Starting phenix.real_space_refine on Fri Mar 6 03:50:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hpo_34935/03_2026/8hpo_34935.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hpo_34935/03_2026/8hpo_34935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hpo_34935/03_2026/8hpo_34935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hpo_34935/03_2026/8hpo_34935.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hpo_34935/03_2026/8hpo_34935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hpo_34935/03_2026/8hpo_34935.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 4 8.98 5 Zn 2 6.06 5 P 10 5.49 5 S 111 5.16 5 C 17688 2.51 5 N 4845 2.21 5 O 5291 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 383 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27951 Number of models: 1 Model: "" Number of chains: 14 Chain: "K" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 2038 Classifications: {'peptide': 413} Incomplete info: {'truncation_to_alanine': 367} Link IDs: {'PTRANS': 16, 'TRANS': 396} Chain breaks: 4 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1279 Unresolved non-hydrogen angles: 1648 Unresolved non-hydrogen dihedrals: 1072 Unresolved non-hydrogen chiralities: 128 Planarities with less than four sites: {'ASP:plan': 21, 'GLU:plan': 32, 'ASN:plan1': 25, 'PHE:plan': 20, 'TRP:plan': 7, 'TYR:plan': 13, 'GLN:plan1': 8, 'HIS:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 652 Chain: "D" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1385 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 6, 'TRANS': 158} Chain breaks: 1 Chain: "F" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3132 Classifications: {'peptide': 392} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 372} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'TPO:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 3057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3057 Classifications: {'peptide': 385} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 366} Chain: "I" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1104 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "A" Number of atoms: 5283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 5283 Classifications: {'peptide': 637} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 19, 'TRANS': 617} Chain breaks: 4 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "H" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1936 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 222} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1116 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 6, 'TRANS': 131} Chain breaks: 1 Chain: "E" Number of atoms: 2077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2077 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 11, 'TRANS': 243} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 5129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 5129 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 17, 'TRANS': 595} Chain breaks: 3 Chain: "J" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1676 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 14, 'TRANS': 194} Chain breaks: 1 Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Classifications: {'peptide': 1} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.03, per 1000 atoms: 0.22 Number of scatterers: 27951 At special positions: 0 Unit cell: (197.834, 130.44, 252.184, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 K 4 19.00 S 111 16.00 P 10 15.00 O 5291 8.00 N 4845 7.00 C 17688 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.25 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN F 502 " pdb="ZN ZN F 502 " - pdb=" ND1 HIS F 188 " pdb=" ZN G 501 " pdb="ZN ZN G 501 " - pdb=" ND1 HIS G 188 " 6974 Ramachandran restraints generated. 3487 Oldfield, 0 Emsley, 3487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6804 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 20 sheets defined 52.3% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'K' and resid 2 through 23 removed outlier: 3.558A pdb=" N ILE K 6 " --> pdb=" O SER K 2 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN K 10 " --> pdb=" O ILE K 6 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS K 11 " --> pdb=" O ALA K 7 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER K 23 " --> pdb=" O ILE K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 27 Processing helix chain 'K' and resid 89 through 91 No H-bonds generated for 'chain 'K' and resid 89 through 91' Processing helix chain 'K' and resid 108 through 117 removed outlier: 3.769A pdb=" N VAL K 114 " --> pdb=" O GLU K 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 308 through 314 removed outlier: 3.625A pdb=" N LEU K 314 " --> pdb=" O ALA K 310 " (cutoff:3.500A) Processing helix chain 'K' and resid 339 through 342 Processing helix chain 'K' and resid 373 through 381 removed outlier: 3.771A pdb=" N ILE K 381 " --> pdb=" O ILE K 377 " (cutoff:3.500A) Processing helix chain 'K' and resid 390 through 397 Processing helix chain 'K' and resid 403 through 407 Processing helix chain 'D' and resid 15 through 35 Processing helix chain 'D' and resid 40 through 55 Processing helix chain 'D' and resid 61 through 141 removed outlier: 3.637A pdb=" N GLN D 65 " --> pdb=" O GLN D 61 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL D 66 " --> pdb=" O TYR D 62 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG D 67 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP D 68 " --> pdb=" O ARG D 64 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU D 76 " --> pdb=" O GLU D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 316 Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 42 through 55 removed outlier: 3.936A pdb=" N ARG F 46 " --> pdb=" O PRO F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 61 removed outlier: 3.849A pdb=" N LYS F 59 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS F 60 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET F 61 " --> pdb=" O TYR F 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 56 through 61' Processing helix chain 'F' and resid 70 through 75 Processing helix chain 'F' and resid 79 through 89 Processing helix chain 'F' and resid 93 through 96 Processing helix chain 'F' and resid 97 through 104 Processing helix chain 'F' and resid 115 through 136 Processing helix chain 'F' and resid 164 through 175 removed outlier: 3.706A pdb=" N LEU F 168 " --> pdb=" O ASN F 164 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG F 175 " --> pdb=" O ILE F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 197 Processing helix chain 'F' and resid 226 through 230 removed outlier: 3.510A pdb=" N LYS F 230 " --> pdb=" O GLY F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 262 Proline residue: F 253 - end of helix Processing helix chain 'F' and resid 287 through 300 removed outlier: 3.535A pdb=" N HIS F 291 " --> pdb=" O SER F 287 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N CYS F 294 " --> pdb=" O GLY F 290 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL F 295 " --> pdb=" O HIS F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 330 removed outlier: 3.565A pdb=" N ASN F 330 " --> pdb=" O THR F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 380 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.771A pdb=" N TYR G 32 " --> pdb=" O VAL G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 55 removed outlier: 3.570A pdb=" N ARG G 46 " --> pdb=" O PRO G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 59 removed outlier: 3.500A pdb=" N LYS G 59 " --> pdb=" O GLY G 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 56 through 59' Processing helix chain 'G' and resid 70 through 75 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 94 through 98 Processing helix chain 'G' and resid 99 through 104 removed outlier: 3.672A pdb=" N LYS G 103 " --> pdb=" O ARG G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 136 removed outlier: 3.521A pdb=" N TYR G 119 " --> pdb=" O GLY G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 177 removed outlier: 3.612A pdb=" N LEU G 168 " --> pdb=" O ASN G 164 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG G 175 " --> pdb=" O ILE G 171 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TYR G 176 " --> pdb=" O GLU G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 197 Processing helix chain 'G' and resid 226 through 230 Processing helix chain 'G' and resid 243 through 262 Proline residue: G 253 - end of helix Processing helix chain 'G' and resid 287 through 300 removed outlier: 4.321A pdb=" N CYS G 294 " --> pdb=" O GLY G 290 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL G 295 " --> pdb=" O HIS G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 314 through 330 removed outlier: 3.677A pdb=" N ASN G 330 " --> pdb=" O THR G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 344 through 348 removed outlier: 3.816A pdb=" N GLY G 348 " --> pdb=" O GLU G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 365 through 380 Processing helix chain 'I' and resid 75 through 88 Processing helix chain 'I' and resid 110 through 119 Processing helix chain 'I' and resid 129 through 134 Processing helix chain 'I' and resid 138 through 141 removed outlier: 3.563A pdb=" N LYS I 141 " --> pdb=" O LEU I 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 138 through 141' Processing helix chain 'I' and resid 142 through 149 Processing helix chain 'I' and resid 159 through 173 Processing helix chain 'I' and resid 179 through 189 removed outlier: 3.810A pdb=" N GLN I 183 " --> pdb=" O ASP I 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 677 removed outlier: 3.598A pdb=" N VAL A 666 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 677 " --> pdb=" O LYS A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 694 removed outlier: 3.553A pdb=" N TYR A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 711 removed outlier: 4.440A pdb=" N PHE A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N TYR A 709 " --> pdb=" O LYS A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 725 removed outlier: 3.575A pdb=" N PHE A 717 " --> pdb=" O ASN A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 764 removed outlier: 3.822A pdb=" N PHE A 764 " --> pdb=" O SER A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 777 Processing helix chain 'A' and resid 802 through 839 removed outlier: 3.563A pdb=" N LEU A 807 " --> pdb=" O TYR A 803 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE A 808 " --> pdb=" O GLU A 804 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS A 809 " --> pdb=" O GLU A 805 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG A 826 " --> pdb=" O GLU A 822 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR A 827 " --> pdb=" O SER A 823 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN A 829 " --> pdb=" O LEU A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 848 Processing helix chain 'A' and resid 861 through 871 Processing helix chain 'A' and resid 875 through 886 removed outlier: 3.705A pdb=" N ILE A 879 " --> pdb=" O ARG A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 894 through 924 removed outlier: 3.876A pdb=" N GLN A 900 " --> pdb=" O LYS A 896 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 903 " --> pdb=" O LYS A 899 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LYS A 914 " --> pdb=" O ARG A 910 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL A 915 " --> pdb=" O GLU A 911 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN A 921 " --> pdb=" O ARG A 917 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LYS A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 928 removed outlier: 3.664A pdb=" N LEU A 928 " --> pdb=" O PHE A 925 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 925 through 928' Processing helix chain 'A' and resid 931 through 942 removed outlier: 5.914A pdb=" N GLN A 937 " --> pdb=" O LEU A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 951 Processing helix chain 'A' and resid 982 through 997 removed outlier: 4.250A pdb=" N TYR A 986 " --> pdb=" O LYS A 982 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP A 987 " --> pdb=" O ASN A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1023 Processing helix chain 'A' and resid 1025 through 1039 Processing helix chain 'A' and resid 1064 through 1069 removed outlier: 3.963A pdb=" N ILE A1068 " --> pdb=" O SER A1064 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU A1069 " --> pdb=" O LEU A1065 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1064 through 1069' Processing helix chain 'A' and resid 1141 through 1173 removed outlier: 3.585A pdb=" N ARG A1157 " --> pdb=" O THR A1153 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLU A1166 " --> pdb=" O LYS A1162 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ARG A1167 " --> pdb=" O GLN A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1184 Processing helix chain 'A' and resid 1189 through 1194 Processing helix chain 'A' and resid 1202 through 1216 Processing helix chain 'A' and resid 1220 through 1232 Processing helix chain 'A' and resid 1236 through 1240 removed outlier: 3.673A pdb=" N LEU A1239 " --> pdb=" O ALA A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1254 removed outlier: 3.829A pdb=" N THR A1246 " --> pdb=" O ILE A1242 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER A1248 " --> pdb=" O LYS A1244 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A1251 " --> pdb=" O GLN A1247 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1274 Processing helix chain 'A' and resid 1280 through 1294 Processing helix chain 'A' and resid 1329 through 1343 Processing helix chain 'A' and resid 1362 through 1372 removed outlier: 3.605A pdb=" N PHE A1366 " --> pdb=" O ARG A1362 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A1370 " --> pdb=" O PHE A1366 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP A1371 " --> pdb=" O GLY A1367 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY A1372 " --> pdb=" O GLN A1368 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 216 Processing helix chain 'H' and resid 230 through 295 removed outlier: 3.711A pdb=" N THR H 254 " --> pdb=" O SER H 250 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR H 287 " --> pdb=" O THR H 283 " (cutoff:3.500A) Processing helix chain 'H' and resid 336 through 342 Processing helix chain 'H' and resid 355 through 380 removed outlier: 3.806A pdb=" N ASP H 361 " --> pdb=" O GLU H 357 " (cutoff:3.500A) Processing helix chain 'H' and resid 393 through 403 Processing helix chain 'C' and resid 8 through 37 Proline residue: C 22 - end of helix removed outlier: 3.772A pdb=" N THR C 25 " --> pdb=" O PHE C 21 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER C 26 " --> pdb=" O PRO C 22 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG C 27 " --> pdb=" O LEU C 23 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 55 Processing helix chain 'C' and resid 64 through 80 