Starting phenix.real_space_refine on Tue May 20 00:19:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qen_13934/05_2025/7qen_13934.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qen_13934/05_2025/7qen_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7qen_13934/05_2025/7qen_13934.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qen_13934/05_2025/7qen_13934.map" model { file = "/net/cci-nas-00/data/ceres_data/7qen_13934/05_2025/7qen_13934.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qen_13934/05_2025/7qen_13934.cif" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 11.62, per 1000 atoms: 0.61 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: 5.25 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 7.09 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: 8.48 Time building geometry restraints manager: 6.08 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: 26513 3.79 - 7.58: 202 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: 10033 17.99 - 35.98: 1341 35.98 - 53.98: 432 53.98 - 71.97: 181 71.97 - 89.96: 20 Dihedral angle restraints: 12007 sinusoidal: 5480 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 12004 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2569 0.072 - 0.143: 481 0.143 - 0.215: 43 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 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: 0.020 Extract box with map and model: 0.850 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 51.250 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.060 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: 0.020 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 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= 0.293 Angle : 0.963 18.938 26740 Z= 0.576 Chirality : 0.055 0.358 3101 Planarity : 0.007 0.093 3141 Dihedral : 19.011 89.959 7743 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 4.07 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (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 TRP 0.017 0.002 TRP D 669 HIS 0.009 0.001 HIS D 435 PHE 0.032 0.002 PHE A 27 TYR 0.024 0.002 TYR D 529 ARG 0.012 0.001 ARG A 965 Details of bonding type rmsd hydrogen bonds : bond 0.13518 ( 1129) hydrogen bonds : angle 6.19740 ( 3275) covalent geometry : bond 0.00565 (19626) covalent geometry : angle 0.96272 (26740) *********************** 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 : 1.965 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: 0.8545 (m-80) cc_final: 0.8105 (m-80) REVERT: B 264 LYS cc_start: 0.8760 (mmtt) cc_final: 0.8289 (tppt) REVERT: B 269 LYS cc_start: 0.8014 (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: 0.8303 (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: 0.6994 (mm-30) REVERT: A 997 GLU cc_start: 0.6888 (tp30) cc_final: 0.6601 (tp30) REVERT: A 1005 LYS cc_start: 0.8048 (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: 0.8089 (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: 0.6803 (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: 0.7125 (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: 0.6644 (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: 0.3460 time to fit residues: 297.7296 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 : 1.982 ------------------------------------------------------------------------------- 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 191 optimal weight: 0.8980 chunk 172 optimal weight: 2.9990 chunk 95 optimal weight: 0.0050 chunk 58 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 177 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 206 optimal weight: 0.5980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 GLN ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 ASN B 235 HIS B 237 GLN 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 D 918 GLN D1031 GLN ** D1123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1158 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.148569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.123795 restraints weight = 29018.199| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.91 r_work: 0.3378 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1552 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= 0.162 Angle : 0.586 8.656 26740 Z= 0.320 Chirality : 0.041 0.169 3101 Planarity : 0.004 0.078 3141 Dihedral : 17.939 86.218 3261 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.40 % Allowed : 14.19 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.16), residues: 2177 helix: -0.32 (0.13), residues: 1303 sheet: 0.25 (0.41), residues: 161 loop : -2.16 (0.21), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1033 HIS 0.004 0.001 HIS B 295 PHE 0.023 0.002 PHE B1264 TYR 0.020 0.002 TYR D 529 ARG 0.008 0.000 ARG D 198 Details of bonding type rmsd hydrogen bonds : bond 0.04373 ( 1129) hydrogen bonds : angle 4.23417 ( 3275) covalent geometry : bond 0.00348 (19626) covalent geometry : angle 0.58564 (26740) *********************** 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 580 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 552 time to evaluate : 2.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 VAL cc_start: 0.8208 (m) cc_final: 0.7717 (t) REVERT: B 252 GLU cc_start: 0.7467 (pm20) cc_final: 0.7139 (pm20) REVERT: B 263 PHE cc_start: 0.8737 (m-80) cc_final: 0.8127 (m-80) REVERT: B 264 LYS cc_start: 0.8711 (mmtt) cc_final: 0.8423 (tppt) REVERT: B 269 LYS cc_start: 0.8268 (mtpt) cc_final: 0.7877 (mtpt) REVERT: B 288 ASN cc_start: 0.8518 (t0) cc_final: 0.8112 (t0) REVERT: B 289 GLU cc_start: 0.8420 (mm-30) cc_final: 0.7949 (mm-30) REVERT: B 312 LYS cc_start: 0.8671 (mptt) cc_final: 0.8425 (mptt) REVERT: B 325 GLU cc_start: 0.8142 (mp0) cc_final: 0.7727 (mp0) REVERT: B 1249 ARG cc_start: 0.7180 (tmm-80) cc_final: 0.6973 (tmm-80) REVERT: B 1260 LYS cc_start: 0.7936 (mttt) cc_final: 0.7673 (mtpp) REVERT: B 1265 ASP cc_start: 0.8255 (t0) cc_final: 0.8032 (t0) REVERT: B 1282 TYR cc_start: 0.8367 (t80) cc_final: 0.7998 (t80) REVERT: B 1292 GLU cc_start: 0.7820 (tp30) cc_final: 0.7566 (tp30) REVERT: B 1294 GLU cc_start: 0.6573 (pm20) cc_final: 0.6029 (pm20) REVERT: B 1324 SER cc_start: 0.8416 (t) cc_final: 0.8078 (p) REVERT: B 1405 LYS cc_start: 0.8793 (mttt) cc_final: 0.8571 (mmtm) REVERT: B 1412 ILE cc_start: 0.8465 (pt) cc_final: 0.8147 (pt) REVERT: A 28 ASN cc_start: 0.7907 (m-40) cc_final: 0.7678 (m-40) REVERT: A 54 MET cc_start: 0.7778 (mmt) cc_final: 0.7429 (mmt) REVERT: A 81 ILE cc_start: 0.8061 (tt) cc_final: 0.7828 (tt) REVERT: A 109 LEU cc_start: 0.8767 (mt) cc_final: 0.8533 (mp) REVERT: A 129 GLN cc_start: 0.7948 (tm-30) cc_final: 0.7364 (tm-30) REVERT: A 160 GLU cc_start: 0.7695 (mp0) cc_final: 0.7181 (mp0) REVERT: A 178 ARG cc_start: 0.7877 (tmm160) cc_final: 0.7368 (ttp-110) REVERT: A 182 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7958 (mm-30) REVERT: A 187 LYS cc_start: 0.8872 (tppt) cc_final: 0.8532 (tppt) REVERT: A 209 LYS cc_start: 0.7704 (mmtm) cc_final: 0.7351 (mmtm) REVERT: A 217 PHE cc_start: 0.7416 (t80) cc_final: 0.7201 (t80) REVERT: A 985 ASN cc_start: 0.8062 (p0) cc_final: 0.7658 (p0) REVERT: A 994 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7893 (mm-30) REVERT: A 1005 LYS cc_start: 0.8434 (mttt) cc_final: 0.8191 (mttp) REVERT: A 1008 GLU cc_start: 0.7831 (tp30) cc_final: 0.7586 (tp30) REVERT: A 1009 LYS cc_start: 0.8473 (tttt) cc_final: 0.8200 (ttmm) REVERT: A 1016 GLU cc_start: 0.8100 (tt0) cc_final: 0.7768 (tt0) REVERT: A 1018 ILE cc_start: 0.8537 (pt) cc_final: 0.8148 (mt) REVERT: A 1023 GLU cc_start: 0.7820 (tp30) cc_final: 0.7528 (tp30) REVERT: A 1082 ILE cc_start: 0.8607 (tp) cc_final: 0.8114 (pt) REVERT: A 1119 ASP cc_start: 0.7509 (p0) cc_final: 0.6955 (p0) REVERT: A 1146 GLU cc_start: 0.8037 (tt0) cc_final: 0.7552 (tt0) REVERT: C 42 LYS cc_start: 0.7638 (mmmt) cc_final: 0.7318 (mmmt) REVERT: C 64 LYS cc_start: 0.8536 (mtmt) cc_final: 0.8020 (mmmm) REVERT: C 99 LYS cc_start: 0.8597 (mtpt) cc_final: 0.8378 (mttp) REVERT: C 189 LYS cc_start: 0.8392 (mmtt) cc_final: 0.8080 (mmmm) REVERT: C 196 ASP cc_start: 0.7939 (t0) cc_final: 0.7586 (t0) REVERT: C 197 GLU cc_start: 0.7765 (pp20) cc_final: 0.7266 (pp20) REVERT: C 277 GLU cc_start: 0.7273 (mp0) cc_final: 0.6875 (mp0) REVERT: C 279 GLU cc_start: 0.7289 (tp30) cc_final: 0.6817 (tp30) REVERT: C 293 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.7890 (tp) REVERT: C 297 