Starting phenix.real_space_refine on Mon Sep 14 12:40:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6flq_4275/09_2026/6flq_4275_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6flq_4275/09_2026/6flq_4275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6flq_4275/09_2026/6flq_4275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6flq_4275/09_2026/6flq_4275.map" model { file = "/net/cci-nas-00/data/ceres_data/6flq_4275/09_2026/6flq_4275_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6flq_4275/09_2026/6flq_4275_neut.cif" } resolution = 3.6 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= 0.006 sd= 0.086 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 Zn 2 6.06 5 P 90 5.49 5 Mg 1 5.21 5 S 105 5.16 5 C 18528 2.51 5 N 5429 2.21 5 O 6046 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30201 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2168 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 14, 'TRANS': 295} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 318 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'ASP:plan': 7, 'PHE:plan': 1, 'ARG:plan': 5, 'GLU:plan': 7, 'ASN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 114 Chain: "B" Number of atoms: 2068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2068 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 13, 'TRANS': 284} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 318 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'ASP:plan': 7, 'PHE:plan': 1, 'ARG:plan': 5, 'GLU:plan': 7, 'ASN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 114 Chain: "C" Number of atoms: 10573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10573 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PTRANS': 56, 'TRANS': 1282} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 10357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 10357 Classifications: {'peptide': 1334} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 55, 'TRANS': 1278} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 709 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "F" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 2447 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 409} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 479} Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1451 Unresolved non-hydrogen angles: 1853 Unresolved non-hydrogen dihedrals: 1145 Unresolved non-hydrogen chiralities: 145 Planarities with less than four sites: {'ASN:plan1': 19, 'GLU:plan': 56, 'ARG:plan': 33, 'PHE:plan': 14, 'TYR:plan': 6, 'GLN:plan1': 19, 'ASP:plan': 42, 'TRP:plan': 4, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 830 Chain: "N" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 647 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain breaks: 1 Chain: "R" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 444 Classifications: {'RNA': 21} Modifications used: {'5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 10, 'rna3p_pyr': 9} Link IDs: {'rna2p': 1, 'rna3p': 19} Chain breaks: 1 Chain: "T" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 785 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15258 SG CYS D 70 108.278 118.706 60.781 1.00110.77 S ATOM 15272 SG CYS D 72 109.338 122.046 60.037 1.00121.27 S ATOM 15404 SG CYS D 88 111.698 119.835 57.627 1.00115.73 S ATOM 21092 SG CYS D 814 110.727 50.721 49.288 1.00 60.52 S ATOM 21657 SG CYS D 888 113.353 53.592 50.117 1.00 50.19 S ATOM 21708 SG CYS D 895 111.072 52.145 52.491 1.00 40.57 S Time building chain proxies: 6.88, per 1000 atoms: 0.23 Number of scatterers: 30201 At special positions: 0 Unit cell: (210.1, 160.6, 154, 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 S 105 16.00 P 90 15.00 Mg 1 11.99 O 6046 8.00 N 5429 7.00 C 18528 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.12 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7172 Finding SS restraints... Secondary structure from input PDB file: 134 helices and 52 sheets defined 38.7% alpha, 13.5% beta 37 base pairs and 68 stacking pairs defined. Time for finding SS restraints: 3.54 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 77 through 87 removed outlier: 4.119A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 161 removed outlier: 3.897A pdb=" N ILE A 159 " --> pdb=" O SER A 156 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER A 161 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 228 removed outlier: 3.741A pdb=" N LEU A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 removed outlier: 3.643A pdb=" N VAL A 232 " --> pdb=" O GLU A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 256 through 260 Processing helix chain 'A' and resid 263 through 272 removed outlier: 3.620A pdb=" N ALA A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.656A pdb=" N LEU A 281 " --> pdb=" O TYR A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'B' and resid 35 through 50 removed outlier: 3.760A pdb=" N LEU B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.536A pdb=" N ILE B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 228 Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 263 through 272 removed outlier: 3.986A pdb=" N ALA B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU B 270 " --> pdb=" O SER B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 284 removed outlier: 3.844A pdb=" N ARG B 284 " --> pdb=" O ASP B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 291 Processing helix chain 'B' and resid 296 through 308 removed outlier: 3.621A pdb=" N THR B 301 " --> pdb=" O LYS B 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 40 removed outlier: 3.523A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 57 removed outlier: 3.857A pdb=" N SER C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 211 removed outlier: 4.036A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 214 No H-bonds generated for 'chain 'C' and resid 212 through 214' Processing helix chain 'C' and resid 216 through 225 removed outlier: 3.588A pdb=" N PHE C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.831A pdb=" N LEU C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 280 removed outlier: 3.641A pdb=" N ASP C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.579A pdb=" N ALA C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLY C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 289 through 294' Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 389 removed outlier: 3.641A pdb=" N ALA C 381 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 removed outlier: 3.524A pdb=" N LEU C 409 " --> pdb=" O PHE C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.804A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE C 426 " --> pdb=" O LYS C 422 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG C 436 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 480 removed outlier: 4.473A pdb=" N ARG C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 Processing helix chain 'C' and resid 495 through 508 removed outlier: 4.147A pdb=" N SER C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 528 removed outlier: 3.605A pdb=" N LYS C 527 " --> pdb=" O GLU C 523 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 612 removed outlier: 3.851A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 removed outlier: 3.610A pdb=" N HIS C 673 " --> pdb=" O PHE C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 686 removed outlier: 3.819A pdb=" N GLN C 686 " --> pdb=" O GLY C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 704 through 712 removed outlier: 3.623A pdb=" N ALA C 709 " --> pdb=" O GLU C 705 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL C 710 " --> pdb=" O ARG C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 741 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 896 through 907 Processing helix chain 'C' and resid 942 through 981 removed outlier: 3.767A pdb=" N LEU C 946 " --> pdb=" O ASP C 942 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN C 952 " --> pdb=" O ILE C 948 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLY C 970 " --> pdb=" O ILE C 966 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU C 971 " --> pdb=" O LEU C 967 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE C 972 " --> pdb=" O GLU C 968 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU C 979 " --> pdb=" O ILE C 975 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 995 through 1000 removed outlier: 3.555A pdb=" N LEU C1000 " --> pdb=" O TRP C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1007 through 1038 removed outlier: 3.714A pdb=" N LEU C1011 " --> pdb=" O LYS C1007 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP C1019 " --> pdb=" O ALA C1015 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU C1026 " --> pdb=" O LYS C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1099 through 1101 No H-bonds generated for 'chain 'C' and resid 1099 through 1101' Processing helix chain 'C' and resid 1102 through 1107 Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 4.082A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1149 removed outlier: 3.746A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1167 through 1175 Processing helix chain 'C' and resid 1185 through 1189 removed outlier: 3.619A pdb=" N ASP C1188 " --> pdb=" O PRO C1185 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLY C1189 " --> pdb=" O VAL C1186 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1185 through 1189' Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.722A pdb=" N ILE C1195 " --> pdb=" O LYS C1191 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY C1202 " --> pdb=" O LEU C1198 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1279 removed outlier: 3.743A pdb=" N VAL C1275 " --> pdb=" O GLY C1271 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TRP C1276 " --> pdb=" O GLU C1272 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA C1277 " --> pdb=" O MET C1273 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1291 removed outlier: 3.801A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) Processing helix chain 'C' and resid 1300 through 1309 removed outlier: 4.028A pdb=" N LYS C1306 " --> pdb=" O THR C1302 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 3.931A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 96 through 101 Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 132 through 140 removed outlier: 