Processing helix chain 'C' and resid 81 through 114 removed outlier: 3.872A pdb=" N GLU C 85 " --> pdb=" O PRO C 81 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N MET C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 147 removed outlier: 3.517A pdb=" N HIS C 135 " --> pdb=" O MET C 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 37 Processing helix chain 'E' and resid 70 through 75 removed outlier: 3.800A pdb=" N GLU E 73 " --> pdb=" O GLN E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.649A pdb=" N ILE E 87 " --> pdb=" O LYS E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 166 Processing helix chain 'E' and resid 173 through 178 Processing helix chain 'E' and resid 180 through 184 Processing helix chain 'E' and resid 189 through 218 removed outlier: 3.862A pdb=" N ALA E 194 " --> pdb=" O LEU E 190 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS E 203 " --> pdb=" O LEU E 199 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN E 213 " --> pdb=" O VAL E 209 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N PHE E 214 " --> pdb=" O ARG E 210 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU E 216 " --> pdb=" O SER E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 302 Processing helix chain 'E' and resid 318 through 374 Processing helix chain 'B' and resid 656 through 660 removed outlier: 3.820A pdb=" N ASN B 659 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 677 removed outlier: 3.530A pdb=" N LYS B 671 " --> pdb=" O THR B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 694 Processing helix chain 'B' and resid 698 through 711 removed outlier: 3.548A pdb=" N TYR B 709 " --> pdb=" O LYS B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 724 Processing helix chain 'B' and resid 771 through 778 removed outlier: 3.513A pdb=" N LEU B 778 " --> pdb=" O CYS B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 840 removed outlier: 3.842A pdb=" N GLU B 805 " --> pdb=" O ASN B 801 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR B 806 " --> pdb=" O GLN B 802 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN B 840 " --> pdb=" O ASN B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 872 removed outlier: 4.163A pdb=" N LYS B 864 " --> pdb=" O MET B 860 " (cutoff:3.500A) Processing helix chain 'B' and resid 876 through 883 Processing helix chain 'B' and resid 892 through 926 removed outlier: 3.631A pdb=" N LYS B 896 " --> pdb=" O PRO B 892 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 897 " --> pdb=" O VAL B 893 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 898 " --> pdb=" O VAL B 894 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN B 900 " --> pdb=" O LYS B 896 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLU B 903 " --> pdb=" O LYS B 899 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL B 915 " --> pdb=" O GLU B 911 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU B 920 " --> pdb=" O TRP B 916 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN B 921 " --> pdb=" O ARG B 917 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LYS B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL B 923 " --> pdb=" O LEU B 919 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE B 925 " --> pdb=" O GLN B 921 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS B 926 " --> pdb=" O LYS B 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 930 through 939 removed outlier: 4.069A pdb=" N LYS B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN B 937 " --> pdb=" O LEU B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 944 through 965 removed outlier: 3.718A pdb=" N LEU B 948 " --> pdb=" O THR B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 997 removed outlier: 4.055A pdb=" N TYR B 986 " --> pdb=" O LYS B 982 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP B 993 " --> pdb=" O LEU B 989 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR B 994 " --> pdb=" O CYS B 990 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 996 " --> pdb=" O ALA B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1003 through 1022 Processing helix chain 'B' and resid 1025 through 1040 Processing helix chain 'B' and resid 1064 through 1070 Processing helix chain 'B' and resid 1141 through 1164 removed outlier: 4.510A pdb=" N MET B1164 " --> pdb=" O GLU B1160 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1175 Processing helix chain 'B' and resid 1189 through 1195 Processing helix chain 'B' and resid 1202 through 1217 Processing helix chain 'B' and resid 1220 through 1232 removed outlier: 3.619A pdb=" N PHE B1224 " --> pdb=" O GLU B1220 " (cutoff:3.500A) Processing helix chain 'B' and resid 1233 through 1240 removed outlier: 3.907A pdb=" N ALA B1236 " --> pdb=" O ASN B1233 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE B1237 " --> pdb=" O ASN B1234 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LYS B1238 " --> pdb=" O LYS B1235 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU B1239 " --> pdb=" O ALA B1236 " (cutoff:3.500A) Processing helix chain 'B' and resid 1241 through 1247 Processing helix chain 'B' and resid 1248 through 1257 removed outlier: 3.637A pdb=" N HIS B1252 " --> pdb=" O SER B1248 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA B1253 " --> pdb=" O LEU B1249 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N HIS B1254 " --> pdb=" O VAL B1250 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET B1257 " --> pdb=" O ALA B1253 " (cutoff:3.500A) Processing helix chain 'B' and resid 1259 through 1274 Processing helix chain 'B' and resid 1279 through 1292 Processing helix chain 'B' and resid 1330 through 1343 removed outlier: 3.680A pdb=" N LEU B1343 " --> pdb=" O THR B1339 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 80 Processing helix chain 'J' and resid 104 through 108 removed outlier: 4.476A pdb=" N SER J 108 " --> pdb=" O THR J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 135 removed outlier: 3.674A pdb=" N ASN J 134 " --> pdb=" O GLY J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 153 removed outlier: 3.879A pdb=" N ILE J 148 " --> pdb=" O THR J 144 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN J 153 " --> pdb=" O GLN J 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 157 through 162 Processing helix chain 'J' and resid 176 through 184 Processing sheet with id=AA1, first strand: chain 'K' and resid 28 through 34 removed outlier: 3.617A pdb=" N HIS K 30 " --> pdb=" O LYS K 442 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 50 through 54 removed outlier: 3.708A pdb=" N SER K 51 " --> pdb=" O SER K 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 50 through 54 removed outlier: 3.708A pdb=" N SER K 51 " --> pdb=" O SER K 74 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TRP K 123 " --> pdb=" O ILE K 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 130 through 134 removed outlier: 7.309A pdb=" N PHE K 157 " --> pdb=" O LYS K 144 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE K 146 " --> pdb=" O ALA K 155 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ALA K 155 " --> pdb=" O ILE K 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 190 through 192 removed outlier: 3.619A pdb=" N THR K 213 " --> pdb=" O LYS K 203 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE K 230 " --> pdb=" O ILE K 214 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP K 218 " --> pdb=" O VAL K 226 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL K 226 " --> pdb=" O ASP K 218 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 238 through 243 removed outlier: 3.735A pdb=" N GLU K 240 " --> pdb=" O CYS K 252 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS K 242 " --> pdb=" O ALA K 250 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER K 253 " --> pdb=" O ILE K 257 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ILE K 257 " --> pdb=" O SER K 253 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TRP K 271 " --> pdb=" O PHE K 260 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 281 through 286 removed outlier: 3.851A pdb=" N CYS K 283 " --> pdb=" O GLY K 297 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR K 298 " --> pdb=" O ALA K 302 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ALA K 302 " --> pdb=" O THR K 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 346 through 349 removed outlier: 3.630A pdb=" N LYS K 346 " --> pdb=" O ILE K 360 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL K 366 " --> pdb=" O TYR K 401 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N TYR K 401 " --> pdb=" O VAL K 366 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N HIS K 368 " --> pdb=" O ALA K 399 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 62 through 64 removed outlier: 7.168A pdb=" N VAL F 21 " --> pdb=" O GLU F 62 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N TYR F 64 " --> pdb=" O VAL F 21 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR F 23 " --> pdb=" O TYR F 64 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL F 267 " --> pdb=" O MET F 306 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL F 308 " --> pdb=" O VAL F 267 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU F 269 " --> pdb=" O VAL F 308 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU F 181 " --> pdb=" O VAL F 268 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N GLN F 270 " --> pdb=" O LEU F 181 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE F 183 " --> pdb=" O GLN F 270 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N VAL F 234 " --> pdb=" O VAL F 203 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N THR F 205 " --> pdb=" O VAL F 234 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N VAL F 236 " --> pdb=" O THR F 205 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER F 207 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N LEU F 238 " --> pdb=" O SER F 207 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N HIS F 209 " --> pdb=" O LEU F 238 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 61 through 64 removed outlier: 6.916A pdb=" N VAL G 21 " --> pdb=" O GLU G 62 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N TYR G 64 " --> pdb=" O VAL G 21 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TYR G 23 " --> pdb=" O TYR G 64 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA G 22 " --> pdb=" O VAL G 143 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ALA G 142 " --> pdb=" O VAL G 307 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL G 267 " --> pdb=" O MET G 306 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N VAL G 308 " --> pdb=" O VAL G 267 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU G 269 " --> pdb=" O VAL G 308 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU G 181 " --> pdb=" O VAL G 268 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLN G 270 " --> pdb=" O LEU G 181 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE G 183 " --> pdb=" O GLN G 270 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N VAL G 234 " --> pdb=" O VAL G 203 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N THR G 205 " --> pdb=" O VAL G 234 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL G 236 " --> pdb=" O THR G 205 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N SER G 207 " --> pdb=" O VAL G 236 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LEU G 238 " --> pdb=" O SER G 207 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N HIS G 209 " --> pdb=" O LEU G 238 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 126 through 127 Processing sheet with id=AB3, first strand: chain 'A' and resid 750 through 751 removed outlier: 3.541A pdb=" N TYR A 755 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 975 through 977 removed outlier: 3.795A pdb=" N MET A1300 " --> pdb=" O ILE A1317 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 90 through 93 Processing sheet with id=AB6, first strand: chain 'B' and resid 734 through 735 removed outlier: 7.406A pdb=" N GLU B 734 " --> pdb=" O SER J 68 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 755 through 757 Processing sheet with id=AB8, first strand: chain 'B' and resid 975 through 977 removed outlier: 3.556A pdb=" N MET B1300 " --> pdb=" O ILE B1317 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 86 through 91 removed outlier: 6.798A pdb=" N ILE J 138 " --> pdb=" O ASN J 86 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLY J 88 " --> pdb=" O ILE J 138 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASP J 225 " --> pdb=" O ILE J 272 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ILE J 272 " --> pdb=" O ASP J 225 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLU J 227 " --> pdb=" O ILE J 270 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE J 270 " --> pdb=" O GLU J 227 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLU J 229 " --> pdb=" O TYR J 268 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 86 through 91 removed outlier: 6.798A pdb=" N ILE J 138 " --> pdb=" O ASN J 86 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLY J 88 " --> pdb=" O ILE J 138 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASP J 225 " --> pdb=" O ILE J 272 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ILE J 272 " --> pdb=" O ASP J 225 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLU J 227 " --> pdb=" O ILE J 270 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE J 270 " --> pdb=" O GLU J 227 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLU J 229 " --> pdb=" O TYR J 268 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR J 213 " --> pdb=" O ILE J 272 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N GLN J 274 " --> pdb=" O THR J 213 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 243 through 244 1384 hydrogen bonds defined for protein. 