Starting phenix.real_space_refine on Mon Aug 25 20:25:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6flq_4275/08_2025/6flq_4275_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6flq_4275/08_2025/6flq_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_4275/08_2025/6flq_4275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6flq_4275/08_2025/6flq_4275.map" model { file = "/net/cci-nas-00/data/ceres_data/6flq_4275/08_2025/6flq_4275_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6flq_4275/08_2025/6flq_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-2.0-5787/lib/python3.9/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: 5.25, per 1000 atoms: 0.17 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: 2.04 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 3.30 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: 6.64 Time building geometry restraints manager: 2.61 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=" CA VAL D 470 " pdb=" C VAL D 470 " ideal model delta sigma weight residual 1.522 1.495 0.028 7.10e-03 1.98e+04 1.52e+01 bond pdb=" CA LYS A 145 " pdb=" CB LYS A 145 " ideal model delta sigma weight residual 1.527 1.460 0.067 1.75e-02 3.27e+03 1.47e+01 bond pdb=" CA PRO D 246 " pdb=" C PRO D 246 " ideal model delta sigma weight residual 1.517 1.552 -0.035 9.30e-03 1.16e+04 1.43e+01 bond pdb=" CB TRP D 115 " pdb=" CG TRP D 115 " ideal model delta sigma weight residual 1.498 1.395 0.103 3.10e-02 1.04e+03 1.10e+01 ... (remaining 30781 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.03: 41367 4.03 - 8.07: 688 8.07 - 12.10: 53 12.10 - 16.13: 3 16.13 - 20.16: 3 Bond angle restraints: 42114 Sorted by residual: 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=" C ASP C1084 " pdb=" N MET C1085 " pdb=" CA MET C1085 " ideal model delta sigma weight residual 120.49 130.59 -10.10 1.42e+00 4.96e-01 5.06e+01 angle pdb=" C ALA C 910 " pdb=" N SER C 911 " pdb=" CA SER C 911 " ideal model delta sigma weight residual 121.70 132.35 -10.65 1.80e+00 3.09e-01 3.50e+01 angle pdb=" C ALA F 11 " pdb=" N VAL F 12 " pdb=" CA VAL F 12 " ideal model delta sigma weight residual 121.70 132.03 -10.33 1.80e+00 3.09e-01 3.29e+01 angle pdb=" C GLN C 41 " pdb=" N ASP C 42 " pdb=" CA ASP C 42 " ideal model delta sigma weight residual 121.59 141.75 -20.16 3.54e+00 7.98e-02 3.24e+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: 3519 0.074 - 0.149: 1178 0.149 - 0.223: 192 0.223 - 0.297: 32 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 28.540 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0214 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= 0.659 Angle : 1.332 20.164 42114 Z= 0.726 Chirality : 0.074 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 aren 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 covalent geometry : bond 0.01562 (30786) covalent geometry : angle 1.33194 (42114) hydrogen bonds : bond 0.17630 ( 1208) hydrogen bonds : angle 7.49232 ( 3363) metal coordination : bond 0.12936 ( 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 : 0.685 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: 0.1621 time to fit residues: 84.8729 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 : 0.800 ------------------------------------------------------------------------------- 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: 5.9990 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... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 84 ASN B 147 GLN C 36 GLN C 273 HIS C 387 ASN C 513 GLN C 526 HIS C 551 HIS C 628 HIS ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 808 ASN C1038 GLN C1070 HIS C1116 HIS C1146 GLN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1299 ASN D 113 HIS D 232 ASN D 365 GLN D 665 GLN D 907 HIS D 910 ASN D 951 GLN D1098 GLN E 29 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5648 r_free = 0.5648 target = 0.360110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5668 r_free = 0.5668 target = 0.351741 restraints weight = 85002.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.5669 r_free = 0.5669 target = 0.352552 restraints weight = 54347.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.5670 r_free = 0.5670 target = 0.352970 restraints weight = 33427.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.5671 r_free = 0.5671 target = 0.353132 restraints weight = 29550.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.5671 r_free = 0.5671 target = 0.353232 restraints weight = 23229.033| |-----------------------------------------------------------------------------| r_work (final): 0.5482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0785 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 30792 Z= 0.188 Angle : 0.756 10.610 42114 Z= 0.399 Chirality : 0.047 0.214 4931 Planarity : 0.007 0.095 5260 Dihedral : 16.428 151.145 5279 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.66 % Favored : 93.29 % Rotamer: Outliers : 2.24 % Allowed : 9.34 % Favored : 88.42 % 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 aren not related in a simple way. whole: -2.94 (0.12), residues: 3846 helix: -0.92 (0.13), residues: 1356 sheet: -2.01 (0.21), residues: 475 loop : -2.75 (0.12), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 143 TYR 0.025 0.002 TYR C1229 PHE 0.024 0.002 PHE D 437 TRP 0.022 0.002 TRP D1193 HIS 0.010 0.002 HIS D 419 Details of bonding type rmsd covalent geometry : bond 0.00402 (30786) covalent geometry : angle 0.75630 (42114) hydrogen bonds : bond 0.04688 ( 1208) hydrogen bonds : angle 5.36213 ( 3363) metal coordination : bond 0.04038 ( 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 289 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 228 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.3071 (pp) cc_final: 0.2769 (pp) REVERT: A 143 ARG cc_start: 0.3094 (mtm-85) cc_final: 0.2871 (mtm180) REVERT: C 429 MET cc_start: -0.3294 (mtp) cc_final: -0.4202 (ptp) REVERT: C 653 MET cc_start: 0.1870 (ttp) cc_final: 0.1156 (mtp) REVERT: C 667 LEU cc_start: -0.0640 (OUTLIER) cc_final: -0.2214 (mt) REVERT: C 711 ASP cc_start: 0.2976 (m-30) cc_final: 0.2421 (m-30) REVERT: C 741 MET cc_start: 0.0064 (mmm) cc_final: -0.0358 (mmm) REVERT: C 1066 MET cc_start: 0.2554 (mmm) cc_final: 0.1840 (mmt) REVERT: C 1073 LYS cc_start: 0.2435 (ptmt) cc_final: 0.1792 (mttp) REVERT: C 1170 MET cc_start: -0.0858 (mmm) cc_final: -0.1558 (mmm) REVERT: C 1262 LYS cc_start: -0.3436 (OUTLIER) cc_final: -0.3795 (ttpt) REVERT: D 372 MET cc_start: 0.1938 (mmp) cc_final: 0.1407 (mmp) REVERT: D 772 TYR cc_start: 0.0641 (t80) cc_final: -0.0308 (t80) REVERT: D 1370 MET cc_start: -0.0072 (tpt) cc_final: -0.0904 (ptt) outliers start: 61 outliers final: 28 residues processed: 283 average time/residue: 0.1595 time to fit residues: 73.0199 Evaluate side-chains 223 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 574 SER 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 765 ILE Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1117 LEU Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1262 LYS Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain D residue 44 ILE 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 342 LEU Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 457 TYR Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 545 HIS 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 1326 GLN 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: 5.9990 chunk 213 optimal weight: 4.9990 chunk 211 optimal weight: 20.0000 chunk 89 optimal weight: 9.9990 chunk 340 optimal weight: 10.0000 chunk 238 optimal weight: 9.9990 chunk 383 optimal weight: 50.0000 chunk 278 optimal weight: 8.9990 chunk 68 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 357 optimal weight: 6.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 GLN C 526 HIS ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 673 HIS ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1146 GLN C1220 GLN C1244 HIS C1256 GLN D 153 ASN D 157 GLN D 469 HIS D 594 GLN ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 910 ASN D1244 GLN D1279 GLN ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5612 r_free = 0.5612 target = 0.353750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.5614 r_free = 0.5614 target = 0.343792 restraints weight = 84938.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.5616 r_free = 0.5616 target = 0.344484 restraints weight = 67442.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.5619 r_free = 0.5619 target = 0.345051 restraints weight = 46786.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.5620 r_free = 0.5620 target = 0.345107 restraints weight = 36514.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.5621 r_free = 0.5621 target = 0.345227 restraints weight = 33596.468| |-----------------------------------------------------------------------------| r_work (final): 0.5431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1649 moved from start: 0.6548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 30792 Z= 0.303 Angle : 1.058 23.645 42114 Z= 0.551 Chirality : 0.055 0.298 4931 Planarity : 0.009 0.116 5260 Dihedral : 17.062 170.169 5271 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.27 % Favored : 89.63 % Rotamer: Outliers : 4.78 % Allowed : 11.80 % Favored : 83.42 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.08 % Twisted Proline : 3.90 % Twisted General : 0.49 % 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 aren not related in a simple way. whole: -3.04 (0.12), residues: 3846 helix: -0.97 (0.13), residues: 1366 sheet: -1.98 (0.21), residues: 501 loop : -2.87 (0.12), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 150 TYR 0.040 0.004 TYR C 26 PHE 0.043 0.004 PHE B 8 TRP 0.027 0.003 TRP D1193 HIS 0.021 0.003 HIS D 907 Details of bonding type rmsd covalent geometry : bond 0.00666 (30786) covalent geometry : angle 1.05829 (42114) hydrogen bonds : bond 0.06814 ( 1208) hydrogen bonds : angle 6.44024 ( 3363) metal coordination : bond 0.01712 ( 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 356 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 226 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.1947 (OUTLIER) cc_final: 0.1525 (pt) REVERT: A 143 ARG cc_start: 0.4542 (mtm-85) cc_final: 0.3360 (mtm180) REVERT: A 152 TYR cc_start: 0.2518 (p90) cc_final: 0.0682 (m-80) REVERT: B 177 TYR cc_start: -0.1264 (OUTLIER) cc_final: -0.2162 (p90) REVERT: B 203 ILE cc_start: -0.0910 (OUTLIER) cc_final: -0.1327 (tt) REVERT: C 26 TYR cc_start: 0.3076 (t80) cc_final: 0.2144 (m-80) REVERT: C 27 LEU cc_start: -0.0462 (OUTLIER) cc_final: -0.1212 (mt) REVERT: C 447 HIS cc_start: 0.1049 (OUTLIER) cc_final: -0.1830 (t-90) REVERT: C 653 MET cc_start: 0.2156 (ttp) cc_final: 0.1037 (mmp) REVERT: C 667 LEU cc_start: 0.2150 (OUTLIER) cc_final: 0.1729 (mp) REVERT: C 790 ASP cc_start: 0.1329 (t0) cc_final: 0.1087 (t0) REVERT: C 1064 ASP cc_start: 0.1828 (OUTLIER) cc_final: 0.0910 (t0) REVERT: C 1170 MET cc_start: -0.0282 (mmm) cc_final: -0.0896 (mmm) REVERT: C 1251 TYR cc_start: 0.6175 (m-80) cc_final: 0.5842 (m-80) REVERT: C 1270 PHE cc_start: 0.3365 (t80) cc_final: 0.3102 (t80) REVERT: D 29 MET cc_start: 0.2179 (tpt) cc_final: 0.1186 (tmm) REVERT: D 582 ILE cc_start: 0.2472 (OUTLIER) cc_final: 0.2017 (pt) REVERT: D 644 MET cc_start: 0.4181 (mpp) cc_final: 0.3671 (mmm) REVERT: D 789 LYS cc_start: 0.2397 (ttpt) cc_final: 0.0948 (mmpt) REVERT: D 1282 TYR cc_start: 0.3949 (m-80) cc_final: 0.3366 (m-80) REVERT: D 1349 GLU cc_start: 0.0749 (OUTLIER) cc_final: -0.0072 (tm-30) REVERT: D 1370 MET cc_start: 0.0350 (tpt) cc_final: -0.0981 (ptt) outliers start: 130 outliers final: 68 residues processed: 338 average time/residue: 0.1637 time to fit residues: 87.6451 Evaluate side-chains 279 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 202 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 116 THR 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 177 TYR Chi-restraints excluded: chain B residue 201 LEU 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 146 VAL Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 285 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 558 VAL Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 586 PHE 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 802 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 892 GLU Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1064 ASP Chi-restraints excluded: chain C residue 1117 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1246 ARG Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1287 LEU Chi-restraints excluded: chain C residue 1292 THR 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 62 PHE 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 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 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 582 ILE Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 708 ASN 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 892 PHE Chi-restraints excluded: chain D residue 898 CYS Chi-restraints excluded: chain D residue 950 ILE Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 1260 MET Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1349 GLU Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain E residue 21 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 78 optimal weight: 0.9980 chunk 119 optimal weight: 30.0000 chunk 177 optimal weight: 6.9990 chunk 331 optimal weight: 0.9990 chunk 250 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 275 optimal weight: 3.9990 chunk 118 optimal weight: 0.0000 chunk 182 optimal weight: 4.9990 chunk 298 optimal weight: 30.0000 chunk 100 optimal weight: 20.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 HIS ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 HIS C 450 ASN ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 HIS C1256 GLN D 206 ASN D 365 GLN D 897 HIS ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5624 r_free = 0.5624 target = 0.354747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.5629 r_free = 0.5629 target = 0.345410 restraints weight = 84600.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.5632 r_free = 0.5632 target = 0.346389 restraints weight = 63851.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.5636 r_free = 0.5636 target = 0.346916 restraints weight = 40940.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.5635 r_free = 0.5635 target = 0.346820 restraints weight = 32186.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.5636 r_free = 0.5636 target = 0.346964 restraints weight = 32592.124| |-----------------------------------------------------------------------------| r_work (final): 0.5447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1515 moved from start: 0.6881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30792 Z= 0.156 Angle : 0.704 13.516 42114 Z= 0.366 Chirality : 0.045 0.237 4931 Planarity : 0.006 0.090 5260 Dihedral : 16.409 159.766 5270 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.44 % Favored : 92.51 % Rotamer: Outliers : 3.31 % Allowed : 14.78 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.08 % Twisted Proline : 3.25 % 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 aren not related in a simple way. whole: -2.45 (0.13), residues: 3846 helix: -0.32 (0.14), residues: 1383 sheet: -1.62 (0.21), residues: 518 loop : -2.68 (0.12), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 801 TYR 0.023 0.002 TYR C 26 PHE 0.023 0.002 PHE B 8 TRP 0.022 0.001 TRP D1193 HIS 0.009 0.001 HIS D 907 Details of bonding type rmsd covalent geometry : bond 0.00336 (30786) covalent geometry : angle 0.70378 (42114) hydrogen bonds : bond 0.04534 ( 1208) hydrogen bonds : angle 5.31286 ( 3363) metal coordination : bond 0.00835 ( 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 298 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 208 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.3874 (tpt-90) cc_final: 0.3453 (mtt90) REVERT: A 162 GLU cc_start: 0.0421 (OUTLIER) cc_final: -0.3513 (mt-10) REVERT: B 203 ILE cc_start: -0.1154 (OUTLIER) cc_final: -0.1552 (tt) REVERT: C 26 TYR cc_start: 0.2433 (t80) cc_final: 0.1806 (m-80) REVERT: C 27 LEU cc_start: -0.1013 (OUTLIER) cc_final: -0.2324 (mt) REVERT: C 90 VAL cc_start: -0.2966 (OUTLIER) cc_final: -0.3403 (p) REVERT: C 429 MET cc_start: -0.2760 (mtp) cc_final: -0.4574 (ptp) REVERT: C 653 MET cc_start: 0.1909 (ttp) cc_final: 0.1086 (mmp) REVERT: C 667 LEU cc_start: 0.0729 (OUTLIER) cc_final: -0.0297 (mt) REVERT: C 741 MET cc_start: 0.0314 (mmm) cc_final: -0.1071 (mmm) REVERT: C 867 GLU cc_start: 0.0669 (OUTLIER) cc_final: -0.0415 (tt0) REVERT: C 1170 MET cc_start: -0.0169 (mmm) cc_final: -0.0872 (mmm) REVERT: D 20 ILE cc_start: 0.0739 (OUTLIER) cc_final: 0.0339 (tt) REVERT: D 644 MET cc_start: 0.4454 (mpp) cc_final: 0.4237 (mmt) REVERT: D 654 ILE cc_start: -0.0285 (OUTLIER) cc_final: -0.0588 (mm) REVERT: D 789 LYS cc_start: 0.2349 (ttpt) cc_final: 0.1149 (mmpt) REVERT: D 905 ARG cc_start: 0.0740 (OUTLIER) cc_final: -0.4183 (ptm160) REVERT: D 1349 GLU cc_start: 0.0395 (OUTLIER) cc_final: -0.0087 (tp30) REVERT: D 1370 MET cc_start: -0.0397 (tpt) cc_final: -0.0681 (ppp) REVERT: E 16 ARG cc_start: 0.1025 (OUTLIER) cc_final: 0.0255 (ptt-90) outliers start: 90 