4.559A pdb=" N VAL D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 192 removed outlier: 3.608A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.906A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 231 removed outlier: 3.643A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR D 218 " --> pdb=" O ARG D 214 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 removed outlier: 3.596A pdb=" N TRP D 236 " --> pdb=" O LYS D 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 233 through 236' Processing helix chain 'D' and resid 256 through 258 No H-bonds generated for 'chain 'D' and resid 256 through 258' Processing helix chain 'D' and resid 263 through 285 removed outlier: 3.889A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 307 removed outlier: 3.631A pdb=" N VAL D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 337 through 342 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 388 removed outlier: 3.700A pdb=" N GLY D 383 " --> pdb=" O PRO D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 404 removed outlier: 4.027A pdb=" N ALA D 397 " --> pdb=" O THR D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 416 removed outlier: 4.362A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU D 414 " --> pdb=" O ASP D 410 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 451 through 456 removed outlier: 3.871A pdb=" N ALA D 455 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 483 removed outlier: 3.784A pdb=" N GLN D 477 " --> pdb=" O THR D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 513 removed outlier: 3.878A pdb=" N LEU D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 539 removed outlier: 3.903A pdb=" N SER D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 580 removed outlier: 3.676A pdb=" N ALA D 577 " --> pdb=" O THR D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 612 removed outlier: 3.709A pdb=" N ILE D 611 " --> pdb=" O THR D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 634 Processing helix chain 'D' and resid 649 through 670 removed outlier: 3.792A pdb=" N SER D 655 " --> pdb=" O HIS D 651 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA D 659 " --> pdb=" O SER D 655 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA D 662 " --> pdb=" O GLU D 658 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLU D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE D 668 " --> pdb=" O ILE D 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.628A pdb=" N ARG D 678 " --> pdb=" O THR D 674 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.591A pdb=" N ILE D 737 " --> pdb=" O SER D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 786 removed outlier: 4.243A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 804 removed outlier: 3.878A pdb=" N TYR D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 839 removed outlier: 4.039A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 removed outlier: 3.736A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 896 through 900 removed outlier: 3.772A pdb=" N GLY D 900 " --> pdb=" O ALA D 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 896 through 900' Processing helix chain 'D' and resid 915 through 925 Processing helix chain 'D' and resid 926 through 930 removed outlier: 3.807A pdb=" N LEU D 930 " --> pdb=" O GLY D 927 " (cutoff:3.500A) Processing helix chain 'D' and resid 1138 through 1146 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.645A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1258 removed outlier: 3.626A pdb=" N GLU D1254 " --> pdb=" O ASP D1250 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1259 through 1261 No H-bonds generated for 'chain 'D' and resid 1259 through 1261' Processing helix chain 'D' and resid 1280 through 1293 removed outlier: 3.598A pdb=" N GLU D1293 " --> pdb=" O ASN D1289 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1327 through 1338 removed outlier: 3.942A pdb=" N ALA D1338 " --> pdb=" O GLU D1334 " (cutoff:3.500A) Processing helix chain 'D' and resid 1348 through 1353 Processing helix chain 'D' and resid 1362 through 1373 removed outlier: 3.515A pdb=" N HIS D1366 " --> pdb=" O GLY D1362 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG D1371 " --> pdb=" O GLN D1367 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 15 through 32 removed outlier: 4.137A pdb=" N LEU E 19 " --> pdb=" O ASN E 15 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG E 25 " --> pdb=" O LEU E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 90 removed outlier: 3.518A pdb=" N LEU E 64 " --> pdb=" O ASN E 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 10 removed outlier: 3.708A pdb=" N ALA F 7 " --> pdb=" O LYS F 3 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU F 10 " --> pdb=" O LEU F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 37 Processing helix chain 'F' and resid 70 through 74 removed outlier: 3.752A pdb=" N GLU F 74 " --> pdb=" O PRO F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 81 Processing helix chain 'F' and resid 103 through 132 Processing helix chain 'F' and resid 201 through 213 removed outlier: 3.934A pdb=" N LEU F 205 " --> pdb=" O LYS F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 218 removed outlier: 4.233A pdb=" N GLY F 217 " --> pdb=" O VAL F 213 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU F 218 " --> pdb=" O PRO F 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 213 through 218' Processing helix chain 'F' and resid 246 through 253 removed outlier: 3.609A pdb=" N GLY F 253 " --> pdb=" O GLY F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 257 Processing helix chain 'F' and resid 258 through 267 removed outlier: 3.536A pdb=" N THR F 264 " --> pdb=" O GLN F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 287 Processing helix chain 'F' and resid 310 through 319 removed outlier: 4.217A pdb=" N GLN F 316 " --> pdb=" O GLY F 312 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY F 319 " --> pdb=" O ALA F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 333 Processing helix chain 'F' and resid 341 through 364 Processing helix chain 'F' and resid 366 through 377 removed outlier: 3.670A pdb=" N VAL F 372 " --> pdb=" O ASP F 368 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU F 376 " --> pdb=" O VAL F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 393 removed outlier: 3.940A pdb=" N GLU F 391 " --> pdb=" O PRO F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 426 Processing helix chain 'F' and resid 431 through 436 Processing helix chain 'F' and resid 441 through 450 Processing helix chain 'F' and resid 455 through 462 Processing helix chain 'F' and resid 463 through 468 Processing helix chain 'F' and resid 474 through 491 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 18 removed outlier: 3.688A pdb=" N ARG A 12 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL A 14 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ILE A 16 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LYS A 25 " --> pdb=" O ILE A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 144 through 149 removed outlier: 6.847A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 91 removed outlier: 3.598A pdb=" N ARG A 91 " --> pdb=" O GLU A 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 102 through 104 Processing sheet with id=AA5, first strand: chain 'A' and resid 108 through 110 removed outlier: 3.658A pdb=" N GLY A 108 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 188 through 189 Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 19 removed outlier: 3.677A pdb=" N HIS B 23 " --> pdb=" O VAL B 19 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 52 through 56 removed outlier: 3.781A pdb=" N ALA B 55 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN B 147 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.646A pdb=" N VAL B 153 " --> pdb=" O ALA B 175 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 187 through 190 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.922A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 5.712A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA C 94 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N GLY C 125 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N LEU C 96 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N TYR C 123 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N VAL C 98 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU C 121 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU C 100 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS C 115 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'C' and resid 148 through 151 Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 159 Processing sheet with id=AB7, first strand: chain 'C' and resid 285 through 286 removed outlier: 3.802A pdb=" N MET C 239 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN C 238 " --> pdb=" O GLU C 231 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 255 through 257 removed outlier: 7.021A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 296 through 297 removed outlier: 4.209A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 529 through 531 removed outlier: 3.554A pdb=" N ASN C 573 " --> pdb=" O ILE C 530 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.252A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC4, first strand: chain 'C' and resid 634 through 637 Processing sheet with id=AC5, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.744A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.501A pdb=" N THR C 757 " --> pdb=" O ILE C 765 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC8, first strand: chain 'C' and resid 1066 through 1067 removed outlier: 3.706A pdb=" N ALA C1067 " --> pdb=" O LEU C1233 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY C1228 " --> pdb=" O VAL C 802 " (cutoff:3.500A) removed outlier: 9.111A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1066 through 1067 removed outlier: 3.706A pdb=" N ALA C1067 " --> pdb=" O LEU C1233 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 816 through 819 removed outlier: 7.413A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 830 through 840 removed outlier: 3.659A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 876 through 877 Processing sheet with id=AD4, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.922A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 887 through 889 