4026 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.72 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.17: 7 1.17 - 1.33: 7550 1.33 - 1.49: 9068 1.49 - 1.65: 11701 1.65 - 1.81: 181 Bond restraints: 28507 Sorted by residual: bond pdb=" N PRO F 10 " pdb=" CA PRO F 10 " ideal model delta sigma weight residual 1.467 1.690 -0.223 1.17e-02 7.31e+03 3.64e+02 bond pdb=" C LYS F 14 " pdb=" N PRO F 15 " ideal model delta sigma weight residual 1.332 1.497 -0.165 8.90e-03 1.26e+04 3.42e+02 bond pdb=" OG1 TPO E 167 " pdb=" P TPO E 167 " ideal model delta sigma weight residual 1.717 1.438 0.279 2.00e-02 2.50e+03 1.94e+02 bond pdb=" C PRO J 123 " pdb=" N PRO J 124 " ideal model delta sigma weight residual 1.329 1.487 -0.158 1.18e-02 7.18e+03 1.80e+02 bond pdb=" C PRO D 294 " pdb=" N PRO D 295 " ideal model delta sigma weight residual 1.332 1.502 -0.170 1.32e-02 5.74e+03 1.67e+02 ... (remaining 28502 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.58: 38360 4.58 - 9.15: 190 9.15 - 13.73: 31 13.73 - 18.31: 4 18.31 - 22.88: 3 Bond angle restraints: 38588 Sorted by residual: angle pdb=" C ASP F 9 " pdb=" N PRO F 10 " pdb=" CA PRO F 10 " ideal model delta sigma weight residual 119.93 138.67 -18.74 1.07e+00 8.73e-01 3.07e+02 angle pdb=" C ASP D 307 " pdb=" CA ASP D 307 " pdb=" CB ASP D 307 " ideal model delta sigma weight residual 110.79 87.91 22.88 1.66e+00 3.63e-01 1.90e+02 angle pdb=" C PRO J 123 " pdb=" N PRO J 124 " pdb=" CA PRO J 124 " ideal model delta sigma weight residual 120.38 133.86 -13.48 1.03e+00 9.43e-01 1.71e+02 angle pdb=" C PRO D 294 " pdb=" N PRO D 295 " pdb=" CA PRO D 295 " ideal model delta sigma weight residual 119.76 130.88 -11.12 1.00e+00 1.00e+00 1.24e+02 angle pdb=" C TPO E 167 " pdb=" CA TPO E 167 " pdb=" CB TPO E 167 " ideal model delta sigma weight residual 109.10 87.88 21.22 2.20e+00 2.07e-01 9.30e+01 ... (remaining 38583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 14471 18.05 - 36.11: 1895 36.11 - 54.16: 637 54.16 - 72.21: 149 72.21 - 90.27: 55 Dihedral angle restraints: 17207 sinusoidal: 6703 harmonic: 10504 Sorted by residual: dihedral pdb=" CA GLU H 342 " pdb=" C GLU H 342 " pdb=" N SER H 343 " pdb=" CA SER H 343 " ideal model delta harmonic sigma weight residual -180.00 -127.56 -52.44 0 5.00e+00 4.00e-02 1.10e+02 dihedral pdb=" C ASP D 307 " pdb=" N ASP D 307 " pdb=" CA ASP D 307 " pdb=" CB ASP D 307 " ideal model delta harmonic sigma weight residual -122.60 -96.67 -25.93 0 2.50e+00 1.60e-01 1.08e+02 dihedral pdb=" CA LYS H 314 " pdb=" C LYS H 314 " pdb=" N THR H 315 " pdb=" CA THR H 315 " ideal model delta harmonic sigma weight residual -180.00 -131.23 -48.77 0 5.00e+00 4.00e-02 9.51e+01 ... (remaining 17204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.150: 4206 0.150 - 0.300: 41 0.300 - 0.450: 12 0.450 - 0.600: 2 0.600 - 0.749: 2 Chirality restraints: 4263 Sorted by residual: chirality pdb=" CA SEP D 309 " pdb=" N SEP D 309 " pdb=" C SEP D 309 " pdb=" CB SEP D 309 " both_signs ideal model delta sigma weight residual False 2.50 1.75 0.75 2.00e-01 2.50e+01 1.40e+01 chirality pdb=" CA TPO F 501 " pdb=" N TPO F 501 " pdb=" C TPO F 501 " pdb=" CB TPO F 501 " both_signs ideal model delta sigma weight residual False 2.53 1.88 0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" CA LYS F 14 " pdb=" N LYS F 14 " pdb=" C LYS F 14 " pdb=" CB LYS F 14 " both_signs ideal model delta sigma weight residual False 2.51 3.07 -0.56 2.00e-01 2.50e+01 7.91e+00 ... (remaining 4260 not shown) Planarity restraints: 5006 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SEP I 174 " 0.088 2.00e-02 2.50e+03 1.78e-01 3.17e+02 pdb=" C SEP I 174 " -0.306 2.00e-02 2.50e+03 pdb=" O SEP I 174 " 0.136 2.00e-02 2.50e+03 pdb=" N ILE I 175 " 0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SEP F 265 " 0.078 2.00e-02 2.50e+03 1.65e-01 2.73e+02 pdb=" C SEP F 265 " -0.284 2.00e-02 2.50e+03 pdb=" O SEP F 265 " 0.130 2.00e-02 2.50e+03 pdb=" N ALA F 266 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 165 " -0.027 2.00e-02 2.50e+03 5.70e-02 3.25e+01 pdb=" C ILE E 165 " 0.098 2.00e-02 2.50e+03 pdb=" O ILE E 165 " -0.038 2.00e-02 2.50e+03 pdb=" N LEU E 166 " -0.033 2.00e-02 2.50e+03 ... (remaining 5003 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.10: 14 2.10 - 2.86: 10373 2.86 - 3.62: 44853 3.62 - 4.38: 77964 4.38 - 5.14: 132570 Nonbonded interactions: 265774 Sorted by model distance: nonbonded pdb=" OE2 GLU D 306 " pdb=" CD2 LEU D 324 " model vdw 1.346 3.460 nonbonded pdb=" N VAL F 2 " pdb=" OD1 ASP F 370 " model vdw 1.416 3.120 nonbonded pdb=" OD1 ASP F 184 " pdb=" K K F 503 " model vdw 1.784 2.850 nonbonded pdb=" OD2 ASP F 186 " pdb="ZN ZN F 502 " model vdw 1.809 2.230 nonbonded pdb=" O GLU I 177 " pdb=" N ASP I 179 " model vdw 1.817 3.120 ... (remaining 265769 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 637 or resid 660 through 1041 or resid 1063 through 1177 o \ r resid 1187 through 1343)) selection = (chain 'B' and (resid 647 or resid 660 through 1069 or resid 1132 through 1343)) \ } ncs_group { reference = (chain 'F' and (resid 2 through 5 or resid 7 through 11 or resid 13 through 264 \ or resid 266 through 364 or resid 366 through 386 or resid 502 through 504)) selection = (chain 'G' and (resid 2 through 5 or resid 7 through 11 or resid 13 through 264 \ or resid 266 through 364 or resid 366 through 503)) } 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: 4.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 27.580 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 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 : 0.008 0.279 28510 Z= 0.415 Angle : 0.978 22.885 38588 Z= 0.573 Chirality : 0.057 0.749 4263 Planarity : 0.007 0.178 5006 Dihedral : 19.273 90.267 10403 Min Nonbonded Distance : 1.346 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.40 % Favored : 93.17 % Rotamer: Outliers : 11.26 % Allowed : 25.32 % Favored : 63.42 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.79 (0.11), residues: 3487 helix: -2.11 (0.10), residues: 1728 sheet: -1.64 (0.23), residues: 389 loop : -3.20 (0.14), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 90 TYR 0.040 0.002 TYR E 373 PHE 0.024 0.002 PHE F 8 TRP 0.020 0.002 TRP A 719 HIS 0.017 0.002 HIS I 173 Details of bonding type rmsd covalent geometry : bond 0.00751 (28507) covalent geometry : angle 0.97833 (38588) hydrogen bonds : bond 0.15981 ( 1367) hydrogen bonds : angle 6.90942 ( 4026) metal coordination : bond 0.06006 ( 2) Misc. bond : bond 0.09054 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6974 Ramachandran restraints generated. 3487 Oldfield, 0 Emsley, 3487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6974 Ramachandran restraints generated. 3487 Oldfield, 0 Emsley, 3487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 3229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 321 poor density : 343 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 47 MET cc_start: 0.7856 (mtp) cc_final: 0.7451 (mtp) REVERT: F 280 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7482 (ptm160) REVERT: F 380 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7898 (tp) REVERT: G 72 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.7390 (tp-100) REVERT: G 99 ARG cc_start: 0.6892 (tpm170) cc_final: 0.6476 (tpm170) REVERT: G 108 ASP cc_start: 0.6946 (m-30) cc_final: 0.6621 (m-30) REVERT: G 384 LYS cc_start: 0.6710 (mmtt) cc_final: 0.6451 (mmtt) REVERT: I 95 LEU cc_start: 0.8366 (mt) cc_final: 0.7915 (mp) REVERT: A 727 GLN cc_start: 0.6823 (pp30) cc_final: 0.6578 (pp30) REVERT: A 801 ASN cc_start: 0.7424 (OUTLIER) cc_final: 0.7027 (m-40) REVERT: A 872 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7494 (t0) REVERT: A 1062 GLU cc_start: 0.2107 (OUTLIER) cc_final: 0.1177 (tp30) REVERT: A 1257 MET cc_start: 0.7283 (ptp) cc_final: 0.7057 (mtp) REVERT: A 1345 HIS cc_start: 0.6955 (OUTLIER) cc_final: 0.6634 (m90) REVERT: H 248 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6443 (tp30) REVERT: H 259 THR cc_start: 0.8176 (t) cc_final: 0.7965 (m) REVERT: H 313 ASN cc_start: 0.7664 (OUTLIER) cc_final: 0.7435 (t0) REVERT: H 345 GLU cc_start: 0.6315 (tt0) cc_final: 0.6079 (pt0) REVERT: C 21 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.7891 (t80) REVERT: C 27 ARG cc_start: 0.6582 (mtp-110) cc_final: 0.6343 (mtm110) REVERT: C 43 MET cc_start: 0.6366 (ttp) cc_final: 0.6097 (ttm) REVERT: C 49 ARG cc_start: 0.7605 (mmt90) cc_final: 0.7361 (mmt180) REVERT: C 55 LYS cc_start: 0.7136 (mmtt) cc_final: 0.6866 (mmmt) REVERT: C 76 TYR cc_start: 0.8164 (OUTLIER) cc_final: 0.7775 (m-80) REVERT: E 42 GLN cc_start: 0.5195 (OUTLIER) cc_final: 0.4948 (pt0) REVERT: B 918 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6851 (tp30) REVERT: B 1223 TRP cc_start: 0.8045 (m100) cc_final: 0.7832 (m100) REVERT: B 1225 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7998 (mm-30) REVERT: B 1291 ARG cc_start: 0.7740 (ttt180) cc_final: 0.7410 (tmm160) REVERT: J 110 ARG cc_start: 0.5301 (OUTLIER) cc_final: 0.5010 (tpm170) REVERT: J 149 GLN cc_start: 0.8319 (tp40) cc_final: 0.8045 (mm-40) REVERT: J 227 GLU cc_start: 0.5709 (mm-30) cc_final: 0.5292 (mm-30) REVERT: J 229 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6985 (mt-10) outliers start: 321 outliers final: 170 residues processed: 636 average time/residue: 0.6260 time to fit residues: 463.7160 Evaluate side-chains 449 residues out of total 3229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 265 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 129 GLN Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 14 LYS Chi-restraints excluded: chain F residue 44 ARG Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 264 PRO Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 280 ARG Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 316 ARG Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 337 ASP Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 380 LEU Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 72 GLN Chi-restraints excluded: chain G residue 98 LYS Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 277 SER Chi-restraints excluded: chain G residue 314 THR Chi-restraints excluded: chain G residue 321 THR Chi-restraints excluded: chain G residue 326 THR Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 172 GLU Chi-restraints excluded: chain I residue 173 HIS Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 802 GLN Chi-restraints excluded: chain A residue 823 SER Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 826 ARG Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 860 MET Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 864 LYS Chi-restraints excluded: chain A residue 868 ARG Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 896 LYS Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1064 SER Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1153 THR Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1233 ASN Chi-restraints excluded: chain A residue 1248 SER Chi-restraints excluded: chain A residue 1262 THR Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1321 ASP Chi-restraints excluded: chain A residue 1345 HIS Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 245 GLN Chi-restraints excluded: chain H residue 248 GLU Chi-restraints excluded: chain H residue 251 CYS Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 313 ASN Chi-restraints excluded: chain H residue 333 GLU Chi-restraints excluded: chain H residue 370 SER Chi-restraints excluded: chain H residue 371 ASP Chi-restraints excluded: chain H residue 396 ILE Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain E residue 371 ARG Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 732 CYS Chi-restraints excluded: chain B residue 734 GLU Chi-restraints excluded: chain B residue 768 SER Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 844 ASN Chi-restraints excluded: chain B residue 858 THR Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 881 ASP Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 890 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain B residue 991 LEU Chi-restraints excluded: chain B residue 999 THR Chi-restraints excluded: chain B residue 1004 ASN Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain B residue 1143 ASN Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1211 SER Chi-restraints excluded: chain B residue 1309 THR Chi-restraints excluded: chain B residue 1321 ASP Chi-restraints excluded: chain B residue 1339 THR Chi-restraints excluded: chain J residue 63 ASP Chi-restraints excluded: chain J residue 68 SER Chi-restraints excluded: chain J residue 69 SER Chi-restraints excluded: chain J residue 71 SER Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 110 ARG Chi-restraints excluded: chain J residue 157 SER Chi-restraints excluded: chain J residue 172 SER Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 259 ILE Chi-restraints excluded: chain J residue 265 TYR Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain J residue 276 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.0670 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.9980 overall best weight: 0.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 141 HIS F 72 GLN F 105 ASN F 231 ASN F 341 ASN F 392 ASN G 38 HIS G 177 HIS I 76 GLN I 82 ASN I 92 HIS I 100 HIS ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 183 GLN ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 GLN A 829 GLN A 930 HIS A 947 GLN A 959 GLN A 983 ASN A1036 HIS A1173 ASN A1252 HIS A1293 HIS A1299 ASN A1345 HIS H 195 GLN H 264 HIS ** H 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 ASN E 89 GLN E 192 ASN E 238 HIS ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 694 GLN B 735 ASN B 900 GLN B 965 HIS B 998 HIS ** B1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1070 HIS B1163 GLN B1206 GLN B1216 ASN B1233 ASN B1234 ASN J 237 GLN J 260 HIS Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.185126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.134381 restraints weight = 39811.515| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.54 r_work: 0.3757 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 28510 Z= 0.155 Angle : 0.677 11.189 38588 Z= 0.355 Chirality : 0.045 0.313 4263 Planarity : 0.005 0.086 5006 Dihedral : 10.767 92.145 4241 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.59 % Favored : 94.18 % Rotamer: Outliers : 7.75 % Allowed : 26.59 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.13), residues: 3487 helix: -0.38 (0.12), residues: 1739 sheet: -1.19 (0.24), residues: 382 loop : -2.43 (0.15), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 674 TYR 0.018 0.002 TYR D 40 PHE 0.016 0.001 PHE D 95 TRP 0.027 0.002 TRP H 403 HIS 0.008 0.001 HIS B 998 Details of bonding type rmsd covalent geometry : bond 0.00335 (28507) covalent geometry : angle 0.67711 (38588) hydrogen bonds : bond 0.06446 ( 1367) hydrogen bonds : angle 4.92291 ( 4026) metal coordination : bond 0.00165 ( 2) Misc. bond : bond 0.00058 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6974 Ramachandran restraints generated. 3487 Oldfield, 0 Emsley, 3487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6974 Ramachandran restraints generated. 