GLU cc_start: 0.7236 (pm20) cc_final: 0.6712 (pm20) REVERT: C 664 GLU cc_start: 0.7584 (mp0) cc_final: 0.6897 (mp0) REVERT: C 705 ASP cc_start: 0.8407 (t0) cc_final: 0.8068 (t0) REVERT: C 709 LYS cc_start: 0.8410 (ttpt) cc_final: 0.8069 (ttpt) REVERT: C 730 GLN cc_start: 0.7800 (mt0) cc_final: 0.7588 (mt0) REVERT: D 89 LYS cc_start: 0.8433 (tptm) cc_final: 0.8054 (mmtt) REVERT: D 105 ILE cc_start: 0.8222 (tt) cc_final: 0.8004 (tt) REVERT: D 117 TYR cc_start: 0.7810 (t80) cc_final: 0.7568 (t80) REVERT: D 158 LYS cc_start: 0.7742 (mtmm) cc_final: 0.7409 (mttp) REVERT: D 165 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7808 (tm-30) REVERT: D 173 LYS cc_start: 0.8114 (tppt) cc_final: 0.7900 (tppt) REVERT: D 202 VAL cc_start: 0.8713 (p) cc_final: 0.8456 (m) REVERT: D 205 GLU cc_start: 0.7383 (tm-30) cc_final: 0.7033 (tm-30) REVERT: D 269 GLN cc_start: 0.8038 (tp-100) cc_final: 0.7795 (tp-100) REVERT: D 277 GLU cc_start: 0.8004 (tt0) cc_final: 0.7783 (tt0) REVERT: D 287 ASP cc_start: 0.7723 (t70) cc_final: 0.7386 (t0) REVERT: D 303 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7985 (tm-30) REVERT: D 341 GLU cc_start: 0.7962 (tp30) cc_final: 0.7667 (tp30) REVERT: D 363 LEU cc_start: 0.7984 (mt) cc_final: 0.7685 (mp) REVERT: D 364 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7697 (mt-10) REVERT: D 424 LYS cc_start: 0.8504 (tppp) cc_final: 0.8255 (mttt) REVERT: D 554 LYS cc_start: 0.8827 (mttt) cc_final: 0.8573 (mtpp) REVERT: D 570 ASP cc_start: 0.7532 (t0) cc_final: 0.7120 (t0) REVERT: D 606 GLU cc_start: 0.8267 (tp30) cc_final: 0.7987 (tp30) REVERT: D 662 GLN cc_start: 0.7438 (tp-100) cc_final: 0.6817 (tm-30) REVERT: D 698 GLU cc_start: 0.7433 (mp0) cc_final: 0.7031 (mp0) REVERT: D 722 LEU cc_start: 0.8950 (tp) cc_final: 0.8625 (tt) REVERT: D 749 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7543 (tm-30) REVERT: D 776 TYR cc_start: 0.8348 (t80) cc_final: 0.7670 (t80) REVERT: D 780 ILE cc_start: 0.8929 (pt) cc_final: 0.8584 (mt) REVERT: D 815 ARG cc_start: 0.8054 (ttm170) cc_final: 0.7808 (mtt90) REVERT: D 867 GLU cc_start: 0.8460 (tp30) cc_final: 0.8162 (tp30) REVERT: D 921 LYS cc_start: 0.8298 (mtpt) cc_final: 0.8070 (mtmt) REVERT: D 924 GLU cc_start: 0.7628 (tt0) cc_final: 0.7192 (tm-30) REVERT: D 942 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7469 (mm-30) REVERT: D 987 LYS cc_start: 0.8732 (ptpt) cc_final: 0.8528 (ptpt) REVERT: D 1017 ASP cc_start: 0.8222 (t70) cc_final: 0.7779 (t0) REVERT: D 1048 LYS cc_start: 0.7907 (mtpt) cc_final: 0.7485 (mtpt) REVERT: D 1055 GLU cc_start: 0.7909 (tp30) cc_final: 0.7666 (tp30) REVERT: D 1064 ASP cc_start: 0.7520 (t0) cc_final: 0.7301 (t0) REVERT: D 1072 ARG cc_start: 0.8138 (ttm110) cc_final: 0.7929 (ttm110) REVERT: D 1109 LYS cc_start: 0.8338 (tptm) cc_final: 0.8088 (tppp) REVERT: D 1139 GLU cc_start: 0.7252 (tm-30) cc_final: 0.6780 (tm-30) REVERT: D 1143 GLN cc_start: 0.7650 (mp10) cc_final: 0.7234 (mp10) outliers start: 28 outliers final: 12 residues processed: 564 average time/residue: 0.3732 time to fit residues: 306.6021 Evaluate side-chains 526 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 513 time to evaluate : 2.032 ------------------------------------------------------------------------------- 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 74 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 1047 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 116 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 144 optimal weight: 0.5980 chunk 122 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 171 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 ASN B 307 ASN B1340 HIS ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1102 GLN C 653 ASN D 72 GLN D 120 GLN D 266 ASN ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1158 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.147848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.123116 restraints weight = 29057.012| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.95 r_work: 0.3372 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19626 Z= 0.166 Angle : 0.567 8.303 26740 Z= 0.308 Chirality : 0.041 0.192 3101 Planarity : 0.004 0.075 3141 Dihedral : 18.132 86.370 3257 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.15 % Allowed : 16.78 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.17), residues: 2177 helix: 0.62 (0.14), residues: 1299 sheet: 0.49 (0.41), residues: 161 loop : -1.78 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 23 HIS 0.006 0.001 HIS D1123 PHE 0.024 0.002 PHE B1302 TYR 0.020 0.002 TYR D1086 ARG 0.006 0.000 ARG D 198 Details of bonding type rmsd hydrogen bonds : bond 0.04219 ( 1129) hydrogen bonds : angle 4.02893 ( 3275) covalent geometry : bond 0.00369 (19626) covalent geometry : angle 0.56730 (26740) *********************** 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 570 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 527 time to evaluate : 2.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 VAL cc_start: 0.8171 (m) cc_final: 0.7659 (t) REVERT: B 213 ARG cc_start: 0.8079 (mtm110) cc_final: 0.7679 (mtm110) REVERT: B 214 LEU cc_start: 0.8784 (mt) cc_final: 0.8490 (mt) REVERT: B 252 GLU cc_start: 0.7450 (pm20) cc_final: 0.7129 (pm20) REVERT: B 263 PHE cc_start: 0.8766 (m-80) cc_final: 0.8153 (m-80) REVERT: B 264 LYS cc_start: 0.8768 (mmtt) cc_final: 0.8415 (tppt) REVERT: B 269 LYS cc_start: 0.8255 (mtpt) cc_final: 0.7950 (mtpt) REVERT: B 288 ASN cc_start: 0.8480 (t0) cc_final: 0.8100 (t0) REVERT: B 289 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7671 (mm-30) REVERT: B 312 LYS cc_start: 0.8585 (mptt) cc_final: 0.8326 (mptt) REVERT: B 325 GLU cc_start: 0.8155 (mp0) cc_final: 0.7733 (mp0) REVERT: B 329 ASP cc_start: 0.7729 (t0) cc_final: 0.7511 (t0) REVERT: B 1249 ARG cc_start: 0.7252 (tmm-80) cc_final: 0.7005 (tmm-80) REVERT: B 1260 LYS cc_start: 0.7906 (mttt) cc_final: 0.7660 (mtpp) REVERT: B 1265 ASP cc_start: 0.8212 (t0) cc_final: 0.7985 (t0) REVERT: B 1292 GLU cc_start: 0.7783 (tp30) cc_final: 0.7474 (tp30) REVERT: B 1294 GLU cc_start: 0.6543 (pm20) cc_final: 0.5837 (pm20) REVERT: B 1324 SER cc_start: 0.8550 (t) cc_final: 0.8225 (p) REVERT: B 1405 LYS cc_start: 0.8807 (mttt) cc_final: 0.8569 (mttm) REVERT: B 1412 ILE cc_start: 0.8424 (pt) cc_final: 0.8124 (pt) REVERT: A 49 LEU cc_start: 0.8578 (mt) cc_final: 0.8365 (mp) REVERT: A 54 MET cc_start: 0.7624 (mmt) cc_final: 0.7296 (mmt) REVERT: A 81 ILE cc_start: 0.7991 (tt) cc_final: 0.7722 (tt) REVERT: A 109 LEU cc_start: 0.8800 (mt) cc_final: 0.8538 (mp) REVERT: A 129 GLN cc_start: 0.7986 (tm-30) cc_final: 0.7396 (tm-30) REVERT: A 160 GLU cc_start: 0.7685 (mp0) cc_final: 0.7103 (mp0) REVERT: A 178 ARG cc_start: 0.7886 (tmm160) cc_final: 0.7356 (ttp-110) REVERT: A 182 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7922 (mm-30) REVERT: A 187 LYS cc_start: 0.8885 (tppt) cc_final: 0.8573 (tppt) REVERT: A 209 LYS cc_start: 0.7755 (mmtm) cc_final: 0.7454 (mmtm) REVERT: A 985 ASN cc_start: 0.8129 (p0) cc_final: 0.7743 (p0) REVERT: A 994 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7915 (mm-30) REVERT: A 1005 LYS cc_start: 0.8441 (mttt) cc_final: 0.8205 (mttp) REVERT: A 1009 LYS cc_start: 0.8462 (tttt) cc_final: 0.8211 (ttmm) REVERT: A 1016 GLU cc_start: 0.8066 (tt0) cc_final: 0.7774 (tt0) REVERT: A 1018 ILE cc_start: 0.8567 (pt) cc_final: 0.8295 (mt) REVERT: A 1082 ILE cc_start: 0.8666 (tp) cc_final: 0.8156 (pt) REVERT: A 1119 ASP cc_start: 0.7556 (p0) cc_final: 0.7028 (p0) REVERT: A 1146 GLU cc_start: 0.8054 (tt0) cc_final: 0.7475 (tt0) REVERT: A 1157 ARG cc_start: 0.8507 (mtp85) cc_final: 0.8002 (mtp85) REVERT: C 42 LYS cc_start: 0.7568 (mmmt) cc_final: 0.7238 (mmmt) REVERT: C 64 LYS cc_start: 0.8569 (mtmt) cc_final: 0.8060 (mmmm) REVERT: C 170 PHE cc_start: 0.8083 (t80) cc_final: 0.7731 (t80) REVERT: C 174 LYS cc_start: 0.8127 (ttmm) cc_final: 0.7768 (ttmm) REVERT: C 189 LYS cc_start: 0.8412 (mmtt) cc_final: 0.8095 (mmmm) REVERT: C 196 ASP cc_start: 0.7914 (t0) cc_final: 0.7570 (t0) REVERT: C 197 GLU cc_start: 0.7776 (pp20) cc_final: 0.7248 (pp20) REVERT: C 277 GLU cc_start: 0.7314 (mp0) cc_final: 0.6881 (mp0) REVERT: C 297 GLU cc_start: 0.7230 (pm20) cc_final: 0.6687 (pm20) REVERT: C 664 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.6991 (mp0) REVERT: C 705 ASP cc_start: 0.8429 (t0) cc_final: 0.8113 (t0) REVERT: C 709 LYS cc_start: 0.8391 (ttpt) cc_final: 