Processing sheet with id=AD6, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.652A pdb=" N GLY D 351 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 7.767A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 1335 through 1339 Processing sheet with id=AD9, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.560A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.580A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.388A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AE2, first strand: chain 'D' and resid 253 through 254 removed outlier: 3.641A pdb=" N VAL D 253 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA D 261 " --> pdb=" O VAL D 253 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'D' and resid 548 through 559 removed outlier: 6.233A pdb=" N GLU D 562 " --> pdb=" O ASP D 558 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 809 through 811 removed outlier: 6.901A pdb=" N VAL D 894 " --> pdb=" O THR D 810 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE6, first strand: chain 'D' and resid 949 through 951 Processing sheet with id=AE7, first strand: chain 'D' and resid 957 through 961 removed outlier: 3.570A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR D 980 " --> pdb=" O VAL D 997 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1025 through 1028 removed outlier: 3.979A pdb=" N ALA D1122 " --> pdb=" O VAL D1027 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE D1106 " --> pdb=" O ARG D1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1034 through 1038 Processing sheet with id=AF1, first strand: chain 'D' and resid 1161 through 1162 Processing sheet with id=AF2, first strand: chain 'D' and resid 1172 through 1176 Processing sheet with id=AF3, first strand: chain 'D' and resid 1278 through 1279 removed outlier: 6.967A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 45 through 49 removed outlier: 3.798A pdb=" N GLN F 96 " --> pdb=" O ARG F 60 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 178 through 182 removed outlier: 6.918A pdb=" N SER F 151 " --> pdb=" O LYS F 143 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N VAL F 145 " --> pdb=" O ASN F 149 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ASN F 149 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N VAL F 197 " --> pdb=" O GLU F 159 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL F 161 " --> pdb=" O VAL F 197 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 221 through 229 removed outlier: 5.289A pdb=" N ILE F 223 " --> pdb=" O LYS F 239 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS F 239 " --> pdb=" O ILE F 223 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 295 through 299 removed outlier: 4.257A pdb=" N SER F 295 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA F 308 " --> pdb=" O SER F 295 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR F 304 " --> pdb=" O ASP F 299 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE F 307 " --> pdb=" O ASN F 337 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET F 339 " --> pdb=" O ILE F 307 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL F 309 " --> pdb=" O MET F 339 " (cutoff:3.500A) 1122 hydrogen bonds defined for protein. 3177 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 93 hydrogen bonds 186 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 68 stacking parallelities Total time for adding SS restraints: 7.78 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.23: 518 1.23 - 1.37: 11090 1.37 - 1.52: 14450 1.52 - 1.67: 4546 1.67 - 1.82: 182 Bond restraints: 30786 Sorted by residual: bond pdb=" C ASP C1084 " pdb=" N MET C1085 " ideal model delta sigma weight residual 1.329 1.078 0.251 1.60e-02 3.91e+03 2.45e+02 bond pdb=" C3' DC T 14 " pdb=" O3' DC T 14 " ideal model delta sigma weight residual 1.435 1.367 0.068 1.30e-02 5.92e+03 2.77e+01 bond pdb=" C3' DA T 19 " pdb=" O3' DA T 19 " ideal model delta sigma weight residual 1.435 1.367 0.068 1.30e-02 5.92e+03 2.72e+01 bond pdb=" C3' DT T 13 " pdb=" O3' DT T 13 " ideal model delta sigma weight residual 1.435 1.370 0.065 1.30e-02 5.92e+03 2.47e+01 bond pdb=" N1 DT T 12 " pdb=" C2 DT T 12 " ideal model delta sigma weight residual 1.376 1.336 0.040 8.00e-03 1.56e+04 2.45e+01 ... (remaining 30781 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.03: 41356 4.03 - 8.07: 699 8.07 - 12.10: 53 12.10 - 16.13: 3 16.13 - 20.16: 3 Bond angle restraints: 42114 Sorted by residual: angle pdb=" C1' G R 25 " pdb=" N9 G R 25 " pdb=" C4 G R 25 " ideal model delta sigma weight residual 126.50 138.39 -11.89 1.30e+00 5.92e-01 8.37e+01 angle pdb=" N ILE D 135 " pdb=" CA ILE D 135 " pdb=" C ILE D 135 " ideal model delta sigma weight residual 112.96 104.36 8.60 1.00e+00 1.00e+00 7.39e+01 angle pdb=" C1' G R 25 " pdb=" N9 G R 25 " pdb=" C8 G R 25 " ideal model delta sigma weight residual 127.00 115.82 11.18 1.30e+00 5.92e-01 7.39e+01 angle pdb=" N1 C R 28 " pdb=" C6 C R 28 " pdb=" C5 C R 28 " ideal model delta sigma weight residual 121.00 125.06 -4.06 5.00e-01 4.00e+00 6.58e+01 angle pdb=" C2 C R 28 " pdb=" N1 C R 28 " pdb=" C6 C R 28 " ideal model delta sigma weight residual 120.30 117.11 3.19 4.00e-01 6.25e+00 6.35e+01 ... (remaining 42109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.01: 17951 31.01 - 62.02: 678 62.02 - 93.03: 48 93.03 - 124.04: 1 124.04 - 155.05: 3 Dihedral angle restraints: 18681 sinusoidal: 7567 harmonic: 11114 Sorted by residual: dihedral pdb=" CA PHE C 57 " pdb=" C PHE C 57 " pdb=" N PRO C 58 " pdb=" CA PRO C 58 " ideal model delta harmonic sigma weight residual 180.00 -94.66 -85.34 0 5.00e+00 4.00e-02 2.91e+02 dihedral pdb=" CA GLU B 29 " pdb=" C GLU B 29 " pdb=" N PRO B 30 " pdb=" CA PRO B 30 " ideal model delta harmonic sigma weight residual 180.00 -122.17 -57.83 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" CA ILE C 198 " pdb=" C ILE C 198 " pdb=" N ASP C 199 " pdb=" CA ASP C 199 " ideal model delta harmonic sigma weight residual -180.00 -126.94 -53.06 0 5.00e+00 4.00e-02 1.13e+02 ... (remaining 18678 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 3485 0.074 - 0.149: 1200 0.149 - 0.223: 203 0.223 - 0.297: 33 0.297 - 0.372: 10 Chirality restraints: 4931 Sorted by residual: chirality pdb=" CB THR D 514 " pdb=" CA THR D 514 " pdb=" OG1 THR D 514 " pdb=" CG2 THR D 514 " both_signs ideal model delta sigma weight residual False 2.55 2.18 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CB VAL C 802 " pdb=" CA VAL C 802 " pdb=" CG1 VAL C 802 " pdb=" CG2 VAL C 802 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CB VAL D1255 " pdb=" CA VAL D1255 " pdb=" CG1 VAL D1255 " pdb=" CG2 VAL D1255 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.90e+00 ... (remaining 4928 not shown) Planarity restraints: 5260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 29 " 0.068 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO B 30 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO B 30 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 30 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 519 " 0.064 5.00e-02 4.00e+02 9.74e-02 1.52e+01 pdb=" N PRO C 520 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO C 520 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 520 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C1229 " -0.022 2.00e-02 2.50e+03 2.62e-02 1.37e+01 pdb=" CG TYR C1229 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR C1229 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR C1229 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C1229 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR C1229 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR C1229 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR C1229 " -0.004 2.00e-02 2.50e+03 ... (remaining 5257 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 133 2.50 - 3.10: 20454 3.10 - 3.70: 43657 3.70 - 4.30: 58208 4.30 - 4.90: 97171 Nonbonded interactions: 219623 Sorted by model distance: nonbonded pdb=" OD2 ASP C 393 " pdb=" NH1 ARG C 394 " model vdw 1.897 3.120 nonbonded pdb=" OD2 ASP D 129 " pdb=" NH1 ARG D 220 " model vdw 1.976 3.120 nonbonded pdb=" NH1 ARG D1341 " pdb=" OE2 GLU D1343 " model vdw 1.980 3.120 nonbonded pdb=" NH1 ARG A 33 " pdb=" OD2 ASP A 199 " model vdw 2.024 3.120 nonbonded pdb=" OH TYR D 68 " pdb=" NH1 ARG D 81 " model vdw 2.046 3.120 ... (remaining 219618 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 6 through 158 or resid 171 through 329)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 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: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 36.460 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0229 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 : 0.016 0.251 30792 Z= 0.719 Angle : 1.345 20.164 42114 Z= 0.793 Chirality : 0.075 0.372 4931 Planarity : 0.009 0.103 5260 Dihedral : 15.269 155.052 11509 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.79 % Favored : 89.08 % Rotamer: Outliers : 1.40 % Allowed : 6.10 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.05 % Twisted Proline : 3.90 % Twisted General : 0.32 % 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: -4.32 (0.11), residues: 3846 helix: -2.70 (0.10), residues: 1360 sheet: -2.43 (0.20), residues: 492 loop : -3.15 (0.11), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG D 352 TYR 0.055 0.005 TYR C1229 PHE 0.061 0.005 PHE D 620 TRP 0.039 0.005 TRP C1276 HIS 0.019 0.005 HIS D 545 Details of bonding type rmsd/Z covalent geometry : bond 0.01568 / 0.72 (30786) covalent geometry : angle 1.34452 / 0.79 (42114) hydrogen bonds : bond 0.17630 / 12.21 ( 1208) hydrogen bonds : angle 7.49232 / 5.18 ( 3363) metal coordination : bond 0.12936 / 6.