3487 Oldfield, 0 Emsley, 3487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 221 poor density : 312 time to evaluate : 1.048 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: D 51 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7778 (tp) REVERT: D 54 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7616 (mt) REVERT: F 47 MET cc_start: 0.8448 (mtp) cc_final: 0.8053 (mtp) REVERT: F 62 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8730 (mt-10) REVERT: F 105 ASN cc_start: 0.8714 (t0) cc_final: 0.8295 (t0) REVERT: F 345 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6177 (mm-30) REVERT: G 72 GLN cc_start: 0.8277 (tm-30) cc_final: 0.7743 (tp-100) REVERT: G 99 ARG cc_start: 0.7238 (tpm170) cc_final: 0.6638 (tpm170) REVERT: G 105 ASN cc_start: 0.8808 (t0) cc_final: 0.8182 (t0) REVERT: G 108 ASP cc_start: 0.7495 (m-30) cc_final: 0.7257 (m-30) REVERT: I 80 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8237 (mp) REVERT: I 103 ASP cc_start: 0.7534 (t0) cc_final: 0.6906 (t0) REVERT: I 117 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7885 (t0) REVERT: A 727 GLN cc_start: 0.6938 (OUTLIER) cc_final: 0.6472 (pp30) REVERT: A 735 ASN cc_start: 0.8291 (OUTLIER) cc_final: 0.7907 (p0) REVERT: A 801 ASN cc_start: 0.7627 (OUTLIER) cc_final: 0.7064 (m-40) REVERT: A 860 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.7792 (mtt) REVERT: A 976 ASP cc_start: 0.7613 (OUTLIER) cc_final: 0.7329 (t70) REVERT: A 1062 GLU cc_start: 0.2013 (OUTLIER) cc_final: 0.0995 (tp30) REVERT: A 1063 MET cc_start: 0.3179 (tpt) cc_final: 0.2628 (tpt) REVERT: A 1202 ASP cc_start: 0.6634 (OUTLIER) cc_final: 0.5899 (t70) REVERT: A 1244 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7683 (mmpt) REVERT: H 220 HIS cc_start: 0.5523 (OUTLIER) cc_final: 0.4731 (p-80) REVERT: H 244 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.6254 (tmm-80) REVERT: H 245 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.6974 (tm-30) REVERT: H 259 THR cc_start: 0.8125 (t) cc_final: 0.7814 (m) REVERT: H 295 ASP cc_start: 0.7817 (m-30) cc_final: 0.7483 (t0) REVERT: H 387 GLU cc_start: 0.7150 (mp0) cc_final: 0.6934 (mp0) REVERT: H 401 HIS cc_start: 0.6665 (m-70) cc_final: 0.6191 (t-170) REVERT: C 19 GLU cc_start: 0.7643 (tp30) cc_final: 0.7130 (tp30) REVERT: C 21 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.8096 (t80) REVERT: C 27 ARG cc_start: 0.7051 (mtp-110) cc_final: 0.6740 (mtm110) REVERT: C 49 ARG cc_start: 0.7702 (mmt90) cc_final: 0.7476 (mmt180) REVERT: C 55 LYS cc_start: 0.7218 (mmtt) cc_final: 0.6799 (mmmt) REVERT: C 67 ARG cc_start: 0.6602 (OUTLIER) cc_final: 0.6304 (ptp90) REVERT: C 76 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.7749 (m-80) REVERT: E 42 GLN cc_start: 0.5367 (OUTLIER) cc_final: 0.4588 (mp10) REVERT: E 329 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7926 (tt0) REVERT: E 354 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7779 (tttt) REVERT: E 372 GLU cc_start: 0.8109 (tt0) cc_final: 0.7836 (tm-30) REVERT: B 674 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.6872 (mmp80) REVERT: B 734 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6364 (pp20) REVERT: B 773 MET cc_start: 0.6126 (tpp) cc_final: 0.5713 (tpp) REVERT: B 834 ILE cc_start: 0.7504 (OUTLIER) cc_final: 0.7252 (mt) REVERT: B 1067 ASP cc_start: 0.6938 (m-30) cc_final: 0.6628 (p0) REVERT: B 1131 GLN cc_start: 0.6360 (OUTLIER) cc_final: 0.6041 (tp40) REVERT: B 1175 ARG cc_start: 0.5304 (ptp-110) cc_final: 0.4741 (ttp-110) REVERT: B 1225 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7965 (mm-30) REVERT: B 1234 ASN cc_start: 0.7550 (OUTLIER) cc_final: 0.7194 (m-40) REVERT: J 64 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6454 (pp) REVERT: J 73 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8038 (mm) REVERT: J 149 GLN cc_start: 0.8481 (tp40) cc_final: 0.8261 (mm-40) REVERT: J 229 GLU cc_start: 0.7236 (mm-30) cc_final: 0.6828 (mt-10) outliers start: 221 outliers final: 85 residues processed: 502 average time/residue: 0.6098 time to fit residues: 357.6686 Evaluate side-chains 379 residues out of total 3229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 264 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 106 HIS Chi-restraints excluded: chain D residue 129 GLN Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 316 ARG Chi-restraints excluded: chain F residue 337 ASP Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 75 CYS Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 117 ASP Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 687 LYS Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain A residue 735 ASN Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 802 GLN Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 826 ARG Chi-restraints excluded: chain A residue 860 MET Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 896 LYS Chi-restraints excluded: chain A residue 927 SER Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1202 ASP Chi-restraints excluded: chain A residue 1244 LYS Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1337 TYR Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 220 HIS Chi-restraints excluded: chain H residue 244 ARG Chi-restraints excluded: chain H residue 245 GLN Chi-restraints excluded: chain H residue 333 GLU Chi-restraints excluded: chain H residue 371 ASP Chi-restraints excluded: chain H residue 396 ILE Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 674 ARG Chi-restraints excluded: chain B residue 734 GLU Chi-restraints excluded: chain B residue 830 CYS Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 917 ARG Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1025 SER Chi-restraints excluded: chain B residue 1131 GLN Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1220 GLU Chi-restraints excluded: chain B residue 1234 ASN Chi-restraints excluded: chain B residue 1266 MET Chi-restraints excluded: chain B residue 1321 ASP Chi-restraints excluded: chain B residue 1341 TYR Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 68 SER Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 111 HIS Chi-restraints excluded: chain J residue 222 THR Chi-restraints excluded: chain J residue 259 ILE Chi-restraints excluded: chain J residue 269 SER Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain J residue 276 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 140 optimal weight: 0.4980 chunk 270 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 24 optimal weight: 50.0000 chunk 240 optimal weight: 0.4980 chunk 32 optimal weight: 50.0000 chunk 114 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 315 optimal weight: 1.9990 chunk 191 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 72 GLN G 330 ASN ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1132 ASN H 198 GLN H 402 GLN E 89 GLN B 886 HIS B1234 ASN ** B1289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 HIS J 183 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.184959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.132530 restraints weight = 39937.978| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 2.24 r_work: 0.3794 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3682 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 28510 Z= 0.154 Angle : 0.640 12.633 38588 Z= 0.332 Chirality : 0.044 0.193 4263 Planarity : 0.004 0.083 5006 Dihedral : 9.009 89.399 4036 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.25 % Favored : 94.58 % Rotamer: Outliers : 7.33 % Allowed : 27.36 % Favored : 65.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.14), residues: 3487 helix: 0.26 (0.12), residues: 1740 sheet: -0.95 (0.24), residues: 384 loop : -2.16 (0.16), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 160 TYR 0.022 0.002 TYR B 682 PHE 0.018 0.001 PHE D 95 TRP 0.016 0.001 TRP H 403 HIS 0.007 0.001 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00344 (28507) covalent geometry : angle 0.64011 (38588) hydrogen bonds : bond 0.06183 ( 1367) hydrogen bonds : angle 4.59052 ( 4026) metal coordination : bond 0.00060 ( 2) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6974 Ramachandran restraints generated. 3487 Oldfield, 0 Emsley, 3487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6974 Ramachandran restraints generated. 3487 Oldfield, 0 Emsley, 3487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 294 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 51 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7808 (tp) REVERT: D 54 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7694 (mt) REVERT: D 113 CYS cc_start: 0.5531 (OUTLIER) cc_final: 0.5007 (t) REVERT: F 8 PHE cc_start: 0.7679 (t80) cc_final: 0.7139 (t80) REVERT: F 47 MET cc_start: 0.8426 (mtp) cc_final: 0.8020 (mtp) REVERT: F 62 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8773 (mt-10) REVERT: F 179 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.6994 (mtm180) REVERT: F 345 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6195 (mm-30) REVERT: G 18 LYS cc_start: 0.7915 (mttp) cc_final: 0.7352 (tttp) REVERT: G 72 GLN cc_start: 0.8199 (tm-30) cc_final: 0.7728 (tp-100) REVERT: G 99 ARG cc_start: 0.7271 (tpm170) cc_final: 0.6718 (tpm170) REVERT: G 105 ASN cc_start: 0.8804 (t0) cc_final: 0.8153 (t0) REVERT: G 375 ASN cc_start: 0.7749 (OUTLIER) cc_final: 0.7460 (p0) REVERT: I 80 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8232 (mp) REVERT: I 103 ASP cc_start: 0.7420 (t0) cc_final: 0.7072 (t0) REVERT: I 106 GLU cc_start: 0.7968 (mp0) cc_final: 0.7706 (mp0) REVERT: I 117 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7922 (t0) REVERT: I 172 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6942 (pp20) REVERT: A 727 GLN cc_start: 0.7005 (OUTLIER) cc_final: 0.6526 (pp30) REVERT: A 735 ASN cc_start: 0.8249 (OUTLIER) cc_final: 0.7890 (p0) REVERT: A 920 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7136 (tm-30) REVERT: A 976 ASP cc_start: 0.7649 (OUTLIER) cc_final: 0.7349 (t70) REVERT: A 1062 GLU cc_start: 0.1949 (OUTLIER) cc_final: 0.1722 (tt0) REVERT: A 1202 ASP cc_start: 0.6555 (OUTLIER) cc_final: 0.5960 (t70) REVERT: A 1244 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7672 (mmpt) REVERT: H 220 HIS cc_start: 0.5435 (OUTLIER) cc_final: 0.4650 (p-80) REVERT: H 244 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.6293 (tmm-80) REVERT: H 245 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.6821 (tm-30) REVERT: H 259 THR cc_start: 0.8151 (t) cc_final: 0.7813 (m) REVERT: H 295 ASP cc_start: 0.7660 (m-30) cc_final: 0.7395 (t0) REVERT: H 401 HIS cc_start: 0.6724 (m-70) cc_final: 0.6416 (t-170) REVERT: C 19 GLU cc_start: 0.7438 (tp30) cc_final: 0.6893 (tp30) REVERT: C 21 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.7977 (t80) REVERT: C 27 ARG cc_start: 0.7130 (mtp-110) cc_final: 0.6816 (mtm110) REVERT: C 49 ARG cc_start: 0.7700 (mmt90) cc_final: 0.7498 (mmt180) REVERT: C 55 LYS cc_start: 0.7369 (mmtt) cc_final: 0.6841 (mmmt) REVERT: C 67 ARG cc_start: 0.6603 (mtm110) cc_final: 0.6290 (ptp90) REVERT: C 76 TYR cc_start: 0.8175 (OUTLIER) cc_final: 0.7806 (m-80) REVERT: C 77 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7107 (pm20) REVERT: C 110 VAL cc_start: 0.7950 (OUTLIER) cc_final: 0.7733 (t) REVERT: E 42 GLN cc_start: 0.4941 (OUTLIER) cc_final: 0.4580 (mp10) REVERT: E 189 ILE cc_start: 0.7210 (OUTLIER) cc_final: 0.6809 (mp) REVERT: B 674 ARG cc_start: 0.7071 (OUTLIER) cc_final: 0.6819 (mmp80) REVERT: B 773 MET cc_start: 0.6031 (tpp) cc_final: 0.5680 (tpp) REVERT: B 834 ILE cc_start: 0.7465 (OUTLIER) cc_final: 0.7235 (mt) REVERT: B 884 HIS cc_start: 0.7319 (OUTLIER) cc_final: 0.6745 (m170) REVERT: B 918 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7387 (tp30) REVERT: B 1131 GLN cc_start: 0.6452 (OUTLIER) cc_final: 0.6031 (tp40) REVERT: B 1175 ARG cc_start: 0.5557 (ptp-110) cc_final: 0.4917 (ttp-110) REVERT: B 1187 LEU cc_start: 0.2756 (OUTLIER) cc_final: 0.2168 (pp) REVERT: B 1225 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7944 (mm-30) REVERT: B 1301 PHE cc_start: 0.5522 (OUTLIER) cc_final: 0.4951 (m-80) REVERT: J 73 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8060 (mm) REVERT: J 149 GLN cc_start: 0.8495 (tp40) cc_final: 0.8275 (mm-40) outliers start: 209 outliers final: 102 residues processed: 466 average time/residue: 0.6050 time to fit residues: 329.3225 Evaluate side-chains 396 residues out of total 3229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 260 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 113 CYS Chi-restraints excluded: chain D residue 129 GLN Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 316 ARG Chi-restraints excluded: chain F residue 337 ASP Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 360 MET Chi-restraints excluded: chain G residue 375 ASN Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 117 ASP Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 172 GLU Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 687 LYS Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain A residue 735 ASN Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 802 GLN Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 826 ARG Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 896 LYS Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 927 SER Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1202 ASP Chi-restraints excluded: chain A residue 1244 LYS Chi-restraints excluded: chain A residue 1266 MET Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1337 TYR Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 220 HIS Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 244 ARG Chi-restraints excluded: chain H residue 245 GLN Chi-restraints excluded: chain H residue 283 THR Chi-restraints excluded: chain H residue 333 GLU Chi-restraints excluded: chain H residue 371 ASP Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 674 ARG Chi-restraints excluded: chain B residue 756 LYS Chi-restraints excluded: chain B residue 830 CYS Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 858 THR Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 884 HIS Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1025 SER Chi-restraints excluded: chain B residue 1131 GLN Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1266 MET Chi-restraints excluded: chain B residue 1289 GLN Chi-restraints excluded: chain B residue 1301 PHE Chi-restraints excluded: chain B residue 1321 ASP Chi-restraints excluded: chain B residue 1323 THR Chi-restraints excluded: chain B residue 1341 TYR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 111 HIS Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 222 THR Chi-restraints excluded: chain J residue 259 ILE Chi-restraints excluded: chain J residue 269 SER Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain J residue 276 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 38 optimal weight: 50.0000 chunk 198 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 291 optimal weight: 2.9990 chunk 271 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 242 optimal weight: 1.9990 chunk 266 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 72 GLN ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 ASN ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 ASN B 801 ASN ** B1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1311 HIS J 79 HIS J 183 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.184857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.134074 restraints weight = 39796.788| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 2.71 r_work: 0.3750 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 28510 Z= 0.165 Angle : 0.638 11.461 38588 Z= 0.332 Chirality : 0.044 0.268 4263 Planarity : 0.004 0.081 5006 Dihedral : 8.746 87.184 4021 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.59 % Favored : 94.21 % Rotamer: Outliers : 7.79 % Allowed : 27.08 % Favored : 65.