0.8079 (ttpt) REVERT: D 31 LEU cc_start: 0.6218 (OUTLIER) cc_final: 0.6010 (tt) REVERT: D 89 LYS cc_start: 0.8460 (tptm) cc_final: 0.8077 (mmtt) REVERT: D 117 TYR cc_start: 0.7884 (t80) cc_final: 0.7514 (t80) REVERT: D 127 GLN cc_start: 0.7959 (pp30) cc_final: 0.7553 (tm-30) REVERT: D 165 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7816 (tm-30) REVERT: D 169 GLU cc_start: 0.7397 (mm-30) cc_final: 0.6899 (mm-30) REVERT: D 173 LYS cc_start: 0.8120 (tppt) cc_final: 0.7910 (tppt) REVERT: D 202 VAL cc_start: 0.8755 (p) cc_final: 0.8480 (m) REVERT: D 205 GLU cc_start: 0.7334 (tm-30) cc_final: 0.6942 (tm-30) REVERT: D 269 GLN cc_start: 0.8093 (tp-100) cc_final: 0.7828 (tp-100) REVERT: D 277 GLU cc_start: 0.7926 (tt0) cc_final: 0.7673 (tt0) REVERT: D 287 ASP cc_start: 0.7665 (t70) cc_final: 0.7448 (t0) REVERT: D 333 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7945 (mt-10) REVERT: D 341 GLU cc_start: 0.8038 (tp30) cc_final: 0.7745 (tp30) REVERT: D 363 LEU cc_start: 0.8010 (mt) cc_final: 0.7712 (mp) REVERT: D 364 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7714 (mt-10) REVERT: D 394 LYS cc_start: 0.7941 (tptp) cc_final: 0.7735 (tptp) REVERT: D 554 LYS cc_start: 0.8846 (mttt) cc_final: 0.8591 (mtpp) REVERT: D 570 ASP cc_start: 0.7630 (t0) cc_final: 0.7241 (t0) REVERT: D 606 GLU cc_start: 0.8274 (tp30) cc_final: 0.7835 (tp30) REVERT: D 662 GLN cc_start: 0.7427 (tp-100) cc_final: 0.6833 (tm-30) REVERT: D 698 GLU cc_start: 0.7480 (mp0) cc_final: 0.6971 (mp0) REVERT: D 722 LEU cc_start: 0.8925 (tp) cc_final: 0.8612 (tt) REVERT: D 749 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7524 (tm-30) REVERT: D 776 TYR cc_start: 0.8384 (t80) cc_final: 0.7726 (t80) REVERT: D 780 ILE cc_start: 0.8972 (pt) cc_final: 0.8610 (mt) REVERT: D 867 GLU cc_start: 0.8466 (tp30) cc_final: 0.8188 (tp30) REVERT: D 921 LYS cc_start: 0.8280 (mtpt) cc_final: 0.8023 (mtmt) REVERT: D 924 GLU cc_start: 0.7603 (tt0) cc_final: 0.7365 (tm-30) REVERT: D 942 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7563 (mm-30) REVERT: D 1004 MET cc_start: 0.7970 (mmm) cc_final: 0.7473 (mmm) REVERT: D 1017 ASP cc_start: 0.8259 (t70) cc_final: 0.7864 (t0) REVERT: D 1036 MET cc_start: 0.8091 (mmm) cc_final: 0.7738 (tpt) REVERT: D 1048 LYS cc_start: 0.7898 (mtpt) cc_final: 0.7148 (mtpt) REVERT: D 1055 GLU cc_start: 0.7967 (tp30) cc_final: 0.7653 (tp30) REVERT: D 1058 LYS cc_start: 0.8563 (mttp) cc_final: 0.8314 (mptt) REVERT: D 1064 ASP cc_start: 0.7484 (t0) cc_final: 0.7255 (t0) REVERT: D 1070 MET cc_start: 0.7392 (tpp) cc_final: 0.6694 (tpp) REVERT: D 1072 ARG cc_start: 0.8121 (ttm110) cc_final: 0.7901 (ttm110) REVERT: D 1077 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7764 (mm-30) REVERT: D 1109 LYS cc_start: 0.8370 (tptm) cc_final: 0.8130 (tppp) REVERT: D 1128 ASN cc_start: 0.8493 (t0) cc_final: 0.8057 (m-40) REVERT: D 1139 GLU cc_start: 0.7295 (tm-30) cc_final: 0.6878 (tm-30) REVERT: D 1143 GLN cc_start: 0.7608 (mp10) cc_final: 0.7256 (mp10) outliers start: 43 outliers final: 21 residues processed: 549 average time/residue: 0.3470 time to fit residues: 280.2645 Evaluate side-chains 525 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 502 time to evaluate : 2.155 ------------------------------------------------------------------------------- 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 268 SER 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 79 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1019 SER Chi-restraints excluded: chain C residue 172 THR 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 217 MET 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 549 ASN 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 1104 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 85 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 111 optimal weight: 0.0980 chunk 176 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 ASN B 266 ASN ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 ASN ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1123 HIS ** 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 = 0.3886 r_free = 0.3886 target = 0.148271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.123491 restraints weight = 29213.878| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.97 r_work: 0.3390 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19626 Z= 0.146 Angle : 0.542 7.003 26740 Z= 0.294 Chirality : 0.040 0.175 3101 Planarity : 0.004 0.071 3141 Dihedral : 17.901 85.420 3257 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.45 % Allowed : 17.98 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.18), residues: 2177 helix: 1.07 (0.14), residues: 1299 sheet: 0.61 (0.40), residues: 161 loop : -1.51 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1033 HIS 0.009 0.001 HIS D1123 PHE 0.024 0.001 PHE B1302 TYR 0.024 0.001 TYR D1086 ARG 0.004 0.000 ARG D 198 Details of bonding type rmsd hydrogen bonds : bond 0.03990 ( 1129) hydrogen bonds : angle 3.88214 ( 3275) covalent geometry : bond 0.00322 (19626) covalent geometry : angle 0.54219 (26740) *********************** 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 570 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 521 time to evaluate : 2.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 VAL cc_start: 0.8088 (m) cc_final: 0.7585 (t) REVERT: B 213 ARG cc_start: 0.8047 (mtm110) cc_final: 0.7747 (mtm110) REVERT: B 214 LEU cc_start: 0.8716 (mt) cc_final: 0.8455 (mt) REVERT: B 252 GLU cc_start: 0.7447 (pm20) cc_final: 0.7157 (pm20) REVERT: B 263 PHE cc_start: 0.8741 (m-80) cc_final: 0.8040 (m-80) REVERT: B 264 LYS cc_start: 0.8696 (mmtt) cc_final: 0.8344 (tppt) REVERT: B 269 LYS cc_start: 0.8316 (mtpt) cc_final: 0.8061 (mtpt) REVERT: B 288 ASN cc_start: 0.8460 (t0) cc_final: 0.8094 (t0) REVERT: B 289 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7631 (mm-30) REVERT: B 312 LYS cc_start: 0.8551 (mptt) cc_final: 0.8325 (mptt) REVERT: B 325 GLU cc_start: 0.8140 (mp0) cc_final: 0.7709 (mp0) REVERT: B 1249 ARG cc_start: 0.7352 (tmm-80) cc_final: 0.7089 (tmm-80) REVERT: B 1260 LYS cc_start: 0.7915 (mttt) cc_final: 0.7678 (mtpp) REVERT: B 1265 ASP cc_start: 0.8264 (t0) cc_final: 0.8038 (t0) REVERT: B 1292 GLU cc_start: 0.7749 (tp30) cc_final: 0.7504 (tp30) REVERT: B 1294 GLU cc_start: 0.6676 (pm20) cc_final: 0.6405 (pm20) REVERT: B 1310 VAL cc_start: 0.8627 (OUTLIER) cc_final: 0.8322 (p) REVERT: B 1324 SER cc_start: 0.8524 (t) cc_final: 0.8219 (p) REVERT: B 1405 LYS cc_start: 0.8841 (mttt) cc_final: 0.8593 (mttm) REVERT: B 1412 ILE cc_start: 0.8418 (pt) cc_final: 0.8118 (pt) REVERT: B 1413 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.8179 (t0) REVERT: A 54 MET cc_start: 0.7549 (mmt) cc_final: 0.7183 (mmt) REVERT: A 81 ILE cc_start: 0.7961 (tt) cc_final: 0.7702 (tt) REVERT: A 109 LEU cc_start: 0.8783 (mt) cc_final: 0.8530 (mp) REVERT: A 129 GLN cc_start: 0.7997 (tm-30) cc_final: 0.7383 (tm-30) REVERT: A 160 GLU cc_start: 0.7688 (mp0) cc_final: 0.7086 (mp0) REVERT: A 178 ARG cc_start: 0.7839 (tmm160) cc_final: 0.7351 (ttp-110) REVERT: A 187 LYS cc_start: 0.8869 (tppt) cc_final: 0.8553 (tppt) REVERT: A 189 GLU cc_start: 0.8136 (tp30) cc_final: 0.7756 (tp30) REVERT: A 209 LYS cc_start: 0.7673 (mmtm) cc_final: 0.7401 (mmtm) REVERT: A 217 PHE cc_start: 0.7262 (t80) cc_final: 0.6684 (t80) REVERT: A 985 ASN cc_start: 0.8149 (p0) cc_final: 0.7734 (p0) REVERT: A 987 MET cc_start: 0.8353 (mmm) cc_final: 0.8116 (mmm) REVERT: A 994 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7880 (mm-30) REVERT: A 1005 LYS cc_start: 0.8404 (mttt) cc_final: 0.8174 (mttp) REVERT: A 1009 LYS cc_start: 0.8434 (tttt) cc_final: 0.8166 (ttmm) REVERT: A 1016 GLU cc_start: 0.8055 (tt0) cc_final: 0.7784 (tt0) REVERT: A 1018 ILE cc_start: 0.8549 (pt) cc_final: 0.8327 (mt) REVERT: A 1082 ILE cc_start: 0.8709 (tp) cc_final: 0.8213 (pt) REVERT: A 1119 ASP cc_start: 0.7562 (p0) cc_final: 0.7040 (p0) REVERT: A 1146 GLU cc_start: 0.8035 (tt0) cc_final: 0.7598 (tt0) REVERT: C 32 GLU cc_start: 0.8187 (tp30) cc_final: 0.7948 (tp30) REVERT: C 42 LYS cc_start: 0.7563 (mmmt) cc_final: 0.7269 (mmmt) REVERT: C 64 LYS cc_start: 0.8555 (mtmt) cc_final: 0.8046 (mmmm) REVERT: C 170 PHE cc_start: 0.8093 (t80) cc_final: 0.7619 (t80) REVERT: C 174 LYS cc_start: 0.8147 (ttmm) cc_final: 0.7814 (ttmm) REVERT: C 189 LYS cc_start: 0.8402 (mmtt) cc_final: 0.8079 (mmmm) REVERT: C 196 ASP