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 296 time to evaluate : 1.041 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: C 12 ARG cc_start: -0.0387 (ttm-80) cc_final: -0.1264 (mmm-85) REVERT: C 175 ARG cc_start: 0.1280 (ttm170) cc_final: 0.0127 (mtm180) REVERT: C 388 LEU cc_start: -0.4191 (OUTLIER) cc_final: -0.4709 (tp) REVERT: C 653 MET cc_start: 0.2366 (ttp) cc_final: 0.0794 (mpp) REVERT: C 711 ASP cc_start: 0.2312 (m-30) cc_final: 0.1787 (m-30) REVERT: C 1170 MET cc_start: -0.2322 (mmm) cc_final: -0.4015 (ptt) REVERT: C 1253 LEU cc_start: 0.4733 (OUTLIER) cc_final: 0.4424 (mt) REVERT: D 237 MET cc_start: -0.1962 (mtt) cc_final: -0.2234 (mtt) REVERT: D 860 ARG cc_start: 0.0345 (tmm-80) cc_final: -0.0290 (ptt180) REVERT: D 1370 MET cc_start: 0.0302 (tpt) cc_final: -0.0155 (ptt) outliers start: 38 outliers final: 11 residues processed: 329 average time/residue: 0.2135 time to fit residues: 111.7208 Evaluate side-chains 213 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 200 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 1117 LEU Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 1155 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 84 ASN ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 HIS C 387 ASN C 513 GLN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1038 GLN C1146 GLN C1237 HIS C1268 GLN C1299 ASN C1313 HIS D 113 HIS D 424 ASN D1010 GLN D1098 GLN D1366 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5652 r_free = 0.5652 target = 0.361471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5669 r_free = 0.5669 target = 0.352938 restraints weight = 85057.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5671 r_free = 0.5671 target = 0.353890 restraints weight = 55185.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.5674 r_free = 0.5674 target = 0.354334 restraints weight = 35277.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.5675 r_free = 0.5675 target = 0.354466 restraints weight = 24388.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.5676 r_free = 0.5676 target = 0.354531 restraints weight = 22901.267| |-----------------------------------------------------------------------------| r_work (final): 0.5491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0529 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 30792 Z= 0.203 Angle : 0.805 12.772 42114 Z= 0.423 Chirality : 0.050 0.238 4931 Planarity : 0.007 0.098 5260 Dihedral : 16.709 153.201 5279 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.99 % Favored : 92.93 % Rotamer: Outliers : 2.50 % Allowed : 8.64 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.05 % Twisted Proline : 3.90 % Twisted General : 0.14 % 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: -2.98 (0.12), residues: 3846 helix: -1.02 (0.13), residues: 1371 sheet: -1.93 (0.21), residues: 500 loop : -2.75 (0.12), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 143 TYR 0.032 0.002 TYR C1229 PHE 0.029 0.002 PHE C 389 TRP 0.018 0.002 TRP D1193 HIS 0.011 0.002 HIS C1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.20 (30786) covalent geometry : angle 0.80506 / 0.42 (42114) hydrogen bonds : bond 0.05805 / 4.12 ( 1208) hydrogen bonds : angle 5.54732 / 3.86 ( 3363) metal coordination : bond 0.04531 / 2.99 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 219 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 PHE cc_start: 0.0005 (OUTLIER) cc_final: -0.0868 (m-80) REVERT: C 210 LEU cc_start: -0.2057 (OUTLIER) cc_final: -0.2675 (mt) REVERT: C 429 MET cc_start: -0.3578 (mtp) cc_final: -0.4051 (ptp) REVERT: C 653 MET cc_start: 0.1917 (ttp) cc_final: 0.0851 (mtp) REVERT: C 711 ASP cc_start: 0.2353 (m-30) cc_final: 0.1839 (m-30) REVERT: C 741 MET cc_start: -0.0102 (mmm) cc_final: -0.0317 (mmm) REVERT: C 1073 LYS cc_start: 0.2020 (ptmt) cc_final: 0.1571 (mttp) REVERT: C 1170 MET cc_start: -0.1030 (mmm) cc_final: -0.1706 (mmm) REVERT: D 372 MET cc_start: 0.1673 (mmp) cc_final: -0.0555 (mmm) REVERT: D 1370 MET cc_start: 0.0275 (tpt) cc_final: -0.0743 (ptt) REVERT: E 7 GLN cc_start: -0.0342 (tp40) cc_final: -0.2164 (pm20) outliers start: 68 outliers final: 36 residues processed: 278 average time/residue: 0.1948 time to fit residues: 87.7190 Evaluate side-chains 229 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 191 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1117 LEU Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1337 VAL Chi-restraints excluded: chain E residue 13 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 14 optimal weight: 0.9980 chunk 213 optimal weight: 10.0000 chunk 211 optimal weight: 20.0000 chunk 89 optimal weight: 30.0000 chunk 340 optimal weight: 50.0000 chunk 238 optimal weight: 0.0570 chunk 383 optimal weight: 50.0000 chunk 278 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 357 optimal weight: 6.9990 overall best weight: 4.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN B 147 GLN C 36 GLN ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 526 HIS ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN C 673 HIS ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1220 GLN C1237 HIS C1256 GLN C1313 HIS D 157 GLN ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 665 GLN ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 907 HIS D 951 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5472 r_free = 0.5472 target = 0.334941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.5379 r_free = 0.5379 target = 0.322706 restraints weight = 81161.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.5406 r_free = 0.5406 target = 0.325733 restraints weight = 50471.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.5422 r_free = 0.5422 target = 0.327481 restraints weight = 32249.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.5432 r_free = 0.5432 target = 0.328521 restraints weight = 22607.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.5438 r_free = 0.5438 target = 0.329258 restraints weight = 17620.317| |-----------------------------------------------------------------------------| r_work (final): 0.5442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1389 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.159 30792 Z= 0.284 Angle : 1.019 27.714 42114 Z= 0.529 Chirality : 0.057 0.644 4931 Planarity : 0.009 0.107 5260 Dihedral : 16.712 158.181 5271 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.10 % Favored : 90.77 % Rotamer: Outliers : 4.96 % Allowed : 11.25 % Favored : 83.79 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.08 % Twisted Proline : 3.90 % Twisted General : 0.19 % 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: -2.91 (0.12), residues: 3846 helix: -0.84 (0.13), residues: 1384 sheet: -2.02 (0.20), residues: 541 loop : -2.79 (0.12), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 150 TYR 0.076 0.003 TYR B 177 PHE 0.046 0.004 PHE D 377 TRP 0.026 0.003 TRP D1193 HIS 0.015 0.002 HIS C1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00633 / 0.28 (30786) covalent geometry : angle 1.01938 / 0.53 (42114) hydrogen bonds : bond 0.06361 / 4.41 ( 1208) hydrogen bonds : angle 5.86863 / 4.11 ( 3363) metal coordination : bond 0.01961 / 1.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 218 time to evaluate : 1.020 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: A 152 TYR cc_start: 0.0304 (p90) cc_final: -0.0500 (p90) REVERT: A 162 GLU cc_start: 0.0859 (OUTLIER) cc_final: -0.3081 (mt-10) REVERT: B 171 LEU cc_start: -0.0725 (OUTLIER) cc_final: -0.1295 (tp) REVERT: B 177 TYR cc_start: -0.2489 (OUTLIER) cc_final: -0.2853 (p90) REVERT: B 203 ILE cc_start: -0.0503 (OUTLIER) cc_final: -0.0978 (tt) REVERT: C 27 LEU cc_start: -0.0882 (OUTLIER) cc_final: -0.3331 (mt) REVERT: C 370 MET cc_start: -0.1226 (mmm) cc_final: -0.1527 (mmm) REVERT: C 447 HIS cc_start: 0.0279 (OUTLIER) cc_final: -0.2788 (t-170) REVERT: C 653 MET cc_start: 0.2213 (ttp) cc_final: 0.0696 (mmp) REVERT: C 667 LEU cc_start: 0.1104 (OUTLIER) cc_final: -0.0331 (tt) REVERT: C 711 ASP cc_start: 0.4037 (m-30) cc_final: 0.3759 (m-30) REVERT: C 741 MET cc_start: 0.0298 (mmm) cc_final: -0.0578 (mmm) REVERT: C 967 LEU cc_start: 0.2339 (OUTLIER) cc_final: 0.2063 (tm) REVERT: C 1066 MET cc_start: 0.2733 (mmm) cc_final: 0.1730 (mmt) REVERT: C 1170 MET cc_start: -0.0720 (mmm) cc_final: -0.1406 (mmm) REVERT: C 1269 ARG cc_start: 0.1294 (ttt90) cc_final: 0.0106 (tpt170) REVERT: D 48 THR cc_start: -0.2285 (OUTLIER) cc_final: -0.2809 (p) REVERT: D 394 ILE cc_start: -0.1336 (OUTLIER) cc_final: -0.1609 (mp) REVERT: D 448 GLN cc_start: 0.3753 (mt0) cc_final: 0.1021 (mm-40) REVERT: D 1095 MET cc_start: -0.1081 (ttt) cc_final: -0.1351 (ttt) REVERT: D 1155 ILE cc_start: -0.4170 (OUTLIER) cc_final: -0.4676 (tp) REVERT: D 1326 GLN cc_start: 0.3310 (OUTLIER) cc_final: 0.1832 (mt0) REVERT: D 1370 MET cc_start: 0.0148 (tpt) cc_final: -0.0842 (ptt) REVERT: E 25 ARG cc_start: 0.1671 (mpt180) cc_final: 0.1121 (mpt180) REVERT: E 30 MET cc_start: -0.1164 (tpt) cc_final: -0.1517 (tpt) outliers start: 135 outliers final: 59 residues processed: 339 average time/residue: 0.1850 time to fit residues: 103.3380 Evaluate side-chains 267 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 196 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 177 TYR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1117 LEU Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1287 LEU Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 457 TYR Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 897 HIS Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 950 ILE Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 1155 ILE Chi-restraints excluded: chain D residue 1326 GLN Chi-restraints excluded: chain D residue 1337 VAL Chi-restraints excluded: chain E residue 10 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 78 optimal weight: 1.9990 chunk 119 optimal weight: 8.9990 chunk 177 optimal weight: 0.9990 chunk 331 optimal weight: 1.9990 chunk 250 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 275 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 182 optimal weight: 0.9990 chunk 298 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 808 ASN C1220 GLN D 157 GLN D 206 ASN D 232 ASN D 469 HIS D 716 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5639 r_free = 0.5639 target = 0.358615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5659 r_free = 0.5659 target = 0.349803 restraints weight = 84853.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.5662 r_free = 0.5662 target = 0.350511 restraints weight = 57771.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.5661 r_free = 0.5661 target = 0.350492 restraints weight = 39027.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.5661 r_free = 0.5661 target = 0.350492 restraints weight = 35519.