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.14), residues: 3487 helix: 0.51 (0.12), residues: 1753 sheet: -0.83 (0.25), residues: 378 loop : -2.00 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 222 TYR 0.025 0.002 TYR B 682 PHE 0.026 0.002 PHE A1305 TRP 0.018 0.002 TRP B 719 HIS 0.009 0.001 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00378 (28507) covalent geometry : angle 0.63785 (38588) hydrogen bonds : bond 0.06256 ( 1367) hydrogen bonds : angle 4.45022 ( 4026) metal coordination : bond 0.00044 ( 2) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6974 Ramachandran restraints generated. 3487 Oldfield, 0 Emsley, 3487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6974 Ramachandran restraints generated. 3487 Oldfield, 0 Emsley, 3487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 222 poor density : 275 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 48 GLN cc_start: 0.7604 (tp40) cc_final: 0.7375 (tp-100) REVERT: D 51 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7839 (tp) REVERT: D 54 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7777 (mt) REVERT: D 113 CYS cc_start: 0.5622 (OUTLIER) cc_final: 0.5095 (t) REVERT: D 307 ASP cc_start: 0.7886 (m-30) cc_final: 0.7617 (m-30) REVERT: F 8 PHE cc_start: 0.7743 (t80) cc_final: 0.7145 (t80) REVERT: F 62 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8786 (mt-10) REVERT: F 179 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.6920 (mtm180) REVERT: F 211 TYR cc_start: 0.7419 (t80) cc_final: 0.7210 (t80) REVERT: G 18 LYS cc_start: 0.7943 (mttp) cc_final: 0.7355 (tttp) REVERT: G 72 GLN cc_start: 0.8330 (tm-30) cc_final: 0.7828 (tp-100) REVERT: G 99 ARG cc_start: 0.7379 (tpm170) cc_final: 0.6849 (tpm170) REVERT: G 105 ASN cc_start: 0.8779 (t0) cc_final: 0.8129 (t0) REVERT: G 375 ASN cc_start: 0.7757 (OUTLIER) cc_final: 0.7470 (p0) REVERT: I 80 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8224 (mp) REVERT: I 103 ASP cc_start: 0.7385 (t0) cc_final: 0.6954 (t0) REVERT: I 106 GLU cc_start: 0.8006 (mp0) cc_final: 0.7683 (mp0) REVERT: I 117 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7886 (t0) REVERT: I 172 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6956 (pp20) REVERT: A 700 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.8063 (m-30) REVERT: A 727 GLN cc_start: 0.7005 (OUTLIER) cc_final: 0.6522 (pp30) REVERT: A 735 ASN cc_start: 0.8289 (OUTLIER) cc_final: 0.7927 (p0) REVERT: A 747 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7478 (mp) REVERT: A 801 ASN cc_start: 0.7726 (OUTLIER) cc_final: 0.6862 (m110) REVERT: A 872 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7602 (t0) REVERT: A 920 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7165 (tm-30) REVERT: A 976 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7313 (t70) REVERT: A 1202 ASP cc_start: 0.6548 (OUTLIER) cc_final: 0.5912 (t70) REVERT: A 1244 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7702 (mmpt) REVERT: H 220 HIS cc_start: 0.5506 (OUTLIER) cc_final: 0.4631 (p-80) REVERT: H 244 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.6553 (tmm-80) REVERT: H 245 GLN cc_start: 0.7571 (OUTLIER) cc_final: 0.6867 (tm-30) REVERT: H 259 THR cc_start: 0.8150 (t) cc_final: 0.7797 (m) REVERT: H 295 ASP cc_start: 0.7762 (m-30) cc_final: 0.7448 (t0) REVERT: H 392 ARG cc_start: 0.6954 (OUTLIER) cc_final: 0.6705 (ptp90) REVERT: H 401 HIS cc_start: 0.6799 (m-70) cc_final: 0.6573 (t-170) REVERT: C 19 GLU cc_start: 0.7518 (tp30) cc_final: 0.6922 (tp30) REVERT: C 21 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.7917 (t80) REVERT: C 27 ARG cc_start: 0.7192 (mtp-110) cc_final: 0.6868 (mtm110) REVERT: C 55 LYS cc_start: 0.7341 (mmtt) cc_final: 0.6803 (mmmt) REVERT: C 76 TYR cc_start: 0.8230 (OUTLIER) cc_final: 0.7823 (m-80) REVERT: C 77 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7256 (pm20) REVERT: C 110 VAL cc_start: 0.8017 (OUTLIER) cc_final: 0.7785 (t) REVERT: B 773 MET cc_start: 0.6170 (tpp) cc_final: 0.5884 (tpp) REVERT: B 788 TRP cc_start: 0.7582 (OUTLIER) cc_final: 0.5771 (m100) REVERT: B 834 ILE cc_start: 0.7521 (OUTLIER) cc_final: 0.7301 (mt) REVERT: B 884 HIS cc_start: 0.7291 (OUTLIER) cc_final: 0.6740 (m170) REVERT: B 918 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7458 (tp30) REVERT: B 975 LEU cc_start: 0.5500 (OUTLIER) cc_final: 0.5292 (mp) REVERT: B 1175 ARG cc_start: 0.5431 (ptp-110) cc_final: 0.4728 (ttp-110) REVERT: B 1187 LEU cc_start: 0.2539 (OUTLIER) cc_final: 0.1967 (pp) REVERT: B 1301 PHE cc_start: 0.5545 (OUTLIER) cc_final: 0.4975 (m-80) REVERT: J 73 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8142 (mm) REVERT: J 216 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6797 (tp) outliers start: 222 outliers final: 116 residues processed: 466 average time/residue: 0.5847 time to fit residues: 320.4786 Evaluate side-chains 391 residues out of total 3229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 239 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 113 CYS Chi-restraints excluded: chain D residue 129 GLN Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 55 TYR Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 316 ARG Chi-restraints excluded: chain F residue 337 ASP Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 277 SER Chi-restraints excluded: chain G residue 314 THR Chi-restraints excluded: chain G residue 360 MET Chi-restraints excluded: chain G residue 375 ASN Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 117 ASP Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 172 GLU Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 687 LYS Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain A residue 735 ASN Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 802 GLN Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 826 ARG Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 896 LYS Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 927 SER Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1202 ASP Chi-restraints excluded: chain A residue 1244 LYS Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1337 TYR Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 214 MET Chi-restraints excluded: chain H residue 220 HIS Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 244 ARG Chi-restraints excluded: chain H residue 245 GLN Chi-restraints excluded: chain H residue 283 THR Chi-restraints excluded: chain H residue 333 GLU Chi-restraints excluded: chain H residue 371 ASP Chi-restraints excluded: chain H residue 392 ARG Chi-restraints excluded: chain H residue 396 ILE Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 756 LYS Chi-restraints excluded: chain B residue 780 ASP Chi-restraints excluded: chain B residue 788 TRP Chi-restraints excluded: chain B residue 830 CYS Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 884 HIS Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1025 SER Chi-restraints excluded: chain B residue 1134 SER Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1220 GLU Chi-restraints excluded: chain B residue 1289 GLN Chi-restraints excluded: chain B residue 1301 PHE Chi-restraints excluded: chain B residue 1321 ASP Chi-restraints excluded: chain B residue 1323 THR Chi-restraints excluded: chain B residue 1341 TYR Chi-restraints excluded: chain J residue 63 ASP Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 111 HIS Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 222 THR Chi-restraints excluded: chain J residue 259 ILE Chi-restraints excluded: chain J residue 269 SER Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain J residue 276 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 266 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 244 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 212 optimal weight: 5.9990 chunk 195 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 78 optimal weight: 0.0270 chunk 164 optimal weight: 1.9990 overall best weight: 0.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 72 GLN ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 ASN A 947 GLN C 71 ASN B1036 HIS ** B1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 HIS J 183 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.186364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.135655 restraints weight = 39648.921| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.57 r_work: 0.3790 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3676 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 28510 Z= 0.137 Angle : 0.602 11.704 38588 Z= 0.312 Chirality : 0.043 0.208 4263 Planarity : 0.004 0.078 5006 Dihedral : 8.253 87.180 4012 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.96 % Favored : 94.92 % Rotamer: Outliers : 6.94 % Allowed : 28.13 % Favored : 64.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.14), residues: 3487 helix: 0.85 (0.12), residues: 1749 sheet: -0.59 (0.25), residues: 379 loop : -1.87 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 160 TYR 0.018 0.001 TYR D 40 PHE 0.015 0.001 PHE D 95 TRP 0.020 0.001 TRP B 719 HIS 0.007 0.001 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00304 (28507) covalent geometry : angle 0.60165 (38588) hydrogen bonds : bond 0.05668 ( 1367) hydrogen bonds : angle 4.29593 ( 4026) metal coordination : bond 0.00021 ( 2) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6974 Ramachandran restraints generated. 3487 Oldfield, 0 Emsley, 3487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6974 Ramachandran restraints generated. 3487 Oldfield, 0 Emsley, 3487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 277 time to evaluate : 1.123 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: D 51 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7789 (tp) REVERT: D 54 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7746 (mt) REVERT: D 113 CYS cc_start: 0.5590 (OUTLIER) cc_final: 0.5099 (t) REVERT: D 307 ASP cc_start: 0.7847 (m-30) cc_final: 0.7560 (m-30) REVERT: F 8 PHE cc_start: 0.7749 (t80) cc_final: 0.7132 (t80) REVERT: F 55 TYR cc_start: 0.8669 (OUTLIER) cc_final: 0.7132 (t80) REVERT: F 62 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8786 (mt-10) REVERT: F 179 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.6953 (mtm180) REVERT: F 211 TYR cc_start: 0.7367 (t80) cc_final: 0.7161 (t80) REVERT: F 345 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6465 (mm-30) REVERT: G 18 LYS cc_start: 0.7907 (mttp) cc_final: 0.7345 (tttt) REVERT: G 72 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7750 (tp-100) REVERT: G 105 ASN cc_start: 0.8729 (t0) cc_final: 0.8059 (t0) REVERT: G 204 MET cc_start: 0.7331 (ttp) cc_final: 0.6990 (ttp) REVERT: G 375 ASN cc_start: 0.7689 (OUTLIER) cc_final: 0.7358 (p0) REVERT: I 80 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8227 (mp) REVERT: I 103 ASP cc_start: 0.7504 (t0) cc_final: 0.6989 (t0) REVERT: I 106 GLU cc_start: 0.7903 (mp0) cc_final: 0.7531 (mp0) REVERT: A 727 GLN cc_start: 0.7068 (OUTLIER) cc_final: 0.6588 (pp30) REVERT: A 735 ASN cc_start: 0.8199 (OUTLIER) cc_final: 0.7863 (p0) REVERT: A 801 ASN cc_start: 0.7455 (OUTLIER) cc_final: 0.7080 (m110) REVERT: A 920 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7055 (tm-30) REVERT: A 946 LYS cc_start: 0.7032 (OUTLIER) cc_final: 0.6807 (mptt) REVERT: A 976 ASP cc_start: 0.7642 (OUTLIER) cc_final: 0.7323 (t70) REVERT: A 1244 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7675 (mmpt) REVERT: A 1266 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7909 (mpp) REVERT: H 220 HIS cc_start: 0.5264 (OUTLIER) cc_final: 0.4498 (p-80) REVERT: H 244 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.6299 (tmm-80) REVERT: H 259 THR cc_start: 0.8189 (t) cc_final: 0.7862 (m) REVERT: H 295 ASP cc_start: 0.7603 (m-30) cc_final: 0.7307 (t0) REVERT: H 392 ARG cc_start: 0.6944 (OUTLIER) cc_final: 0.6660 (ptp90) REVERT: H 401 HIS cc_start: 0.6802 (m-70) cc_final: 0.6545 (t-170) REVERT: C 21 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.7766 (t80) REVERT: C 55 LYS cc_start: 0.7381 (mmtt) cc_final: 0.6918 (mmmt) REVERT: C 76 TYR cc_start: 0.8203 (OUTLIER) cc_final: 0.7772 (m-80) REVERT: C 77 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7276 (pm20) REVERT: C 110 VAL cc_start: 0.7895 (OUTLIER) cc_final: 0.7690 (t) REVERT: E 32 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7169 (ttp-170) REVERT: E 97 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7032 (mm-30) REVERT: E 189 ILE cc_start: 0.7189 (OUTLIER) cc_final: 0.6874 (mp) REVERT: E 329 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.8017 (tt0) REVERT: B 773 MET cc_start: 0.6080 (tpp) cc_final: 0.5695 (tpp) REVERT: B 788 TRP cc_start: 0.7356 (OUTLIER) cc_final: 0.5196 (m100) REVERT: B 834 ILE cc_start: 0.7373 (OUTLIER) cc_final: 0.7149 (mt) REVERT: B 884 HIS cc_start: 0.7207 (OUTLIER) cc_final: 0.6650 (m170) REVERT: B 897 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7633 (mmt-90) REVERT: B 918 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7508 (tp30) REVERT: B 1164 MET cc_start: 0.6478 (pmt) cc_final: 0.6187 (pmt) REVERT: B 1175 ARG cc_start: 0.5455 (ptp-110) cc_final: 0.4774 (mtm-85) REVERT: B 1187 LEU cc_start: 0.2761 (OUTLIER) cc_final: 0.2260 (pp) REVERT: B 1301 PHE cc_start: 0.5424 (OUTLIER) cc_final: 0.4871 (m-80) outliers start: 198 outliers final: 106 residues processed: 445 average time/residue: 0.6190 time to fit residues: 323.0926 Evaluate side-chains 387 residues out of total 3229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 246 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 113 CYS Chi-restraints excluded: chain D residue 129 GLN Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 55 TYR Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 316 ARG Chi-restraints excluded: chain F residue 337 ASP Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 72 GLN Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 360 MET Chi-restraints excluded: chain G residue 375 ASN Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 197 MET Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 687 LYS Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain A residue 735 ASN Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 802 GLN Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 826 ARG Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 896 LYS Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 927 SER Chi-restraints excluded: chain A residue 946 LYS Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1244 LYS Chi-restraints excluded: chain A residue 1266 MET Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1337 TYR Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 214 MET Chi-restraints excluded: chain H residue 220 HIS Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 244 ARG Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 333 GLU Chi-restraints excluded: chain H residue 371 ASP Chi-restraints excluded: chain H residue 392 ARG Chi-restraints excluded: chain H residue 396 ILE Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 780 ASP Chi-restraints excluded: chain B residue 788 TRP Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 830 CYS Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 857 HIS Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 884 HIS Chi-restraints excluded: chain B residue 897 ARG Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1025 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1134 SER Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1301 PHE Chi-restraints excluded: chain B residue 1321 ASP Chi-restraints excluded: chain B residue 1341 TYR Chi-restraints excluded: chain J residue 63 ASP Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 111 HIS Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 222 THR Chi-restraints excluded: chain J residue 259 ILE Chi-restraints excluded: chain J residue 269 SER Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain J residue 276 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 112 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 221 optimal weight: 0.5980 chunk 243 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 171 optimal weight: 0.7980 chunk 347 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 202 optimal weight: 5.9990 chunk 206 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 48 GLN G 231 ASN ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 ASN ** B1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 HIS J 183 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.187174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.135364 restraints weight = 40175.820| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.50 r_work: 0.3807 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3695 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 28510 Z= 0.128 Angle : 0.594 11.538 38588 Z= 0.306 Chirality : 0.042 0.195 4263 Planarity : 0.004 0.077 5006 Dihedral : 7.893 88.078 4004 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.88 % Favored : 95.04 % Rotamer: Outliers : 6.17 % Allowed : 29.25 % Favored : 64.