cc_start: 0.7937 (t0) cc_final: 0.7644 (t0) REVERT: C 197 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7300 (pp20) REVERT: C 277 GLU cc_start: 0.7281 (mp0) cc_final: 0.6872 (mp0) REVERT: C 293 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8000 (tp) REVERT: C 297 GLU cc_start: 0.7268 (pm20) cc_final: 0.6711 (pm20) REVERT: C 664 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7421 (mm-30) REVERT: C 705 ASP cc_start: 0.8367 (t0) cc_final: 0.8063 (t0) REVERT: C 709 LYS cc_start: 0.8405 (ttpt) cc_final: 0.8084 (ttpt) REVERT: D 31 LEU cc_start: 0.6177 (OUTLIER) cc_final: 0.5960 (tt) REVERT: D 89 LYS cc_start: 0.8425 (tptm) cc_final: 0.8017 (mmtt) REVERT: D 105 ILE cc_start: 0.8323 (tt) cc_final: 0.8071 (pt) REVERT: D 117 TYR cc_start: 0.7840 (t80) cc_final: 0.7512 (t80) REVERT: D 127 GLN cc_start: 0.7962 (pp30) cc_final: 0.7542 (tm-30) REVERT: D 173 LYS cc_start: 0.8072 (tppt) cc_final: 0.7438 (tppt) REVERT: D 202 VAL cc_start: 0.8719 (p) cc_final: 0.8454 (m) REVERT: D 205 GLU cc_start: 0.7337 (tm-30) cc_final: 0.6907 (tm-30) REVERT: D 269 GLN cc_start: 0.8033 (tp-100) cc_final: 0.7777 (tp-100) REVERT: D 277 GLU cc_start: 0.7960 (tt0) cc_final: 0.7627 (tt0) REVERT: D 287 ASP cc_start: 0.7621 (t70) cc_final: 0.7324 (t0) REVERT: D 303 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7997 (tm-30) REVERT: D 312 GLN cc_start: 0.8241 (mm-40) cc_final: 0.7664 (mm-40) REVERT: D 341 GLU cc_start: 0.8041 (tp30) cc_final: 0.7736 (tp30) REVERT: D 364 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7762 (mt-10) REVERT: D 385 ILE cc_start: 0.8839 (mt) cc_final: 0.8571 (mt) REVERT: D 424 LYS cc_start: 0.8532 (tttt) cc_final: 0.8131 (tttt) REVERT: D 554 LYS cc_start: 0.8855 (mttt) cc_final: 0.8603 (mtpp) REVERT: D 570 ASP cc_start: 0.7587 (t0) cc_final: 0.7253 (t0) REVERT: D 606 GLU cc_start: 0.8313 (tp30) cc_final: 0.7846 (tp30) REVERT: D 662 GLN cc_start: 0.7409 (tp-100) cc_final: 0.6949 (tm-30) REVERT: D 698 GLU cc_start: 0.7506 (mp0) cc_final: 0.6970 (mp0) REVERT: D 749 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7489 (tm-30) REVERT: D 776 TYR cc_start: 0.8359 (t80) cc_final: 0.7755 (t80) REVERT: D 780 ILE cc_start: 0.8953 (pt) cc_final: 0.8634 (mt) REVERT: D 791 MET cc_start: 0.8566 (tmm) cc_final: 0.8166 (tmm) REVERT: D 867 GLU cc_start: 0.8377 (tp30) cc_final: 0.8124 (tp30) REVERT: D 921 LYS cc_start: 0.8267 (mtpt) cc_final: 0.8039 (mtmt) REVERT: D 924 GLU cc_start: 0.7618 (tt0) cc_final: 0.7366 (tm-30) REVERT: D 942 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7589 (mm-30) REVERT: D 1004 MET cc_start: 0.7886 (mmm) cc_final: 0.7378 (mmm) REVERT: D 1017 ASP cc_start: 0.8256 (t70) cc_final: 0.7949 (t0) REVERT: D 1036 MET cc_start: 0.8151 (mmm) cc_final: 0.7913 (mmt) REVERT: D 1055 GLU cc_start: 0.7959 (tp30) cc_final: 0.7637 (tp30) REVERT: D 1058 LYS cc_start: 0.8513 (mttp) cc_final: 0.8283 (mptt) REVERT: D 1064 ASP cc_start: 0.7458 (t0) cc_final: 0.7255 (t0) REVERT: D 1070 MET cc_start: 0.7381 (tpp) cc_final: 0.7013 (tpp) REVERT: D 1072 ARG cc_start: 0.8127 (ttm110) cc_final: 0.7896 (ttm110) REVERT: D 1077 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7863 (mm-30) REVERT: D 1109 LYS cc_start: 0.8364 (tptm) cc_final: 0.8110 (tppp) REVERT: D 1128 ASN cc_start: 0.8496 (t0) cc_final: 0.8069 (m-40) REVERT: D 1139 GLU cc_start: 0.7341 (tm-30) cc_final: 0.6855 (tm-30) REVERT: D 1143 GLN cc_start: 0.7622 (mp10) cc_final: 0.7218 (mp10) outliers start: 49 outliers final: 19 residues processed: 547 average time/residue: 0.3411 time to fit residues: 275.2914 Evaluate side-chains 529 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 504 time to evaluate : 2.095 ------------------------------------------------------------------------------- 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 296 LYS Chi-restraints excluded: chain B residue 1310 VAL Chi-restraints excluded: chain B residue 1314 LYS Chi-restraints excluded: chain B residue 1413 ASP 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 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 78 SER Chi-restraints excluded: chain D residue 407 LEU 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 Chi-restraints excluded: chain D residue 1104 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 29 optimal weight: 0.3980 chunk 67 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 91 optimal weight: 0.0870 chunk 139 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 189 optimal weight: 4.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 ASN C 23 ASN C 659 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** ** D 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1123 HIS ** 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 = 0.3887 r_free = 0.3887 target = 0.148347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.123664 restraints weight = 29180.219| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.97 r_work: 0.3382 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2394 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= 0.144 Angle : 0.541 9.582 26740 Z= 0.294 Chirality : 0.040 0.168 3101 Planarity : 0.003 0.069 3141 Dihedral : 17.815 88.825 3257 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.05 % Allowed : 17.93 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.18), residues: 2177 helix: 1.27 (0.14), residues: 1300 sheet: 0.73 (0.40), residues: 161 loop : -1.34 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1033 HIS 0.010 0.001 HIS D1123 PHE 0.024 0.001 PHE B1302 TYR 0.022 0.001 TYR D1086 ARG 0.004 0.000 ARG A1157 Details of bonding type rmsd hydrogen bonds : bond 0.03972 ( 1129) hydrogen bonds : angle 3.83998 ( 3275) covalent geometry : bond 0.00320 (19626) covalent geometry : angle 0.54148 (26740) *********************** 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 580 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 519 time to evaluate : 2.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 VAL cc_start: 0.8031 (m) cc_final: 0.7524 (t) REVERT: B 214 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8354 (tp) REVERT: B 216 ASP cc_start: 0.7790 (m-30) cc_final: 0.7557 (m-30) REVERT: B 252 GLU cc_start: 0.7426 (pm20) cc_final: 0.7026 (pm20) REVERT: B 263 PHE cc_start: 0.8732 (m-80) cc_final: 0.7979 (m-80) REVERT: B 264 LYS cc_start: 0.8755 (mmtt) cc_final: 0.8411 (tppt) REVERT: B 269 LYS cc_start: 0.8323 (mtpt) cc_final: 0.7975 (mtpt) REVERT: B 281 GLU cc_start: 0.8030 (tp30) cc_final: 0.7672 (tp30) REVERT: B 288 ASN cc_start: 0.8439 (t0) cc_final: 0.8069 (t0) REVERT: B 289 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7829 (mm-30) REVERT: B 292 ASP cc_start: 0.7438 (t0) cc_final: 0.7157 (t0) REVERT: B 312 LYS cc_start: 0.8573 (mptt) cc_final: 0.8360 (mptt) REVERT: B 325 GLU cc_start: 0.8147 (mp0) cc_final: 0.7698 (mp0) REVERT: B 1249 ARG cc_start: 0.7379 (tmm-80) cc_final: 0.7093 (tmm-80) REVERT: B 1260 LYS cc_start: 0.7884 (mttt) cc_final: 0.7638 (mtpp) REVERT: B 1265 ASP cc_start: 0.8272 (t0) cc_final: 0.8022 (t0) REVERT: B 1281 MET cc_start: 0.8111 (mmm) cc_final: 0.7661 (mpp) REVERT: B 1317 TRP cc_start: 0.8430 (m100) cc_final: 0.8127 (m100) REVERT: B 1322 ASN cc_start: 0.8167 (p0) cc_final: 0.7661 (t0) REVERT: B 1405 LYS cc_start: 0.8836 (mttt) cc_final: 0.8577 (mttm) REVERT: B 1412 ILE cc_start: 0.8408 (pt) cc_final: 0.8139 (pt) REVERT: A 81 ILE cc_start: 0.7953 (tt) cc_final: 0.7696 (tt) REVERT: A 109 LEU cc_start: 0.8780 (mt) cc_final: 0.8516 (mp) REVERT: A 129 GLN cc_start: 0.8002 (tm-30) cc_final: 0.7388 (tm-30) REVERT: A 160 GLU cc_start: 0.7744 (mp0) cc_final: 0.7153 (mp0) REVERT: A 175 GLU cc_start: 0.7565 (tp30) cc_final: 0.7253 (tp30) REVERT: A 178 ARG cc_start: 0.7846 (tmm160) cc_final: 0.7283 (ttp-110) REVERT: A 187 LYS cc_start: 0.8865 (tppt) cc_final: 0.8546 (tppt) REVERT: A 208 GLU cc_start: 0.6431 (OUTLIER) cc_final: 0.6208 (pp20) REVERT: A 209 LYS cc_start: 0.7721 (mmtm) cc_final: 0.7336 (mmtm) REVERT: A 217 PHE cc_start: 0.7258 (t80) cc_final: 0.6630 (t80) REVERT: A 957 GLU cc_start: 0.3339 (OUTLIER) cc_final: 0.2946 (mp0) REVERT: A 985 ASN cc_start: 0.8158 (p0) cc_final: 0.7763 (p0) REVERT: A 987 MET cc_start: 0.8391 (mmm) cc_final: 0.8128 (mmm) REVERT: A 997 GLU cc_start: 0.7356 (tp30) cc_final: 0.7054 (tp30) REVERT: A 1005 LYS cc_start: 0.8390 (mttt) cc_final: 0.8123 (mttp) REVERT: A 1009 LYS cc_start: 0.8450 (tttt) cc_final: 0.8236 (ttmm) REVERT: A 1018 