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5661 r_free = 0.5661 target = 0.350492 restraints weight = 35518.995| |-----------------------------------------------------------------------------| r_work (final): 0.5470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1080 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 30792 Z= 0.142 Angle : 0.678 16.028 42114 Z= 0.357 Chirality : 0.046 0.296 4931 Planarity : 0.006 0.095 5260 Dihedral : 16.352 155.943 5269 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.63 % Favored : 93.32 % Rotamer: Outliers : 3.16 % Allowed : 13.64 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.08 % Twisted Proline : 3.90 % Twisted General : 0.08 % 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: -2.34 (0.13), residues: 3846 helix: -0.20 (0.14), residues: 1379 sheet: -1.73 (0.21), residues: 529 loop : -2.59 (0.12), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 211 TYR 0.018 0.002 TYR D 144 PHE 0.020 0.002 PHE B 8 TRP 0.018 0.001 TRP D1193 HIS 0.007 0.001 HIS C1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (30786) covalent geometry : angle 0.67789 / 0.36 (42114) hydrogen bonds : bond 0.04519 / 3.20 ( 1208) hydrogen bonds : angle 5.26638 / 3.68 ( 3363) metal coordination : bond 0.00495 / 0.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 206 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 TYR cc_start: 0.0540 (p90) cc_final: -0.0355 (p90) REVERT: C 27 LEU cc_start: -0.0990 (OUTLIER) cc_final: -0.2806 (mt) REVERT: C 164 THR cc_start: 0.3349 (OUTLIER) cc_final: 0.3107 (m) REVERT: C 429 MET cc_start: -0.2293 (OUTLIER) cc_final: -0.3500 (ttm) REVERT: C 447 HIS cc_start: 0.0217 (OUTLIER) cc_final: -0.3070 (t-170) REVERT: C 653 MET cc_start: 0.2042 (ttp) cc_final: 0.0711 (mmp) REVERT: C 667 LEU cc_start: 0.0419 (OUTLIER) cc_final: -0.0858 (tt) REVERT: C 681 MET cc_start: -0.0293 (OUTLIER) cc_final: -0.1050 (tpp) REVERT: C 741 MET cc_start: 0.0089 (mmm) cc_final: -0.0857 (mmm) REVERT: C 967 LEU cc_start: 0.2443 (OUTLIER) cc_final: 0.2149 (tm) REVERT: C 1066 MET cc_start: 0.2672 (mmm) cc_final: 0.2231 (mmt) REVERT: C 1170 MET cc_start: -0.0709 (mmm) cc_final: -0.1424 (mmm) REVERT: C 1269 ARG cc_start: 0.0707 (ttt90) cc_final: -0.0227 (tpt170) REVERT: D 20 ILE cc_start: 0.0019 (OUTLIER) cc_final: -0.0384 (tt) REVERT: D 447 ILE cc_start: 0.6409 (mt) cc_final: 0.6068 (pt) REVERT: D 448 GLN cc_start: 0.2937 (mt0) cc_final: 0.1067 (mm-40) REVERT: D 485 MET cc_start: 0.3391 (ttm) cc_final: 0.2357 (ttm) REVERT: D 582 ILE cc_start: 0.2272 (OUTLIER) cc_final: 0.1914 (pt) REVERT: D 609 TYR cc_start: 0.1076 (t80) cc_final: 0.0349 (t80) REVERT: D 1095 MET cc_start: 0.0924 (ttt) cc_final: 0.0654 (ttt) REVERT: D 1189 MET cc_start: -0.2109 (ppp) cc_final: -0.2418 (ttp) REVERT: D 1370 MET cc_start: -0.0204 (tpt) cc_final: -0.0643 (ptt) outliers start: 86 outliers final: 49 residues processed: 273 average time/residue: 0.1962 time to fit residues: 87.2455 Evaluate side-chains 247 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 189 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1064 ASP Chi-restraints excluded: chain C residue 1116 HIS Chi-restraints excluded: chain C residue 1117 LEU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1287 LEU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 457 TYR Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 890 THR Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 1229 VAL Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1326 GLN Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain E residue 21 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 81 optimal weight: 9.9990 chunk 231 optimal weight: 4.9990 chunk 59 optimal weight: 50.0000 chunk 152 optimal weight: 7.9990 chunk 91 optimal weight: 40.0000 chunk 66 optimal weight: 20.0000 chunk 29 optimal weight: 50.0000 chunk 136 optimal weight: 0.0770 chunk 349 optimal weight: 40.0000 chunk 377 optimal weight: 30.0000 chunk 25 optimal weight: 50.0000 overall best weight: 8.6148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS B 147 GLN ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 526 HIS ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 688 GLN C 760 ASN C 832 HIS ** C1070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1146 GLN C1220 GLN C1244 HIS C1288 GLN D 153 ASN ** D 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 594 GLN D 792 ASN ** D 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1244 GLN D1279 GLN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5419 r_free = 0.5419 target = 0.326138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.5314 r_free = 0.5314 target = 0.312763 restraints weight = 80703.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.5330 r_free = 0.5330 target = 0.314840 restraints weight = 54698.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.5336 r_free = 0.5336 target = 0.315633 restraints weight = 41853.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.5347 r_free = 0.5347 target = 0.316881 restraints weight = 33803.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.5346 r_free = 0.5346 target = 0.317008 restraints weight = 28010.155| |-----------------------------------------------------------------------------| r_work (final): 0.5343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2192 moved from start: 0.6961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.291 30792 Z= 0.453 Angle : 1.355 24.602 42114 Z= 0.709 Chirality : 0.068 0.546 4931 Planarity : 0.012 0.186 5260 Dihedral : 17.340 170.345 5268 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 23.80 Ramachandran Plot: Outliers : 0.44 % Allowed : 12.06 % Favored : 87.49 % Rotamer: Outliers : 6.76 % Allowed : 14.85 % Favored : 78.38 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.08 % Twisted Proline : 3.90 % Twisted General : 0.92 % 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: -3.17 (0.12), residues: 3846 helix: -1.03 (0.13), residues: 1334 sheet: -1.80 (0.22), residues: 487 loop : -3.03 (0.12), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG C 548 TYR 0.061 0.005 TYR C 26 PHE 0.068 0.005 PHE C 389 TRP 0.030 0.004 TRP D1020 HIS 0.026 0.004 HIS D 907 Details of bonding type rmsd/Z covalent geometry : bond 0.01000 / 0.45 (30786) covalent geometry : angle 1.35498 / 0.71 (42114) hydrogen bonds : bond 0.09030 / 6.21 ( 1208) hydrogen bonds : angle 7.24221 / 5.09 ( 3363) metal coordination : bond 0.02660 / 1.50 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 207 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 GLU cc_start: 0.1171 (OUTLIER) cc_final: -0.3504 (tt0) REVERT: B 171 LEU cc_start: -0.0197 (OUTLIER) cc_final: -0.0714 (tp) REVERT: C 26 TYR cc_start: 0.3299 (t80) cc_final: 0.2131 (m-80) REVERT: C 27 LEU cc_start: -0.0369 (OUTLIER) cc_final: -0.1205 (mt) REVERT: C 384 LEU cc_start: 0.3256 (OUTLIER) cc_final: 0.2479 (tp) REVERT: C 425 ILE cc_start: -0.2686 (OUTLIER) cc_final: -0.2949 (mm) REVERT: C 429 MET cc_start: -0.2037 (mtp) cc_final: -0.4484 (ppp) REVERT: C 447 HIS cc_start: 0.1282 (OUTLIER) cc_final: -0.1309 (t-170) REVERT: C 459 MET cc_start: 0.2401 (mmm) cc_final: 0.1328 (mmp) REVERT: C 492 MET cc_start: -0.0048 (mmm) cc_final: -0.0397 (mtt) REVERT: C 653 MET cc_start: 0.1864 (ttp) cc_final: 0.0589 (mmp) REVERT: C 741 MET cc_start: 0.0485 (mmm) cc_final: -0.0486 (mmm) REVERT: C 801 ARG cc_start: 0.6678 (mmm-85) cc_final: 0.6326 (mmm-85) REVERT: C 820 GLU cc_start: -0.2237 (OUTLIER) cc_final: -0.2561 (mt-10) REVERT: C 867 GLU cc_start: 0.1357 (OUTLIER) cc_final: 0.0079 (tt0) REVERT: C 913 VAL cc_start: -0.1852 (OUTLIER) cc_final: -0.2666 (p) REVERT: C 929 ILE cc_start: 0.0171 (OUTLIER) cc_final: -0.0070 (mt) REVERT: C 941 LYS cc_start: 0.4926 (mttp) cc_final: 0.4016 (mttp) REVERT: C 967 LEU cc_start: 0.2547 (OUTLIER) cc_final: 0.2287 (tm) REVERT: C 1115 THR cc_start: 0.1108 (OUTLIER) cc_final: 0.0833 (m) REVERT: C 1170 MET cc_start: -0.0425 (mmm) cc_final: -0.1155 (mmm) REVERT: C 1235 LEU cc_start: 0.3011 (OUTLIER) cc_final: 0.2667 (mt) REVERT: C 1262 LYS cc_start: -0.1534 (OUTLIER) cc_final: -0.2005 (tptp) REVERT: C 1269 ARG cc_start: 0.1836 (ttt180) cc_final: 0.0774 (ttt180) REVERT: C 1321 GLU cc_start: 0.1744 (OUTLIER) cc_final: -0.0208 (tt0) REVERT: D 330 MET cc_start: 0.1695 (ppp) cc_final: 0.1471 (ppp) REVERT: D 449 LEU cc_start: 0.4477 (OUTLIER) cc_final: 0.4254 (mt) REVERT: D 513 MET cc_start: 0.4354 (ttt) cc_final: 0.4106 (mtp) REVERT: D 582 ILE cc_start: 0.2026 (OUTLIER) cc_final: 0.1609 (pt) REVERT: D 644 MET cc_start: 0.4418 (mpp) cc_final: 0.3883 (mpp) REVERT: D 654 ILE cc_start: 0.0442 (OUTLIER) cc_final: -0.0138 (mt) REVERT: D 789 LYS cc_start: 0.2756 (ttpt) cc_final: 0.1168 (mmtm) REVERT: D 905 ARG cc_start: 0.1417 (OUTLIER) cc_final: -0.4131 (ptm160) REVERT: D 1095 MET cc_start: -0.1167 (ttt) cc_final: -0.1400 (ttt) REVERT: D 1189 MET cc_start: -0.0746 (ppp) cc_final: -0.1106 (ttp) REVERT: D 1344 LEU cc_start: 0.3504 (OUTLIER) cc_final: 0.1288 (pp) REVERT: D 1352 ILE cc_start: -0.0906 (OUTLIER) cc_final: -0.1598 (mm) REVERT: D 1370 MET cc_start: 0.1210 (tpt) cc_final: -0.1329 (ptt) outliers start: 184 outliers final: 113 residues processed: 366 average time/residue: 0.1927 time to fit residues: 114.1383 Evaluate side-chains 325 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 191 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 211 ARG Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 692 THR Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 820 GLU Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 867 GLU Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 892 GLU Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1064 ASP Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1116 HIS Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1240 ASP Chi-restraints excluded: chain C residue 1243 MET Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1262 LYS Chi-restraints excluded: chain C residue 1287 LEU Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1321 GLU Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 890 THR Chi-restraints excluded: chain D residue 892 PHE Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 950 ILE Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1229 VAL Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1279 GLN Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1341 ARG Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1352 ILE Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain D residue 1361 THR Chi-restraints excluded: chain E residue 21 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 181 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 35 optimal weight: 20.0000 chunk 352 optimal weight: 50.0000 chunk 388 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 320 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 277 optimal weight: 0.2980 chunk 293 optimal weight: 0.0170 overall best weight: 1.4422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1146 GLN ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 817 HIS D 897 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5461 r_free = 0.5461 target = 0.330737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5364 r_free = 0.5364 target = 0.318789 restraints weight = 82324.