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.14), residues: 3487 helix: 1.07 (0.12), residues: 1752 sheet: -0.50 (0.25), residues: 381 loop : -1.77 (0.16), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 168 TYR 0.017 0.001 TYR D 29 PHE 0.023 0.001 PHE A1305 TRP 0.023 0.001 TRP B 719 HIS 0.007 0.001 HIS H 220 Details of bonding type rmsd covalent geometry : bond 0.00282 (28507) covalent geometry : angle 0.59389 (38588) hydrogen bonds : bond 0.05404 ( 1367) hydrogen bonds : angle 4.17416 ( 4026) metal coordination : bond 0.00038 ( 2) Misc. bond : bond 0.00000 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6974 Ramachandran restraints generated. 3487 Oldfield, 0 Emsley, 3487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6974 Ramachandran restraints generated. 3487 Oldfield, 0 Emsley, 3487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 263 time to evaluate : 0.855 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: D 51 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7784 (tp) REVERT: D 54 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7796 (mt) REVERT: D 94 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6993 (mt-10) REVERT: D 113 CYS cc_start: 0.5659 (OUTLIER) cc_final: 0.5169 (t) REVERT: D 307 ASP cc_start: 0.7793 (m-30) cc_final: 0.7489 (m-30) REVERT: F 55 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.7126 (t80) REVERT: F 179 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.6946 (mtm180) REVERT: F 211 TYR cc_start: 0.7327 (t80) cc_final: 0.7123 (t80) REVERT: F 345 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6438 (mm-30) REVERT: G 72 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7772 (tp-100) REVERT: G 105 ASN cc_start: 0.8739 (t0) cc_final: 0.8082 (t0) REVERT: G 375 ASN cc_start: 0.7658 (OUTLIER) cc_final: 0.7316 (p0) REVERT: I 80 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8177 (mp) REVERT: I 103 ASP cc_start: 0.7516 (t0) cc_final: 0.7058 (t0) REVERT: I 106 GLU cc_start: 0.7883 (mp0) cc_final: 0.7573 (mp0) REVERT: I 196 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8857 (pttt) REVERT: A 727 GLN cc_start: 0.7093 (OUTLIER) cc_final: 0.6641 (pp30) REVERT: A 735 ASN cc_start: 0.8162 (OUTLIER) cc_final: 0.7852 (p0) REVERT: A 779 ASN cc_start: 0.7911 (OUTLIER) cc_final: 0.7703 (t0) REVERT: A 872 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7499 (t0) REVERT: A 920 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7022 (tm-30) REVERT: A 946 LYS cc_start: 0.7018 (OUTLIER) cc_final: 0.6749 (mptt) REVERT: A 976 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7360 (t0) REVERT: A 1063 MET cc_start: 0.2846 (tpt) cc_final: 0.0687 (pmm) REVERT: A 1244 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7635 (mmpt) REVERT: A 1281 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8416 (ptpp) REVERT: H 214 MET cc_start: 0.4517 (OUTLIER) cc_final: 0.3628 (mpt) REVERT: H 220 HIS cc_start: 0.5273 (OUTLIER) cc_final: 0.4501 (p-80) REVERT: H 244 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.6254 (tmm-80) REVERT: H 259 THR cc_start: 0.8185 (t) cc_final: 0.7852 (m) REVERT: H 295 ASP cc_start: 0.7616 (m-30) cc_final: 0.7300 (t0) REVERT: H 392 ARG cc_start: 0.6924 (OUTLIER) cc_final: 0.6638 (ptp90) REVERT: C 21 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.7678 (t80) REVERT: C 55 LYS cc_start: 0.7383 (mmtt) cc_final: 0.6931 (mmmt) REVERT: C 67 ARG cc_start: 0.6518 (mtm110) cc_final: 0.6258 (ptp90) REVERT: C 76 TYR cc_start: 0.8174 (OUTLIER) cc_final: 0.7779 (m-80) REVERT: C 77 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7315 (pm20) REVERT: C 140 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7506 (ptmm) REVERT: E 32 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7127 (ttp-170) REVERT: E 56 GLU cc_start: 0.7246 (mp0) cc_final: 0.6348 (mt-10) REVERT: E 97 GLU cc_start: 0.7319 (mm-30) cc_final: 0.7050 (mm-30) REVERT: E 189 ILE cc_start: 0.7198 (OUTLIER) cc_final: 0.6956 (mp) REVERT: E 329 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.8022 (tt0) REVERT: B 648 VAL cc_start: 0.7840 (OUTLIER) cc_final: 0.7496 (t) REVERT: B 731 LYS cc_start: 0.7801 (tppt) cc_final: 0.7515 (tppp) REVERT: B 773 MET cc_start: 0.5968 (tpp) cc_final: 0.5594 (tpp) REVERT: B 788 TRP cc_start: 0.7293 (OUTLIER) cc_final: 0.4882 (m100) REVERT: B 834 ILE cc_start: 0.7367 (OUTLIER) cc_final: 0.7151 (mt) REVERT: B 884 HIS cc_start: 0.7180 (OUTLIER) cc_final: 0.6639 (m170) REVERT: B 897 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7616 (mmt-90) REVERT: B 918 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7453 (tp30) REVERT: B 1175 ARG cc_start: 0.5445 (ptp-110) cc_final: 0.4668 (mtm-85) REVERT: B 1187 LEU cc_start: 0.2723 (OUTLIER) cc_final: 0.2222 (pp) REVERT: B 1226 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7586 (pm20) REVERT: B 1301 PHE cc_start: 0.5448 (OUTLIER) cc_final: 0.4867 (m-80) REVERT: J 109 ASP cc_start: 0.5967 (OUTLIER) cc_final: 0.5425 (p0) REVERT: J 216 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6583 (tt) outliers start: 176 outliers final: 95 residues processed: 413 average time/residue: 0.6266 time to fit residues: 302.8273 Evaluate side-chains 379 residues out of total 3229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 242 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 113 CYS Chi-restraints excluded: chain D residue 129 GLN Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain F residue 55 TYR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 316 ARG Chi-restraints excluded: chain F residue 337 ASP Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 72 GLN Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 277 SER Chi-restraints excluded: chain G residue 375 ASN Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 196 LYS Chi-restraints excluded: chain I residue 197 MET Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 687 LYS Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain A residue 735 ASN Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 779 ASN Chi-restraints excluded: chain A residue 802 GLN Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 826 ARG Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 896 LYS Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 927 SER Chi-restraints excluded: chain A residue 946 LYS Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1244 LYS Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1281 LYS Chi-restraints excluded: chain A residue 1313 SER Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1337 TYR Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 214 MET Chi-restraints excluded: chain H residue 220 HIS Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 244 ARG Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 371 ASP Chi-restraints excluded: chain H residue 392 ARG Chi-restraints excluded: chain H residue 396 ILE Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 780 ASP Chi-restraints excluded: chain B residue 788 TRP Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 830 CYS Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 857 HIS Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 884 HIS Chi-restraints excluded: chain B residue 897 ARG Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1025 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1134 SER Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1226 GLU Chi-restraints excluded: chain B residue 1301 PHE Chi-restraints excluded: chain B residue 1321 ASP Chi-restraints excluded: chain B residue 1341 TYR Chi-restraints excluded: chain J residue 63 ASP Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 109 ASP Chi-restraints excluded: chain J residue 111 HIS Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 222 THR Chi-restraints excluded: chain J residue 259 ILE Chi-restraints excluded: chain J residue 276 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 279 optimal weight: 5.9990 chunk 347 optimal weight: 0.8980 chunk 277 optimal weight: 1.9990 chunk 36 optimal weight: 50.0000 chunk 143 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 54 optimal weight: 0.0030 chunk 234 optimal weight: 0.6980 chunk 210 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 99 optimal weight: 0.0470 overall best weight: 0.7290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 148 ASN ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 ASN B1036 HIS ** B1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 HIS ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 183 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.187176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.135582 restraints weight = 39944.570| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 2.63 r_work: 0.3798 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3684 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 28510 Z= 0.129 Angle : 0.592 12.501 38588 Z= 0.305 Chirality : 0.042 0.188 4263 Planarity : 0.004 0.076 5006 Dihedral : 7.663 88.754 3991 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.76 % Favored : 95.15 % Rotamer: Outliers : 6.66 % Allowed : 29.08 % Favored : 64.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.14), residues: 3487 helix: 1.17 (0.12), residues: 1757 sheet: -0.38 (0.26), residues: 381 loop : -1.68 (0.16), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 168 TYR 0.018 0.001 TYR D 29 PHE 0.016 0.001 PHE D 95 TRP 0.026 0.001 TRP B 719 HIS 0.007 0.001 HIS H 220 Details of bonding type rmsd covalent geometry : bond 0.00287 (28507) covalent geometry : angle 0.59204 (38588) hydrogen bonds : bond 0.05397 ( 1367) hydrogen bonds : angle 4.11570 ( 4026) metal coordination : bond 0.00063 ( 2) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6974 Ramachandran restraints generated. 3487 Oldfield, 0 Emsley, 3487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6974 Ramachandran restraints generated. 3487 Oldfield, 0 Emsley, 3487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 260 time to evaluate : 1.134 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: D 51 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7808 (tp) REVERT: D 113 CYS cc_start: 0.5676 (OUTLIER) cc_final: 0.5192 (t) REVERT: D 307 ASP cc_start: 0.7817 (m-30) cc_final: 0.7505 (m-30) REVERT: F 8 PHE cc_start: 0.7656 (t80) cc_final: 0.7115 (t80) REVERT: F 55 TYR cc_start: 0.8652 (OUTLIER) cc_final: 0.7125 (t80) REVERT: F 99 ARG cc_start: 0.8480 (mtp85) cc_final: 0.8173 (mtp-110) REVERT: F 179 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.6926 (mtm180) REVERT: F 211 TYR cc_start: 0.7310 (t80) cc_final: 0.7104 (t80) REVERT: F 345 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6410 (mm-30) REVERT: G 41 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7359 (mttt) REVERT: G 72 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7768 (tp-100) REVERT: G 105 ASN cc_start: 0.8741 (t0) cc_final: 0.8082 (t0) REVERT: G 204 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6792 (ttp) REVERT: G 375 ASN cc_start: 0.7638 (OUTLIER) cc_final: 0.7295 (p0) REVERT: I 80 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8206 (mp) REVERT: I 103 ASP cc_start: 0.7546 (t0) cc_final: 0.7074 (t0) REVERT: I 106 GLU cc_start: 0.7891 (mp0) cc_final: 0.7569 (mp0) REVERT: I 117 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7932 (t0) REVERT: I 172 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6742 (pp20) REVERT: I 196 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8860 (pttt) REVERT: A 639 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7628 (tt) REVERT: A 727 GLN cc_start: 0.7100 (OUTLIER) cc_final: 0.6666 (pp30) REVERT: A 735 ASN cc_start: 0.8153 (OUTLIER) cc_final: 0.7843 (p0) REVERT: A 756 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.6914 (mttm) REVERT: A 779 ASN cc_start: 0.7898 (OUTLIER) cc_final: 0.7675 (t0) REVERT: A 801 ASN cc_start: 0.7382 (OUTLIER) cc_final: 0.6972 (m110) REVERT: A 872 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7589 (t0) REVERT: A 976 ASP cc_start: 0.7533 (OUTLIER) cc_final: 0.7094 (t70) REVERT: A 1063 MET cc_start: 0.2943 (tpt) cc_final: 0.0786 (pmm) REVERT: A 1244 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7586 (mmpt) REVERT: A 1281 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8469 (ptpp) REVERT: H 214 MET cc_start: 0.4602 (OUTLIER) cc_final: 0.3700 (mpt) REVERT: H 220 HIS cc_start: 0.5294 (OUTLIER) cc_final: 0.4504 (p-80) REVERT: H 244 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.6340 (tmm-80) REVERT: H 259 THR cc_start: 0.8192 (t) cc_final: 0.7860 (m) REVERT: H 295 ASP cc_start: 0.7642 (m-30) cc_final: 0.7316 (t0) REVERT: H 392 ARG cc_start: 0.6973 (OUTLIER) cc_final: 0.6741 (ptp90) REVERT: C 21 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.7722 (t80) REVERT: C 55 LYS cc_start: 0.7414 (mmtt) cc_final: 0.6980 (mmmt) REVERT: C 76 TYR cc_start: 0.8211 (OUTLIER) cc_final: 0.7802 (m-80) REVERT: C 77 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7278 (pm20) REVERT: C 140 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7545 (ptmm) REVERT: E 32 