cc_final: 0.7698 (mmtp) REVERT: C 99 LYS cc_start: 0.8109 (mtpt) cc_final: 0.7888 (mtmt) REVERT: C 189 LYS cc_start: 0.8088 (mmtt) cc_final: 0.7713 (mmmm) REVERT: C 196 ASP cc_start: 0.7537 (t0) cc_final: 0.7143 (t0) REVERT: C 197 GLU cc_start: 0.7412 (pp20) cc_final: 0.6948 (pp20) REVERT: C 211 ASP cc_start: 0.7507 (OUTLIER) cc_final: 0.7232 (m-30) REVERT: C 277 GLU cc_start: 0.7204 (mp0) cc_final: 0.6714 (mp0) REVERT: C 279 GLU cc_start: 0.6804 (tp30) cc_final: 0.6540 (tp30) REVERT: C 288 ILE cc_start: 0.8248 (pt) cc_final: 0.8022 (pt) REVERT: C 297 GLU cc_start: 0.6896 (pm20) cc_final: 0.6459 (pm20) REVERT: C 643 LYS cc_start: 0.7438 (mtmm) cc_final: 0.7121 (mtmm) REVERT: C 653 ASN cc_start: 0.7850 (m-40) cc_final: 0.7618 (m110) REVERT: C 659 ASN cc_start: 0.8098 (m-40) cc_final: 0.7882 (m110) REVERT: C 691 LYS cc_start: 0.8031 (mtpp) cc_final: 0.7777 (mtpp) REVERT: C 705 ASP cc_start: 0.7724 (t0) cc_final: 0.7421 (t0) REVERT: C 709 LYS cc_start: 0.8144 (ttpt) cc_final: 0.7832 (ttpt) REVERT: C 718 ILE cc_start: 0.6892 (pt) cc_final: 0.6686 (mt) REVERT: C 743 ASN cc_start: 0.7829 (t0) cc_final: 0.6466 (t0) REVERT: D 6 LEU cc_start: 0.7779 (tp) cc_final: 0.7533 (tt) REVERT: D 62 PHE cc_start: 0.7767 (t80) cc_final: 0.7559 (t80) REVERT: D 78 SER cc_start: 0.7302 (t) cc_final: 0.6966 (t) REVERT: D 89 LYS cc_start: 0.8300 (tptm) cc_final: 0.7856 (tptm) REVERT: D 105 ILE cc_start: 0.8160 (tt) cc_final: 0.7772 (pt) REVERT: D 165 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7478 (tm-30) REVERT: D 167 LEU cc_start: 0.7981 (mt) cc_final: 0.7768 (mt) REVERT: D 169 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6632 (mm-30) REVERT: D 173 LYS cc_start: 0.7910 (tppt) cc_final: 0.7669 (tppt) REVERT: D 202 VAL cc_start: 0.8549 (p) cc_final: 0.8307 (m) REVERT: D 205 GLU cc_start: 0.7006 (tm-30) cc_final: 0.6781 (tm-30) REVERT: D 213 SER cc_start: 0.8616 (t) cc_final: 0.7794 (t) REVERT: D 217 MET cc_start: 0.6884 (mpp) cc_final: 0.6484 (mpp) REVERT: D 260 LEU cc_start: 0.8797 (tp) cc_final: 0.8465 (tt) REVERT: D 269 GLN cc_start: 0.7900 (tp-100) cc_final: 0.7562 (tp-100) REVERT: D 277 GLU cc_start: 0.7367 (tt0) cc_final: 0.7035 (pt0) REVERT: D 287 ASP cc_start: 0.7632 (t70) cc_final: 0.7431 (t0) REVERT: D 303 GLU cc_start: 0.7548 (tm-30) cc_final: 0.7347 (tm-30) REVERT: D 322 ASN cc_start: 0.8178 (t0) cc_final: 0.7928 (t0) REVERT: D 341 GLU cc_start: 0.7381 (tp30) cc_final: 0.6941 (tp30) REVERT: D 364 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6824 (mt-10) REVERT: D 365 GLU cc_start: 0.6643 (mt-10) cc_final: 0.6420 (mt-10) REVERT: D 385 ILE cc_start: 0.8850 (mt) cc_final: 0.8609 (mt) REVERT: D 542 LYS cc_start: 0.7797 (tttt) cc_final: 0.7516 (ttpp) REVERT: D 554 LYS cc_start: 0.8348 (mttt) cc_final: 0.8027 (mtpp) REVERT: D 606 GLU cc_start: 0.7607 (tp30) cc_final: 0.7267 (tp30) REVERT: D 698 GLU cc_start: 0.6589 (mp0) cc_final: 0.6263 (mp0) REVERT: D 722 LEU cc_start: 0.8664 (tp) cc_final: 0.8285 (tt) REVERT: D 749 GLU cc_start: 0.7497 (tm-30) cc_final: 0.7197 (tm-30) REVERT: D 773 LYS cc_start: 0.8054 (tptt) cc_final: 0.7803 (tptt) REVERT: D 815 ARG cc_start: 0.7859 (ttm170) cc_final: 0.7305 (mtm-85) REVERT: D 819 MET cc_start: 0.7145 (mmt) cc_final: 0.6925 (mmt) REVERT: D 921 LYS cc_start: 0.8205 (mtpt) cc_final: 0.7995 (mtmt) REVERT: D 952 ASP cc_start: 0.7468 (t0) cc_final: 0.7243 (t0) REVERT: D 970 SER cc_start: 0.8222 (t) cc_final: 0.7666 (p) REVERT: D 990 ASP cc_start: 0.7624 (t0) cc_final: 0.7416 (t0) REVERT: D 993 ILE cc_start: 0.8244 (mt) cc_final: 0.8025 (mt) REVERT: D 1017 ASP cc_start: 0.7789 (t70) cc_final: 0.7392 (t0) REVERT: D 1027 ASN cc_start: 0.7649 (t0) cc_final: 0.7263 (t0) REVERT: D 1048 LYS cc_start: 0.7871 (mtpt) cc_final: 0.6040 (mtpt) REVERT: D 1055 GLU cc_start: 0.7116 (tp30) cc_final: 0.6750 (tp30) REVERT: D 1058 LYS cc_start: 0.8392 (mttt) cc_final: 0.8179 (mttp) REVERT: D 1105 GLU cc_start: 0.7704 (pm20) cc_final: 0.7415 (pm20) REVERT: D 1109 LYS cc_start: 0.8210 (tptm) cc_final: 0.7934 (tppp) REVERT: D 1139 GLU cc_start: 0.7021 (tm-30) cc_final: 0.6523 (tm-30) outliers start: 4 outliers final: 2 residues processed: 591 average time/residue: 0.1469 time to fit residues: 128.8909 Evaluate side-chains 529 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 526 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain C residue 211 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 0.0000 chunk 212 optimal weight: 0.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 150 GLN ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 ASN B 235 HIS B 237 GLN B 359 ASN B1243 ASN B1283 GLN B1361 ASN A 34 ASN A 135 GLN A 212 ASN C 68 ASN C 71 ASN C 313 ASN C 725 ASN C 738 ASN D 70 GLN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 GLN D 351 HIS ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 GLN D 657 GLN ** D1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1123 HIS D1158 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.148022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.122358 restraints weight = 29090.699| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.02 r_work: 0.3382 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19626 Z= 0.168 Angle : 0.656 8.098 26740 Z= 0.350 Chirality : 0.045 0.193 3101 Planarity : 0.005 0.079 3141 Dihedral : 18.106 65.569 3199 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.40 % Allowed : 14.09 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.16), residues: 2177 helix: -0.39 (0.13), residues: 1298 sheet: 0.26 (0.42), residues: 161 loop : -2.27 (0.20), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 198 TYR 0.024 0.002 TYR D 776 PHE 0.024 0.002 PHE B1264 TRP 0.014 0.002 TRP A1033 HIS 0.005 0.001 HIS D1123 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 (19626) covalent geometry : angle 0.65647 / 0.35 (26740) hydrogen bonds : bond 0.04773 / 5.32 ( 1129) hydrogen bonds : angle 4.49866 / 5.11 ( 3275) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 541 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 VAL cc_start: 0.8265 (m) cc_final: 0.7764 (t) REVERT: B 252 GLU cc_start: 0.7518 (pm20) cc_final: 0.7190 (pm20) REVERT: B 263 PHE cc_start: 0.8734 (m-80) cc_final: 0.8226 (m-80) REVERT: B 264 LYS cc_start: 0.8718 (mmtt) cc_final: 0.8431 (tppt) REVERT: B 269 LYS cc_start: 0.8250 (mtpt) cc_final: 0.7866 (mtpt) REVERT: B 288 ASN cc_start: 0.8509 (t0) cc_final: 0.8086 (t0) REVERT: B 289 GLU cc_start: 0.8433 (mm-30) cc_final: 0.7893 (mm-30) REVERT: B 312 LYS cc_start: 0.8680 (mptt) cc_final: 0.8412 (mptt) REVERT: B 325 GLU cc_start: 0.8133 (mp0) cc_final: 0.7805 (mp0) REVERT: B 1249 ARG cc_start: 0.7180 (tmm-80) cc_final: 0.6978 (tmm-80) REVERT: B 1260 LYS cc_start: 0.7984 (mttt) cc_final: 0.7720 (mtpp) REVERT: B 1271 PHE cc_start: 0.8381 (t80) cc_final: 0.8159 (t80) REVERT: B 1282 TYR cc_start: 0.8362 (t80) cc_final: 0.8035 (t80) REVERT: B 1292 GLU cc_start: 0.7791 (tp30) cc_final: 0.7536 (tp30) REVERT: B 1294 GLU cc_start: 0.6389 (pm20) cc_final: 0.5738 (pm20) REVERT: B 1373 THR cc_start: 0.8577 (m) cc_final: 0.8367 (t) REVERT: B 1405 LYS cc_start: 0.8854 (mttt) cc_final: 0.8522 (mttp) REVERT: B 1412 ILE cc_start: 0.8503 (pt) cc_final: 0.8215 (pt) REVERT: A 28 ASN cc_start: 0.7864 (m-40) cc_final: 0.7657 (m-40) REVERT: A 54 MET cc_start: 0.7828 (mmt) cc_final: 0.7465 (mmt) REVERT: A 81 ILE cc_start: 0.8060 (tt) cc_final: 0.7787 (tt) REVERT: A 109 LEU cc_start: 0.8780 (mt) cc_final: 0.8574 (mp) REVERT: A 129 GLN cc_start: 0.7963 (tm-30) cc_final: 0.7374 (tm-30) REVERT: A 156 MET cc_start: 0.7845 (mtm) cc_final: 0.7638 (mtp) REVERT: A 160 GLU cc_start: 0.7647 (mp0) cc_final: 0.7309 (mp0) REVERT: A 178 ARG cc_start: 0.7893 (tmm160) cc_final: 0.7429 (ttp-110) REVERT: A 187 LYS cc_start: 0.8847 (tppt) cc_final: 0.8514 (tppt) REVERT: A 200 THR cc_start: 0.8002 (t) cc_final: 0.7789 (m) REVERT: A 209 LYS cc_start: 0.7634 (mmtm) cc_final: 0.7294 (mmtm) REVERT: A 217 PHE cc_start: 0.7479 (t80) cc_final: 0.7206 (t80) REVERT: A 985 ASN cc_start: 0.8057 (p0) cc_final: 0.7631 (p0) REVERT: A 994 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7863 (mm-30) REVERT: A 1005 LYS cc_start: 0.8420 (mttt) cc_final: 0.8161 (mttp) REVERT: A 1009 LYS cc_start: 0.8536 (tttt) cc_final: 0.8270 (ttmm) REVERT: A 1011 LYS cc_start: 0.8739 (tttt) cc_final: 0.8486 (ttpt) REVERT: A 1016 GLU cc_start: 0.8062 (tt0) cc_final: 0.7741 (tt0) REVERT: A 1018 ILE cc_start: 0.8527 (pt) cc_final: 0.8141 (mt) REVERT: A 1023 GLU cc_start: 0.7803 (tp30) cc_final: 0.7514 (tp30) REVERT: A 1082 ILE cc_start: 0.8605 (tp) cc_final: 0.8156 (pt) REVERT: A 1146 GLU cc_start: 0.8164 (tt0) cc_final: 0.7600 (tt0) REVERT: C 32 GLU cc_start: 0.8258 (tp30) cc_final: 0.8036 (mm-30) REVERT: C 42 LYS cc_start: 0.7630 (mmmt) cc_final: 0.7325 (mmmt) REVERT: C 64 LYS cc_start: 0.8530 (mtmt) cc_final: 0.8036 (mmmm) REVERT: C 170 PHE cc_start: 0.8239 (t80) cc_final: 0.7955 (t80) REVERT: C 189 LYS cc_start: 0.8392 (mmtt) cc_final: 0.8082 (mmmm) REVERT: C 196 ASP cc_start: 0.7940 (t0) cc_final: 0.7588 (t0) REVERT: C 197 GLU cc_start: 0.7804 (pp20) cc_final: 0.7319 (pp20) REVERT: C 277 GLU cc_start: 0.7248 (mp0) cc_final: 0.6889 (mp0) REVERT: C 279 GLU cc_start: 0.7276 (tp30) cc_final: 0.7055 (tp30) REVERT: C 297 GLU cc_start: 0.7252 (pm20) cc_final: 0.6740 (pm20) REVERT: C 643 LYS cc_start: 0.7650 (mtmm) cc_final: 0.7410 (mtmm) REVERT: C 709 LYS cc_start: 0.8418 (ttpt) cc_final: 0.8106 (ttpt) REVERT: C 730 GLN cc_start: 0.7848 (mt0) cc_final: 0.7617 (mt0) REVERT: C 743 ASN cc_start: 0.7775 (t0) cc_final: 0.7543 (t0) REVERT: C 745 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7078 (mm-30) REVERT: D 78 SER cc_start: 0.7586 (t) cc_final: 0.7337 (t) REVERT: D 89 LYS cc_start: 0.8421 (tptm) cc_final: 0.8051 (mmtt) REVERT: D 105 ILE cc_start: 0.8255 (tt) cc_final: 0.7804 (pt) REVERT: D 117 TYR cc_start: 0.7886 (t80) cc_final: 0.7542 (t80) REVERT: D 158 LYS cc_start: 