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.5373 r_free = 0.5373 target = 0.320880 restraints weight = 55773.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.5389 r_free = 0.5389 target = 0.322193 restraints weight = 39297.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.5395 r_free = 0.5395 target = 0.323154 restraints weight = 30437.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.5396 r_free = 0.5396 target = 0.323481 restraints weight = 23597.855| |-----------------------------------------------------------------------------| r_work (final): 0.5397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1851 moved from start: 0.6784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30792 Z= 0.162 Angle : 0.765 17.640 42114 Z= 0.406 Chirality : 0.049 0.316 4931 Planarity : 0.006 0.090 5260 Dihedral : 16.647 168.589 5266 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.09 % Favored : 91.86 % Rotamer: Outliers : 4.15 % Allowed : 17.43 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.05 % Twisted Proline : 3.90 % Twisted General : 0.30 % 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: -2.61 (0.13), residues: 3846 helix: -0.41 (0.14), residues: 1348 sheet: -1.53 (0.22), residues: 509 loop : -2.84 (0.12), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 180 TYR 0.019 0.002 TYR C 395 PHE 0.032 0.002 PHE B 8 TRP 0.023 0.002 TRP D1193 HIS 0.008 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (30786) covalent geometry : angle 0.76487 / 0.41 (42114) hydrogen bonds : bond 0.05280 / 3.64 ( 1208) hydrogen bonds : angle 5.97281 / 4.19 ( 3363) metal coordination : bond 0.00457 / 0.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 197 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 TYR cc_start: 0.2099 (t80) cc_final: 0.1674 (m-80) REVERT: C 27 LEU cc_start: -0.0496 (OUTLIER) cc_final: -0.1349 (mt) REVERT: C 130 MET cc_start: 0.3055 (ptp) cc_final: 0.2531 (ptt) REVERT: C 211 ARG cc_start: 0.3674 (OUTLIER) cc_final: 0.2007 (ptm160) REVERT: C 429 MET cc_start: -0.2548 (mtp) cc_final: -0.4271 (ppp) REVERT: C 447 HIS cc_start: 0.1408 (OUTLIER) cc_final: -0.1203 (t-170) REVERT: C 459 MET cc_start: 0.1386 (mmm) cc_final: 0.1011 (mmm) REVERT: C 653 MET cc_start: 0.1732 (ttp) cc_final: 0.0703 (mmp) REVERT: C 667 LEU cc_start: 0.1022 (OUTLIER) cc_final: 0.0076 (mt) REVERT: C 741 MET cc_start: -0.0112 (mmm) cc_final: -0.1122 (mmm) REVERT: C 799 ASN cc_start: 0.0270 (OUTLIER) cc_final: -0.0523 (p0) REVERT: C 801 ARG cc_start: 0.6491 (mmm-85) cc_final: 0.6211 (mmm-85) REVERT: C 922 ASN cc_start: 0.0191 (OUTLIER) cc_final: -0.0405 (m-40) REVERT: C 941 LYS cc_start: 0.3988 (mttp) cc_final: 0.3148 (ptpp) REVERT: C 967 LEU cc_start: 0.2653 (OUTLIER) cc_final: 0.2397 (tm) REVERT: C 1048 LYS cc_start: 0.1284 (OUTLIER) cc_final: 0.0040 (mttt) REVERT: C 1170 MET cc_start: -0.0242 (mmm) cc_final: -0.1036 (mmm) REVERT: C 1269 ARG cc_start: 0.1129 (ttt180) cc_final: 0.0229 (ttt180) REVERT: C 1321 GLU cc_start: 0.0780 (OUTLIER) cc_final: -0.0995 (tt0) REVERT: D 20 ILE cc_start: 0.1313 (OUTLIER) cc_final: 0.0779 (tt) REVERT: D 789 LYS cc_start: 0.2475 (ttpt) cc_final: 0.1148 (mmpt) REVERT: D 905 ARG cc_start: 0.0796 (OUTLIER) cc_final: -0.4174 (ptm160) REVERT: D 1193 TRP cc_start: 0.2723 (OUTLIER) cc_final: -0.2870 (m100) REVERT: D 1282 TYR cc_start: 0.3598 (m-80) cc_final: 0.3090 (m-80) REVERT: D 1370 MET cc_start: 0.0460 (tpt) cc_final: -0.0722 (ptt) REVERT: E 30 MET cc_start: -0.0930 (tpt) cc_final: -0.1226 (tpt) outliers start: 113 outliers final: 76 residues processed: 294 average time/residue: 0.1906 time to fit residues: 91.5090 Evaluate side-chains 278 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 190 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 211 ARG Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 820 GLU Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 840 SER Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 922 ASN Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1048 LYS Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1064 ASP Chi-restraints excluded: chain C residue 1116 HIS Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1234 LYS Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1287 LEU Chi-restraints excluded: chain C residue 1305 TYR Chi-restraints excluded: chain C residue 1321 GLU Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 165 TYR Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 457 TYR Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 892 PHE Chi-restraints excluded: chain D residue 897 HIS Chi-restraints excluded: chain D residue 898 CYS Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1193 TRP Chi-restraints excluded: chain D residue 1229 VAL Chi-restraints excluded: chain D residue 1257 VAL Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain E residue 21 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 371 optimal weight: 20.0000 chunk 271 optimal weight: 20.0000 chunk 137 optimal weight: 8.9990 chunk 377 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 285 optimal weight: 3.9990 chunk 365 optimal weight: 3.9990 chunk 376 optimal weight: 6.9990 chunk 272 optimal weight: 7.9990 chunk 198 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 HIS ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1146 GLN ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5600 r_free = 0.5600 target = 0.351325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5593 r_free = 0.5593 target = 0.341233 restraints weight = 83987.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.5597 r_free = 0.5597 target = 0.342043 restraints weight = 68979.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.5602 r_free = 0.5602 target = 0.342625 restraints weight = 46665.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.5602 r_free = 0.5602 target = 0.342630 restraints weight = 37386.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.5603 r_free = 0.5603 target = 0.342765 restraints weight = 33352.537| |-----------------------------------------------------------------------------| r_work (final): 0.5411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1836 moved from start: 0.7424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 30792 Z= 0.257 Angle : 0.898 20.891 42114 Z= 0.477 Chirality : 0.052 0.477 4931 Planarity : 0.007 0.120 5260 Dihedral : 16.687 164.928 5264 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.15 % Favored : 88.79 % Rotamer: Outliers : 5.04 % Allowed : 17.65 % Favored : 77.32 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.08 % Twisted Proline : 3.90 % Twisted General : 0.35 % 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: -2.67 (0.13), residues: 3846 helix: -0.48 (0.14), residues: 1356 sheet: -1.59 (0.22), residues: 505 loop : -2.86 (0.12), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 352 TYR 0.035 0.003 TYR C 26 PHE 0.046 0.003 PHE B 8 TRP 0.019 0.002 TRP D1193 HIS 0.061 0.003 HIS D 897 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.26 (30786) covalent geometry : angle 0.89835 / 0.48 (42114) hydrogen bonds : bond 0.06198 / 4.27 ( 1208) hydrogen bonds : angle 6.19972 / 4.34 ( 3363) metal coordination : bond 0.01769 / 1.00 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 204 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.3553 (tpt-90) cc_final: 0.3204 (mtt90) REVERT: A 65 LEU cc_start: -0.2328 (OUTLIER) cc_final: -0.3235 (mp) REVERT: B 171 LEU cc_start: 0.0937 (OUTLIER) cc_final: 0.0027 (tp) REVERT: B 203 ILE cc_start: -0.0821 (OUTLIER) cc_final: -0.1193 (tt) REVERT: C 26 TYR cc_start: 0.3218 (t80) cc_final: 0.2127 (m-80) REVERT: C 27 LEU cc_start: -0.0605 (OUTLIER) cc_final: -0.1098 (mt) REVERT: C 130 MET cc_start: 0.3027 (ptp) cc_final: 0.2442 (ptt) REVERT: C 211 ARG cc_start: 0.3885 (OUTLIER) cc_final: 0.1302 (ptm160) REVERT: C 429 MET cc_start: -0.2149 (OUTLIER) cc_final: -0.4394 (ppp) REVERT: C 447 HIS cc_start: 0.1125 (OUTLIER) cc_final: -0.1776 (t-170) REVERT: C 459 MET cc_start: 0.1244 (mmm) cc_final: 0.0790 (mmm) REVERT: C 522 SER cc_start: 0.5008 (OUTLIER) cc_final: 0.3644 (m) REVERT: C 549 ASP cc_start: 0.1079 (OUTLIER) cc_final: -0.1076 (m-30) REVERT: C 653 MET cc_start: 0.1913 (ttp) cc_final: 0.0856 (mmp) REVERT: C 741 MET cc_start: 0.0220 (mmm) cc_final: -0.0691 (mmm) REVERT: C 866 ASP cc_start: 0.0477 (OUTLIER) cc_final: -0.0390 (p0) REVERT: C 867 GLU cc_start: 0.1299 (OUTLIER) cc_final: -0.0222 (tt0) REVERT: C 922 ASN cc_start: 0.0755 (OUTLIER) cc_final: 0.0306 (m-40) REVERT: C 941 LYS cc_start: 0.4084 (mttp) cc_final: 0.3174 (ptpp) REVERT: C 1048 LYS cc_start: 0.0947 (OUTLIER) cc_final: 0.0261 (mtpt) REVERT: C 1107 MET cc_start: 0.3187 (tpp) cc_final: 0.2823 (tpp) REVERT: C 1170 MET cc_start: 0.0048 (mmm) cc_final: -0.0772 (mmm) REVERT: C 1195 ILE cc_start: 0.5952 (mt) cc_final: 0.5621 (tp) REVERT: C 1262 LYS cc_start: -0.1932 (OUTLIER) cc_final: -0.2352 (tptm) REVERT: C 1269 ARG cc_start: 0.1053 (ttt180) cc_final: 0.0341 (ttt180) REVERT: C 1321 GLU cc_start: 0.1071 (OUTLIER) cc_final: -0.0971 (tt0) REVERT: D 20 ILE cc_start: 0.0914 (OUTLIER) cc_final: 0.0313 (tt) REVERT: D 448 GLN cc_start: 0.5280 (mt0) cc_final: 0.4661 (mm-40) REVERT: D 582 ILE cc_start: 0.2492 (OUTLIER) cc_final: 0.1999 (pt) REVERT: D 698 MET cc_start: -0.3015 (tpt) cc_final: -0.3661 (tmm) REVERT: D 789 LYS cc_start: 0.2167 (ttpt) cc_final: 0.1418 (mmpt) REVERT: D 905 ARG cc_start: 0.0752 (OUTLIER) cc_final: -0.4299 (ptm160) REVERT: D 1193 TRP cc_start: 0.3079 (OUTLIER) cc_final: -0.1945 (m100) REVERT: D 1282 TYR cc_start: 0.4016 (m-80) cc_final: 0.3134 (m-80) REVERT: D 1284 ARG cc_start: 0.1619 (ttt90) cc_final: -0.0229 (ttt90) REVERT: D 1370 MET cc_start: 0.0496 (tpt) cc_final: -0.1461 (ptt) REVERT: E 30 MET cc_start: -0.0821 (tpt) cc_final: -0.1208 (tpt) REVERT: E 58 LEU cc_start: -0.1526 (OUTLIER) cc_final: -0.1783 (pp) outliers start: 137 outliers final: 96 residues processed: 324 average time/residue: 0.1980 time to fit residues: 103.4866 Evaluate side-chains 306 