outliers final: 55 residues processed: 283 average time/residue: 0.1708 time to fit residues: 76.2545 Evaluate side-chains 258 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 192 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 214 ASN 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 377 THR Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 574 SER 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 748 ILE Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 820 GLU Chi-restraints excluded: chain C residue 867 GLU Chi-restraints excluded: chain C residue 908 GLU Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1116 HIS Chi-restraints excluded: chain C residue 1229 TYR Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1240 ASP Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain C residue 1287 LEU Chi-restraints excluded: chain C residue 1305 TYR Chi-restraints excluded: chain D residue 20 ILE 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 165 TYR Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 882 VAL 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 1273 ASP Chi-restraints excluded: chain D residue 1279 GLN Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain D residue 1349 GLU Chi-restraints excluded: chain E residue 16 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 81 optimal weight: 8.9990 chunk 231 optimal weight: 0.6980 chunk 59 optimal weight: 50.0000 chunk 152 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 29 optimal weight: 50.0000 chunk 136 optimal weight: 0.9980 chunk 349 optimal weight: 7.9990 chunk 377 optimal weight: 50.0000 chunk 25 optimal weight: 40.0000 overall best weight: 4.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 ASN ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1136 GLN C1288 GLN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 594 GLN ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 921 GLN ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5590 r_free = 0.5590 target = 0.349150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.5582 r_free = 0.5582 target = 0.339001 restraints weight = 84160.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.5587 r_free = 0.5587 target = 0.339859 restraints weight = 68214.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.5591 r_free = 0.5591 target = 0.340387 restraints weight = 44602.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.5591 r_free = 0.5591 target = 0.340360 restraints weight = 36433.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.5593 r_free = 0.5593 target = 0.340485 restraints weight = 33688.467| |-----------------------------------------------------------------------------| r_work (final): 0.5395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1988 moved from start: 0.8765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 30792 Z= 0.264 Angle : 0.945 20.083 42114 Z= 0.494 Chirality : 0.052 0.256 4931 Planarity : 0.007 0.117 5260 Dihedral : 16.838 175.326 5263 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.10 % Favored : 88.85 % Rotamer: Outliers : 5.15 % Allowed : 16.14 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.08 % Twisted Proline : 1.95 % Twisted General : 0.38 % 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 aren not related in a simple way. whole: -2.64 (0.13), residues: 3846 helix: -0.44 (0.14), residues: 1332 sheet: -1.39 (0.22), residues: 480 loop : -2.87 (0.12), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 801 TYR 0.028 0.003 TYR C 26 PHE 0.054 0.003 PHE B 8 TRP 0.018 0.002 TRP D 409 HIS 0.015 0.002 HIS C 447 Details of bonding type rmsd covalent geometry : bond 0.00582 (30786) covalent geometry : angle 0.94476 (42114) hydrogen bonds : bond 0.06435 ( 1208) hydrogen bonds : angle 6.29136 ( 3363) metal coordination : bond 0.01598 ( 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 348 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 208 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 12 ARG cc_start: 0.3987 (tpt-90) cc_final: 0.3356 (mtm180) REVERT: A 162 GLU cc_start: 0.0254 (OUTLIER) cc_final: -0.4421 (tt0) REVERT: B 203 ILE cc_start: -0.0801 (OUTLIER) cc_final: -0.1249 (tt) REVERT: C 27 LEU cc_start: -0.1076 (OUTLIER) cc_final: -0.1416 (mt) REVERT: C 384 LEU cc_start: 0.2283 (OUTLIER) cc_final: 0.1315 (tp) REVERT: C 429 MET cc_start: -0.1776 (mtp) cc_final: -0.4566 (ptp) REVERT: C 447 HIS cc_start: 0.1699 (OUTLIER) cc_final: -0.0966 (t70) REVERT: C 572 ILE cc_start: 0.0707 (OUTLIER) cc_final: 0.0490 (mm) REVERT: C 653 MET cc_start: 0.1639 (ttp) cc_final: 0.0771 (mmp) REVERT: C 667 LEU cc_start: 0.1341 (OUTLIER) cc_final: 0.0910 (mp) REVERT: C 681 MET cc_start: 0.1042 (tpp) cc_final: 0.0786 (mmm) REVERT: C 685 MET cc_start: 0.4223 (mtm) cc_final: 0.3961 (mtm) REVERT: C 741 MET cc_start: 0.0543 (mmm) cc_final: -0.0392 (mmm) REVERT: C 867 GLU cc_start: 0.0986 (OUTLIER) cc_final: -0.1037 (pt0) REVERT: C 943 LYS cc_start: 0.1343 (OUTLIER) cc_final: 0.1049 (tppt) REVERT: C 1170 MET cc_start: 0.0438 (mmm) cc_final: -0.0243 (mmm) REVERT: C 1195 ILE cc_start: 0.6011 (mt) cc_final: 0.5666 (tp) REVERT: C 1293 VAL cc_start: 0.0238 (OUTLIER) cc_final: -0.0189 (p) REVERT: C 1321 GLU cc_start: 0.0765 (OUTLIER) cc_final: -0.0614 (tp30) REVERT: D 29 MET cc_start: 0.2225 (tpt) cc_final: 0.0996 (tmm) REVERT: D 102 MET cc_start: 0.3684 (tpt) cc_final: 0.2676 (tpt) REVERT: D 219 LYS cc_start: 0.1198 (mtpt) cc_final: 0.0347 (mmtt) REVERT: D 400 MET cc_start: -0.0271 (ttp) cc_final: -0.2054 (mpp) REVERT: D 644 MET cc_start: 0.4366 (mpp) cc_final: 0.3459 (mmt) REVERT: D 654 ILE cc_start: 0.0663 (OUTLIER) cc_final: 0.0279 (mm) REVERT: D 789 LYS cc_start: 0.2554 (ttpt) cc_final: 0.1480 (mmmt) REVERT: D 1193 TRP cc_start: 0.2778 (OUTLIER) cc_final: -0.2421 (m100) REVERT: D 1349 GLU cc_start: 0.1050 (OUTLIER) cc_final: -0.1176 (tp30) REVERT: D 1370 MET cc_start: 0.0509 (tpt) cc_final: -0.1352 (ptm) REVERT: E 30 MET cc_start: -0.1075 (tpt) cc_final: -0.1439 (tpt) outliers start: 140 outliers final: 83 residues processed: 326 average time/residue: 0.1607 time to fit residues: 83.8435 Evaluate side-chains 291 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 194 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 162 GLU 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 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 57 PHE Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 165 HIS 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 377 THR Chi-restraints excluded: chain C residue 384 LEU 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 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 609 ILE Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 728 ASP Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 820 GLU Chi-restraints excluded: chain C residue 840 SER Chi-restraints excluded: chain C residue 867 GLU Chi-restraints excluded: chain C residue 908 GLU Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 943 LYS Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1229 TYR 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 1246 ARG Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain C residue 1287 LEU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1305 TYR Chi-restraints excluded: chain C residue 1321 GLU Chi-restraints excluded: chain D residue 62 PHE 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 97 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 165 TYR Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 371 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 491 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 889 ASP Chi-restraints excluded: chain D residue 892 PHE Chi-restraints excluded: chain D residue 898 CYS Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 1193 TRP Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1273 ASP Chi-restraints excluded: chain D residue 1279 GLN Chi-restraints excluded: chain D residue 1287 ILE Chi-restraints excluded: chain D residue 1302 TYR Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1337 VAL Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain D residue 1349 GLU Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1357 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 181 optimal weight: 6.9990 chunk 120 optimal weight: 40.0000 chunk 35 optimal weight: 30.0000 chunk 352 optimal weight: 0.5980 chunk 388 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 320 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 277 optimal weight: 5.9990 chunk 293 optimal weight: 6.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 GLN ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 ASN ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 HIS C 658 GLN ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 688 GLN C1157 GLN C1256 GLN ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 665 GLN ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5585 r_free = 0.5585 target = 0.347869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5573 r_free = 0.5573 target = 0.337845 restraints weight = 83855.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5581 r_free = 0.5581 target = 0.338905 restraints weight = 68436.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.5585 r_free = 0.5585 target = 0.339200 restraints weight = 44263.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.5585 r_free = 0.5585 target = 0.339195 restraints weight = 35232.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5585 r_free = 0.5585 target = 0.339195 restraints weight = 33731.468| |-----------------------------------------------------------------------------| r_work (final): 0.5384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2045 moved from start: 0.9694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 30792 Z= 0.236 Angle : 0.860 18.428 42114 Z= 0.450 Chirality : 0.049 0.249 4931 Planarity : 0.007 0.098 5260 Dihedral : 16.761 165.141 5262 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.88 % Favored : 90.07 % Rotamer: Outliers : 4.96 % Allowed : 17.65 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.08 % Twisted Proline : 1.95 % Twisted General : 0.22 % 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 aren not related in a simple way. whole: -2.50 (0.13), residues: 3846 helix: -0.30 (0.14), residues: 1339 sheet: -1.27 (0.23), residues: 456 loop : -2.81 (0.12), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 540 TYR 0.035 0.003 TYR C1281 PHE 0.047 0.003 PHE B 8 TRP 0.020 0.002 TRP D1193 HIS 0.011 0.002 HIS D1366 Details of bonding type rmsd covalent geometry : bond 0.00523 (30786) covalent geometry : angle 0.86011 (42114) hydrogen bonds : bond 0.05880 ( 1208) hydrogen bonds : angle 6.04034 ( 3363) metal coordination : bond 0.01819 ( 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 349 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 214 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.3524 (tpt-90) cc_final: 0.2867 (mtm180) REVERT: A 39 LEU cc_start: 0.1016 (OUTLIER) cc_final: 0.0471 (mp) REVERT: A 162 GLU cc_start: 0.0690 (OUTLIER) cc_final: -0.0303 (mm-30) REVERT: B 203 ILE cc_start: -0.0546 (OUTLIER) cc_final: -0.1014 (tt) REVERT: C 258 ASN cc_start: 0.0399 (OUTLIER) cc_final: 0.0111 (m110) REVERT: C 384 LEU cc_start: 0.2740 (OUTLIER) cc_final: 0.2024 (tt) REVERT: C 447 HIS cc_start: 0.1472 (OUTLIER) cc_final: -0.0637 (t70) REVERT: C 488 MET cc_start: 0.0797 (ttt) cc_final: 0.0378 (ptt) REVERT: C 653 MET cc_start: 0.1818 (ttp) cc_final: 