0.7733 (mtmm) cc_final: 0.7433 (mttp) REVERT: D 165 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7802 (tm-30) REVERT: D 169 GLU cc_start: 0.7412 (mm-30) cc_final: 0.7002 (mm-30) REVERT: D 173 LYS cc_start: 0.8111 (tppt) cc_final: 0.7829 (tppt) REVERT: D 202 VAL cc_start: 0.8701 (p) cc_final: 0.8457 (m) REVERT: D 205 GLU cc_start: 0.7413 (tm-30) cc_final: 0.7080 (tm-30) REVERT: D 241 MET cc_start: 0.8243 (tpt) cc_final: 0.7293 (tpp) REVERT: D 269 GLN cc_start: 0.8072 (tp-100) cc_final: 0.7829 (tp-100) REVERT: D 277 GLU cc_start: 0.8112 (tt0) cc_final: 0.7858 (tt0) REVERT: D 287 ASP cc_start: 0.7751 (t70) cc_final: 0.7441 (t0) REVERT: D 303 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7991 (tm-30) REVERT: D 341 GLU cc_start: 0.7970 (tp30) cc_final: 0.7714 (tp30) REVERT: D 363 LEU cc_start: 0.8006 (mt) cc_final: 0.7715 (mp) REVERT: D 364 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7674 (mt-10) REVERT: D 385 ILE cc_start: 0.8913 (mt) cc_final: 0.8665 (mt) REVERT: D 420 LYS cc_start: 0.8826 (tttt) cc_final: 0.8550 (ttmt) REVERT: D 424 LYS cc_start: 0.8503 (tppp) cc_final: 0.8239 (mttt) REVERT: D 542 LYS cc_start: 0.8106 (tttt) cc_final: 0.7820 (ttpp) REVERT: D 554 LYS cc_start: 0.8813 (mttt) cc_final: 0.8556 (mtpp) REVERT: D 570 ASP cc_start: 0.7500 (t0) cc_final: 0.7022 (t0) REVERT: D 606 GLU cc_start: 0.8253 (tp30) cc_final: 0.8001 (tp30) REVERT: D 662 GLN cc_start: 0.7458 (tp-100) cc_final: 0.7135 (tm-30) REVERT: D 698 GLU cc_start: 0.7416 (mp0) cc_final: 0.6991 (mp0) REVERT: D 749 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7560 (tm-30) REVERT: D 776 TYR cc_start: 0.8329 (t80) cc_final: 0.7608 (t80) REVERT: D 780 ILE cc_start: 0.8970 (pt) cc_final: 0.8541 (mt) REVERT: D 815 ARG cc_start: 0.8040 (ttm170) cc_final: 0.7510 (mtm110) REVERT: D 819 MET cc_start: 0.8009 (mmt) cc_final: 0.7802 (mmt) REVERT: D 867 GLU cc_start: 0.8438 (tp30) cc_final: 0.8136 (tp30) REVERT: D 921 LYS cc_start: 0.8289 (mtpt) cc_final: 0.8037 (mtmt) REVERT: D 924 GLU cc_start: 0.7681 (tt0) cc_final: 0.7175 (tm-30) REVERT: D 942 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7455 (mm-30) REVERT: D 1017 ASP cc_start: 0.8151 (t70) cc_final: 0.7739 (t0) REVERT: D 1048 LYS cc_start: 0.7906 (mtpt) cc_final: 0.7306 (mtpt) REVERT: D 1055 GLU cc_start: 0.7870 (tp30) cc_final: 0.7557 (tp30) REVERT: D 1109 LYS cc_start: 0.8307 (tptm) cc_final: 0.8056 (tppp) REVERT: D 1139 GLU cc_start: 0.7259 (tm-30) cc_final: 0.6765 (tm-30) REVERT: D 1166 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7244 (mm-30) outliers start: 28 outliers final: 12 residues processed: 552 average time/residue: 0.1460 time to fit residues: 119.7891 Evaluate side-chains 527 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 514 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 1295 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 584 MET Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 988 SER Chi-restraints excluded: chain D residue 1047 VAL Chi-restraints excluded: chain D residue 1166 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 101 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 177 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 220 optimal weight: 0.2980 chunk 225 optimal weight: 0.1980 chunk 128 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 ASN B 307 ASN B1283 GLN B1340 HIS ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 653 ASN C 725 ASN D 72 GLN D 120 GLN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1158 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.148647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.122882 restraints weight = 29193.822| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.04 r_work: 0.3386 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19626 Z= 0.141 Angle : 0.591 8.422 26740 Z= 0.317 Chirality : 0.042 0.173 3101 Planarity : 0.004 0.072 3141 Dihedral : 17.943 66.955 3195 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.90 % Allowed : 16.58 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.17), residues: 2177 helix: 0.37 (0.14), residues: 1301 sheet: 0.56 (0.42), residues: 161 loop : -1.97 (0.21), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D1032 TYR 0.020 0.002 TYR D1086 PHE 0.025 0.002 PHE B1302 TRP 0.012 0.002 TRP A1033 HIS 0.005 0.001 HIS D1123 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (19626) covalent geometry : angle 0.59095 / 0.32 (26740) hydrogen bonds : bond 0.04368 / 4.90 ( 1129) hydrogen bonds : angle 4.22838 / 4.78 ( 3275) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 525 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 ARG cc_start: 0.8139 (mtm110) cc_final: 0.7804 (mtp-110) REVERT: B 252 GLU cc_start: 0.7414 (pm20) cc_final: 0.6989 (pm20) REVERT: B 263 PHE cc_start: 0.8735 (m-80) cc_final: 0.8180 (m-80) REVERT: B 264 LYS cc_start: 0.8742 (mmtt) cc_final: 0.8413 (tppt) REVERT: B 269 LYS cc_start: 0.8262 (mtpt) cc_final: 0.7871 (mtpt) REVERT: B 288 ASN cc_start: 0.8511 (t0) cc_final: 0.8032 (t0) REVERT: B 289 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7700 (mm-30) REVERT: B 312 LYS cc_start: 0.8662 (mptt) cc_final: 0.8405 (mptt) REVERT: B 325 GLU cc_start: 0.8154 (mp0) cc_final: 0.7713 (mp0) REVERT: B 1260 LYS cc_start: 0.7935 (mttt) cc_final: 0.7685 (mtpp) REVERT: B 1271 PHE cc_start: 0.8289 (t80) cc_final: 0.8056 (t80) REVERT: B 1281 MET cc_start: 0.7842 (mmt) cc_final: 0.7571 (mpp) REVERT: B 1282 TYR cc_start: 0.8363 (t80) cc_final: 0.8014 (t80) REVERT: B 1292 GLU cc_start: 0.7769 (tp30) cc_final: 0.7468 (tp30) REVERT: B 1373 THR cc_start: 0.8502 (m) cc_final: 0.8270 (t) REVERT: B 1405 LYS cc_start: 0.8884 (mttt) cc_final: 0.8616 (mmtm) REVERT: B 1412 ILE cc_start: 0.8478 (pt) cc_final: 0.8176 (pt) REVERT: A 28 ASN cc_start: 0.7884 (m-40) cc_final: 0.7664 (m-40) REVERT: A 54 MET cc_start: 0.7766 (mmt) cc_final: 0.7417 (mmt) REVERT: A 64 ASP cc_start: 0.7388 (t0) cc_final: 0.7104 (m-30) REVERT: A 81 ILE cc_start: 0.8016 (tt) cc_final: 0.7759 (tt) REVERT: A 109 LEU cc_start: 0.8775 (mt) cc_final: 0.8544 (mp) REVERT: A 129 GLN cc_start: 0.7944 (tm-30) cc_final: 0.7342 (tm-30) REVERT: A 160 GLU cc_start: 0.7711 (mp0) cc_final: 0.7255 (mp0) REVERT: A 178 ARG cc_start: 0.7853 (tmm160) cc_final: 0.7361 (ttp-110) REVERT: A 187 LYS cc_start: 0.8865 (tppt) cc_final: 0.8513 (tppt) REVERT: A 209 LYS cc_start: 0.7654 (mmtm) cc_final: 0.7277 (mmtm) REVERT: A 985 ASN cc_start: 0.8058 (p0) cc_final: 0.7660 (p0) REVERT: A 994 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7877 (mm-30) REVERT: A 1005 LYS cc_start: 0.8468 (mttt) cc_final: 0.8210 (mttp) REVERT: A 1009 LYS cc_start: 0.8509 (tttt) cc_final: 0.8240 (ttmm) REVERT: A 1018 ILE cc_start: 0.8528 (pt) cc_final: 0.8196 (mt) REVERT: A 1082 ILE cc_start: 0.8619 (tp) cc_final: 0.8153 (pt) REVERT: A 1119 ASP cc_start: 0.7567 (p0) cc_final: 0.7070 (p0) REVERT: A 1146 GLU cc_start: 0.8174 (tt0) cc_final: 0.7558 (tt0) REVERT: C 42 LYS cc_start: 0.7638 (mmmt) cc_final: 0.7322 (mmmt) REVERT: C 64 LYS cc_start: 0.8515 (mtmt) cc_final: 0.8021 (mmmm) REVERT: C 170 PHE cc_start: 0.8196 (t80) cc_final: 0.7991 (t80) REVERT: C 189 LYS cc_start: 0.8398 (mmtt) cc_final: 0.8080 (mmmm) REVERT: C 196 ASP cc_start: 0.7941 (t0) cc_final: 0.7597 (t0) REVERT: C 197 GLU cc_start: 0.7804 (pp20) cc_final: 0.7316 (pp20) REVERT: C 203 LEU cc_start: 0.8554 (pp) cc_final: 0.8269 (pp) REVERT: C 277 GLU cc_start: 0.7284 (mp0) cc_final: 0.6869 (mp0) REVERT: C 293 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.7951 (tp) REVERT: C 297 GLU cc_start: 0.7245 (pm20) cc_final: 0.6716 (pm20) REVERT: C 643 LYS cc_start: 0.7657 (mtmm) cc_final: 0.7434 (mtmm) REVERT: C 664 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7057 (mp0) REVERT: C 709 LYS cc_start: 0.8413 (ttpt) cc_final: 0.8108 (ttpt) REVERT: C 730 GLN cc_start: 0.7781 (mt0) cc_final: 0.7568 (mt0) REVERT: C 743 ASN cc_start: 0.7761 (t0) cc_final: 0.7538 (t0) REVERT: C 745 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7137 (mm-30) REVERT: D 31 LEU cc_start: 0.6231 (OUTLIER) cc_final: 0.6026 (tt) REVERT: D 78 SER cc_start: 0.7663 (t) cc_final: 0.7446 (t) REVERT: D 89 LYS cc_start: 0.8425 (tptm) cc_final: 0.8053 (mmtt) REVERT: D 105 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7989 (tt) REVERT: D 117 TYR cc_start: 0.7871 (t80) cc_final: 0.7493 (t80) REVERT: D 165 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7782 (tm-30) REVERT: D 169 GLU cc_start: 0.7389 (mm-30) cc_final: 0.6986 (mm-30) REVERT: D 173 LYS cc_start: 0.8087 (tppt) cc_final: 0.7865 (tppt) REVERT: D 202 VAL cc_start: 0.8702 (p) cc_final: 0.8463 (m) REVERT: D 205 GLU cc_start: 0.7398 (tm-30) cc_final: 0.7028 (tm-30) REVERT: D 269 GLN cc_start: 0.8072 (tp-100) cc_final: 0.7810 (tp-100) REVERT: D 277 GLU cc_start: 0.8063 (tt0) cc_final: 0.7797 (pt0) REVERT: D 287 ASP cc_start: 0.7738 (t70) cc_final: 0.7446 (t0) REVERT: D 303 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7989 (tm-30) REVERT: D 341 GLU cc_start: 0.8017 (tp30) cc_final: 0.7744 (tp30) REVERT: D 363 LEU cc_start: 0.8013 (mt) cc_final: 0.7694 (mp) REVERT: D 364 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7789 (mt-10) REVERT: D 424 LYS cc_start: 0.8511 (tppp) cc_final: 0.8237 (mttt) REVERT: D 428 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7687 (ttmm) REVERT: D 542 LYS cc_start: 0.8141 (tttt) cc_final: 0.7922 (ttpp) REVERT: D 554 LYS cc_start: 0.8840 (mttt) cc_final: 0.8583 (mtpp) REVERT: D 570 ASP cc_start: 0.7550 (t0) cc_final: 0.7158 (t0) REVERT: D 606 GLU cc_start: 0.8222 (tp30) cc_final: 0.8000 (tp30) REVERT: D 677 LYS cc_start: 0.8007 (mmtp) cc_final: 0.7768 (mmtm) REVERT: D 698 GLU cc_start: 0.7409 (mp0) cc_final: 0.6989 (mp0) REVERT: D 749 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7575 (tm-30) REVERT: D 776 TYR cc_start: 0.8357 (t80) cc_final: 0.7767 (t80) REVERT: D 780 ILE cc_start: 0.8962 (pt) cc_final: 0.8563 (mt) REVERT: D 815 ARG cc_start: 0.8052 (ttm170) cc_final: 0.7521 (mtm110) REVERT: D 819 MET cc_start: 0.8076 (mmt) cc_final: 0.7845 (mmt) REVERT: D 867 GLU cc_start: 0.8463 (tp30) cc_final: 0.8169 (tp30) REVERT: D 921 LYS cc_start: 0.8251 (mtpt) cc_final: 0.7999 (mtmt) REVERT: D 942 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7535 (mm-30) REVERT: D 1017 ASP cc_start: 0.8207 (t70) cc_final: 0.7880 (t0) REVERT: D 1055 GLU cc_start: 0.7908 (tp30) cc_final: 0.7594 (tp30) REVERT: D 1058 LYS cc_start: 0.8596 (mttp) cc_final: 0.8259 (mptt) REVERT: D 1064 ASP cc_start: 0.7454 (t0) cc_final: 0.7148 (t0) REVERT: D 1109 LYS cc_start: 0.8334 (tptm) cc_final: 0.8097 (tppp) REVERT: D 1139 GLU cc_start: 0.7293 (tm-30) cc_final: 0.6844 (tm-30) REVERT: D 1143 GLN cc_start: 0.7621 (mp10) cc_final: 0.7239 (mp10) outliers start: 38 outliers final: 16 residues processed: 542 average time/residue: 0.1496 time to fit residues: 120.0852 Evaluate side-chains 530 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 509 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 1374 LYS Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 664 GLU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 988 SER Chi-restraints excluded: chain D residue 1047 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 117 optimal weight: 0.6980 chunk 199 optimal weight: 0.7980 chunk 43 optimal weight: 0.0570 chunk 222 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 180 optimal weight: 0.5980 chunk 178 optimal weight: 2.9990 chunk 224 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 ASN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1031 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.148573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.122902 restraints weight = 29152.294| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.02 r_work: 0.3384 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19626 Z= 0.140 Angle : 0.576 8.710 26740 Z= 0.308 Chirality : 0.042 0.172 3101 Planarity : 0.004 0.070 3141 Dihedral : 17.954 67.975 3195 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.05 % Allowed : 17.73 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.18), residues: 2177 helix: 0.77 (0.14), residues: 1299 sheet: 0.51 (0.41), residues: 166 loop : -1.70 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 198 TYR 0.026 0.001 TYR D1086 PHE 0.025 0.001 PHE B1302 TRP 0.011 0.001 TRP A 23 HIS 0.009 0.001 HIS D1123 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (19626) covalent geometry : angle 0.57626 / 0.31 (26740) hydrogen bonds : bond 0.04185 / 4.69 ( 1129) hydrogen bonds : angle 4.10431 / 4.62 ( 3275) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 519 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 250 ASP cc_start: 0.7819 (t0) cc_final: 0.7483 (t0) REVERT: B 252 GLU cc_start: 0.7394 (pm20) cc_final: 0.7024 (pm20) REVERT: B 263 PHE cc_start: 0.8743 (m-80) cc_final: 0.8154 (m-80) REVERT: B 264 LYS cc_start: 0.8747 (mmtt) cc_final: 0.8400 (tppt) REVERT: B 269 LYS cc_start: 0.8251 (mtpt) cc_final: 0.7882 (mtpt) REVERT: B 288 ASN cc_start: 0.8503 (t0) cc_final: 0.8104 (t0) REVERT: B 289 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7789 (mm-30) REVERT: B 312 LYS cc_start: 0.8651 (mptt) cc_final: 0.8408 (mptt) REVERT: B 325 GLU cc_start: 0.8182 (mp0) cc_final: 0.7751 (mp0) REVERT: B 329 ASP cc_start: 0.7776 (t0) cc_final: 0.7536 (t0) REVERT: B 344 MET cc_start: 0.7666 (tmm) cc_final: 0.7466 (tmm) REVERT: B 1260 LYS cc_start: 0.7929 (mttt) cc_final: 0.7687 (mtpp) REVERT: B 1281 MET cc_start: 0.7757 (mmp) cc_final: 0.7390 (mpp) REVERT: B 1282 TYR cc_start: 0.8331 (t80) cc_final: 0.7985 (t80) REVERT: B 1405 LYS cc_start: 0.8877 (mttt) cc_final: 0.8633 (mmtm) REVERT: B 1412 ILE cc_start: 0.8456 (pt) cc_final: 0.8151 (pt) REVERT: A 54 MET cc_start: 0.7667 (mmt) cc_final: 0.7254 (mmt) REVERT: A 64 ASP cc_start: 0.7336 (t0) cc_final: 0.7019 (m-30) REVERT: A 81 ILE cc_start: 0.8008 (tt) cc_final: 0.7729 (tt) REVERT: A 109 LEU cc_start: 0.8779 (mt) cc_final: 0.8543 (mp) REVERT: A 129 GLN cc_start: 0.7924 (tm-30) cc_final: 0.7312 (tm-30) REVERT: A 160 GLU cc_start: 0.7677 (mp0) cc_final: 0.7114 (mp0) REVERT: A 178 ARG cc_start: 0.7854 (tmm160) cc_final: 0.7345 (ttp-110) REVERT: A 187 LYS cc_start: 0.8851 (tppt) cc_final: 0.8506 (tppt) REVERT: A 209 LYS cc_start: 0.7716 (mmtm) cc_final: 0.7346 (mmtm) REVERT: A 985 ASN cc_start: 0.8052 (p0) cc_final: 0.7658 (p0) REVERT: A 994 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7877 (mm-30) REVERT: A 997 GLU cc_start: 0.7563 (tp30) cc_final: 0.7261 (tp30) REVERT: A 1005 LYS cc_start: 0.8473 (mttt) cc_final: 0.8228 (mttp) REVERT: A 1009 LYS cc_start: 0.8489 (tttt) cc_final: 0.8231 (ttmm) REVERT: A 1016 GLU cc_start: 0.8137 (tt0) cc_final: 0.7867 (tt0) REVERT: A 1018 ILE cc_start: 0.8484 (pt) cc_final: 0.8134 (mt) REVERT: A 1082 ILE cc_start: 0.8614 (tp) cc_final: 0.8181 (pt) REVERT: A 1119 ASP cc_start: 0.7565 (p0) cc_final: 0.7049 (p0) REVERT: A 1146 GLU cc_start: 0.8093 (tt0) cc_final: 0.7515 (tt0) REVERT: C 32 GLU cc_start: 0.8205 (tp30) cc_final: 0.7838 (mm-30) REVERT: C 42 LYS cc_start: 0.7638 (mmmt) cc_final: 0.7305 (mmmt) REVERT: C 64 LYS cc_start: 0.8586 (mtmt) cc_final: 0.8072 (mmmm) REVERT: C 189 LYS cc_start: 0.8399 (mmtt) cc_final: 0.8077 (mmmm) REVERT: C 196 ASP cc_start: 0.7972 (t0) cc_final: 0.7628 (t0) REVERT: C 197 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7322 (pp20) REVERT: C 203 LEU cc_start: 0.8448 (pp) cc_final: 0.8229 (pp) REVERT: C 211 ASP cc_start: 0.8016 (m-30) cc_final: 0.7802 (m-30) REVERT: C 277 GLU cc_start: 0.7280 (mp0) cc_final: 0.6884 (mp0) REVERT: C 293 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.7974 (tp) REVERT: C 297 GLU cc_start: 0.7257 (pm20) cc_final: 0.6696 (pm20) REVERT: C 643 LYS cc_start: 0.7679 (mtmm) cc_final: 0.7456 (mtmm) REVERT: C 664 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7103 (mp0) REVERT: C 709 LYS cc_start: 0.8419 (ttpt) cc_final: 0.8102 (ttpt) REVERT: C 730 GLN cc_start: 0.7788 (mt0) cc_final: 0.7583 (mt0) REVERT: C 743 ASN cc_start: 0.7727 (t0) cc_final: 0.7503 (t0) REVERT: C 745 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7069 (mm-30) REVERT: D 31 LEU cc_start: 0.6227 (OUTLIER) cc_final: 0.6013 (tt) REVERT: D 89 LYS cc_start: 0.8429 (tptm) cc_final: 0.8063 (mmtt) REVERT: D 105 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7974 (tt) REVERT: D 165 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7821 (tm-30) REVERT: D 169 GLU cc_start: 0.7397 (mm-30) cc_final: 0.6992 (mm-30) REVERT: D 202 VAL cc_start: 0.8709 (p) cc_final: 0.8464 (m) REVERT: D 205 GLU cc_start: 0.7435 (tm-30) cc_final: 0.7034 (tm-30) REVERT: D 269 GLN cc_start: 0.8084 (tp-100) cc_final: 0.7825 (tp-100) REVERT: D 277 GLU cc_start: 0.8004 (tt0) cc_final: 0.7689 (tt0) REVERT: D 287 ASP cc_start: 0.7704 (t70) cc_final: 0.7421 (t0) REVERT: D 303 GLU cc_start: 0.8287 (tm-30) cc_final: 0.8005 (tm-30) REVERT: D 341 GLU cc_start: 0.8067 (tp30) cc_final: 0.7800 (tp30) REVERT: D 364 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7685 (mt-10) REVERT: D 424 LYS cc_start: 0.8519 (tppp) cc_final: 0.8263 (mttt) REVERT: D 428 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7668 (ttmm) REVERT: D 554 LYS cc_start: 0.8848 (mttt) cc_final: 0.8595 (mtpp) REVERT: D 570 ASP cc_start: 0.7567 (t0) cc_final: 0.7152 (t0) REVERT: D 606 GLU cc_start: 0.8229 (tp30) cc_final: 0.7790 (tp30) REVERT: D 662 GLN cc_start: 0.7396 (tp-100) cc_final: 0.6956 (tm-30) REVERT: D 677 LYS cc_start: 0.7999 (mmtp) cc_final: 0.7706 (mmtm) REVERT: D 698 GLU cc_start: 0.7433 (mp0) cc_final: 0.6991 (mp0) REVERT: D 749 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7530 (tm-30) REVERT: D 776 TYR cc_start: 0.8345 (t80) cc_final: 0.7757 (t80) REVERT: D 780 ILE cc_start: 0.8934 (pt) cc_final: 0.8565 (mt) REVERT: D 791 MET cc_start: 0.8553 (tmm) cc_final: 0.8055 (tmm) REVERT: D 819 MET cc_start: 0.8067 (mmt) cc_final: 0.7851 (mmt) REVERT: D 867 GLU cc_start: 0.8467 (tp30) cc_final: 0.8168 (tp30) REVERT: D 921 LYS cc_start: 0.8277 (mtpt) cc_final: 0.8047 (mtmt) REVERT: D 942 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7530 (mm-30) REVERT: D 1017 ASP cc_start: 0.8279 (t70) cc_final: 0.8057 (t0) REVERT: D 1048 LYS cc_start: 0.7754 (mtpt) cc_final: 0.7370 (mtpt) REVERT: D 1055 GLU cc_start: 0.7926 (tp30) cc_final: 0.7607 (tp30) REVERT: D 1058 LYS cc_start: 0.8558 (mttp) cc_final: 0.8311 (mptt) REVERT: D 1064 ASP cc_start: 0.7469 (t0) cc_final: 0.7161 (t0) REVERT: D 1072 ARG cc_start: 0.8145 (ttm110) cc_final: 0.7910 (ttm110) REVERT: D 1109 LYS cc_start: 0.8331 (tptm) cc_final: 0.8086 (tppp) REVERT: D 1139 GLU cc_start: 0.7297 (tm-30) cc_final: 0.6843 (tm-30) outliers start: 41 outliers final: 21 residues processed: 540 average time/residue: 0.1466 time to fit residues: 117.7660 Evaluate side-chains 525 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 498 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 664 GLU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 988 SER Chi-restraints excluded: chain D residue 995 SER Chi-restraints excluded: chain D residue 1047 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 15 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 174 optimal weight: 0.0030 chunk 146 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 ASN C 212 ASN C 725 ASN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.148035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.122125 restraints weight = 29092.906| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.08 r_work: 0.3376 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19626 Z= 0.157 Angle : 0.579 9.256 26740 Z= 0.309 Chirality : 0.042 0.167 3101 Planarity : 0.004 0.070 3141 Dihedral : 17.941 68.535 3195 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.50 % Allowed : 18.08 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.18), residues: 