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 190 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 211 ARG Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 820 GLU Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 840 SER Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 867 GLU Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 922 ASN Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1048 LYS Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1116 HIS Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1234 LYS Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1262 LYS Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1287 LEU Chi-restraints excluded: chain C residue 1305 TYR Chi-restraints excluded: chain C residue 1321 GLU Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 165 TYR Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 890 THR Chi-restraints excluded: chain D residue 892 PHE Chi-restraints excluded: chain D residue 897 HIS Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 950 ILE Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1193 TRP Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1229 VAL Chi-restraints excluded: chain D residue 1257 VAL Chi-restraints excluded: chain D residue 1287 ILE Chi-restraints excluded: chain D residue 1302 TYR Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 66 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 98 optimal weight: 0.9990 chunk 375 optimal weight: 30.0000 chunk 23 optimal weight: 3.9990 chunk 372 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 20.0000 chunk 182 optimal weight: 0.9980 chunk 154 optimal weight: 0.4980 chunk 95 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 229 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 GLN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 897 HIS D1259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5621 r_free = 0.5621 target = 0.353843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.5623 r_free = 0.5623 target = 0.344337 restraints weight = 84165.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.5628 r_free = 0.5628 target = 0.345410 restraints weight = 62685.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.5632 r_free = 0.5632 target = 0.345740 restraints weight = 37732.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.5633 r_free = 0.5633 target = 0.345869 restraints weight = 29504.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.5634 r_free = 0.5634 target = 0.345997 restraints weight = 25405.146| |-----------------------------------------------------------------------------| r_work (final): 0.5440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1616 moved from start: 0.7344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 30792 Z= 0.136 Angle : 0.685 15.155 42114 Z= 0.363 Chirality : 0.046 0.330 4931 Planarity : 0.006 0.088 5260 Dihedral : 16.373 159.911 5264 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.54 % Favored : 92.41 % Rotamer: Outliers : 3.71 % Allowed : 18.82 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.08 % Twisted Proline : 1.95 % Twisted General : 0.03 % 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: -2.24 (0.13), residues: 3846 helix: -0.03 (0.14), residues: 1361 sheet: -1.44 (0.22), residues: 515 loop : -2.66 (0.13), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 352 TYR 0.016 0.001 TYR D 165 PHE 0.019 0.002 PHE B 8 TRP 0.020 0.001 TRP D1193 HIS 0.020 0.001 HIS D 897 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 (30786) covalent geometry : angle 0.68495 / 0.36 (42114) hydrogen bonds : bond 0.04614 / 3.20 ( 1208) hydrogen bonds : angle 5.54279 / 3.88 ( 3363) metal coordination : bond 0.00971 / 0.49 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 192 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 203 ILE cc_start: -0.1123 (OUTLIER) cc_final: -0.1508 (tt) REVERT: C 26 TYR cc_start: 0.2456 (t80) cc_final: 0.1638 (m-80) REVERT: C 27 LEU cc_start: -0.0937 (OUTLIER) cc_final: -0.2072 (mt) REVERT: C 130 MET cc_start: 0.2798 (ptp) cc_final: 0.2313 (ptt) REVERT: C 211 ARG cc_start: 0.3604 (OUTLIER) cc_final: 0.0999 (ptm160) REVERT: C 429 MET cc_start: -0.2269 (mtp) cc_final: -0.4094 (ppp) REVERT: C 447 HIS cc_start: 0.0985 (OUTLIER) cc_final: -0.1782 (t-170) REVERT: C 488 MET cc_start: 0.1002 (ttt) cc_final: 0.0626 (ttt) REVERT: C 522 SER cc_start: 0.4066 (OUTLIER) cc_final: 0.3332 (p) REVERT: C 549 ASP cc_start: 0.0931 (OUTLIER) cc_final: -0.1318 (m-30) REVERT: C 653 MET cc_start: 0.1644 (ttp) cc_final: 0.0849 (mmp) REVERT: C 667 LEU cc_start: 0.0321 (OUTLIER) cc_final: -0.0724 (mt) REVERT: C 741 MET cc_start: 0.0274 (mmm) cc_final: -0.0683 (mmm) REVERT: C 799 ASN cc_start: -0.0230 (OUTLIER) cc_final: -0.1101 (p0) REVERT: C 922 ASN cc_start: 0.0275 (OUTLIER) cc_final: -0.0361 (m-40) REVERT: C 941 LYS cc_start: 0.3539 (mttp) cc_final: 0.2983 (ptpt) REVERT: C 1048 LYS cc_start: 0.0984 (OUTLIER) cc_final: 0.0070 (mttt) REVERT: C 1107 MET cc_start: 0.2727 (tpp) cc_final: 0.2369 (tpp) REVERT: C 1170 MET cc_start: 0.0124 (mmm) cc_final: -0.0684 (mmm) REVERT: C 1195 ILE cc_start: 0.5899 (mt) cc_final: 0.5589 (tp) REVERT: C 1269 ARG cc_start: 0.0556 (ttt180) cc_final: -0.0084 (ttt180) REVERT: C 1321 GLU cc_start: 0.0416 (OUTLIER) cc_final: -0.1236 (tp30) REVERT: D 20 ILE cc_start: 0.0837 (OUTLIER) cc_final: 0.0379 (tt) REVERT: D 448 GLN cc_start: 0.4654 (mt0) cc_final: 0.3901 (mm-40) REVERT: D 513 MET cc_start: 0.4669 (OUTLIER) cc_final: 0.3945 (ttp) REVERT: D 698 MET cc_start: -0.2911 (tpt) cc_final: -0.3446 (tmm) REVERT: D 789 LYS cc_start: 0.2437 (ttpt) cc_final: 0.1396 (mmpt) REVERT: D 905 ARG cc_start: 0.0689 (OUTLIER) cc_final: -0.4141 (ptm160) REVERT: D 1193 TRP cc_start: 0.2530 (OUTLIER) cc_final: -0.2615 (m100) REVERT: D 1282 TYR cc_start: 0.3677 (m-80) cc_final: 0.3244 (m-80) REVERT: D 1370 MET cc_start: 0.0441 (tpt) cc_final: -0.0463 (ppp) outliers start: 101 outliers final: 71 residues processed: 279 average time/residue: 0.2011 time to fit residues: 90.5081 Evaluate side-chains 274 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 188 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 211 ARG Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 820 GLU Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 840 SER Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 922 ASN Chi-restraints excluded: chain C residue 1048 LYS Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1116 HIS Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1287 LEU Chi-restraints excluded: chain C residue 1305 TYR Chi-restraints excluded: chain C residue 1321 GLU Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 75 TYR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 165 TYR Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 457 TYR Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 809 VAL Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 892 PHE Chi-restraints excluded: chain D residue 897 HIS Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1193 TRP Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1229 VAL Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain E residue 21 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 237 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 4 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 238 optimal weight: 1.9990 chunk 290 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 chunk 387 optimal weight: 20.0000 chunk 314 optimal weight: 7.9990 chunk 271 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 897 HIS ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5450 r_free = 0.5450 target = 0.329059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.5343 r_free = 0.5343 target = 0.316269 restraints weight = 81770.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.5354 r_free = 0.5354 target = 0.318050 restraints weight = 54831.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.5365 r_free = 0.5365 target = 0.319088 restraints weight = 42529.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.5373 r_free = 0.5373 target = 0.320178 restraints weight = 33058.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 67)----------------| | r_work = 0.5383 r_free = 0.5383 target = 0.321301 restraints weight = 27608.686| |-----------------------------------------------------------------------------| r_work (final): 0.5381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2006 moved from start: 0.7655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 30792 Z= 0.177 Angle : 0.743 17.188 42114 Z= 0.392 Chirality : 0.047 0.337 4931 Planarity : 0.006 0.091 5260 Dihedral : 16.366 159.024 5263 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.41 % Favored : 90.54 % Rotamer: Outliers : 3.75 % Allowed : 19.04 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.08 % Twisted Proline : 2.60 % Twisted General : 0.08 % 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: -2.20 (0.13), residues: 3846 helix: -0.02 (0.14), residues: 1378 sheet: -1.30 (0.23), residues: 494 loop : -2.67 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C1301 TYR 0.032 0.002 TYR D 144 PHE 0.034 0.002 PHE B 8 TRP 0.017 0.001 TRP D1193 HIS 0.045 0.002 HIS D 897 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (30786) covalent geometry : angle 0.74289 / 0.39 (42114) hydrogen bonds : bond 0.05020 / 3.48 ( 1208) hydrogen bonds : angle 5.62798 / 3.92 ( 3363) metal coordination : bond 0.01269 / 0.72 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 188 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: B 203 ILE cc_start: -0.0602 (OUTLIER) cc_final: -0.0961 (tt) REVERT: C 26 TYR cc_start: 0.2918 (t80) cc_final: 0.1367 (m-80) REVERT: C 27 LEU cc_start: -0.0539 (OUTLIER) cc_final: -0.1199 (mt) REVERT: C 130 MET cc_start: 0.3011 (ptp) cc_final: 0.2490 (ptt) REVERT: C 211 ARG cc_start: 0.3872 (OUTLIER) cc_final: 0.1116 (ptm160) REVERT: C 384 LEU cc_start: 0.2878 (OUTLIER) cc_final: 0.2184 (tt) REVERT: C 447 HIS cc_start: 0.0895 (OUTLIER) cc_final: -0.1503 (t-170) REVERT: C 522 SER cc_start: 0.4762 (OUTLIER) cc_final: 0.3275 (m) REVERT: C 549 ASP cc_start: 0.1158 (OUTLIER) cc_final: -0.1144 (m-30) REVERT: C 653 MET cc_start: 0.1361 (ttp) cc_final: 0.0520 (mmp) REVERT: C 667 LEU cc_start: 0.1159 (OUTLIER) cc_final: 0.0216 (mt) REVERT: C 741 MET cc_start: -0.0173 (mmm) cc_final: -0.1053 (mmm) REVERT: C 867 GLU cc_start: 0.1461 (OUTLIER) cc_final: 0.0259 (tt0) REVERT: C 922 ASN