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7052 (ttp-170) REVERT: E 56 GLU cc_start: 0.7222 (mp0) cc_final: 0.6312 (mt-10) REVERT: E 97 GLU cc_start: 0.7303 (mm-30) cc_final: 0.7077 (mm-30) REVERT: E 329 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.8010 (tt0) REVERT: B 648 VAL cc_start: 0.7878 (OUTLIER) cc_final: 0.7511 (t) REVERT: B 716 LEU cc_start: 0.4827 (OUTLIER) cc_final: 0.4612 (mp) REVERT: B 731 LYS cc_start: 0.7811 (tppt) cc_final: 0.7551 (tppp) REVERT: B 773 MET cc_start: 0.5958 (OUTLIER) cc_final: 0.5593 (tpp) REVERT: B 788 TRP cc_start: 0.7121 (OUTLIER) cc_final: 0.5090 (m100) REVERT: B 834 ILE cc_start: 0.7344 (OUTLIER) cc_final: 0.7136 (mt) REVERT: B 884 HIS cc_start: 0.7141 (OUTLIER) cc_final: 0.6615 (m170) REVERT: B 897 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7623 (mmt-90) REVERT: B 918 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7463 (tp30) REVERT: B 1175 ARG cc_start: 0.5409 (ptp-110) cc_final: 0.4732 (mtm-85) REVERT: B 1187 LEU cc_start: 0.2698 (OUTLIER) cc_final: 0.2265 (pp) REVERT: B 1226 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7467 (pm20) REVERT: B 1301 PHE cc_start: 0.5435 (OUTLIER) cc_final: 0.4864 (m-80) REVERT: J 109 ASP cc_start: 0.5962 (OUTLIER) cc_final: 0.5432 (p0) REVERT: J 216 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6573 (tt) outliers start: 190 outliers final: 95 residues processed: 419 average time/residue: 0.6225 time to fit residues: 307.2012 Evaluate side-chains 379 residues out of total 3229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 238 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 113 CYS Chi-restraints excluded: chain D residue 129 GLN Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain F residue 55 TYR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 316 ARG Chi-restraints excluded: chain F residue 337 ASP Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 72 GLN Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 204 MET Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 277 SER Chi-restraints excluded: chain G residue 375 ASN Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 117 ASP Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 172 GLU Chi-restraints excluded: chain I residue 196 LYS Chi-restraints excluded: chain I residue 197 MET Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 687 LYS Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain A residue 735 ASN Chi-restraints excluded: chain A residue 756 LYS Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 779 ASN Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 802 GLN Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 826 ARG Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 896 LYS Chi-restraints excluded: chain A residue 927 SER Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1244 LYS Chi-restraints excluded: chain A residue 1281 LYS Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1337 TYR Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 214 MET Chi-restraints excluded: chain H residue 220 HIS Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 244 ARG Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 371 ASP Chi-restraints excluded: chain H residue 392 ARG Chi-restraints excluded: chain H residue 396 ILE Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 780 ASP Chi-restraints excluded: chain B residue 788 TRP Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 830 CYS Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 857 HIS Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 884 HIS Chi-restraints excluded: chain B residue 897 ARG Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1025 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1134 SER Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1226 GLU Chi-restraints excluded: chain B residue 1301 PHE Chi-restraints excluded: chain B residue 1321 ASP Chi-restraints excluded: chain B residue 1341 TYR Chi-restraints excluded: chain J residue 63 ASP Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 109 ASP Chi-restraints excluded: chain J residue 111 HIS Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 222 THR Chi-restraints excluded: chain J residue 259 ILE Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain J residue 276 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 283 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 chunk 228 optimal weight: 3.9990 chunk 255 optimal weight: 0.5980 chunk 276 optimal weight: 9.9990 chunk 212 optimal weight: 5.9990 chunk 300 optimal weight: 2.9990 chunk 286 optimal weight: 9.9990 chunk 32 optimal weight: 50.0000 chunk 152 optimal weight: 4.9990 chunk 251 optimal weight: 0.0670 overall best weight: 1.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 HIS B 801 ASN ** B1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 HIS J 134 ASN J 183 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.184159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.132506 restraints weight = 40162.553| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.77 r_work: 0.3743 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 28510 Z= 0.196 Angle : 0.670 13.152 38588 Z= 0.348 Chirality : 0.046 0.289 4263 Planarity : 0.005 0.079 5006 Dihedral : 7.708 87.165 3980 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.79 % Favored : 94.06 % Rotamer: Outliers : 6.10 % Allowed : 29.50 % Favored : 64.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.14), residues: 3487 helix: 0.89 (0.12), residues: 1761 sheet: -0.39 (0.26), residues: 381 loop : -1.68 (0.16), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 168 TYR 0.024 0.002 TYR D 40 PHE 0.026 0.002 PHE D 95 TRP 0.026 0.002 TRP B 719 HIS 0.009 0.001 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00462 (28507) covalent geometry : angle 0.67002 (38588) hydrogen bonds : bond 0.06455 ( 1367) hydrogen bonds : angle 4.27121 ( 4026) metal coordination : bond 0.00131 ( 2) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6974 Ramachandran restraints generated. 3487 Oldfield, 0 Emsley, 3487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6974 Ramachandran restraints generated. 3487 Oldfield, 0 Emsley, 3487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 244 time to evaluate : 1.257 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: F 8 PHE cc_start: 0.7812 (t80) cc_final: 0.7207 (t80) REVERT: F 17 ASP cc_start: 0.7420 (OUTLIER) cc_final: 0.6996 (p0) REVERT: F 55 TYR cc_start: 0.8711 (OUTLIER) cc_final: 0.7154 (t80) REVERT: F 179 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.6950 (mtm180) REVERT: F 211 TYR cc_start: 0.7425 (t80) cc_final: 0.7187 (t80) REVERT: F 345 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6603 (mm-30) REVERT: G 72 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7812 (tp-100) REVERT: G 105 ASN cc_start: 0.8757 (t0) cc_final: 0.8143 (t0) REVERT: G 375 ASN cc_start: 0.7748 (OUTLIER) cc_final: 0.7454 (p0) REVERT: I 103 ASP cc_start: 0.7568 (t0) cc_final: 0.7214 (t0) REVERT: I 106 GLU cc_start: 0.7930 (mp0) cc_final: 0.7687 (mp0) REVERT: I 117 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.8007 (t0) REVERT: I 179 ASP cc_start: 0.7274 (p0) cc_final: 0.6872 (t0) REVERT: I 196 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8848 (pttt) REVERT: A 727 GLN cc_start: 0.7099 (OUTLIER) cc_final: 0.6646 (pp30) REVERT: A 735 ASN cc_start: 0.8395 (OUTLIER) cc_final: 0.8003 (p0) REVERT: A 756 LYS cc_start: 0.7420 (OUTLIER) cc_final: 0.7048 (mttm) REVERT: A 779 ASN cc_start: 0.8002 (OUTLIER) cc_final: 0.7802 (t0) REVERT: A 801 ASN cc_start: 0.7686 (OUTLIER) cc_final: 0.7185 (m-40) REVERT: A 920 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7234 (tm-30) REVERT: A 1063 MET cc_start: 0.2808 (tpt) cc_final: 0.0686 (pmm) REVERT: A 1244 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7643 (mmpt) REVERT: A 1281 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8429 (ptpp) REVERT: H 220 HIS cc_start: 0.5475 (OUTLIER) cc_final: 0.4696 (p-80) REVERT: H 244 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.6695 (tmm-80) REVERT: H 248 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7504 (tp30) REVERT: H 259 THR cc_start: 0.8161 (t) cc_final: 0.7810 (m) REVERT: H 295 ASP cc_start: 0.7923 (m-30) cc_final: 0.7512 (t0) REVERT: H 392 ARG cc_start: 0.7023 (OUTLIER) cc_final: 0.6715 (ptp90) REVERT: H 401 HIS cc_start: 0.6901 (m-70) cc_final: 0.6586 (t-170) REVERT: C 21 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.7911 (t80) REVERT: C 55 LYS cc_start: 0.7424 (mmtt) cc_final: 0.6980 (mmmt) REVERT: C 76 TYR cc_start: 0.8248 (OUTLIER) cc_final: 0.7850 (m-80) REVERT: C 77 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7303 (pm20) REVERT: C 110 VAL cc_start: 0.8042 (OUTLIER) cc_final: 0.7825 (t) REVERT: C 140 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7619 (ptmm) REVERT: E 32 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7174 (ttp-170) REVERT: E 329 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.8033 (tt0) REVERT: B 648 VAL cc_start: 0.7964 (OUTLIER) cc_final: 0.7576 (t) REVERT: B 731 LYS cc_start: 0.7859 (tppt) cc_final: 0.7595 (tppp) REVERT: B 773 MET cc_start: 0.6195 (OUTLIER) cc_final: 0.5912 (tpp) REVERT: B 788 TRP cc_start: 0.7395 (OUTLIER) cc_final: 0.5119 (m100) REVERT: B 884 HIS cc_start: 0.7135 (OUTLIER) cc_final: 0.6602 (m170) REVERT: B 897 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7744 (mmt-90) REVERT: B 918 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7449 (tp30) REVERT: B 939 ASP cc_start: 0.7437 (m-30) cc_final: 0.7215 (m-30) REVERT: B 1175 ARG cc_start: 0.5496 (ptp-110) cc_final: 0.4699 (mtm-85) REVERT: B 1226 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7478 (pm20) REVERT: B 1301 PHE cc_start: 0.5652 (OUTLIER) cc_final: 0.5065 (m-80) REVERT: J 109 ASP cc_start: 0.5945 (OUTLIER) cc_final: 0.5426 (p0) REVERT: J 216 LEU cc_start: 0.6914 (OUTLIER) cc_final: 0.6628 (tt) outliers start: 174 outliers final: 100 residues processed: 396 average time/residue: 0.5890 time to fit residues: 275.1525 Evaluate side-chains 370 residues out of total 3229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 233 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 113 CYS Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 55 TYR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 316 ARG Chi-restraints excluded: chain F residue 337 ASP Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 72 GLN Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 277 SER Chi-restraints excluded: chain G residue 375 ASN Chi-restraints excluded: chain I residue 117 ASP Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 196 LYS Chi-restraints excluded: chain I residue 197 MET Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 687 LYS Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain A residue 735 ASN Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 756 LYS Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 779 ASN Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 802 GLN Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 826 ARG Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 896 LYS Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 927 SER Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1244 LYS Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1281 LYS Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1337 TYR Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 220 HIS Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 244 ARG Chi-restraints excluded: chain H residue 248 GLU Chi-restraints excluded: chain H residue 251 CYS Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 371 ASP Chi-restraints excluded: chain H residue 392 ARG Chi-restraints excluded: chain H residue 394 SER Chi-restraints excluded: chain H residue 396 ILE Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 780 ASP Chi-restraints excluded: chain B residue 788 TRP Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 830 CYS Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 858 THR Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 884 HIS Chi-restraints excluded: chain B residue 897 ARG Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 1025 SER Chi-restraints excluded: chain B residue 1134 SER Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1226 GLU Chi-restraints excluded: chain B residue 1301 PHE Chi-restraints excluded: chain B residue 1321 ASP Chi-restraints excluded: chain B residue 1341 TYR Chi-restraints excluded: chain J residue 63 ASP Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 109 ASP Chi-restraints excluded: chain J residue 111 HIS Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 222 THR Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 259 ILE Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain J residue 276 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 345 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 225 optimal weight: 20.0000 chunk 261 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 82 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 191 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 ASN E 192 ASN ** B1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 HIS J 183 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.186873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.136499 restraints weight = 40181.173| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 2.62 r_work: 0.3809 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3698 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 28510 Z= 0.137 Angle : 0.615 13.420 38588 Z= 0.318 Chirality : 0.043 0.270 4263 Planarity : 0.004 0.077 5006 Dihedral : 7.286 75.441 3977 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.67 % Favored : 95.21 % Rotamer: Outliers : 4.98 % Allowed : 30.62 % Favored : 64.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.14), residues: 3487 helix: 1.13 (0.12), residues: 1756 sheet: -0.36 (0.26), residues: 377 loop : -1.61 (0.16), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG I 168 TYR 0.018 0.001 TYR D 40 PHE 0.017 0.001 PHE D 95 TRP 0.030 0.001 TRP B 719 HIS 0.007 0.001 HIS H 220 Details of bonding type rmsd covalent geometry : bond 0.00304 (28507) covalent geometry : angle 0.61504 (38588) hydrogen bonds : bond 0.05583 ( 1367) hydrogen bonds : angle 4.15256 ( 4026) metal coordination : bond 0.00068 ( 2) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6974 Ramachandran restraints generated. 3487 Oldfield, 0 Emsley, 3487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6974 Ramachandran restraints generated. 