2177 helix: 0.94 (0.14), residues: 1300 sheet: 0.56 (0.40), residues: 166 loop : -1.52 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 198 TYR 0.028 0.002 TYR D1086 PHE 0.028 0.002 PHE B1302 TRP 0.011 0.001 TRP A1033 HIS 0.009 0.001 HIS D1123 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (19626) covalent geometry : angle 0.57861 / 0.31 (26740) hydrogen bonds : bond 0.04191 / 4.71 ( 1129) hydrogen bonds : angle 4.05192 / 4.55 ( 3275) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 508 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 VAL cc_start: 0.8103 (m) cc_final: 0.7623 (t) REVERT: B 250 ASP cc_start: 0.7888 (t0) cc_final: 0.7501 (t0) REVERT: B 252 GLU cc_start: 0.7472 (pm20) cc_final: 0.7109 (pm20) REVERT: B 263 PHE cc_start: 0.8746 (m-80) cc_final: 0.8171 (m-80) REVERT: B 264 LYS cc_start: 0.8771 (mmtt) cc_final: 0.8404 (tppt) REVERT: B 269 LYS cc_start: 0.8282 (mtpt) cc_final: 0.7930 (mtpt) REVERT: B 288 ASN cc_start: 0.8475 (t0) cc_final: 0.8096 (t0) REVERT: B 289 GLU cc_start: 0.8362 (mm-30) cc_final: 0.7813 (mm-30) REVERT: B 312 LYS cc_start: 0.8657 (mptt) cc_final: 0.8429 (mptt) REVERT: B 325 GLU cc_start: 0.8190 (mp0) cc_final: 0.7738 (mp0) REVERT: B 344 MET cc_start: 0.7690 (tmm) cc_final: 0.7449 (tmm) REVERT: B 1260 LYS cc_start: 0.7937 (mttt) cc_final: 0.7680 (mtpp) REVERT: B 1281 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7531 (mpp) REVERT: B 1282 TYR cc_start: 0.8323 (t80) cc_final: 0.7975 (t80) REVERT: B 1373 THR cc_start: 0.8531 (m) cc_final: 0.8316 (t) REVERT: B 1405 LYS cc_start: 0.8885 (mttt) cc_final: 0.8634 (mttm) REVERT: B 1412 ILE cc_start: 0.8426 (pt) cc_final: 0.8146 (pt) REVERT: A 49 LEU cc_start: 0.8575 (mt) cc_final: 0.8369 (mp) REVERT: A 54 MET cc_start: 0.7655 (mmt) cc_final: 0.6989 (mmm) REVERT: A 64 ASP cc_start: 0.7342 (t0) cc_final: 0.7034 (m-30) REVERT: A 81 ILE cc_start: 0.8018 (tt) cc_final: 0.7745 (tt) REVERT: A 109 LEU cc_start: 0.8814 (mt) cc_final: 0.8560 (mp) REVERT: A 129 GLN cc_start: 0.7998 (tm-30) cc_final: 0.7365 (tm-30) REVERT: A 156 MET cc_start: 0.7745 (mtm) cc_final: 0.7527 (mtp) REVERT: A 160 GLU cc_start: 0.7696 (mp0) cc_final: 0.7173 (mp0) REVERT: A 178 ARG cc_start: 0.7871 (tmm160) cc_final: 0.7387 (ttp-110) REVERT: A 187 LYS cc_start: 0.8873 (tppt) cc_final: 0.8522 (tppt) REVERT: A 209 LYS cc_start: 0.7745 (mmtm) cc_final: 0.7447 (mmtm) REVERT: A 985 ASN cc_start: 0.8115 (p0) cc_final: 0.7725 (p0) REVERT: A 994 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7943 (mm-30) REVERT: A 997 GLU cc_start: 0.7519 (tp30) cc_final: 0.7213 (tp30) REVERT: A 1005 LYS cc_start: 0.8455 (mttt) cc_final: 0.8202 (mttp) REVERT: A 1009 LYS cc_start: 0.8497 (tttt) cc_final: 0.8236 (ttmm) REVERT: A 1016 GLU cc_start: 0.8160 (tt0) cc_final: 0.7866 (tt0) REVERT: A 1018 ILE cc_start: 0.8508 (pt) cc_final: 0.8211 (mt) REVERT: A 1026 ARG cc_start: 0.7914 (ttp80) cc_final: 0.7655 (tmt170) REVERT: A 1061 LYS cc_start: 0.7677 (mmmm) cc_final: 0.7439 (mmmm) REVERT: A 1082 ILE cc_start: 0.8651 (tp) cc_final: 0.8192 (pt) REVERT: A 1119 ASP cc_start: 0.7598 (p0) cc_final: 0.7074 (p0) REVERT: A 1146 GLU cc_start: 0.8106 (tt0) cc_final: 0.7567 (tt0) REVERT: C 42 LYS cc_start: 0.7623 (mmmt) cc_final: 0.7271 (mmmt) REVERT: C 64 LYS cc_start: 0.8585 (mtmt) cc_final: 0.8054 (mmmm) REVERT: C 189 LYS cc_start: 0.8393 (mmtt) cc_final: 0.8048 (mmmm) REVERT: C 196 ASP cc_start: 0.8022 (t0) cc_final: 0.7684 (t0) REVERT: C 197 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7314 (pp20) REVERT: C 203 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8230 (pp) REVERT: C 211 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7795 (m-30) REVERT: C 277 GLU cc_start: 0.7287 (mp0) cc_final: 0.6870 (mp0) REVERT: C 293 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8007 (tp) REVERT: C 297 GLU cc_start: 0.7275 (pm20) cc_final: 0.6700 (pm20) REVERT: C 664 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: C 709 LYS cc_start: 0.8416 (ttpt) cc_final: 0.8104 (ttpt) REVERT: C 730 GLN cc_start: 0.7829 (mt0) cc_final: 0.7625 (mt0) REVERT: D 31 LEU cc_start: 0.6284 (OUTLIER) cc_final: 0.6078 (tt) REVERT: D 89 LYS cc_start: 0.8436 (tptm) cc_final: 0.8057 (mmtt) REVERT: D 105 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7971 (tt) REVERT: D 165 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7825 (tm-30) REVERT: D 169 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7015 (mm-30) REVERT: D 202 VAL cc_start: 0.8751 (p) cc_final: 0.8499 (m) REVERT: D 205 GLU cc_start: 0.7500 (tm-30) cc_final: 0.7075 (tm-30) REVERT: D 269 GLN cc_start: 0.8097 (tp-100) cc_final: 0.7808 (tp-100) REVERT: D 277 GLU cc_start: 0.8088 (tt0) cc_final: 0.7705 (tt0) REVERT: D 287 ASP cc_start: 0.7748 (t70) cc_final: 0.7419 (t0) REVERT: D 341 GLU cc_start: 0.8122 (tp30) cc_final: 0.7826 (tp30) REVERT: D 424 LYS cc_start: 0.8529 (tppp) cc_final: 0.8307 (tttt) REVERT: D 428 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7669 (ttmm) REVERT: D 554 LYS cc_start: 0.8852 (mttt) cc_final: 0.8593 (mtpp) REVERT: D 570 ASP cc_start: 0.7640 (t0) cc_final: 0.7256 (t0) REVERT: D 606 GLU cc_start: 0.8266 (tp30) cc_final: 0.7803 (tp30) REVERT: D 662 GLN cc_start: 0.7487 (tp-100) cc_final: 0.7152 (tm-30) REVERT: D 677 LYS cc_start: 0.7967 (mmtp) cc_final: 0.7710 (mmtm) REVERT: D 698 GLU cc_start: 0.7500 (mp0) cc_final: 0.7023 (mp0) REVERT: D 749 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7597 (tm-30) REVERT: D 776 TYR cc_start: 0.8360 (t80) cc_final: 0.7778 (t80) REVERT: D 780 ILE cc_start: 0.8937 (pt) cc_final: 0.8569 (mt) REVERT: D 791 MET cc_start: 0.8618 (tmm) cc_final: 0.8077 (tmm) REVERT: D 819 MET cc_start: 0.8071 (mmt) cc_final: 0.7820 (mmt) REVERT: D 867 GLU cc_start: 0.8459 (tp30) cc_final: 0.8168 (tp30) REVERT: D 921 LYS cc_start: 0.8272 (mtpt) cc_final: 0.8035 (mtmt) REVERT: D 942 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7566 (mm-30) REVERT: D 1004 MET cc_start: 0.7997 (mmm) cc_final: 0.7473 (mmm) REVERT: D 1017 ASP cc_start: 0.8261 (t70) cc_final: 0.8009 (t0) REVERT: D 1048 LYS cc_start: 0.7788 (mtpt) cc_final: 0.7444 (mtpt) REVERT: D 1055 GLU cc_start: 0.7972 (tp30) cc_final: 0.7659 (tp30) REVERT: D 1058 LYS cc_start: 0.8599 (mttp) cc_final: 0.8298 (mptt) REVERT: D 1064 ASP cc_start: 0.7466 (t0) cc_final: 0.7228 (t0) REVERT: D 1109 LYS cc_start: 0.8349 (tptm) cc_final: 0.8095 (tppp) REVERT: D 1139 GLU cc_start: 0.7357 (tm-30) cc_final: 0.6859 (tm-30) REVERT: D 1143 GLN cc_start: 0.7648 (mp10) cc_final: 0.7232 (mp10) outliers start: 50 outliers final: 27 residues processed: 533 average time/residue: 0.1500 time to fit residues: 118.9064 Evaluate side-chains 527 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 491 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 1281 MET Chi-restraints excluded: chain B residue 1295 LEU Chi-restraints excluded: chain B residue 1307 THR Chi-restraints excluded: chain B residue 1314 LYS Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 664 GLU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 988 SER Chi-restraints excluded: chain D residue 1032 ARG Chi-restraints excluded: chain D residue 1047 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 196 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 181 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 202 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 161 optimal weight: 0.0020 chunk 220 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 ASN C 725 ASN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.146257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.120305 restraints weight = 28993.756| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.05 r_work: 0.3349 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 19626 Z= 0.239 Angle : 0.622 6.908 26740 Z= 0.332 Chirality : 0.045 0.180 3101 Planarity : 0.004 0.074 3141 Dihedral : 17.929 69.484 3195 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.70 % Allowed : 18.93 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.18), residues: 2177 helix: 0.90 (0.14), residues: 1302 sheet: 0.51 (0.40), residues: 166 loop : -1.47 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1384 TYR 0.029 0.002 TYR D1086 PHE 0.027 0.002 PHE B1302 TRP 0.015 0.002 TRP A1033 HIS 0.010 0.001 HIS D1123 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.24 (19626) covalent geometry : angle 0.62213 / 0.33 (26740) hydrogen bonds : bond 0.04585 / 5.15 ( 1129) hydrogen bonds : angle 4.14045 / 4.65 ( 3275) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 504 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 VAL cc_start: 0.8287 (m) cc_final: 0.7892 (t) REVERT: B 250 ASP cc_start: 0.7937 (t0) cc_final: 0.7515 (t0) REVERT: B 252 GLU cc_start: 0.7487 (pm20) cc_final: 0.7106 (pm20) REVERT: B 263 PHE cc_start: 0.8777 (m-80) cc_final: 0.8337 (m-80) REVERT: B 264 LYS cc_start: 0.8780 (mmtt) cc_final: 0.8444 (tppt) REVERT: B 288 ASN cc_start: 0.8455 (t0) cc_final: 0.8080 (t0) REVERT: B 289 GLU cc_start: 0.8384 (mm-30) cc_final: 0.7815 (mm-30) REVERT: B 292 ASP cc_start: 0.7539 (t0) cc_final: 0.7197 (t0) REVERT: B 312 LYS cc_start: 0.8670 (mptt) cc_final: 0.8417 (mptt) REVERT: B 325 GLU cc_start: 0.8185 (mp0) cc_final: 0.7724 (mp0) REVERT: B 329 ASP cc_start: 0.7721 (t0) cc_final: 0.7505 (t0) REVERT: B 1260 LYS cc_start: 0.7967 (mttt) cc_final: 0.7709 (mtpp) REVERT: B 1281 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.7426 (mpp) REVERT: B 1405 LYS cc_start: 0.8901 (mttt) cc_final: 0.8632 (mttm) REVERT: B 1412 ILE cc_start: 0.8433 (pt) cc_final: 0.8153 (pt) REVERT: A 49 LEU cc_start: 0.8558 (mt) cc_final: 0.8352 (mp) REVERT: A 54 MET cc_start: 0.7662 (mmt) cc_final: 0.7397 (mmp) REVERT: A 81 ILE cc_start: 0.8056 (tt) cc_final: 0.7772 (tt) REVERT: A 109 LEU cc_start: 0.8846 (mt) cc_final: 0.8579 (mp) REVERT: A 129 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7416 (tm-30) REVERT: A 156 MET cc_start: 