ILE cc_start: 0.8527 (pt) cc_final: 0.8248 (mt) REVERT: A 1082 ILE cc_start: 0.8711 (tp) cc_final: 0.8209 (pt) REVERT: A 1119 ASP cc_start: 0.7602 (p0) cc_final: 0.7085 (p0) REVERT: A 1146 GLU cc_start: 0.8030 (tt0) cc_final: 0.7597 (tt0) REVERT: A 1157 ARG cc_start: 0.8492 (mtp85) cc_final: 0.7976 (mtp85) REVERT: C 42 LYS cc_start: 0.7573 (mmmt) cc_final: 0.7275 (mmmt) REVERT: C 64 LYS cc_start: 0.8555 (mtmt) cc_final: 0.8050 (mmmm) REVERT: C 170 PHE cc_start: 0.8107 (t80) cc_final: 0.7627 (t80) REVERT: C 174 LYS cc_start: 0.8182 (ttmm) cc_final: 0.7811 (ttmm) REVERT: C 189 LYS cc_start: 0.8401 (mmtt) cc_final: 0.8077 (mmmm) REVERT: C 196 ASP cc_start: 0.7972 (t0) cc_final: 0.7627 (t0) REVERT: C 197 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7346 (pp20) REVERT: C 277 GLU cc_start: 0.7289 (mp0) cc_final: 0.6788 (mp0) REVERT: C 293 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8016 (tp) REVERT: C 297 GLU cc_start: 0.7395 (pm20) cc_final: 0.6837 (pm20) REVERT: C 664 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7024 (mp0) REVERT: C 705 ASP cc_start: 0.8391 (t0) cc_final: 0.8082 (t0) REVERT: C 709 LYS cc_start: 0.8434 (ttpt) cc_final: 0.8123 (ttpt) REVERT: D 31 LEU cc_start: 0.6220 (OUTLIER) cc_final: 0.5993 (tt) REVERT: D 89 LYS cc_start: 0.8426 (tptm) cc_final: 0.7995 (mmtt) REVERT: D 117 TYR cc_start: 0.7842 (t80) cc_final: 0.7486 (t80) REVERT: D 127 GLN cc_start: 0.7976 (pp30) cc_final: 0.7449 (tm-30) REVERT: D 169 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7140 (mm-30) REVERT: D 173 LYS cc_start: 0.7986 (tppt) cc_final: 0.7402 (tppt) REVERT: D 202 VAL cc_start: 0.8734 (p) cc_final: 0.8445 (m) REVERT: D 205 GLU cc_start: 0.7381 (tm-30) cc_final: 0.6940 (tm-30) REVERT: D 218 PHE cc_start: 0.8201 (m-80) cc_final: 0.7933 (m-80) REVERT: D 269 GLN cc_start: 0.8045 (tp-100) cc_final: 0.7774 (tp-100) REVERT: D 277 GLU cc_start: 0.7943 (tt0) cc_final: 0.7600 (tt0) REVERT: D 287 ASP cc_start: 0.7598 (t70) cc_final: 0.7349 (t0) REVERT: D 303 GLU cc_start: 0.8312 (tm-30) cc_final: 0.8023 (tm-30) REVERT: D 341 GLU cc_start: 0.8088 (tp30) cc_final: 0.7772 (tp30) REVERT: D 364 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7699 (mt-10) REVERT: D 385 ILE cc_start: 0.8832 (mt) cc_final: 0.8545 (mt) REVERT: D 428 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7490 (ttmm) REVERT: D 554 LYS cc_start: 0.8875 (mttt) cc_final: 0.8580 (mtpp) REVERT: D 570 ASP cc_start: 0.7579 (t0) cc_final: 0.7250 (t0) REVERT: D 606 GLU cc_start: 0.8259 (tp30) cc_final: 0.7794 (tp30) REVERT: D 662 GLN cc_start: 0.7429 (tp-100) cc_final: 0.6949 (tm-30) REVERT: D 698 GLU cc_start: 0.7570 (mp0) cc_final: 0.7039 (mp0) REVERT: D 726 LEU cc_start: 0.8705 (mp) cc_final: 0.8503 (mt) REVERT: D 749 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7472 (tm-30) REVERT: D 776 TYR cc_start: 0.8341 (t80) cc_final: 0.7728 (t80) REVERT: D 780 ILE cc_start: 0.8965 (pt) cc_final: 0.8610 (mt) REVERT: D 791 MET cc_start: 0.8564 (tmm) cc_final: 0.8131 (tmm) REVERT: D 858 LEU cc_start: 0.8644 (tp) cc_final: 0.8273 (tt) REVERT: D 860 TYR cc_start: 0.8242 (t80) cc_final: 0.7858 (t80) REVERT: D 867 GLU cc_start: 0.8353 (tp30) cc_final: 0.8137 (tp30) REVERT: D 921 LYS cc_start: 0.8298 (mtpt) cc_final: 0.8038 (mtmt) REVERT: D 924 GLU cc_start: 0.7626 (tt0) cc_final: 0.7319 (tm-30) REVERT: D 942 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7564 (mm-30) REVERT: D 983 THR cc_start: 0.8375 (p) cc_final: 0.8122 (p) REVERT: D 1004 MET cc_start: 0.7907 (mmm) cc_final: 0.7375 (mmm) REVERT: D 1017 ASP cc_start: 0.8253 (t70) cc_final: 0.7984 (t0) REVERT: D 1036 MET cc_start: 0.8171 (mmm) cc_final: 0.7916 (mmt) REVERT: D 1055 GLU cc_start: 0.8028 (tp30) cc_final: 0.7744 (tp30) REVERT: D 1058 LYS cc_start: 0.8548 (mttp) cc_final: 0.8342 (mptt) REVERT: D 1070 MET cc_start: 0.7298 (tpp) cc_final: 0.6920 (tpp) REVERT: D 1077 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7790 (mm-30) REVERT: D 1128 ASN cc_start: 0.8493 (t0) cc_final: 0.8086 (m-40) REVERT: D 1139 GLU cc_start: 0.7472 (tm-30) cc_final: 0.6956 (tm-30) REVERT: D 1143 GLN cc_start: 0.7635 (mt0) cc_final: 0.7280 (mp10) outliers start: 61 outliers final: 35 residues processed: 553 average time/residue: 0.3314 time to fit residues: 270.6111 Evaluate side-chains 547 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 504 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 1314 LYS Chi-restraints excluded: chain A residue 18 THR 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 107 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 957 GLU Chi-restraints excluded: chain A residue 1013 LYS 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 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 84 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 236 ILE 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 414 VAL Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 748 LEU 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 Chi-restraints excluded: chain D residue 1104 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 162 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 189 optimal weight: 0.1980 chunk 30 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 92 optimal weight: 0.2980 chunk 107 optimal weight: 5.9990 chunk 222 optimal weight: 1.9990 chunk 178 optimal weight: 0.1980 chunk 134 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 ASN C 659 ASN D 262 ASN ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 657 GLN ** D1123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1158 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.147750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.123091 restraints weight = 29286.839| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.98 r_work: 0.3371 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 19626 Z= 0.165 Angle : 0.558 9.257 26740 Z= 0.302 Chirality : 0.041 0.350 3101 Planarity : 0.003 0.069 3141 Dihedral : 17.769 84.059 3257 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.70 % Allowed : 19.48 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.18), residues: 2177 helix: 1.34 (0.14), residues: 1298 sheet: 0.80 (0.40), residues: 161 loop : -1.24 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1033 HIS 0.008 0.001 HIS D1123 PHE 0.024 0.002 PHE B1302 TYR 0.018 0.002 TYR D1086 ARG 0.004 0.000 ARG A1157 Details of bonding type rmsd hydrogen bonds : bond 0.04099 ( 1129) hydrogen bonds : angle 3.88070 ( 3275) covalent geometry : bond 0.00371 (19626) covalent geometry : angle 0.55756 (26740) *********************** 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 573 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 519 time to evaluate : 2.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 VAL cc_start: 0.8043 (m) cc_final: 0.7559 (t) REVERT: B 213 ARG cc_start: 0.8051 (mtm110) cc_final: 0.7688 (mtm110) REVERT: B 214 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8371 (tp) REVERT: B 252 GLU cc_start: 0.7413 (pm20) cc_final: 0.6976 (pm20) REVERT: B 263 PHE cc_start: 0.8722 (m-80) cc_final: 0.8039 (m-80) REVERT: B 264 LYS cc_start: 0.8782 (mmtt) cc_final: 0.8450 (tppt) REVERT: B 269 LYS cc_start: 0.8329 (mtpt) cc_final: 0.8018 (mtpt) REVERT: B 288 ASN cc_start: 0.8451 (t0) cc_final: 0.8102 (t0) REVERT: B 289 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7875 (mm-30) REVERT: B 292 ASP cc_start: 0.7531 (t0) cc_final: 0.7222 (t0) REVERT: B 312 LYS cc_start: 0.8585 (mptt) cc_final: 0.8370 (mptt) REVERT: B 325 GLU cc_start: 0.8142 (mp0) cc_final: 0.7715 (mp0) REVERT: B 329 ASP cc_start: 0.7798 (t0) cc_final: 0.7531 (t0) REVERT: B 1249 ARG cc_start: 0.7399 (tmm-80) cc_final: 0.7119 (tmm-80) REVERT: B 1260 LYS cc_start: 0.7954 (mttt) cc_final: 0.7697 (mtpp) REVERT: B 1265 ASP cc_start: 0.8289 (t0) cc_final: 0.8034 (t0) REVERT: B 1281 MET cc_start: 0.8097 (mmm) cc_final: 0.7550 (mpp) REVERT: B 1322 ASN cc_start: 0.8199 (p0) cc_final: 0.7677 (t0) REVERT: B 1405 LYS cc_start: 0.8873 (mttt) cc_final: 0.8605 (mttm) REVERT: B 1412 ILE cc_start: 0.8426 (pt) cc_final: 0.8150 (pt) REVERT: A 81 ILE cc_start: 0.7994 (tt) cc_final: 0.7728 (tt) REVERT: A 109 LEU cc_start: 0.8791 (mt) cc_final: 0.8526 (mp) REVERT: A 160 GLU cc_start: 0.7769 (mp0) cc_final: 0.7198 (mp0) REVERT: A 175 GLU cc_start: 0.7567 (tp30) cc_final: 0.7284 (tp30) REVERT: A 178 ARG cc_start: 0.7862 (tmm160) cc_final: 0.7339 (ttp-110) REVERT: A 182 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7944 (mm-30) REVERT: A 187 LYS cc_start: 0.8904 (tppt) cc_final: 0.8581 (tppt) REVERT: A 208 GLU cc_start: 0.6492 (OUTLIER) cc_final: 0.6274 (pp20) REVERT: A 209 LYS cc_start: 0.7711 (mmtm) cc_final: 0.7352 (mmtm) REVERT: A 217 PHE cc_start: 0.7324 (t80) cc_final: 0.6714 (t80) REVERT: A 957 GLU cc_start: 0.3369 (OUTLIER) cc_final: 0.3037 (mp0) REVERT: A 985 ASN cc_start: 0.8168 (p0) cc_final: 0.7771 (p0) REVERT: A 987 MET cc_start: 0.8462 (mmm) cc_final: 0.8243 (mmm) REVERT: A 997 GLU cc_start: 0.7385 (tp30) cc_final: 0.7137 (tp30) REVERT: A 1005 LYS cc_start: 0.8435 (mttt) cc_final: 0.8179 (mttp) REVERT: A 1009 LYS cc_start: 0.8472 (tttt) cc_final: 0.8246 (ttmm) REVERT: A 1016 GLU cc_start: 0.8084 (tt0) cc_final: 0.7834 (tt0) REVERT: A 1061 LYS cc_start: 0.7659 (mmmm) cc_final: 0.7379 (mmmm) REVERT: A 1082 ILE cc_start: 0.8718 (tp) cc_final: 0.8395 (tp) REVERT: A 1119 ASP cc_start: 0.7656 (p0) cc_final: 0.7160 (p0) REVERT: A 1146 GLU cc_start: 0.8054 (tt0) cc_final: 0.7592 (tt0) REVERT: C 42 LYS cc_start: 0.7626 (mmmt) cc_final: 0.7314 (mmmt) REVERT: C 64 LYS cc_start: 0.8476 (mtmt) cc_final: 0.7976 (mmmm) REVERT: C 99 LYS cc_start: 0.8672 (mtmt) cc_final: 0.8198 (mtpt) REVERT: C 170 PHE cc_start: 0.8107 (t80) cc_final: 0.7629 (t80) REVERT: C 174 LYS cc_start: 0.8223 (ttmm) cc_final: 0.7904 (ttmm) REVERT: C 189 LYS cc_start: 0.8418 (mmtt) cc_final: 0.8124 (mmmm) REVERT: C 196 ASP cc_start: 0.8005 (t0) cc_final: 0.7662 (t0) REVERT: C 197 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7371 (pp20) REVERT: C 211 ASP cc_start: 0.8066 (m-30) cc_final: 0.7866 (m-30) REVERT: C 277 GLU cc_start: 0.7294 (mp0) cc_final: 0.6785 (mp0) REVERT: C 293 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.8006 (tp) REVERT: C 297 GLU cc_start: 0.7423 (pm20) cc_final: 0.6863 (pm20) REVERT: C 664 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7450 (mm-30) REVERT: C 705 ASP cc_start: 0.8410 (t0) cc_final: 0.8099 (t0) REVERT: C 709 LYS cc_start: 0.8440 (ttpt) cc_final: 0.8135 (ttpt) REVERT: D 31 LEU cc_start: 0.6205 (OUTLIER) cc_final: 0.5988 (tt) REVERT: D 89 LYS cc_start: 0.8434 (tptm) cc_final: 0.7996 (mmtt) REVERT: D 117 TYR cc_start: 0.7887 (t80) cc_final: 0.7576 (t80) REVERT: D 127 GLN cc_start: 0.7942 (pp30) cc_final: 0.7424 (tm-30) REVERT: D 173 LYS cc_start: 0.7978 (tppt) cc_final: 0.7400 (tppt) REVERT: D 202 VAL cc_start: 0.8754 (p) cc_final: 0.8471 (m) REVERT: D 205 GLU cc_start: 0.7378 (tm-30) cc_final: 0.6931 (tm-30) REVERT: D 269 GLN cc_start: 0.8075 (tp-100) cc_final: 0.7820 (tp-100) REVERT: D 277 GLU cc_start: 0.8017 (tt0) cc_final: 0.7647 (tt0) REVERT: D 287 ASP cc_start: 0.7675 (t70) cc_final: 0.7376 (t0) REVERT: D 303 GLU cc_start: 0.8357 (tm-30) cc_final: 0.8092 (tm-30) REVERT: D 341 GLU cc_start: 0.8164 (tp30) cc_final: 0.7822 (tp30) REVERT: D 364 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7860 (mt-10) REVERT: D 385 ILE cc_start: 0.8841 (mt) cc_final: 0.8567 (mt) REVERT: D 428 LYS cc_start: 0.7909 (mttp) cc_final: 0.7511 (ttmm) REVERT: D 554 LYS cc_start: 0.8896 (mttt) cc_final: 0.8590 (mtpp) REVERT: D 570 ASP cc_start: 0.7652 (t0) cc_final: 0.7289 (t0) REVERT: D 606 GLU cc_start: 0.8315 (tp30) cc_final: 0.7850 (tp30) REVERT: D 662 GLN cc_start: 0.7491 (tp-100) cc_final: 0.7074 (tm-30) REVERT: D 698 GLU cc_start: 0.7616 (mp0) cc_final: 0.7090 (mp0) REVERT: D 749 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7530 (tm-30) REVERT: D 776 TYR cc_start: 0.8362 (t80) cc_final: 0.7727 (t80) REVERT: D 780 ILE cc_start: 0.8994 (pt) cc_final: 0.8620 (mt) REVERT: D 791 MET cc_start: 0.8585 (tmm) cc_final: 0.8132 (tmm) REVERT: D 867 GLU cc_start: 0.8393 (tp30) cc_final: 0.8149 (tp30) REVERT: D 921 LYS cc_start: 0.8317 (mtpt) cc_final: 0.8062 (mtmt) REVERT: D 983 THR cc_start: 0.8380 (p) cc_final: 0.8161 (p) REVERT: D 1004 MET cc_start: 0.7914 (mmm) cc_final: 0.7420 (mmm) REVERT: D 1012 VAL cc_start: 0.8269 (m) cc_final: 0.7875 (p) REVERT: D 1017 ASP cc_start: 0.8329 (t70) cc_final: 0.8022 (t0) REVERT: D 1021 ARG cc_start: 0.7827 (mtp180) cc_final: 0.7537 (mtp180) REVERT: D 1055 GLU cc_start: 0.8083 (tp30) cc_final: 0.7773 (tp30) REVERT: D 1058 LYS cc_start: 0.8584 (mttp) cc_final: 0.8358 (mptt) REVERT: D 1077 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7810 (mm-30) REVERT: D 1128 ASN cc_start: 0.8501 (t0) cc_final: 0.8100 (m-40) REVERT: D 1137 LYS cc_start: 0.8075 (tptp) cc_final: 0.7699 (tptp) REVERT: D 1139 GLU cc_start: 0.7511 (tm-30) cc_final: 0.6980 (tm-30) outliers start: 54 outliers final: 32 residues processed: 550 average time/residue: 0.3420 time to fit residues: 276.6086 Evaluate side-chains 547 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 508 time to evaluate : 2.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 1314 LYS Chi-restraints excluded: chain A residue 18 THR 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 208 GLU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 957 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 203 LEU Chi-restraints excluded: chain C residue 206 ASN 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 84 LEU 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 323 SER Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 980 LEU Chi-restraints excluded: chain D residue 988 SER Chi-restraints excluded: chain D residue 999 LEU Chi-restraints excluded: chain D residue 1047 VAL Chi-restraints excluded: chain D residue 1056 MET Chi-restraints excluded: chain D residue 1104 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 123 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 191 optimal weight: 1.9990 chunk 203 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 175 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 135 optimal weight: 0.9980 chunk 119 optimal weight: 0.0050 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 ASN A 71 GLN C 659 ASN D 184 GLN ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 657 GLN D1010 ASN ** D1123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1158 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.148529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.124005 restraints weight = 29048.214| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.93 r_work: 0.3387 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19626 Z= 0.138 Angle : 0.555 12.700 26740 Z= 0.297 Chirality : 0.041 0.323 3101 Planarity : 0.003 0.067 3141 Dihedral : 17.656 83.288 3257 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.35 % Allowed : 20.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.18), residues: 2177 helix: 1.47 (0.14), residues: 1300 sheet: 0.88 (0.40), residues: 161 loop : -1.16 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1033 HIS 0.008 0.001 HIS D1123 PHE 0.023 0.001 PHE D1107 TYR 0.017 0.001 TYR D1086 ARG 0.005 0.000 ARG B1318 Details of bonding type rmsd hydrogen bonds : bond 0.03897 ( 1129) hydrogen bonds : angle 3.80491 ( 3275) covalent geometry : bond 0.00306 (19626) covalent geometry : angle 0.55512 (26740) *********************** 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 567 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 520 time to evaluate : 2.