0.1152 (mmp) REVERT: C 681 MET cc_start: 0.1424 (OUTLIER) cc_final: 0.0814 (mmt) REVERT: C 867 GLU cc_start: 0.1346 (OUTLIER) cc_final: -0.0369 (tt0) REVERT: C 943 LYS cc_start: 0.0531 (OUTLIER) cc_final: 0.0187 (tppt) REVERT: C 1170 MET cc_start: 0.0577 (mmm) cc_final: -0.0206 (mmm) REVERT: C 1182 ILE cc_start: 0.2980 (mt) cc_final: 0.2062 (mt) REVERT: C 1312 ASN cc_start: 0.7068 (t0) cc_final: 0.6842 (t0) REVERT: C 1321 GLU cc_start: 0.0930 (OUTLIER) cc_final: -0.0148 (tp30) REVERT: D 322 ARG cc_start: 0.4487 (mtt-85) cc_final: 0.3425 (mtt-85) REVERT: D 400 MET cc_start: 0.0280 (ttp) cc_final: -0.1121 (mpp) REVERT: D 460 ASP cc_start: 0.0244 (OUTLIER) cc_final: 0.0023 (t0) REVERT: D 698 MET cc_start: -0.2861 (tpt) cc_final: -0.3619 (tmm) REVERT: D 789 LYS cc_start: 0.2694 (ttpt) cc_final: 0.1819 (mmmt) REVERT: D 892 PHE cc_start: 0.3424 (OUTLIER) cc_final: -0.0530 (p90) REVERT: D 905 ARG cc_start: 0.0983 (OUTLIER) cc_final: -0.4155 (ptm160) REVERT: D 1193 TRP cc_start: 0.2976 (OUTLIER) cc_final: -0.2601 (m100) REVERT: D 1284 ARG cc_start: 0.1467 (ttt90) cc_final: -0.0783 (ttt180) REVERT: D 1344 LEU cc_start: 0.3259 (OUTLIER) cc_final: 0.1538 (mm) REVERT: D 1349 GLU cc_start: 0.1294 (OUTLIER) cc_final: 0.0652 (pm20) outliers start: 135 outliers final: 82 residues processed: 330 average time/residue: 0.1593 time to fit residues: 84.7707 Evaluate side-chains 303 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 205 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 33 ARG 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 202 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 258 ASN 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 447 HIS Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 558 VAL 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 728 ASP Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 820 GLU Chi-restraints excluded: chain C residue 840 SER Chi-restraints excluded: chain C residue 867 GLU Chi-restraints excluded: chain C residue 908 GLU Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 943 LYS Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1116 HIS Chi-restraints excluded: chain C residue 1229 TYR 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 1246 ARG Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1321 GLU Chi-restraints excluded: chain D residue 62 PHE 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 188 LEU Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 460 ASP Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 889 ASP 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 909 ILE Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1193 TRP Chi-restraints excluded: chain D residue 1273 ASP Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1287 ILE Chi-restraints excluded: chain D residue 1302 TYR Chi-restraints excluded: chain D residue 1337 VAL Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain D residue 1349 GLU 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 E residue 16 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 371 optimal weight: 50.0000 chunk 271 optimal weight: 0.0050 chunk 137 optimal weight: 0.7980 chunk 377 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 285 optimal weight: 9.9990 chunk 365 optimal weight: 9.9990 chunk 376 optimal weight: 20.0000 chunk 272 optimal weight: 7.9990 chunk 198 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 ASN C 450 ASN C 518 ASN ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 GLN C1307 ASN D 430 HIS D 488 ASN ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5441 r_free = 0.5441 target = 0.327140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.5338 r_free = 0.5338 target = 0.314599 restraints weight = 82183.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.5344 r_free = 0.5344 target = 0.317103 restraints weight = 58534.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.5355 r_free = 0.5355 target = 0.318013 restraints weight = 41532.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.5356 r_free = 0.5356 target = 0.318228 restraints weight = 33591.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.5359 r_free = 0.5359 target = 0.318522 restraints weight = 33728.257| |-----------------------------------------------------------------------------| r_work (final): 0.5351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2143 moved from start: 0.9714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 30792 Z= 0.142 Angle : 0.694 11.647 42114 Z= 0.363 Chirality : 0.045 0.242 4931 Planarity : 0.005 0.090 5260 Dihedral : 16.298 157.107 5260 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.10 % Favored : 90.85 % Rotamer: Outliers : 3.71 % Allowed : 19.15 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.08 % Twisted Proline : 1.30 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -2.13 (0.13), residues: 3846 helix: 0.05 (0.14), residues: 1365 sheet: -1.22 (0.22), residues: 480 loop : -2.62 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 202 TYR 0.025 0.001 TYR C1231 PHE 0.048 0.002 PHE D 377 TRP 0.019 0.001 TRP D1193 HIS 0.007 0.001 HIS D1366 Details of bonding type rmsd covalent geometry : bond 0.00306 (30786) covalent geometry : angle 0.69449 (42114) hydrogen bonds : bond 0.04600 ( 1208) hydrogen bonds : angle 5.40843 ( 3363) metal coordination : bond 0.01697 ( 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 307 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 206 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 HIS cc_start: 0.3164 (OUTLIER) cc_final: -0.1746 (t70) REVERT: A 162 GLU cc_start: 0.1522 (OUTLIER) cc_final: 0.0608 (mm-30) REVERT: A 172 LEU cc_start: 0.5362 (OUTLIER) cc_final: 0.4712 (tp) REVERT: B 203 ILE cc_start: -0.0443 (OUTLIER) cc_final: -0.0902 (tt) REVERT: C 239 MET cc_start: -0.0680 (ptt) cc_final: -0.1150 (ptt) REVERT: C 265 LYS cc_start: 0.1039 (OUTLIER) cc_final: 0.0514 (ttmp) REVERT: C 429 MET cc_start: -0.2805 (mtp) cc_final: -0.5009 (ptp) REVERT: C 447 HIS cc_start: 0.0794 (OUTLIER) cc_final: -0.1670 (m170) REVERT: C 522 SER cc_start: 0.4690 (OUTLIER) cc_final: 0.3274 (p) REVERT: C 653 MET cc_start: 0.1373 (ttp) cc_final: 0.0879 (mmp) REVERT: C 667 LEU cc_start: 0.0758 (OUTLIER) cc_final: 0.0032 (mt) REVERT: C 681 MET cc_start: 0.1317 (tpp) cc_final: 0.1009 (mmm) REVERT: C 685 MET cc_start: 0.4472 (mtm) cc_final: 0.4222 (mtm) REVERT: C 867 GLU cc_start: 0.1897 (OUTLIER) cc_final: -0.0034 (pt0) REVERT: C 943 LYS cc_start: 0.0994 (OUTLIER) cc_final: 0.0537 (tppt) REVERT: C 1038 GLN cc_start: -0.0828 (OUTLIER) cc_final: -0.1054 (tt0) REVERT: C 1170 MET cc_start: -0.0128 (mmm) cc_final: -0.0739 (mmm) REVERT: C 1321 GLU cc_start: 0.0412 (OUTLIER) cc_final: -0.0799 (tm-30) REVERT: D 322 ARG cc_start: 0.3749 (mtt-85) cc_final: 0.2925 (mtt-85) REVERT: D 400 MET cc_start: 0.0130 (ttp) cc_final: -0.0960 (mpp) REVERT: D 475 GLU cc_start: 0.1364 (OUTLIER) cc_final: 0.0415 (mt-10) REVERT: D 484 MET cc_start: 0.6417 (ttt) cc_final: 0.5942 (ttp) REVERT: D 609 TYR cc_start: 0.1106 (t80) cc_final: -0.0574 (t80) REVERT: D 698 MET cc_start: -0.3750 (tpt) cc_final: -0.4134 (tmm) REVERT: D 892 PHE cc_start: 0.2869 (OUTLIER) cc_final: -0.0954 (p90) REVERT: D 905 ARG cc_start: 0.1010 (OUTLIER) cc_final: -0.4061 (ptm160) REVERT: D 1025 MET cc_start: -0.3351 (ptp) cc_final: -0.4684 (tpp) REVERT: D 1193 TRP cc_start: 0.2461 (OUTLIER) cc_final: -0.2371 (m100) REVERT: D 1370 MET cc_start: 0.0366 (tpt) cc_final: -0.1102 (ptm) outliers start: 101 outliers final: 59 residues processed: 289 average time/residue: 0.1767 time to fit residues: 82.7861 Evaluate side-chains 268 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 193 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 164 ASP 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 33 ARG Chi-restraints excluded: chain B residue 35 PHE 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 202 VAL Chi-restraints excluded: chain B residue 203 ILE 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 156 PHE 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 377 THR Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 518 ASN Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 728 ASP Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 820 GLU Chi-restraints excluded: chain C residue 867 GLU Chi-restraints excluded: chain C residue 908 GLU Chi-restraints excluded: chain C residue 943 LYS Chi-restraints excluded: chain C residue 1038 GLN 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 1243 MET Chi-restraints excluded: chain C residue 1274 GLU 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 1321 GLU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 165 TYR Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 474 LEU 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 545 HIS Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 892 PHE 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 1196 LEU Chi-restraints excluded: chain D residue 1273 ASP Chi-restraints excluded: chain D residue 1279 GLN Chi-restraints excluded: chain D residue 1302 TYR Chi-restraints excluded: chain D residue 1351 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 98 optimal weight: 7.9990 chunk 375 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 372 optimal weight: 40.0000 chunk 34 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 182 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 229 optimal weight: 0.3980 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 GLN ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 ASN ** 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 = 0.5593 r_free = 0.5593 target = 0.348928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5580 r_free = 0.5580 target = 0.338399 restraints weight = 83528.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5590 r_free = 0.5590 target = 0.339671 restraints weight = 64554.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.5593 r_free = 0.5593 target = 0.339715 restraints weight = 40786.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.5595 r_free = 0.5595 target = 0.339878 restraints weight = 35349.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.5597 r_free = 0.5597 target = 0.340037 restraints weight = 30953.450| |-----------------------------------------------------------------------------| r_work (final): 0.5413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2037 moved from start: 1.0268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 30792 Z= 0.186 Angle : 0.783 17.714 42114 Z= 0.407 Chirality : 0.047 0.279 4931 Planarity : 0.006 0.088 5260 Dihedral : 16.414 163.702 5260 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.35 % Favored : 89.60 % Rotamer: Outliers : 4.12 % Allowed : 19.26 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.08 % Twisted Proline : 1.30 % Twisted General : 0.11 % 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 aren not related in a simple way. whole: -2.12 (0.13), residues: 3846 helix: 0.04 (0.14), residues: 1357 sheet: -1.04 (0.24), residues: 438 loop : -2.62 (0.12), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 33 TYR 0.025 0.002 TYR C1281 PHE 0.050 0.002 PHE D 377 TRP 0.015 0.002 TRP D1193 HIS 0.012 0.002 HIS C 447 Details of bonding type rmsd covalent geometry : bond 0.00411 (30786) covalent geometry : angle 0.78291 (42114) hydrogen bonds : bond 0.05258 ( 1208) hydrogen bonds : angle 5.66005 ( 3363) metal coordination : bond 0.01745 ( 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 