3487 Oldfield, 0 Emsley, 3487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 247 time to evaluate : 1.110 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: D 51 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7841 (tp) REVERT: F 8 PHE cc_start: 0.7808 (t80) cc_final: 0.7228 (t80) REVERT: F 17 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.7044 (p0) REVERT: F 55 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.7208 (t80) REVERT: F 99 ARG cc_start: 0.8512 (mtp85) cc_final: 0.8223 (mtp-110) REVERT: F 179 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7013 (mtm180) REVERT: F 211 TYR cc_start: 0.7310 (t80) cc_final: 0.7094 (t80) REVERT: G 41 LYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7371 (mttt) REVERT: G 72 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7776 (tp-100) REVERT: G 105 ASN cc_start: 0.8731 (t0) cc_final: 0.8112 (t0) REVERT: G 306 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8266 (ttp) REVERT: G 375 ASN cc_start: 0.7678 (OUTLIER) cc_final: 0.7349 (p0) REVERT: I 103 ASP cc_start: 0.7511 (t0) cc_final: 0.7029 (t0) REVERT: I 106 GLU cc_start: 0.7810 (mp0) cc_final: 0.7488 (mp0) REVERT: I 196 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8832 (pttt) REVERT: A 639 ILE cc_start: 0.7894 (OUTLIER) cc_final: 0.7659 (tt) REVERT: A 727 GLN cc_start: 0.7147 (OUTLIER) cc_final: 0.6725 (pp30) REVERT: A 735 ASN cc_start: 0.8204 (OUTLIER) cc_final: 0.7870 (p0) REVERT: A 756 LYS cc_start: 0.7308 (OUTLIER) cc_final: 0.6946 (mttm) REVERT: A 779 ASN cc_start: 0.7916 (OUTLIER) cc_final: 0.7703 (t0) REVERT: A 801 ASN cc_start: 0.7414 (OUTLIER) cc_final: 0.6889 (m-40) REVERT: A 1063 MET cc_start: 0.2970 (tpt) cc_final: 0.1027 (pmm) REVERT: A 1068 ILE cc_start: 0.5845 (OUTLIER) cc_final: 0.5560 (mt) REVERT: A 1244 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7587 (mmpt) REVERT: A 1281 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8391 (ptpp) REVERT: H 220 HIS cc_start: 0.5467 (OUTLIER) cc_final: 0.4711 (p-80) REVERT: H 244 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.6412 (tmm-80) REVERT: H 259 THR cc_start: 0.8125 (t) cc_final: 0.7844 (m) REVERT: H 295 ASP cc_start: 0.7806 (m-30) cc_final: 0.7397 (t0) REVERT: C 21 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.7727 (t80) REVERT: C 55 LYS cc_start: 0.7387 (mmtt) cc_final: 0.6969 (mmmt) REVERT: C 76 TYR cc_start: 0.8208 (OUTLIER) cc_final: 0.7756 (m-80) REVERT: C 77 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7280 (pm20) REVERT: C 140 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7612 (ptmm) REVERT: E 32 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7118 (ttp-170) REVERT: E 329 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7966 (tt0) REVERT: B 648 VAL cc_start: 0.7893 (OUTLIER) cc_final: 0.7519 (t) REVERT: B 773 MET cc_start: 0.6081 (OUTLIER) cc_final: 0.5709 (tpp) REVERT: B 788 TRP cc_start: 0.7225 (OUTLIER) cc_final: 0.4757 (m100) REVERT: B 884 HIS cc_start: 0.7105 (OUTLIER) cc_final: 0.6606 (m170) REVERT: B 897 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7757 (mmt-90) REVERT: B 918 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7490 (tp30) REVERT: B 939 ASP cc_start: 0.7363 (m-30) cc_final: 0.7160 (m-30) REVERT: B 1226 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7463 (pm20) REVERT: B 1301 PHE cc_start: 0.5636 (OUTLIER) cc_final: 0.5044 (m-80) REVERT: J 109 ASP cc_start: 0.5972 (OUTLIER) cc_final: 0.5451 (p0) REVERT: J 216 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6581 (tt) outliers start: 142 outliers final: 88 residues processed: 370 average time/residue: 0.6124 time to fit residues: 267.2124 Evaluate side-chains 362 residues out of total 3229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 238 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 55 TYR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 316 ARG Chi-restraints excluded: chain F residue 337 ASP Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 72 GLN Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 306 MET Chi-restraints excluded: chain G residue 375 ASN Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 196 LYS Chi-restraints excluded: chain I residue 197 MET Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 687 LYS Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain A residue 735 ASN Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 756 LYS Chi-restraints excluded: chain A residue 779 ASN Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 826 ARG Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 896 LYS Chi-restraints excluded: chain A residue 927 SER Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1068 ILE Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1244 LYS Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1281 LYS Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1337 TYR Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 220 HIS Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 244 ARG Chi-restraints excluded: chain H residue 251 CYS Chi-restraints excluded: chain H residue 371 ASP Chi-restraints excluded: chain H residue 396 ILE Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 780 ASP Chi-restraints excluded: chain B residue 788 TRP Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 830 CYS Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 857 HIS Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 884 HIS Chi-restraints excluded: chain B residue 897 ARG Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1025 SER Chi-restraints excluded: chain B residue 1134 SER Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1226 GLU Chi-restraints excluded: chain B residue 1301 PHE Chi-restraints excluded: chain B residue 1321 ASP Chi-restraints excluded: chain B residue 1341 TYR Chi-restraints excluded: chain J residue 63 ASP Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 109 ASP Chi-restraints excluded: chain J residue 111 HIS Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 222 THR Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 259 ILE Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain J residue 276 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 108 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 253 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 315 optimal weight: 0.6980 chunk 210 optimal weight: 5.9990 chunk 132 optimal weight: 0.2980 chunk 239 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 261 optimal weight: 0.7980 chunk 207 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 150 HIS ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 HIS J 183 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.187511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.136214 restraints weight = 39963.467| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 2.65 r_work: 0.3806 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3692 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 28510 Z= 0.128 Angle : 0.604 13.231 38588 Z= 0.313 Chirality : 0.043 0.268 4263 Planarity : 0.004 0.076 5006 Dihedral : 7.029 74.184 3972 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.93 % Favored : 94.98 % Rotamer: Outliers : 4.56 % Allowed : 31.18 % Favored : 64.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.14), residues: 3487 helix: 1.23 (0.12), residues: 1754 sheet: -0.28 (0.26), residues: 377 loop : -1.53 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG I 168 TYR 0.016 0.001 TYR D 40 PHE 0.023 0.001 PHE A1305 TRP 0.033 0.001 TRP B 719 HIS 0.007 0.001 HIS H 220 Details of bonding type rmsd covalent geometry : bond 0.00281 (28507) covalent geometry : angle 0.60359 (38588) hydrogen bonds : bond 0.05313 ( 1367) hydrogen bonds : angle 4.08945 ( 4026) metal coordination : bond 0.00073 ( 2) Misc. bond : bond 0.00001 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6974 Ramachandran restraints generated. 3487 Oldfield, 0 Emsley, 3487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6974 Ramachandran restraints generated. 3487 Oldfield, 0 Emsley, 3487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 251 time to evaluate : 1.003 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: D 51 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7817 (tp) REVERT: D 307 ASP cc_start: 0.7854 (m-30) cc_final: 0.7624 (m-30) REVERT: F 8 PHE cc_start: 0.7781 (t80) cc_final: 0.7179 (t80) REVERT: F 17 ASP cc_start: 0.7436 (OUTLIER) cc_final: 0.7058 (p0) REVERT: F 55 TYR cc_start: 0.8628 (OUTLIER) cc_final: 0.7206 (t80) REVERT: F 99 ARG cc_start: 0.8486 (mtp85) cc_final: 0.8184 (mtp-110) REVERT: F 179 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.6965 (mtm180) REVERT: F 211 TYR cc_start: 0.7269 (t80) cc_final: 0.7025 (t80) REVERT: F 220 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7874 (tp30) REVERT: G 41 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7339 (mttt) REVERT: G 72 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7642 (tp-100) REVERT: G 105 ASN cc_start: 0.8706 (t0) cc_final: 0.8126 (t0) REVERT: G 306 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8266 (ttp) REVERT: G 375 ASN cc_start: 0.7656 (OUTLIER) cc_final: 0.7319 (p0) REVERT: I 103 ASP cc_start: 0.7503 (t0) cc_final: 0.7012 (t0) REVERT: I 106 GLU cc_start: 0.7849 (mp0) cc_final: 0.7541 (mp0) REVERT: I 196 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8847 (pttt) REVERT: A 639 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7651 (tt) REVERT: A 727 GLN cc_start: 0.7074 (OUTLIER) cc_final: 0.6676 (pp30) REVERT: A 735 ASN cc_start: 0.8128 (OUTLIER) cc_final: 0.7826 (p0) REVERT: A 801 ASN cc_start: 0.7307 (OUTLIER) cc_final: 0.6742 (m-40) REVERT: A 1244 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7412 (mmpt) REVERT: A 1281 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8408 (ptpp) REVERT: A 1308 ARG cc_start: 0.7930 (mpt-90) cc_final: 0.7645 (ptp90) REVERT: H 220 HIS cc_start: 0.5599 (OUTLIER) cc_final: 0.4858 (p-80) REVERT: H 244 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.6396 (tmm-80) REVERT: H 259 THR cc_start: 0.8177 (t) cc_final: 0.7880 (m) REVERT: H 295 ASP cc_start: 0.7627 (m-30) cc_final: 0.7198 (t0) REVERT: C 21 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.7626 (t80) REVERT: C 76 TYR cc_start: 0.8206 (OUTLIER) cc_final: 0.7738 (m-80) REVERT: C 77 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7262 (pm20) REVERT: C 127 ASN cc_start: 0.7736 (m-40) cc_final: 0.7246 (t160) REVERT: C 140 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7600 (ptmm) REVERT: E 32 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7026 (ttp-170) REVERT: E 56 GLU cc_start: 0.7271 (mp0) cc_final: 0.6407 (mt-10) REVERT: E 322 GLN cc_start: 0.7407 (pp30) cc_final: 0.7036 (pp30) REVERT: E 329 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.8066 (tt0) REVERT: B 648 VAL cc_start: 0.7895 (OUTLIER) cc_final: 0.7546 (t) REVERT: B 773 MET cc_start: 0.5947 (OUTLIER) cc_final: 0.5580 (tpp) REVERT: B 788 TRP cc_start: 0.7002 (OUTLIER) cc_final: 0.4923 (m100) REVERT: B 897 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7593 (mmt-90) REVERT: B 918 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7475 (tp30) REVERT: B 1226 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7369 (pm20) REVERT: B 1301 PHE cc_start: 0.5519 (OUTLIER) cc_final: 0.4989 (m-80) REVERT: J 109 ASP cc_start: 0.5970 (OUTLIER) cc_final: 0.5458 (p0) REVERT: J 216 LEU cc_start: 0.6801 (OUTLIER) cc_final: 0.6524 (tt) outliers start: 130 outliers final: 85 residues processed: 368 average time/residue: 0.6220 time to fit residues: 270.8825 Evaluate side-chains 351 residues out of total 3229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 234 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 55 TYR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 316 ARG Chi-restraints excluded: chain F residue 337 ASP Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 72 GLN Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 306 MET Chi-restraints excluded: chain G residue 375 ASN Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 196 LYS Chi-restraints excluded: chain I residue 197 MET Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain A residue 735 ASN Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 826 ARG Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 896 LYS Chi-restraints excluded: chain A residue 927 SER Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1244 LYS Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1281 LYS Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1337 TYR Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 220 HIS Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 244 ARG Chi-restraints excluded: chain H residue 251 CYS Chi-restraints excluded: chain H residue 371 ASP Chi-restraints excluded: chain H residue 396 ILE Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 788 TRP Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 830 CYS Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 897 ARG Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1025 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1134 SER Chi-restraints excluded: chain B residue 1226 GLU Chi-restraints excluded: chain B residue 1301 PHE Chi-restraints excluded: chain B residue 1321 ASP Chi-restraints excluded: chain B residue 1341 TYR Chi-restraints excluded: chain J residue 63 ASP Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 109 ASP Chi-restraints excluded: chain J residue 111 HIS Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 222 THR Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 259 ILE Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain J residue 276 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 105 optimal weight: 1.9990 chunk 213 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 182 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 296 optimal weight: 0.9980 chunk 29 optimal weight: 8.9990 chunk 336 optimal weight: 0.0170 chunk 286 optimal weight: 7.9990 chunk 7 optimal weight: 30.0000 chunk 121 optimal weight: 0.5980 overall best weight: 1.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 GLN J 79 HIS J 183 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.185524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.134815 restraints weight = 39961.398| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 2.92 r_work: 0.3761 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 28510 Z= 0.169 Angle : 0.648 13.393 38588 Z= 0.335 Chirality : 0.045 0.304 4263 Planarity : 0.005 0.076 5006 Dihedral : 7.180 74.434 3970 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.28 % Favored : 94.61 % Rotamer: Outliers : 4.84 % Allowed : 31.08 % Favored : 64.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.14), residues: 3487 helix: 1.08 (0.12), residues: 1762 sheet: -0.28 (0.26), residues: 378 loop : -1.52 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 168 TYR 0.023 0.002 TYR D 40 PHE 0.022 0.002 PHE D 95 TRP 0.028 0.002 TRP B 719 HIS 0.007 0.001 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00394 (28507) covalent geometry : angle 0.64776 (38588) hydrogen bonds : bond 0.06012 ( 1367) hydrogen bonds : angle 4.15888 ( 4026) metal coordination : bond 0.00064 ( 2) Misc. bond : bond 0.00009 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20467.81 seconds wall clock time: 345 minutes 49.45 seconds (20749.45 seconds total)