cc_start: 0.0809 (OUTLIER) cc_final: 0.0095 (t0) REVERT: C 941 LYS cc_start: 0.3474 (mttp) cc_final: 0.3153 (ptpt) REVERT: C 1048 LYS cc_start: 0.1356 (OUTLIER) cc_final: 0.0737 (mtpt) REVERT: C 1107 MET cc_start: 0.2876 (tpp) cc_final: 0.2489 (tpp) REVERT: C 1170 MET cc_start: 0.0157 (mmm) cc_final: -0.0695 (mmm) REVERT: C 1195 ILE cc_start: 0.5873 (mt) cc_final: 0.5578 (tp) REVERT: C 1269 ARG cc_start: 0.1319 (ttt180) cc_final: 0.0587 (ttt180) REVERT: C 1321 GLU cc_start: 0.1128 (OUTLIER) cc_final: -0.0734 (tp30) REVERT: D 20 ILE cc_start: 0.1180 (OUTLIER) cc_final: 0.0633 (tt) REVERT: D 448 GLN cc_start: 0.5252 (mt0) cc_final: 0.4647 (mt0) REVERT: D 698 MET cc_start: -0.3009 (tpt) cc_final: -0.3511 (tmm) REVERT: D 789 LYS cc_start: 0.2301 (ttpt) cc_final: 0.1324 (mmpt) REVERT: D 905 ARG cc_start: 0.0871 (OUTLIER) cc_final: -0.4152 (ptm160) REVERT: D 1193 TRP cc_start: 0.2381 (OUTLIER) cc_final: -0.2404 (m100) REVERT: D 1282 TYR cc_start: 0.3776 (m-80) cc_final: 0.3035 (m-80) REVERT: D 1284 ARG cc_start: 0.1574 (ttt90) cc_final: -0.0097 (ttt90) REVERT: D 1370 MET cc_start: 0.0574 (tpt) cc_final: -0.0936 (ptt) outliers start: 102 outliers final: 83 residues processed: 279 average time/residue: 0.1992 time to fit residues: 89.4773 Evaluate side-chains 284 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 186 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 211 ARG Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 820 GLU Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 840 SER Chi-restraints excluded: chain C residue 867 GLU Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 922 ASN Chi-restraints excluded: chain C residue 1048 LYS Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1116 HIS Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1234 LYS Chi-restraints excluded: chain C residue 1243 MET Chi-restraints excluded: chain C residue 1287 LEU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1305 TYR Chi-restraints excluded: chain C residue 1321 GLU Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 75 TYR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 165 TYR Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 457 TYR Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 892 PHE Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1193 TRP Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1229 VAL Chi-restraints excluded: chain D residue 1257 VAL Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain D residue 1361 THR Chi-restraints excluded: chain E residue 21 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 70 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 194 optimal weight: 0.5980 chunk 296 optimal weight: 40.0000 chunk 233 optimal weight: 5.9990 chunk 195 optimal weight: 4.9990 chunk 336 optimal weight: 0.0670 chunk 46 optimal weight: 0.0770 chunk 208 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 overall best weight: 1.3480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1157 GLN ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5621 r_free = 0.5621 target = 0.353727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.5631 r_free = 0.5631 target = 0.344227 restraints weight = 83683.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.5630 r_free = 0.5630 target = 0.345277 restraints weight = 60520.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.5634 r_free = 0.5634 target = 0.345675 restraints weight = 38515.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.5635 r_free = 0.5635 target = 0.345727 restraints weight = 27403.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.5636 r_free = 0.5636 target = 0.345895 restraints weight = 26492.480| |-----------------------------------------------------------------------------| r_work (final): 0.5441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1637 moved from start: 0.7704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30792 Z= 0.133 Angle : 0.666 13.879 42114 Z= 0.352 Chirality : 0.045 0.339 4931 Planarity : 0.005 0.086 5260 Dihedral : 16.218 157.053 5263 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.54 % Favored : 92.41 % Rotamer: Outliers : 3.38 % Allowed : 19.34 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.08 % Twisted Proline : 1.30 % Twisted General : 0.03 % 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: -1.98 (0.13), residues: 3846 helix: 0.18 (0.14), residues: 1378 sheet: -1.17 (0.23), residues: 483 loop : -2.54 (0.13), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 211 TYR 0.022 0.001 TYR D 144 PHE 0.023 0.002 PHE B 8 TRP 0.017 0.001 TRP D1193 HIS 0.009 0.001 HIS D 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (30786) covalent geometry : angle 0.66563 / 0.35 (42114) hydrogen bonds : bond 0.04349 / 3.01 ( 1208) hydrogen bonds : angle 5.33369 / 3.72 ( 3363) metal coordination : bond 0.00450 / 0.26 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 190 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 203 ILE cc_start: -0.0779 (OUTLIER) cc_final: -0.1239 (tt) REVERT: C 26 TYR cc_start: 0.2501 (t80) cc_final: 0.0950 (m-80) REVERT: C 27 LEU cc_start: -0.1124 (OUTLIER) cc_final: -0.2129 (mt) REVERT: C 130 MET cc_start: 0.2918 (ptp) cc_final: 0.2541 (ptt) REVERT: C 211 ARG cc_start: 0.3365 (OUTLIER) cc_final: 0.0728 (ptm160) REVERT: C 384 LEU cc_start: 0.2835 (OUTLIER) cc_final: 0.2097 (tt) REVERT: C 429 MET cc_start: -0.4315 (mtt) cc_final: -0.4699 (mtt) REVERT: C 447 HIS cc_start: 0.0924 (OUTLIER) cc_final: -0.1900 (t-170) REVERT: C 522 SER cc_start: 0.4121 (OUTLIER) cc_final: 0.3294 (p) REVERT: C 549 ASP cc_start: 0.1020 (OUTLIER) cc_final: -0.1333 (m-30) REVERT: C 653 MET cc_start: 0.1828 (ttp) cc_final: 0.1037 (mmp) REVERT: C 667 LEU cc_start: 0.0632 (OUTLIER) cc_final: -0.0413 (mt) REVERT: C 741 MET cc_start: 0.0446 (mmm) cc_final: -0.0451 (mmm) REVERT: C 799 ASN cc_start: -0.0313 (OUTLIER) cc_final: -0.1184 (p0) REVERT: C 922 ASN cc_start: 0.0643 (OUTLIER) cc_final: 0.0050 (t0) REVERT: C 941 LYS cc_start: 0.3473 (mttp) cc_final: 0.2901 (mttp) REVERT: C 1048 LYS cc_start: 0.1054 (OUTLIER) cc_final: 0.0238 (mtpt) REVERT: C 1107 MET cc_start: 0.2633 (tpp) cc_final: 0.2346 (tpp) REVERT: C 1170 MET cc_start: 0.0162 (mmm) cc_final: -0.0652 (mmm) REVERT: C 1195 ILE cc_start: 0.5943 (mt) cc_final: 0.5628 (tp) REVERT: C 1269 ARG cc_start: 0.0329 (ttt180) cc_final: -0.0265 (ttt180) REVERT: C 1321 GLU cc_start: 0.0739 (OUTLIER) cc_final: -0.1007 (tp30) REVERT: D 448 GLN cc_start: 0.4633 (mt0) cc_final: 0.3746 (mm-40) REVERT: D 609 TYR cc_start: 0.1004 (t80) cc_final: -0.0733 (t80) REVERT: D 698 MET cc_start: -0.2892 (tpt) cc_final: -0.3384 (tmm) REVERT: D 789 LYS cc_start: 0.2417 (ttpt) cc_final: 0.1412 (mmpt) REVERT: D 905 ARG cc_start: 0.0800 (OUTLIER) cc_final: -0.4118 (ptm160) REVERT: D 1193 TRP cc_start: 0.2401 (OUTLIER) cc_final: -0.2600 (m100) REVERT: D 1282 TYR cc_start: 0.3917 (m-80) cc_final: 0.3423 (m-80) REVERT: D 1370 MET cc_start: 0.0476 (tpt) cc_final: -0.0495 (ppp) outliers start: 92 outliers final: 73 residues processed: 272 average time/residue: 0.1839 time to fit residues: 81.1262 Evaluate side-chains 274 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 187 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 211 ARG Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 840 SER Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 922 ASN Chi-restraints excluded: chain C residue 1048 LYS Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1116 HIS Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1234 LYS Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1321 GLU Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 75 TYR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 165 TYR Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 890 THR Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1193 TRP Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1229 VAL Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain D residue 1361 THR Chi-restraints excluded: chain E residue 21 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 367 optimal weight: 10.0000 chunk 246 optimal weight: 0.0470 chunk 331 optimal weight: 5.9990 chunk 154 optimal weight: 0.5980 chunk 155 optimal weight: 0.9980 chunk 192 optimal weight: 2.9990 chunk 370 optimal weight: 50.0000 chunk 352 optimal weight: 50.0000 chunk 272 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 125 optimal weight: 20.0000 overall best weight: 1.5282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5463 r_free = 0.5463 target = 0.330655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5357 r_free = 0.5357 target = 0.318401 restraints weight = 82352.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.5381 r_free = 0.5381 target = 0.320744 restraints weight = 53397.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.5384 r_free = 0.5384 target = 0.321660 restraints weight = 39222.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.5395 r_free = 0.5395 target = 0.322759 restraints weight = 29946.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.5396 r_free = 0.5396 target = 0.323067 restraints weight = 25273.538| |-----------------------------------------------------------------------------| r_work (final): 0.5395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1906 moved from start: 0.7715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 30792 Z= 0.155 Angle : 0.757 59.178 42114 Z= 0.416 Chirality : 0.045 0.339 4931 Planarity : 0.005 0.086 5260 Dihedral : 16.213 157.007 5263 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.67 % Favored : 92.28 % Rotamer: Outliers : 3.57 % Allowed : 19.15 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.08 % Twisted Proline : 1.30 % Twisted General : 0.03 % 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: -1.96 (0.13), residues: 3846 helix: 0.19 (0.14), residues: 1378 sheet: -1.14 (0.23), residues: 475 loop : -2.53 (0.13), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 211 TYR 0.025 0.001 TYR D 144 PHE 0.023 0.001 PHE B 8 TRP 0.017 0.001 TRP D1193 HIS 0.008 0.001 HIS D 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (30786) covalent geometry : angle 0.75665 / 0.42 (42114) hydrogen bonds : bond 0.04367 / 3.02 ( 1208) hydrogen bonds : angle 5.33016 / 3.72 ( 3363) metal coordination : bond 0.00422 / 0.23 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5058.77 seconds wall clock time: 88 minutes 4.32 seconds (5284.32 seconds total)