0.7860 (mtm) cc_final: 0.7630 (mtp) REVERT: A 160 GLU cc_start: 0.7716 (mp0) cc_final: 0.7201 (mp0) REVERT: A 178 ARG cc_start: 0.7895 (tmm160) cc_final: 0.7383 (ttp-110) REVERT: A 187 LYS cc_start: 0.8892 (tppt) cc_final: 0.8547 (tppt) REVERT: A 204 GLU cc_start: 0.7638 (mp0) cc_final: 0.7346 (mp0) REVERT: A 209 LYS cc_start: 0.7764 (mmtm) cc_final: 0.7488 (mmtm) REVERT: A 985 ASN cc_start: 0.8159 (p0) cc_final: 0.7760 (p0) REVERT: A 994 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7969 (mm-30) REVERT: A 997 GLU cc_start: 0.7534 (tp30) cc_final: 0.7174 (tp30) REVERT: A 1005 LYS cc_start: 0.8479 (mttt) cc_final: 0.8219 (mttp) REVERT: A 1009 LYS cc_start: 0.8507 (tttt) cc_final: 0.8250 (ttmm) REVERT: A 1018 ILE cc_start: 0.8528 (pt) cc_final: 0.8292 (mt) REVERT: A 1026 ARG cc_start: 0.7991 (ttp80) cc_final: 0.7738 (tmt170) REVERT: A 1061 LYS cc_start: 0.7678 (mmmm) cc_final: 0.7455 (mmmm) REVERT: A 1082 ILE cc_start: 0.8684 (tp) cc_final: 0.8211 (pt) REVERT: A 1119 ASP cc_start: 0.7630 (p0) cc_final: 0.7105 (p0) REVERT: A 1146 GLU cc_start: 0.8083 (tt0) cc_final: 0.7556 (tt0) REVERT: C 42 LYS cc_start: 0.7613 (mmmt) cc_final: 0.7265 (mmmt) REVERT: C 64 LYS cc_start: 0.8620 (mtmt) cc_final: 0.8083 (mmmm) REVERT: C 99 LYS cc_start: 0.8572 (mttt) cc_final: 0.8070 (mtmt) REVERT: C 174 LYS cc_start: 0.8166 (ttmm) cc_final: 0.7954 (ttmm) REVERT: C 189 LYS cc_start: 0.8441 (mmtt) cc_final: 0.8101 (mmmm) REVERT: C 196 ASP cc_start: 0.8009 (t0) cc_final: 0.7682 (t0) REVERT: C 197 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7254 (pp20) REVERT: C 203 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8279 (pp) REVERT: C 211 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7825 (m-30) REVERT: C 277 GLU cc_start: 0.7340 (mp0) cc_final: 0.6867 (mp0) REVERT: C 293 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.7968 (tp) REVERT: C 297 GLU cc_start: 0.7292 (pm20) cc_final: 0.6757 (pm20) REVERT: C 664 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7025 (mp0) REVERT: C 709 LYS cc_start: 0.8414 (ttpt) cc_final: 0.8101 (ttpt) REVERT: C 730 GLN cc_start: 0.7865 (mt0) cc_final: 0.7630 (mt0) REVERT: C 745 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7344 (mm-30) REVERT: D 8 GLU cc_start: 0.7971 (pm20) cc_final: 0.7741 (pm20) REVERT: D 31 LEU cc_start: 0.6313 (OUTLIER) cc_final: 0.6097 (tt) REVERT: D 89 LYS cc_start: 0.8464 (tptm) cc_final: 0.8046 (mmtt) REVERT: D 127 GLN cc_start: 0.8008 (pp30) cc_final: 0.7486 (tm-30) REVERT: D 165 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7828 (tm-30) REVERT: D 169 GLU cc_start: 0.7475 (mm-30) cc_final: 0.6969 (mm-30) REVERT: D 202 VAL cc_start: 0.8813 (p) cc_final: 0.8527 (m) REVERT: D 205 GLU cc_start: 0.7474 (tm-30) cc_final: 0.7038 (tm-30) REVERT: D 261 LEU cc_start: 0.8183 (mt) cc_final: 0.7979 (mp) REVERT: D 269 GLN cc_start: 0.8121 (tp-100) cc_final: 0.7865 (tp-100) REVERT: D 277 GLU cc_start: 0.8100 (tt0) cc_final: 0.7716 (tt0) REVERT: D 287 ASP cc_start: 0.7713 (t70) cc_final: 0.7408 (t0) REVERT: D 333 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7864 (mt-10) REVERT: D 341 GLU cc_start: 0.8217 (tp30) cc_final: 0.7899 (tp30) REVERT: D 363 LEU cc_start: 0.8087 (mt) cc_final: 0.7807 (mp) REVERT: D 424 LYS cc_start: 0.8512 (tppp) cc_final: 0.8259 (mttt) REVERT: D 428 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7743 (ttmm) REVERT: D 554 LYS cc_start: 0.8869 (mttt) cc_final: 0.8612 (mtpp) REVERT: D 570 ASP cc_start: 0.7729 (t0) cc_final: 0.7372 (t0) REVERT: D 606 GLU cc_start: 0.8307 (tp30) cc_final: 0.7844 (tp30) REVERT: D 662 GLN cc_start: 0.7576 (tp-100) cc_final: 0.7308 (tm-30) REVERT: D 677 LYS cc_start: 0.7978 (mmtp) cc_final: 0.7774 (mmtm) REVERT: D 698 GLU cc_start: 0.7573 (mp0) cc_final: 0.7050 (mp0) REVERT: D 749 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7637 (tm-30) REVERT: D 776 TYR cc_start: 0.8406 (t80) cc_final: 0.7724 (t80) REVERT: D 780 ILE cc_start: 0.9020 (pt) cc_final: 0.8594 (mt) REVERT: D 791 MET cc_start: 0.8603 (tmm) cc_final: 0.8039 (tmm) REVERT: D 819 MET cc_start: 0.8144 (mmt) cc_final: 0.7888 (mmt) REVERT: D 867 GLU cc_start: 0.8455 (tp30) cc_final: 0.8164 (tp30) REVERT: D 921 LYS cc_start: 0.8293 (mtpt) cc_final: 0.8053 (mtmt) REVERT: D 942 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7564 (mm-30) REVERT: D 1004 MET cc_start: 0.7998 (mmm) cc_final: 0.7480 (mmm) REVERT: D 1017 ASP cc_start: 0.8310 (t70) cc_final: 0.8055 (t0) REVERT: D 1048 LYS cc_start: 0.7861 (mtpt) cc_final: 0.7502 (mtpt) REVERT: D 1109 LYS cc_start: 0.8386 (tptm) cc_final: 0.8135 (tppp) REVERT: D 1139 GLU cc_start: 0.7450 (tm-30) cc_final: 0.6948 (tm-30) REVERT: D 1143 GLN cc_start: 0.7627 (mp10) cc_final: 0.7197 (mp10) outliers start: 54 outliers final: 27 residues processed: 530 average time/residue: 0.1426 time to fit residues: 112.7427 Evaluate side-chains 533 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 498 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 1281 MET Chi-restraints excluded: chain B residue 1314 LYS Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 664 GLU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 857 THR Chi-restraints excluded: chain D residue 988 SER Chi-restraints excluded: chain D residue 995 SER Chi-restraints excluded: chain D residue 1036 MET Chi-restraints excluded: chain D residue 1047 VAL Chi-restraints excluded: chain D residue 1056 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 161 optimal weight: 0.4980 chunk 7 optimal weight: 0.0000 chunk 139 optimal weight: 0.9990 chunk 184 optimal weight: 0.9980 chunk 105 optimal weight: 0.0670 chunk 84 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 chunk 61 optimal weight: 0.3980 chunk 178 optimal weight: 0.9980 overall best weight: 0.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 ASN A 71 GLN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1158 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.148710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.122885 restraints weight = 29165.013| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.09 r_work: 0.3385 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19626 Z= 0.124 Angle : 0.573 9.737 26740 Z= 0.305 Chirality : 0.041 0.252 3101 Planarity : 0.004 0.066 3141 Dihedral : 17.878 69.198 3195 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.25 % Allowed : 20.33 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.18), residues: 2177 helix: 1.20 (0.14), residues: 1304 sheet: 0.59 (0.40), residues: 166 loop : -1.26 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1157 TYR 0.023 0.001 TYR D1086 PHE 0.029 0.001 PHE B1302 TRP 0.011 0.001 TRP A 23 HIS 0.004 0.001 HIS D1123 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (19626) covalent geometry : angle 0.57282 / 0.30 (26740) hydrogen bonds : bond 0.04038 / 4.54 ( 1129) hydrogen bonds : angle 3.98838 / 4.48 ( 3275) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 514 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 VAL cc_start: 0.8032 (m) cc_final: 0.7510 (t) REVERT: B 250 ASP cc_start: 0.7901 (t0) cc_final: 0.7480 (t0) REVERT: B 252 GLU cc_start: 0.7494 (pm20) cc_final: 0.7081 (pm20) REVERT: B 263 PHE cc_start: 0.8747 (m-80) cc_final: 0.8083 (m-80) REVERT: B 264 LYS cc_start: 0.8770 (mmtt) cc_final: 0.8425 (tppt) REVERT: B 269 LYS cc_start: 0.8284 (mtpt) cc_final: 0.7916 (mtpt) REVERT: B 288 ASN cc_start: 0.8502 (t0) cc_final: 0.8127 (t0) REVERT: B 289 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7745 (mm-30) REVERT: B 292 ASP cc_start: 0.7503 (t0) cc_final: 0.7104 (t0) REVERT: B 312 LYS cc_start: 0.8593 (mptt) cc_final: 0.8356 (mptt) REVERT: B 325 GLU cc_start: 0.8171 (mp0) cc_final: 0.7722 (mp0) REVERT: B 1260 LYS cc_start: 0.7922 (mttt) cc_final: 0.7659 (mtpp) REVERT: B 1281 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.7533 (mpp) REVERT: B 1282 TYR cc_start: 0.8243 (t80) cc_final: 0.7832 (t80) REVERT: B 1373 THR cc_start: 0.8533 (t) cc_final: 0.8323 (t) REVERT: B 1405 LYS cc_start: 0.8879 (mttt) cc_final: 0.8615 (mttm) REVERT: B 1412 ILE cc_start: 0.8396 (pt) cc_final: 0.8130 (pt) REVERT: A 48 VAL cc_start: 0.7983 (OUTLIER) cc_final: 0.7728 (p) REVERT: A 54 MET cc_start: 0.7589 (mmt) cc_final: 0.7342 (mmp) REVERT: A 81 ILE cc_start: 0.8015 (tt) cc_final: 0.7783 (tt) REVERT: A 109 LEU cc_start: 0.8785 (mt) cc_final: 0.8543 (mp) REVERT: A 129 GLN cc_start: 0.8002 (tm-30) cc_final: 0.7362 (tm-30) REVERT: A 156 MET cc_start: 0.7819 (mtm) cc_final: 0.7608 (mtp) REVERT: A 160 GLU cc_start: 0.7706 (mp0) cc_final: 0.7166 (mp0) REVERT: A 178 ARG cc_start: 0.7865 (tmm160) cc_final: 0.7384 (ttp-110) REVERT: A 187 LYS cc_start: 0.8869 (tppt) cc_final: 0.8548 (tppt) REVERT: A 209 LYS cc_start: 0.7639 (mmtm) cc_final: 0.7306 (mmtm) REVERT: A 217 PHE cc_start: 0.7331 (t80) cc_final: 0.6771 (t80) REVERT: A 987 MET cc_start: 0.8390 (mmm) cc_final: 0.8162 (mmm) REVERT: A 994 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7920 (mm-30) REVERT: A 1005 LYS cc_start: 0.8430 (mttt) cc_final: 0.8174 (mttp) REVERT: A 1009 LYS cc_start: 0.8485 (tttt) cc_final: 0.8218 (ttmm) REVERT: A 1016 GLU cc_start: 0.8122 (tt0) cc_final: 0.7863 (tt0) REVERT: A 1018 ILE cc_start: 0.8505 (pt) cc_final: 0.8238 (mt) REVERT: A 1026 ARG cc_start: 0.7873 (ttp80) cc_final: 0.7607 (tmt170) REVERT: A 1061 LYS cc_start: 0.7685 (mmmm) cc_final: 0.7375 (mmmm) REVERT: A 1082 ILE cc_start: 0.8675 (tp) cc_final: 0.8187 (pt) REVERT: A 1119 ASP cc_start: 0.7621 (p0) cc_final: 0.7127 (p0) REVERT: A 1146 GLU cc_start: 0.8044 (tt0) cc_final: 0.7597 (tt0) REVERT: C 42 LYS cc_start: 0.7621 (mmmt) cc_final: 0.7301 (mmmt) REVERT: C 64 LYS cc_start: 0.8566 (mtmt) cc_final: 0.8034 (mmmm) REVERT: C 174 LYS cc_start: 0.8137 (ttmm) cc_final: 0.7863 (ttmm) REVERT: C 189 LYS cc_start: 0.8389 (mmtt) cc_final: 0.8076 (mmmm) REVERT: C 196 ASP cc_start: 0.7994 (t0) cc_final: 0.7678 (t0) REVERT: C 197 