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 VAL cc_start: 0.7984 (m) cc_final: 0.7466 (t) REVERT: B 214 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8342 (tp) REVERT: B 224 PHE cc_start: 0.8796 (m-80) cc_final: 0.8468 (m-80) REVERT: B 252 GLU cc_start: 0.7413 (pm20) cc_final: 0.7054 (pm20) REVERT: B 263 PHE cc_start: 0.8703 (m-80) cc_final: 0.7873 (m-80) REVERT: B 264 LYS cc_start: 0.8740 (mmtt) cc_final: 0.8439 (tppt) REVERT: B 269 LYS cc_start: 0.8349 (mtpt) cc_final: 0.8008 (mtpt) REVERT: B 288 ASN cc_start: 0.8429 (t0) cc_final: 0.8057 (t0) REVERT: B 289 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7822 (mm-30) REVERT: B 292 ASP cc_start: 0.7469 (t0) cc_final: 0.7185 (t0) REVERT: B 325 GLU cc_start: 0.8162 (mp0) cc_final: 0.7730 (mp0) REVERT: B 1249 ARG cc_start: 0.7410 (tmm-80) cc_final: 0.7131 (tmm-80) REVERT: B 1260 LYS cc_start: 0.7938 (mttt) cc_final: 0.7679 (mtpp) REVERT: B 1265 ASP cc_start: 0.8244 (t0) cc_final: 0.8017 (t0) REVERT: B 1282 TYR cc_start: 0.8321 (t80) cc_final: 0.8034 (t80) REVERT: B 1322 ASN cc_start: 0.8154 (p0) cc_final: 0.7605 (t0) REVERT: B 1405 LYS cc_start: 0.8845 (mttt) cc_final: 0.8581 (mttm) REVERT: B 1412 ILE cc_start: 0.8426 (pt) cc_final: 0.8146 (pt) REVERT: B 1413 ASP cc_start: 0.8637 (m-30) cc_final: 0.8415 (t0) REVERT: A 54 MET cc_start: 0.7641 (mmm) cc_final: 0.7279 (mmp) REVERT: A 81 ILE cc_start: 0.7963 (tt) cc_final: 0.7705 (tt) REVERT: A 109 LEU cc_start: 0.8751 (mt) cc_final: 0.8482 (mp) REVERT: A 129 GLN cc_start: 0.7991 (tm-30) cc_final: 0.7411 (tm-30) REVERT: A 160 GLU cc_start: 0.7718 (mp0) cc_final: 0.7156 (mp0) REVERT: A 178 ARG cc_start: 0.7758 (tmm160) cc_final: 0.7257 (ttp-170) REVERT: A 187 LYS cc_start: 0.8907 (tppt) cc_final: 0.8584 (tppt) REVERT: A 208 GLU cc_start: 0.6420 (OUTLIER) cc_final: 0.6193 (pp20) REVERT: A 209 LYS cc_start: 0.7670 (mmtm) cc_final: 0.7294 (mmtm) REVERT: A 217 PHE cc_start: 0.7254 (t80) cc_final: 0.6644 (t80) REVERT: A 985 ASN cc_start: 0.8156 (p0) cc_final: 0.7748 (p0) REVERT: A 987 MET cc_start: 0.8400 (mmm) cc_final: 0.8160 (mmm) REVERT: A 991 GLU cc_start: 0.7967 (tp30) cc_final: 0.7698 (tp30) REVERT: A 997 GLU cc_start: 0.7352 (tp30) cc_final: 0.7121 (tp30) REVERT: A 1005 LYS cc_start: 0.8407 (mttt) cc_final: 0.8157 (mttp) REVERT: A 1009 LYS cc_start: 0.8412 (tttt) cc_final: 0.8202 (ttmm) REVERT: A 1061 LYS cc_start: 0.7615 (mmmm) cc_final: 0.7343 (mmmm) REVERT: A 1082 ILE cc_start: 0.8723 (tp) cc_final: 0.8409 (tp) REVERT: A 1119 ASP cc_start: 0.7604 (p0) cc_final: 0.7139 (p0) REVERT: A 1146 GLU cc_start: 0.8028 (tt0) cc_final: 0.7688 (tt0) REVERT: C 42 LYS cc_start: 0.7633 (mmmt) cc_final: 0.7300 (mmmt) REVERT: C 64 LYS cc_start: 0.8453 (mtmt) cc_final: 0.8113 (mtpt) REVERT: C 170 PHE cc_start: 0.8072 (t80) cc_final: 0.7591 (t80) REVERT: C 174 LYS cc_start: 0.8187 (ttmm) cc_final: 0.7874 (ttmm) REVERT: C 189 LYS cc_start: 0.8428 (mmtt) cc_final: 0.8103 (mmmm) REVERT: C 196 ASP cc_start: 0.7976 (t0) cc_final: 0.7630 (t0) REVERT: C 197 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7316 (pp20) REVERT: C 211 ASP cc_start: 0.7996 (m-30) cc_final: 0.7771 (m-30) REVERT: C 277 GLU cc_start: 0.7231 (mp0) cc_final: 0.6722 (mp0) REVERT: C 293 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.8009 (tp) REVERT: C 297 GLU cc_start: 0.7343 (pm20) cc_final: 0.6812 (pm20) REVERT: C 664 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7033 (mp0) REVERT: C 705 ASP cc_start: 0.8344 (t0) cc_final: 0.8022 (t0) REVERT: C 709 LYS cc_start: 0.8424 (ttpt) cc_final: 0.8126 (ttpt) REVERT: D 31 LEU cc_start: 0.6144 (OUTLIER) cc_final: 0.5937 (tt) REVERT: D 89 LYS cc_start: 0.8417 (tptm) cc_final: 0.8021 (tttp) REVERT: D 117 TYR cc_start: 0.7827 (t80) cc_final: 0.7508 (t80) REVERT: D 173 LYS cc_start: 0.7899 (tppt) cc_final: 0.7323 (tppt) REVERT: D 202 VAL cc_start: 0.8694 (p) cc_final: 0.8403 (m) REVERT: D 205 GLU cc_start: 0.7350 (tm-30) cc_final: 0.6904 (tm-30) REVERT: D 243 ASN cc_start: 0.7991 (m-40) cc_final: 0.7681 (m110) REVERT: D 269 GLN cc_start: 0.8008 (tp-100) cc_final: 0.7768 (tp-100) REVERT: D 277 GLU cc_start: 0.7981 (tt0) cc_final: 0.7616 (tt0) REVERT: D 287 ASP cc_start: 0.7588 (t70) cc_final: 0.7303 (t0) REVERT: D 303 GLU cc_start: 0.8308 (tm-30) cc_final: 0.8046 (tm-30) REVERT: D 341 GLU cc_start: 0.8119 (tp30) cc_final: 0.7795 (tp30) REVERT: D 364 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7765 (mt-10) REVERT: D 385 ILE cc_start: 0.8820 (mt) cc_final: 0.8537 (mt) REVERT: D 428 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7468 (ttmm) REVERT: D 554 LYS cc_start: 0.8872 (mttt) cc_final: 0.8580 (mtpp) REVERT: D 570 ASP cc_start: 0.7550 (t0) cc_final: 0.7251 (t0) REVERT: D 605 ILE cc_start: 0.8695 (mm) cc_final: 0.8467 (tp) REVERT: D 606 GLU cc_start: 0.8274 (tp30) cc_final: 0.7781 (tp30) REVERT: D 662 GLN cc_start: 0.7423 (tp-100) cc_final: 0.7049 (tm-30) REVERT: D 698 GLU cc_start: 0.7529 (mp0) cc_final: 0.6984 (mp0) REVERT: D 749 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7466 (tm-30) REVERT: D 776 TYR cc_start: 0.8342 (t80) cc_final: 0.7713 (t80) REVERT: D 780 ILE cc_start: 0.8951 (pt) cc_final: 0.8630 (mt) REVERT: D 791 MET cc_start: 0.8570 (tmm) cc_final: 0.8079 (tmm) REVERT: D 867 GLU cc_start: 0.8394 (tp30) cc_final: 0.8154 (tp30) REVERT: D 921 LYS cc_start: 0.8311 (mtpt) cc_final: 0.8055 (mtmt) REVERT: D 983 THR cc_start: 0.8365 (p) cc_final: 0.8156 (p) REVERT: D 1004 MET cc_start: 0.7893 (mmm) cc_final: 0.7396 (mmm) REVERT: D 1017 ASP cc_start: 0.8279 (t70) cc_final: 0.7946 (t0) REVERT: D 1021 ARG cc_start: 0.7865 (mtp180) cc_final: 0.7570 (mtp180) REVERT: D 1036 MET cc_start: 0.8218 (tpp) cc_final: 0.7908 (tpp) REVERT: D 1055 GLU cc_start: 0.8073 (tp30) cc_final: 0.7818 (tp30) REVERT: D 1077 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7693 (mm-30) REVERT: D 1128 ASN cc_start: 0.8494 (t0) cc_final: 0.8099 (m-40) REVERT: D 1137 LYS cc_start: 0.8095 (tptp) cc_final: 0.7734 (tptp) REVERT: D 1139 GLU cc_start: 0.7538 (tm-30) cc_final: 0.7015 (tm-30) outliers start: 47 outliers final: 32 residues processed: 548 average time/residue: 0.3424 time to fit residues: 277.1541 Evaluate side-chains 560 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 521 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 1314 LYS Chi-restraints excluded: chain A residue 18 THR 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 186 SER Chi-restraints excluded: chain A residue 208 GLU 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 203 LEU Chi-restraints excluded: chain C residue 206 ASN 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 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 748 LEU Chi-restraints excluded: chain D residue 988 SER Chi-restraints excluded: chain D residue 999 LEU Chi-restraints excluded: chain D residue 1047 VAL Chi-restraints excluded: chain D residue 1056 MET Chi-restraints excluded: chain D residue 1060 LEU Chi-restraints excluded: chain D residue 1104 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 115 optimal weight: 0.8980 chunk 94 optimal weight: 0.5980 chunk 96 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 151 optimal weight: 0.5980 chunk 149 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 184 optimal weight: 0.5980 chunk 197 optimal weight: 0.4980 chunk 187 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 657 GLN D1010 ASN ** 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 = 0.3890 r_free = 0.3890 target = 0.148645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.124430 restraints weight = 29051.114| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.95 r_work: 0.3387 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19626 Z= 0.140 Angle : 0.556 10.045 26740 Z= 0.300 Chirality : 0.041 0.305 3101 Planarity : 0.003 0.067 3141 Dihedral : 17.599 82.885 3257 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.55 % Allowed : 20.53 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.18), residues: 2177 helix: 1.55 (0.14), residues: 1298 sheet: 0.95 (0.40), residues: 161 loop : -1.08 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1033 HIS 0.009 0.001 HIS D1123 PHE 0.023 0.001 PHE B1302 TYR 0.015 0.001 TYR D 776 ARG 0.005 0.000 ARG D 311 Details of bonding type rmsd hydrogen bonds : bond 0.03934 ( 1129) hydrogen bonds : angle 3.80241 ( 3275) covalent geometry : bond 0.00312 (19626) covalent geometry : angle 0.55611 (26740) *********************** 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 566 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 515 time to evaluate : 2.