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7311 (pp20) REVERT: C 211 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7793 (m-30) REVERT: C 277 GLU cc_start: 0.7289 (mp0) cc_final: 0.6822 (mp0) REVERT: C 293 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.7977 (tp) REVERT: C 297 GLU cc_start: 0.7378 (pm20) cc_final: 0.6804 (pm20) REVERT: C 664 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: C 709 LYS cc_start: 0.8389 (ttpt) cc_final: 0.8075 (ttpt) REVERT: C 730 GLN cc_start: 0.7832 (mt0) cc_final: 0.7621 (mt0) REVERT: D 31 LEU cc_start: 0.6261 (OUTLIER) cc_final: 0.6054 (tt) REVERT: D 89 LYS cc_start: 0.8430 (tptm) cc_final: 0.8016 (mmtt) REVERT: D 105 ILE cc_start: 0.8364 (tt) cc_final: 0.8123 (pt) REVERT: D 169 GLU cc_start: 0.7391 (mm-30) cc_final: 0.6870 (mm-30) REVERT: D 173 LYS cc_start: 0.7983 (tppt) cc_final: 0.7401 (tppt) REVERT: D 202 VAL cc_start: 0.8698 (p) cc_final: 0.8438 (m) REVERT: D 205 GLU cc_start: 0.7467 (tm-30) cc_final: 0.7001 (tm-30) REVERT: D 269 GLN cc_start: 0.8097 (tp-100) cc_final: 0.7824 (tp-100) REVERT: D 277 GLU cc_start: 0.8021 (tt0) cc_final: 0.7628 (tt0) REVERT: D 287 ASP cc_start: 0.7650 (t70) cc_final: 0.7393 (t0) REVERT: D 333 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7838 (mt-10) REVERT: D 341 GLU cc_start: 0.8164 (tp30) cc_final: 0.7843 (tp30) REVERT: D 385 ILE cc_start: 0.8868 (mt) cc_final: 0.8576 (mt) REVERT: D 428 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7637 (ttmm) REVERT: D 554 LYS cc_start: 0.8877 (mttt) cc_final: 0.8644 (mmmm) REVERT: D 570 ASP cc_start: 0.7577 (t0) cc_final: 0.7223 (t0) REVERT: D 606 GLU cc_start: 0.8324 (tp30) cc_final: 0.7839 (tp30) REVERT: D 662 GLN cc_start: 0.7538 (tp-100) cc_final: 0.7077 (tm-30) REVERT: D 698 GLU cc_start: 0.7541 (mp0) cc_final: 0.7026 (mp0) REVERT: D 749 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7554 (tm-30) REVERT: D 776 TYR cc_start: 0.8379 (t80) cc_final: 0.7775 (t80) REVERT: D 780 ILE cc_start: 0.8944 (pt) cc_final: 0.8592 (mt) REVERT: D 791 MET cc_start: 0.8588 (tmm) cc_final: 0.8034 (tmm) REVERT: D 819 MET cc_start: 0.8107 (mmt) cc_final: 0.7840 (mmt) REVERT: D 867 GLU cc_start: 0.8429 (tp30) cc_final: 0.8133 (tp30) REVERT: D 921 LYS cc_start: 0.8242 (mtpt) cc_final: 0.7980 (mtmt) REVERT: D 924 GLU cc_start: 0.7619 (tt0) cc_final: 0.7266 (tm-30) REVERT: D 942 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7546 (mm-30) REVERT: D 980 LEU cc_start: 0.8344 (tp) cc_final: 0.8117 (mt) REVERT: D 983 THR cc_start: 0.8380 (p) cc_final: 0.8120 (p) REVERT: D 1004 MET cc_start: 0.7933 (mmm) cc_final: 0.7403 (mmm) REVERT: D 1017 ASP cc_start: 0.8239 (t70) cc_final: 0.7968 (t0) REVERT: D 1048 LYS cc_start: 0.7844 (mtpt) cc_final: 0.7558 (mtpt) REVERT: D 1055 GLU cc_start: 0.8220 (tp30) cc_final: 0.7799 (tp30) REVERT: D 1077 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7809 (mm-30) REVERT: D 1109 LYS cc_start: 0.8335 (tptm) cc_final: 0.8071 (tppp) REVERT: D 1110 ILE cc_start: 0.8198 (mt) cc_final: 0.7996 (mp) REVERT: D 1139 GLU cc_start: 0.7421 (tm-30) cc_final: 0.6913 (tm-30) REVERT: D 1143 GLN cc_start: 0.7632 (mp10) cc_final: 0.7192 (mp10) outliers start: 45 outliers final: 25 residues processed: 536 average time/residue: 0.1479 time to fit residues: 118.2594 Evaluate side-chains 540 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 507 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 1281 MET Chi-restraints excluded: chain B residue 1307 THR Chi-restraints excluded: chain B residue 1314 LYS Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 664 GLU Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 770 VAL Chi-restraints excluded: chain D residue 988 SER Chi-restraints excluded: chain D residue 999 LEU Chi-restraints excluded: chain D residue 1032 ARG Chi-restraints excluded: chain D residue 1047 VAL Chi-restraints excluded: chain D residue 1056 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 173 optimal weight: 0.7980 chunk 182 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 188 optimal weight: 0.6980 chunk 96 optimal weight: 0.0270 chunk 169 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 ASN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.148421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.123464 restraints weight = 28997.087| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.99 r_work: 0.3376 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19626 Z= 0.147 Angle : 0.582 8.322 26740 Z= 0.311 Chirality : 0.042 0.199 3101 Planarity : 0.004 0.067 3141 Dihedral : 17.828 69.250 3195 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.85 % Allowed : 21.28 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.18), residues: 2177 helix: 1.30 (0.14), residues: 1299 sheet: 0.71 (0.40), residues: 166 loop : -1.21 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 311 TYR 0.021 0.002 TYR D1086 PHE 0.027 0.002 PHE B1302 TRP 0.011 0.001 TRP A1033 HIS 0.013 0.001 HIS D1123 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (19626) covalent geometry : angle 0.58197 / 0.31 (26740) hydrogen bonds : bond 0.04086 / 4.59 ( 1129) hydrogen bonds : angle 3.95760 / 4.44 ( 3275) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 523 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 VAL cc_start: 0.8116 (m) cc_final: 0.7643 (t) REVERT: B 242 GLU cc_start: 0.7143 (pm20) cc_final: 0.6793 (pm20) REVERT: B 250 ASP cc_start: 0.7874 (t0) cc_final: 0.7449 (t0) REVERT: B 252 GLU cc_start: 0.7496 (pm20) cc_final: 0.7068 (pm20) REVERT: B 263 PHE cc_start: 0.8756 (m-80) cc_final: 0.8035 (m-80) REVERT: B 264 LYS cc_start: 0.8698 (mmtt) cc_final: 0.8370 (tppt) REVERT: B 269 LYS cc_start: 0.8257 (mtpt) cc_final: 0.7846 (mtpt) REVERT: B 288 ASN cc_start: 0.8489 (t0) cc_final: 0.8118 (t0) REVERT: B 289 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7682 (mm-30) REVERT: B 292 ASP cc_start: 0.7476 (t0) cc_final: 0.7145 (t0) REVERT: B 312 LYS cc_start: 0.8546 (mptt) cc_final: 0.8323 (mptt) REVERT: B 325 GLU cc_start: 0.8201 (mp0) cc_final: 0.7745 (mp0) REVERT: B 1260 LYS cc_start: 0.7936 (mttt) cc_final: 0.7677 (mtpp) REVERT: B 1281 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.7506 (mpp) REVERT: B 1282 TYR cc_start: 0.8260 (t80) cc_final: 0.7843 (t80) REVERT: B 1373 THR cc_start: 0.8516 (t) cc_final: 0.8315 (t) REVERT: B 1405 LYS cc_start: 0.8877 (mttt) cc_final: 0.8619 (mttm) REVERT: B 1412 ILE cc_start: 0.8411 (pt) cc_final: 0.8145 (pt) REVERT: A 54 MET cc_start: 0.7623 (mmt) cc_final: 0.7360 (mmp) REVERT: A 81 ILE cc_start: 0.7995 (tt) cc_final: 0.7719 (tt) REVERT: A 109 LEU cc_start: 0.8784 (mt) cc_final: 0.8539 (mp) REVERT: A 129 GLN cc_start: 0.8008 (tm-30) cc_final: 0.7372 (tm-30) REVERT: A 156 MET cc_start: 0.7826 (mtm) cc_final: 0.7608 (mtp) REVERT: A 160 GLU cc_start: 0.7722 (mp0) cc_final: 0.7207 (mp0) REVERT: A 178 ARG cc_start: 0.7877 (tmm160) cc_final: 0.7388 (ttp-110) REVERT: A 187 LYS cc_start: 0.8864 (tppt) cc_final: 0.8545 (tppt) REVERT: A 209 LYS cc_start: 0.7674 (mmtm) cc_final: 0.7372 (mmtm) REVERT: A 217 PHE cc_start: 0.7305 (t80) cc_final: 0.6803 (t80) REVERT: A 987 MET cc_start: 0.8384 (mmm) cc_final: 0.8148 (mmm) REVERT: A 994 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7938 (mm-30) REVERT: A 1005 LYS cc_start: 0.8441 (mttt) cc_final: 0.8149 (mttp) REVERT: A 1009 LYS cc_start: 0.8465 (tttt) cc_final: 0.8204 (ttmm) REVERT: A 1016 GLU cc_start: 0.8138 (tt0) cc_final: 0.7882 (tt0) REVERT: A 1018 ILE cc_start: 0.8486 (pt) cc_final: 0.8213 (mt) REVERT: A 1026 ARG cc_start: 0.7894 (ttp80) cc_final: 0.7622 (tmt170) REVERT: A 1061 LYS cc_start: 0.7696 (mmmm) cc_final: 0.7385 (mmmm) REVERT: A 1082 ILE cc_start: 0.8689 (tp) cc_final: 0.8230 (pt) REVERT: A 1119 ASP cc_start: 0.7620 (p0) cc_final: 0.7132 (p0) REVERT: A 1146 GLU cc_start: 0.8078 (tt0) cc_final: 0.7625 (tt0) REVERT: C 42 LYS cc_start: 0.7607 (mmmt) cc_final: 0.7292 (mmmt) REVERT: C 64 LYS cc_start: 0.8569 (mtmt) cc_final: 0.8044 (mmmm) REVERT: C 174 LYS cc_start: 0.8142 (ttmm) cc_final: 0.7858 (ttmm) REVERT: C 189 LYS cc_start: 0.8409 (mmtt) cc_final: 0.8071 (mmmm) REVERT: C 196 ASP cc_start: 0.7954 (t0) cc_final: 0.7622 (t0) REVERT: C 197 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7302 (pp20) REVERT: C 211 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7744 (m-30) REVERT: C 277 GLU cc_start: 0.7293 (mp0) cc_final: 0.6819 (mp0) REVERT: C 293 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.7986 (tp) REVERT: C 297 GLU cc_start: 0.7377 (pm20) cc_final: 0.6821 (pm20) REVERT: C 664 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7027 (mp0) REVERT: C 709 LYS cc_start: 0.8392 (ttpt) cc_final: 0.8083 (ttpt) REVERT: C 730 GLN cc_start: 0.7858 (mt0) cc_final: 0.7638 (mt0) REVERT: D 31 LEU cc_start: 0.6210 (OUTLIER) cc_final: 0.6005 (tt) REVERT: D 89 LYS cc_start: 0.8387 (tptm) cc_final: 0.7967 (mmtt) REVERT: D 105 ILE cc_start: 0.8362 (tt) cc_final: 0.8066 (pt) REVERT: D 168 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7076 (mt) REVERT: D 169 GLU cc_start: 0.7360 (mm-30) cc_final: 0.7062 (mm-30) REVERT: D 173 LYS cc_start: 0.7953 (tppt) cc_final: 0.7390 (tppt) REVERT: D 202 VAL cc_start: 0.8717 (p) cc_final: 0.8454 (m) REVERT: D 205 GLU cc_start: 0.7477 (tm-30) cc_final: 0.7046 (tm-30) REVERT: D 269 GLN cc_start: 0.8123 (tp-100) cc_final: 0.7853 (tp-100) REVERT: D 277 GLU cc_start: 0.8048 (tt0) cc_final: 0.7654 (tt0) REVERT: D 287 ASP cc_start: 0.7659 (t70) cc_final: 0.7364 (t0) REVERT: D 303 GLU cc_start: 0.8308 (tm-30) cc_final: 0.8005 (tm-30) REVERT: D 333 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7791 (mt-10) REVERT: D 341 GLU cc_start: 0.8157 (tp30) cc_final: 0.7844 (tp30) REVERT: D 363 LEU cc_start: 0.8014 (mt) cc_final: 0.7718 (mp) REVERT: D 385 ILE cc_start: 0.8848 (mt) cc_final: 0.8570 (mt) REVERT: D 424 LYS cc_start: 0.8559 (tttt) cc_final: 0.8280 (tttt) REVERT: D 428 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7621 (ttmm) REVERT: D 554 LYS cc_start: 0.8871 (mttt) cc_final: 0.8562 (mtpp) REVERT: D 570 ASP cc_start: 0.7602 (t0) cc_final: 0.7231 (t0) REVERT: D 582 LYS cc_start: 0.8581 (mtpt) cc_final: 0.8326 (mtpt) REVERT: D 606 GLU cc_start: 0.8321 (tp30) cc_final: 0.7823 (tp30) REVERT: D 662 GLN cc_start: 0.7546 (tp-100) cc_final: 0.7160 (tm-30) REVERT: D 698 GLU cc_start: 0.7558 (mp0) cc_final: 0.7009 (mp0) REVERT: D 749 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7511 (tm-30) REVERT: D 776 TYR cc_start: 0.8375 (t80) cc_final: 0.7738 (t80) REVERT: D 780 ILE cc_start: 0.8965 (pt) cc_final: 0.8601 (mt) REVERT: D 791 MET cc_start: 0.8602 (tmm) cc_final: 0.8013 (tmm) REVERT: D 819 MET cc_start: 0.8126 (mmt) cc_final: 0.7887 (mmt) REVERT: D 867 GLU cc_start: 0.8409 (tp30) cc_final: 0.8165 (tp30) REVERT: D 921 LYS cc_start: 0.8263 (mtpt) cc_final: 0.8022 (mtmt) REVERT: D 924 GLU cc_start: 0.7619 (tt0) cc_final: 0.7261 (tm-30) REVERT: D 942 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7560 (mm-30) REVERT: D 980 LEU cc_start: 0.8367 (tp) cc_final: 0.8163 (mt) REVERT: D 983 THR cc_start: 0.8381 (p) cc_final: 0.8129 (p) REVERT: D 1004 MET cc_start: 0.7950 (mmm) cc_final: 0.7419 (mmm) REVERT: D 1048 LYS cc_start: 0.7831 (mtpt) cc_final: 0.7571 (mtpt) REVERT: D 1055 GLU cc_start: 0.8220 (tp30) cc_final: 0.7757 (tp30) REVERT: D 1109 LYS cc_start: 0.8379 (tptm) cc_final: 0.8127 (tppp) REVERT: D 1139 GLU cc_start: 0.7451 (tm-30) cc_final: 0.6950 (tm-30) REVERT: D 1143 GLN cc_start: 0.7601 (mp10) cc_final: 0.7174 (mp10) outliers start: 37 outliers final: 24 residues processed: 542 average time/residue: 0.1467 time to fit residues: 119.4567 Evaluate side-chains 536 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 504 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 1281 MET Chi-restraints excluded: chain B residue 1307 THR Chi-restraints excluded: chain B residue 1314 LYS Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 664 GLU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 770 VAL Chi-restraints excluded: chain D residue 857 THR Chi-restraints excluded: chain D residue 988 SER Chi-restraints excluded: chain D residue 999 LEU Chi-restraints excluded: chain D residue 1032 ARG Chi-restraints excluded: chain D residue 1047 VAL Chi-restraints excluded: chain D residue 1056 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 5 optimal weight: 5.9990 chunk 212 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 chunk 133 optimal weight: 0.5980 chunk 149 optimal weight: 0.9980 chunk 207 optimal weight: 0.3980 chunk 37 optimal weight: 0.9990 chunk 192 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 ASN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.147712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.122777 restraints weight = 28824.196| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.00 r_work: 0.3370 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19626 Z= 0.161 Angle : 0.602 10.432 26740 Z= 0.317 Chirality : 0.042 0.195 3101 Planarity : 0.004 0.068 3141 Dihedral : 17.788 69.505 3195 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.10 % Allowed : 21.33 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.18), residues: 2177 helix: 1.29 (0.14), residues: 1302 sheet: 0.79 (0.40), residues: 166 loop : -1.14 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1157 TYR 0.021 0.001 TYR D1086 PHE 0.030 0.002 PHE B1302 TRP 0.012 0.001 TRP A1033 HIS 0.012 0.001 HIS D1123 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (19626) covalent geometry : angle 0.60169 / 0.32 (26740) hydrogen bonds : bond 0.04178 / 4.70 ( 1129) hydrogen bonds : angle 3.98540 / 4.46 ( 3275) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 505 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 VAL cc_start: 0.8107 (m) cc_final: 0.7638 (t) REVERT: B 250 ASP cc_start: 0.7910 (t0) cc_final: 0.7453 (t0) REVERT: B 252 GLU cc_start: 0.7492 (pm20) cc_final: 0.7070 (pm20) REVERT: B 263 PHE cc_start: 0.8737 (m-80) cc_final: 0.8100 (m-80) REVERT: B 264 LYS cc_start: 0.8769 (mmtt) cc_final: 0.8435 (tppt) REVERT: B 269 LYS cc_start: 0.8253 (mtpt) cc_final: 0.7874 (mtpt) REVERT: B 288 ASN cc_start: 0.8486 (t0) cc_final: 0.8111 (t0) REVERT: B 289 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7674 (mm-30) REVERT: B 292 ASP cc_start: 0.7495 (t0) cc_final: 0.7171 (t0) REVERT: B 325 GLU cc_start: 0.8193 (mp0) cc_final: 0.7692 (mp0) REVERT: B 1260 LYS cc_start: 0.7926 (mttt) cc_final: 0.7664 (mtpp) REVERT: B 1281 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7544 (mpp) REVERT: B 1405 LYS cc_start: 0.8869 (mttt) cc_final: 0.8590 (mttm) REVERT: B 1412 ILE cc_start: 0.8408 (pt) cc_final: 0.8148 (pt) REVERT: A 54 MET cc_start: 0.7615 (mmt) cc_final: 0.7349 (mmp) REVERT: A 81 ILE cc_start: 0.7998 (tt) cc_final: 0.7726 (tt) REVERT: A 109 LEU cc_start: 0.8784 (mt) cc_final: 0.8524 (mp) REVERT: A 129 GLN cc_start: 0.8027 (tm-30) cc_final: 0.7388 (tm-30) REVERT: A 156 MET cc_start: 0.7854 (mtm) cc_final: 0.7632 (mtp) REVERT: A 160 GLU cc_start: 0.7724 (mp0) cc_final: 0.7219 (mp0) REVERT: A 178 ARG cc_start: 0.7875 (tmm160) cc_final: 0.7409 (ttp-110) REVERT: A 187 LYS cc_start: 0.8881 (tppt) cc_final: 0.8556 (tppt) REVERT: A 209 LYS cc_start: 0.7702 (mmtm) cc_final: 0.7352 (mmtm) REVERT: A 994 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7930 (mm-30) REVERT: A 1005 LYS cc_start: 0.8436 (mttt) cc_final: 0.8138 (mttp) REVERT: A 1009 LYS cc_start: 0.8477 (tttt) cc_final: 0.8207 (ttmm) REVERT: A 1016 GLU cc_start: 0.8141 (tt0) cc_final: 0.7871 (tt0) REVERT: A 1018 ILE cc_start: 0.8547 (pt) cc_final: 0.8303 (mt) REVERT: A 1026 ARG cc_start: 0.7907 (ttp80) cc_final: 0.7638 (tmt170) REVERT: A 1061 LYS cc_start: 0.7700 (mmmm) cc_final: 0.7371 (mmmm) REVERT: A 1082 ILE cc_start: 0.8705 (tp) cc_final: 0.8236 (pt) REVERT: A 1119 ASP cc_start: 0.7638 (p0) cc_final: 0.7149 (p0) REVERT: A 1146 GLU cc_start: 0.8055 (tt0) cc_final: 0.7601 (tt0) REVERT: C 42 LYS cc_start: 0.7632 (mmmt) cc_final: 0.7333 (mmmt) REVERT: C 64 LYS cc_start: 0.8472 (mtmt) cc_final: 0.7965 (mmmm) REVERT: C 174 LYS cc_start: 0.8137 (ttmm) cc_final: 0.7849 (ttmm) REVERT: C 189 LYS cc_start: 0.8412 (mmtt) cc_final: 0.8089 (mmmm) REVERT: C 196 ASP cc_start: 0.7982 (t0) cc_final: 0.7664 (t0) REVERT: C 197 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7295 (pp20) REVERT: C 211 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7793 (m-30) REVERT: C 277 GLU cc_start: 0.7278 (mp0) cc_final: 0.6811 (mp0) REVERT: C 293 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.7969 (tp) REVERT: C 297 GLU cc_start: 0.7393 (pm20) cc_final: 0.6858 (pm20) REVERT: C 664 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: C 709 LYS cc_start: 0.8382 (ttpt) cc_final: 0.8061 (ttpt) REVERT: C 730 GLN cc_start: 0.7839 (mt0) cc_final: 0.7612 (mt0) REVERT: D 31 LEU cc_start: 0.6272 (OUTLIER) cc_final: 0.6065 (tt) REVERT: D 89 LYS cc_start: 0.8382 (tptm) cc_final: 0.7940 (mmtt) REVERT: D 105 ILE cc_start: 0.8368 (tt) cc_final: 0.8099 (pt) REVERT: D 169 GLU cc_start: 0.7412 (mm-30) cc_final: 0.7100 (mm-30) REVERT: D 173 LYS cc_start: 0.7919 (tppt) cc_final: 0.7340 (tppt) REVERT: D 205 GLU cc_start: 0.7330 (tm-30) cc_final: 0.6896 (tm-30) REVERT: D 269 GLN cc_start: 0.8154 (tp-100) cc_final: 0.7875 (tp-100) REVERT: D 277 GLU cc_start: 0.8057 (tt0) cc_final: 0.7660 (tt0) REVERT: D 287 ASP cc_start: 0.7644 (t70) cc_final: 0.7351 (t0) REVERT: D 303 GLU cc_start: 0.8313 (tm-30) cc_final: 0.8011 (tm-30) REVERT: D 333 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7874 (mt-10) REVERT: D 341 GLU cc_start: 0.8181 (tp30) cc_final: 0.7867 (tp30) REVERT: D 363 LEU cc_start: 0.8027 (mt) cc_final: 0.7723 (mp) REVERT: D 385 ILE cc_start: 0.8854 (mt) cc_final: 0.8587 (mt) REVERT: D 424 LYS cc_start: 0.8553 (tttt) cc_final: 0.8143 (tttt) REVERT: D 428 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7653 (ttmm) REVERT: D 554 LYS cc_start: 0.8886 (mttt) cc_final: 0.8576 (mtpp) REVERT: D 570 ASP cc_start: 0.7605 (t0) cc_final: 0.7244 (t0) REVERT: D 582 LYS cc_start: 0.8596 (mtpt) cc_final: 0.8347 (mtpt) REVERT: D 606 GLU cc_start: 0.8335 (tp30) cc_final: 0.7843 (tp30) REVERT: D 662 GLN cc_start: 0.7575 (tp-100) cc_final: 0.7234 (tm-30) REVERT: D 698 GLU cc_start: 0.7579 (mp0) cc_final: 0.7065 (mp0) REVERT: D 749 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7526 (tm-30) REVERT: D 776 TYR cc_start: 0.8375 (t80) cc_final: 0.7726 (t80) REVERT: D 780 ILE cc_start: 0.8970 (pt) cc_final: 0.8593 (mt) REVERT: D 791 MET cc_start: 0.8613 (tmm) cc_final: 0.8008 (tmm) REVERT: D 819 MET cc_start: 0.8140 (mmt) cc_final: 0.7900 (mmt) REVERT: D 867 GLU cc_start: 0.8391 (tp30) cc_final: 0.8159 (tp30) REVERT: D 921 LYS cc_start: 0.8276 (mtpt) cc_final: 0.8024 (mtmt) REVERT: D 942 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7557 (mm-30) REVERT: D 980 LEU cc_start: 0.8399 (tp) cc_final: 0.8180 (mt) REVERT: D 983 THR cc_start: 0.8379 (p) cc_final: 0.8137 (p) REVERT: D 1004 MET cc_start: 0.7938 (mmm) cc_final: 0.7400 (mmm) REVERT: D 1048 LYS cc_start: 0.7862 (mtpt) cc_final: 0.7638 (mtpt) REVERT: D 1055 GLU cc_start: 0.8269 (tp30) cc_final: 0.7907 (tp30) REVERT: D 1077 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7835 (mm-30) REVERT: D 1109 LYS cc_start: 0.8402 (tptm) cc_final: 0.8146 (tppp) REVERT: D 1139 GLU cc_start: 0.7486 (tm-30) cc_final: 0.6992 (tm-30) REVERT: D 1143 GLN cc_start: 0.7600 (mp10) cc_final: 0.7179 (mp10) outliers start: 42 outliers final: 26 residues processed: 527 average time/residue: 0.1466 time to fit residues: 115.1038 Evaluate side-chains 536 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 503 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 1281 MET Chi-restraints excluded: chain B residue 1307 THR Chi-restraints excluded: chain B residue 1314 LYS Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 664 