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 VAL cc_start: 0.8060 (m) cc_final: 0.7537 (t) REVERT: B 214 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8329 (tp) REVERT: B 216 ASP cc_start: 0.7848 (m-30) cc_final: 0.7230 (m-30) REVERT: B 224 PHE cc_start: 0.8812 (m-80) cc_final: 0.8437 (m-80) REVERT: B 252 GLU cc_start: 0.7387 (pm20) cc_final: 0.7053 (pm20) REVERT: B 264 LYS cc_start: 0.8798 (mmtt) cc_final: 0.8499 (tppt) REVERT: B 269 LYS cc_start: 0.8314 (mtpt) cc_final: 0.7946 (mtpt) REVERT: B 288 ASN cc_start: 0.8444 (t0) cc_final: 0.8064 (t0) REVERT: B 289 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7359 (mm-30) REVERT: B 292 ASP cc_start: 0.7464 (t0) cc_final: 0.7179 (t0) REVERT: B 325 GLU cc_start: 0.8162 (mp0) cc_final: 0.7720 (mp0) REVERT: B 329 ASP cc_start: 0.7754 (t0) cc_final: 0.7423 (t0) REVERT: B 1249 ARG cc_start: 0.7397 (tmm-80) cc_final: 0.7120 (tmm-80) REVERT: B 1260 LYS cc_start: 0.7934 (mttt) cc_final: 0.7676 (mtpp) REVERT: B 1265 ASP cc_start: 0.8256 (t0) cc_final: 0.7988 (t0) REVERT: B 1281 MET cc_start: 0.8041 (mmm) cc_final: 0.7520 (mpp) REVERT: B 1282 TYR cc_start: 0.8300 (t80) cc_final: 0.8012 (t80) REVERT: B 1322 ASN cc_start: 0.8168 (p0) cc_final: 0.7630 (t0) REVERT: B 1405 LYS cc_start: 0.8818 (mttt) cc_final: 0.8538 (mttm) REVERT: B 1412 ILE cc_start: 0.8405 (pt) cc_final: 0.8137 (pt) REVERT: A 54 MET cc_start: 0.7609 (mmm) cc_final: 0.7257 (mmp) REVERT: A 81 ILE cc_start: 0.7936 (tt) cc_final: 0.7679 (tt) REVERT: A 109 LEU cc_start: 0.8757 (mt) cc_final: 0.8488 (mp) REVERT: A 160 GLU cc_start: 0.7711 (mp0) cc_final: 0.7145 (mp0) REVERT: A 175 GLU cc_start: 0.7570 (tp30) cc_final: 0.6949 (tp30) REVERT: A 178 ARG cc_start: 0.7741 (tmm160) cc_final: 0.7179 (ttp-110) REVERT: A 187 LYS cc_start: 0.8899 (tppt) cc_final: 0.8562 (tppt) REVERT: A 208 GLU cc_start: 0.6421 (OUTLIER) cc_final: 0.6184 (pp20) REVERT: A 209 LYS cc_start: 0.7686 (mmtm) cc_final: 0.7230 (mmtm) REVERT: A 217 PHE cc_start: 0.7288 (t80) cc_final: 0.6640 (t80) REVERT: A 985 ASN cc_start: 0.8153 (p0) cc_final: 0.7750 (p0) REVERT: A 987 MET cc_start: 0.8422 (mmm) cc_final: 0.8162 (mmm) REVERT: A 991 GLU cc_start: 0.7941 (tp30) cc_final: 0.7694 (tp30) REVERT: A 997 GLU cc_start: 0.7380 (tp30) cc_final: 0.7162 (tp30) REVERT: A 1005 LYS cc_start: 0.8396 (mttt) cc_final: 0.8138 (mttp) REVERT: A 1009 LYS cc_start: 0.8393 (tttt) cc_final: 0.8183 (ttmm) REVERT: A 1061 LYS cc_start: 0.7583 (mmmm) cc_final: 0.7310 (mmmm) REVERT: A 1082 ILE cc_start: 0.8720 (tp) cc_final: 0.8407 (tp) REVERT: A 1119 ASP cc_start: 0.7597 (p0) cc_final: 0.7149 (p0) REVERT: A 1146 GLU cc_start: 0.7992 (tt0) cc_final: 0.7639 (tt0) REVERT: C 64 LYS cc_start: 0.8438 (mtmt) cc_final: 0.8091 (mtpt) REVERT: C 170 PHE cc_start: 0.8035 (t80) cc_final: 0.7572 (t80) REVERT: C 174 LYS cc_start: 0.8193 (ttmm) cc_final: 0.7852 (ttmm) REVERT: C 189 LYS cc_start: 0.8439 (mmtt) cc_final: 0.8098 (mmmm) REVERT: C 196 ASP cc_start: 0.7962 (t0) cc_final: 0.7609 (t0) REVERT: C 197 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7151 (pp20) REVERT: C 211 ASP cc_start: 0.7985 (m-30) cc_final: 0.7756 (m-30) REVERT: C 277 GLU cc_start: 0.7263 (mp0) cc_final: 0.6737 (mp0) REVERT: C 293 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.7994 (tp) REVERT: C 297 GLU cc_start: 0.7350 (pm20) cc_final: 0.6824 (pm20) REVERT: C 664 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7402 (mm-30) REVERT: C 705 ASP cc_start: 0.8322 (t0) cc_final: 0.8017 (t0) REVERT: C 709 LYS cc_start: 0.8426 (ttpt) cc_final: 0.8125 (ttpt) REVERT: D 31 LEU cc_start: 0.6158 (OUTLIER) cc_final: 0.5931 (tt) REVERT: D 89 LYS cc_start: 0.8419 (tptm) cc_final: 0.8030 (mmtt) REVERT: D 117 TYR cc_start: 0.7837 (t80) cc_final: 0.7497 (t80) REVERT: D 202 VAL cc_start: 0.8672 (p) cc_final: 0.8401 (m) REVERT: D 205 GLU cc_start: 0.7345 (tm-30) cc_final: 0.6896 (tm-30) REVERT: D 243 ASN cc_start: 0.7994 (m-40) cc_final: 0.7681 (m110) REVERT: D 269 GLN cc_start: 0.8048 (tp-100) cc_final: 0.7787 (tp-100) REVERT: D 277 GLU cc_start: 0.7937 (tt0) cc_final: 0.7572 (tt0) REVERT: D 287 ASP cc_start: 0.7571 (t70) cc_final: 0.7284 (t0) REVERT: D 303 GLU cc_start: 0.8306 (tm-30) cc_final: 0.8025 (tm-30) REVERT: D 333 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7775 (mt-10) REVERT: D 341 GLU cc_start: 0.8153 (tp30) cc_final: 0.7803 (tp30) REVERT: D 364 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7754 (mt-10) REVERT: D 385 ILE cc_start: 0.8825 (mt) cc_final: 0.8537 (mt) REVERT: D 428 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7528 (ttmm) REVERT: D 554 LYS cc_start: 0.8880 (mttt) cc_final: 0.8583 (mtpp) REVERT: D 570 ASP cc_start: 0.7560 (t0) cc_final: 0.7271 (t0) REVERT: D 605 ILE cc_start: 0.8685 (mm) cc_final: 0.8453 (tp) REVERT: D 606 GLU cc_start: 0.8255 (tp30) cc_final: 0.7765 (tp30) REVERT: D 662 GLN cc_start: 0.7437 (tp-100) cc_final: 0.7008 (tm-30) REVERT: D 698 GLU cc_start: 0.7514 (mp0) cc_final: 0.6977 (mp0) REVERT: D 749 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7447 (tm-30) REVERT: D 776 TYR cc_start: 0.8347 (t80) cc_final: 0.7727 (t80) REVERT: D 778 ILE cc_start: 0.8855 (tp) cc_final: 0.8620 (tp) REVERT: D 780 ILE cc_start: 0.8949 (pt) cc_final: 0.8629 (mt) REVERT: D 791 MET cc_start: 0.8573 (tmm) cc_final: 0.8109 (tmm) REVERT: D 867 GLU cc_start: 0.8385 (tp30) cc_final: 0.8153 (tp30) REVERT: D 921 LYS cc_start: 0.8296 (mtpt) cc_final: 0.8045 (mtmt) REVERT: D 1004 MET cc_start: 0.7864 (mmm) cc_final: 0.7345 (mmm) REVERT: D 1012 VAL cc_start: 0.8273 (m) cc_final: 0.7936 (p) REVERT: D 1017 ASP cc_start: 0.8274 (t70) cc_final: 0.7963 (t0) REVERT: D 1021 ARG cc_start: 0.7896 (mtp180) cc_final: 0.7609 (mtp180) REVERT: D 1055 GLU cc_start: 0.8068 (tp30) cc_final: 0.7771 (tp30) REVERT: D 1109 LYS cc_start: 0.8361 (tptm) cc_final: 0.8098 (tppp) REVERT: D 1128 ASN cc_start: 0.8487 (t0) cc_final: 0.8076 (m-40) REVERT: D 1137 LYS cc_start: 0.8074 (tptp) cc_final: 0.7727 (tptp) REVERT: D 1139 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7042 (tm-30) outliers start: 51 outliers final: 34 residues processed: 543 average time/residue: 0.3329 time to fit residues: 267.5489 Evaluate side-chains 544 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 503 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 1314 LYS Chi-restraints excluded: chain B residue 1375 ASN Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 208 GLU 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 206 ASN Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 664 GLU 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 84 LEU Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 368 GLN 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 980 LEU Chi-restraints excluded: chain D residue 988 SER Chi-restraints excluded: chain D residue 999 LEU Chi-restraints excluded: chain D residue 1047 VAL Chi-restraints excluded: chain D residue 1056 MET Chi-restraints excluded: chain D residue 1104 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.3671 > 50: distance: 2 - 26: 29.389 distance: 6 - 37: 29.132 distance: 14 - 46: 31.061 distance: 19 - 26: 29.190 distance: 26 - 27: 49.969 distance: 27 - 28: 21.448 distance: 27 - 30: 15.780 distance: 28 - 29: 16.917 distance: 28 - 37: 35.198 distance: 30 - 31: 31.888 distance: 31 - 32: 16.888 distance: 31 - 33: 20.029 distance: 32 - 34: 47.491 distance: 33 - 35: 23.179 distance: 34 - 36: 25.848 distance: 35 - 36: 41.541 distance: 37 - 38: 27.515 distance: 38 - 39: 43.447 distance: 38 - 41: 34.598 distance: 39 - 40: 4.061 distance: 39 - 46: 35.430 distance: 41 - 42: 46.856 distance: 42 - 43: 40.296 distance: 43 - 44: 29.276 distance: 43 - 45: 48.947 distance: 46 - 47: 23.540 distance: 47 - 48: 32.577 distance: 47 - 50: 34.950 distance: 48 - 49: 14.208 distance: 48 - 53: 45.969 distance: 50 - 51: 36.704 distance: 50 - 52: 21.659 distance: 53 - 54: 8.523 distance: 54 - 55: 44.406 distance: 54 - 57: 55.089 distance: 55 - 56: 33.307 distance: 55 - 60: 38.914 distance: 57 - 58: 8.177 distance: 57 - 59: 42.813 distance: 60 - 61: 17.736 distance: 61 - 62: 20.914 distance: 61 - 64: 26.703 distance: 62 - 63: 28.456 distance: 62 - 68: 18.573 distance: 65 - 66: 53.122 distance: 65 - 67: 45.613 distance: 68 - 69: 44.221 distance: 69 - 70: 30.123 distance: 69 - 72: 21.035 distance: 70 - 71: 22.440 distance: 70 - 79: 23.876 distance: 72 - 73: 32.315 distance: 73 - 74: 37.507 distance: 74 - 75: 29.689 distance: 75 - 76: 16.645 distance: 76 - 77: 45.891 distance: 76 - 78: 45.449 distance: 79 - 80: 37.869 distance: 80 - 81: 20.657 distance: 80 - 83: 25.586 distance: 81 - 82: 43.341 distance: 81 - 88: 20.615 distance: 83 - 84: 43.811 distance: 84 - 85: 32.614 distance: 85 - 86: 44.831 distance: 85 - 87: 27.825 distance: 88 - 89: 28.514 distance: 89 - 90: 44.684 distance: 89 - 92: 51.816 distance: 90 - 91: 53.502 distance: 90 - 94: 7.959 distance: 92 - 93: 65.657 distance: 95 - 96: 38.221 distance: 95 - 98: 59.234 distance: 96 - 97: 32.451 distance: 96 - 106: 30.187 distance: 98 - 99: 45.406 distance: 99 - 100: 39.706 distance: 100 - 102: 11.296 distance: 101 - 103: 51.805 distance: 102 - 104: 30.489 distance: 103 - 104: 47.708 distance: 104 - 105: 55.727 distance: 106 - 107: 67.138 distance: 106 - 112: 40.337 distance: 107 - 108: 62.105 distance: 107 - 110: 60.797 distance: 108 - 109: 48.058 distance: 108 - 113: 26.774 distance: 110 - 111: 26.734 distance: 111 - 112: 27.409