GLU Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 770 VAL Chi-restraints excluded: chain D residue 857 THR Chi-restraints excluded: chain D residue 988 SER Chi-restraints excluded: chain D residue 999 LEU Chi-restraints excluded: chain D residue 1032 ARG Chi-restraints excluded: chain D residue 1047 VAL Chi-restraints excluded: chain D residue 1056 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 26 optimal weight: 0.9990 chunk 197 optimal weight: 0.5980 chunk 62 optimal weight: 0.0050 chunk 7 optimal weight: 0.0870 chunk 183 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 192 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 overall best weight: 0.4372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 ASN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.148630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.122964 restraints weight = 29163.547| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.07 r_work: 0.3383 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19626 Z= 0.132 Angle : 0.589 9.203 26740 Z= 0.312 Chirality : 0.041 0.181 3101 Planarity : 0.004 0.066 3141 Dihedral : 17.756 69.270 3195 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.90 % Allowed : 21.68 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.18), residues: 2177 helix: 1.40 (0.14), residues: 1296 sheet: 0.83 (0.40), residues: 166 loop : -1.10 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 311 TYR 0.018 0.001 TYR D1086 PHE 0.029 0.002 PHE B1302 TRP 0.011 0.001 TRP A1033 HIS 0.010 0.001 HIS D1123 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (19626) covalent geometry : angle 0.58875 / 0.31 (26740) hydrogen bonds : bond 0.04035 / 4.53 ( 1129) hydrogen bonds : angle 3.93317 / 4.39 ( 3275) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 505 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 VAL cc_start: 0.8081 (m) cc_final: 0.7569 (t) REVERT: B 242 GLU cc_start: 0.7037 (pm20) cc_final: 0.6823 (pm20) REVERT: B 250 ASP cc_start: 0.7888 (t0) cc_final: 0.7305 (t0) REVERT: B 252 GLU cc_start: 0.7481 (pm20) cc_final: 0.6991 (pm20) REVERT: B 263 PHE cc_start: 0.8721 (m-80) cc_final: 0.8013 (m-80) REVERT: B 264 LYS cc_start: 0.8735 (mmtt) cc_final: 0.8382 (tppt) REVERT: B 269 LYS cc_start: 0.8242 (mtpt) cc_final: 0.7853 (mtpt) REVERT: B 288 ASN cc_start: 0.8482 (t0) cc_final: 0.8096 (t0) REVERT: B 289 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7744 (mm-30) REVERT: B 292 ASP cc_start: 0.7501 (t0) cc_final: 0.7136 (t0) REVERT: B 325 GLU cc_start: 0.8195 (mp0) cc_final: 0.7678 (mp0) REVERT: B 1260 LYS cc_start: 0.7916 (mttt) cc_final: 0.7662 (mtpp) REVERT: B 1405 LYS cc_start: 0.8859 (mttt) cc_final: 0.8579 (mttm) REVERT: B 1412 ILE cc_start: 0.8396 (pt) cc_final: 0.8133 (pt) REVERT: A 54 MET cc_start: 0.7592 (mmt) cc_final: 0.7329 (mmp) REVERT: A 81 ILE cc_start: 0.7978 (tt) cc_final: 0.7709 (tt) REVERT: A 109 LEU cc_start: 0.8763 (mt) cc_final: 0.8510 (mp) REVERT: A 129 GLN cc_start: 0.7981 (tm-30) cc_final: 0.7344 (tm-30) REVERT: A 156 MET cc_start: 0.7843 (mtm) cc_final: 0.7622 (mtp) REVERT: A 160 GLU cc_start: 0.7715 (mp0) cc_final: 0.7189 (mp0) REVERT: A 178 ARG cc_start: 0.7883 (tmm160) cc_final: 0.7384 (ttp-110) REVERT: A 187 LYS cc_start: 0.8857 (tppt) cc_final: 0.8516 (tppt) REVERT: A 209 LYS cc_start: 0.7645 (mmtm) cc_final: 0.7374 (mmtm) REVERT: A 217 PHE cc_start: 0.7331 (t80) cc_final: 0.7015 (t80) REVERT: A 994 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7953 (mm-30) REVERT: A 1005 LYS cc_start: 0.8428 (mttt) cc_final: 0.8130 (mttp) REVERT: A 1009 LYS cc_start: 0.8468 (tttt) cc_final: 0.8196 (ttmm) REVERT: A 1016 GLU cc_start: 0.8133 (tt0) cc_final: 0.7872 (tt0) REVERT: A 1018 ILE cc_start: 0.8471 (pt) cc_final: 0.8209 (mt) REVERT: A 1026 ARG cc_start: 0.7877 (ttp80) cc_final: 0.7602 (tmt170) REVERT: A 1061 LYS cc_start: 0.7663 (mmmm) cc_final: 0.7345 (mmmm) REVERT: A 1082 ILE cc_start: 0.8699 (tp) cc_final: 0.8214 (pt) REVERT: A 1119 ASP cc_start: 0.7642 (p0) cc_final: 0.7149 (p0) REVERT: A 1146 GLU cc_start: 0.8050 (tt0) cc_final: 0.7622 (tt0) REVERT: C 32 GLU cc_start: 0.8175 (tp30) cc_final: 0.7937 (tp30) REVERT: C 42 LYS cc_start: 0.7632 (mmmt) cc_final: 0.7305 (mmmt) REVERT: C 64 LYS cc_start: 0.8438 (mtmt) cc_final: 0.7934 (mmmm) REVERT: C 174 LYS cc_start: 0.8117 (ttmm) cc_final: 0.7833 (ttmm) REVERT: C 189 LYS cc_start: 0.8376 (mmtt) cc_final: 0.8065 (mmmm) REVERT: C 196 ASP cc_start: 0.7938 (t0) cc_final: 0.7603 (t0) REVERT: C 197 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7295 (pp20) REVERT: C 211 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7742 (m-30) REVERT: C 277 GLU cc_start: 0.7270 (mp0) cc_final: 0.6802 (mp0) REVERT: C 293 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.7980 (tp) REVERT: C 297 GLU cc_start: 0.7382 (pm20) cc_final: 0.6826 (pm20) REVERT: C 664 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7387 (mm-30) REVERT: C 709 LYS cc_start: 0.8359 (ttpt) cc_final: 0.8039 (ttpt) REVERT: C 730 GLN cc_start: 0.7835 (mt0) cc_final: 0.7611 (mt0) REVERT: D 89 LYS cc_start: 0.8376 (tptm) cc_final: 0.7931 (mmtt) REVERT: D 105 ILE cc_start: 0.8317 (tt) cc_final: 0.8058 (pt) REVERT: D 164 MET cc_start: 0.7791 (tpp) cc_final: 0.7449 (tpp) REVERT: D 169 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7070 (mm-30) REVERT: D 173 LYS cc_start: 0.7863 (tppt) cc_final: 0.7259 (tppt) REVERT: D 205 GLU cc_start: 0.7323 (tm-30) cc_final: 0.6885 (tm-30) REVERT: D 277 GLU cc_start: 0.8033 (tt0) cc_final: 0.7633 (tt0) REVERT: D 287 ASP cc_start: 0.7626 (t70) cc_final: 0.7368 (t0) REVERT: D 303 GLU cc_start: 0.8305 (tm-30) cc_final: 0.8001 (tm-30) REVERT: D 333 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7879 (mt-10) REVERT: D 341 GLU cc_start: 0.8143 (tp30) cc_final: 0.7812 (tp30) REVERT: D 363 LEU cc_start: 0.8015 (mt) cc_final: 0.7699 (mp) REVERT: D 385 ILE cc_start: 0.8839 (mt) cc_final: 0.8570 (mt) REVERT: D 424 LYS cc_start: 0.8538 (tttt) cc_final: 0.8168 (tttt) REVERT: D 428 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7612 (ttmm) REVERT: D 554 LYS cc_start: 0.8881 (mttt) cc_final: 0.8573 (mtpp) REVERT: D 570 ASP cc_start: 0.7561 (t0) cc_final: 0.7227 (t0) REVERT: D 582 LYS cc_start: 0.8575 (mtpt) cc_final: 0.8329 (mtpt) REVERT: D 606 GLU cc_start: 0.8319 (tp30) cc_final: 0.7817 (tp30) REVERT: D 661 ASP cc_start: 0.7365 (p0) cc_final: 0.6981 (p0) REVERT: D 662 GLN cc_start: 0.7567 (tp-100) cc_final: 0.6968 (tm-30) REVERT: D 698 GLU cc_start: 0.7525 (mp0) cc_final: 0.6966 (mp0) REVERT: D 749 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7501 (tm-30) REVERT: D 776 TYR cc_start: 0.8377 (t80) cc_final: 0.7732 (t80) REVERT: D 780 ILE cc_start: 0.8962 (pt) cc_final: 0.8614 (mt) REVERT: D 791 MET cc_start: 0.8593 (tmm) cc_final: 0.8018 (tmm) REVERT: D 819 MET cc_start: 0.8132 (mmt) cc_final: 0.7889 (mmt) REVERT: D 867 GLU cc_start: 0.8378 (tp30) cc_final: 0.8113 (tp30) REVERT: D 921 LYS cc_start: 0.8223 (mtpt) cc_final: 0.7967 (mtmt) REVERT: D 942 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7598 (mm-30) REVERT: D 980 LEU cc_start: 0.8375 (tp) cc_final: 0.8139 (mt) REVERT: D 983 THR cc_start: 0.8332 (p) cc_final: 0.8117 (p) REVERT: D 1004 MET cc_start: 0.7903 (mmm) cc_final: 0.7364 (mmm) REVERT: D 1055 GLU cc_start: 0.8262 (tp30) cc_final: 0.7902 (tp30) REVERT: D 1064 ASP cc_start: 0.7446 (t0) cc_final: 0.7202 (t0) REVERT: D 1077 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7831 (mm-30) REVERT: D 1137 LYS cc_start: 0.8075 (tptp) cc_final: 0.7700 (tptp) REVERT: D 1139 GLU cc_start: 0.7480 (tm-30) cc_final: 0.6964 (tm-30) REVERT: D 1143 GLN cc_start: 0.7619 (mp10) cc_final: 0.7241 (mp10) outliers start: 38 outliers final: 27 residues processed: 524 average time/residue: 0.1423 time to fit residues: 111.6951 Evaluate side-chains 538 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 506 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 1307 THR Chi-restraints excluded: chain B residue 1314 LYS Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 664 GLU Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 770 VAL Chi-restraints excluded: chain D residue 857 THR Chi-restraints excluded: chain D residue 988 SER Chi-restraints excluded: chain D residue 999 LEU Chi-restraints excluded: chain D residue 1032 ARG Chi-restraints excluded: chain D residue 1047 VAL Chi-restraints excluded: chain D residue 1056 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 38 optimal weight: 0.4980 chunk 202 optimal weight: 0.0870 chunk 204 optimal weight: 1.9990 chunk 195 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 179 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 ASN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 GLN ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1158 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.148494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.124569 restraints weight = 29052.081| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.79 r_work: 0.3406 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19626 Z= 0.140 Angle : 0.597 10.338 26740 Z= 0.314 Chirality : 0.042 0.193 3101 Planarity : 0.003 0.067 3141 Dihedral : 17.710 69.115 3195 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.95 % Allowed : 21.48 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.18), residues: 2177 helix: 1.44 (0.14), residues: 1297 sheet: 0.86 (0.40), residues: 166 loop : -1.08 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 311 TYR 0.017 0.001 TYR D1086 PHE 0.030 0.001 PHE B1302 TRP 0.011 0.001 TRP A1033 HIS 0.009 0.001 HIS D1123 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (19626) covalent geometry : angle 0.59678 / 0.31 (26740) hydrogen bonds : bond 0.04056 / 4.55 ( 1129) hydrogen bonds : angle 3.92929 / 4.37 ( 3275) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5077.93 seconds wall clock time: 87 minutes 43.87 seconds (5263.87 seconds total)