306 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 194 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.3237 (tpt-90) cc_final: 0.2686 (mtm180) REVERT: A 160 HIS cc_start: 0.2954 (OUTLIER) cc_final: -0.1908 (t-90) REVERT: A 162 GLU cc_start: 0.0566 (OUTLIER) cc_final: -0.0276 (mm-30) REVERT: A 188 GLU cc_start: 0.0667 (OUTLIER) cc_final: -0.0096 (tm-30) REVERT: B 203 ILE cc_start: -0.0745 (OUTLIER) cc_final: -0.1243 (tt) REVERT: C 239 MET cc_start: 0.0077 (ptt) cc_final: -0.0386 (ptt) REVERT: C 265 LYS cc_start: 0.1731 (OUTLIER) cc_final: 0.1090 (ttmp) REVERT: C 429 MET cc_start: -0.1904 (mtp) cc_final: -0.4800 (ptp) REVERT: C 447 HIS cc_start: 0.1364 (OUTLIER) cc_final: -0.1141 (t70) REVERT: C 522 SER cc_start: 0.5279 (OUTLIER) cc_final: 0.3634 (m) REVERT: C 653 MET cc_start: 0.1810 (ttp) cc_final: 0.1378 (mmp) REVERT: C 667 LEU cc_start: 0.0881 (OUTLIER) cc_final: 0.0643 (mt) REVERT: C 681 MET cc_start: 0.1114 (OUTLIER) cc_final: 0.0472 (mmm) REVERT: C 685 MET cc_start: 0.4320 (mtm) cc_final: 0.3217 (mtt) REVERT: C 867 GLU cc_start: 0.1747 (OUTLIER) cc_final: 0.0171 (tt0) REVERT: C 893 THR cc_start: 0.2649 (OUTLIER) cc_final: 0.2244 (p) REVERT: C 943 LYS cc_start: 0.0655 (OUTLIER) cc_final: 0.0289 (mmmt) REVERT: C 1038 GLN cc_start: -0.0089 (OUTLIER) cc_final: -0.0568 (tt0) REVERT: C 1170 MET cc_start: 0.0689 (mmm) cc_final: -0.0151 (mmm) REVERT: C 1304 MET cc_start: 0.2694 (tpt) cc_final: 0.2286 (tpt) REVERT: C 1321 GLU cc_start: 0.1061 (OUTLIER) cc_final: 0.0086 (tp30) REVERT: D 29 MET cc_start: 0.2300 (tpt) cc_final: 0.1432 (tmm) REVERT: D 400 MET cc_start: -0.0028 (ttp) cc_final: -0.0384 (mpp) REVERT: D 475 GLU cc_start: 0.1301 (OUTLIER) cc_final: 0.0390 (mt-10) REVERT: D 484 MET cc_start: 0.6450 (ttt) cc_final: 0.5938 (ttp) REVERT: D 581 MET cc_start: 0.3811 (tmm) cc_final: 0.2833 (ttp) REVERT: D 609 TYR cc_start: 0.1245 (t80) cc_final: -0.0121 (t80) REVERT: D 698 MET cc_start: -0.3191 (tpt) cc_final: -0.3923 (tmm) REVERT: D 892 PHE cc_start: 0.3062 (OUTLIER) cc_final: -0.0824 (p90) REVERT: D 905 ARG cc_start: 0.1034 (OUTLIER) cc_final: -0.4204 (tpt90) REVERT: D 1284 ARG cc_start: 0.1501 (ttt90) cc_final: -0.0939 (ttt180) REVERT: D 1344 LEU cc_start: 0.3195 (OUTLIER) cc_final: 0.1448 (mm) outliers start: 112 outliers final: 75 residues processed: 285 average time/residue: 0.1713 time to fit residues: 78.9140 Evaluate side-chains 281 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 188 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 33 ARG 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 192 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 203 ILE 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 90 VAL Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 728 ASP Chi-restraints excluded: chain C residue 820 GLU Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 867 GLU Chi-restraints excluded: chain C residue 893 THR Chi-restraints excluded: chain C residue 908 GLU Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 943 LYS Chi-restraints excluded: chain C residue 955 GLN Chi-restraints excluded: chain C residue 1038 GLN 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 1229 TYR 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 1246 ARG Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain C residue 1287 LEU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1321 GLU Chi-restraints excluded: chain D residue 90 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 195 GLU Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 474 LEU 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 545 HIS Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 809 VAL Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 877 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 930 LEU Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1273 ASP Chi-restraints excluded: chain D residue 1279 GLN Chi-restraints excluded: chain D residue 1287 ILE Chi-restraints excluded: chain D residue 1302 TYR Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain E residue 16 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 237 optimal weight: 0.8980 chunk 143 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 238 optimal weight: 0.9990 chunk 290 optimal weight: 10.0000 chunk 139 optimal weight: 7.9990 chunk 387 optimal weight: 8.9990 chunk 314 optimal weight: 6.9990 chunk 271 optimal weight: 0.0970 chunk 164 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN C 518 ASN ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1288 GLN D 232 ASN ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5615 r_free = 0.5615 target = 0.351626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5610 r_free = 0.5610 target = 0.341743 restraints weight = 84478.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.5619 r_free = 0.5619 target = 0.343093 restraints weight = 62505.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.5623 r_free = 0.5623 target = 0.343468 restraints weight = 38183.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.5623 r_free = 0.5623 target = 0.343425 restraints weight = 29232.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.5624 r_free = 0.5624 target = 0.343532 restraints weight = 30566.534| |-----------------------------------------------------------------------------| r_work (final): 0.5441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1818 moved from start: 1.0192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 30792 Z= 0.125 Angle : 0.657 13.480 42114 Z= 0.342 Chirality : 0.044 0.285 4931 Planarity : 0.005 0.090 5260 Dihedral : 16.120 154.859 5260 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.54 % Favored : 92.41 % Rotamer: Outliers : 2.83 % Allowed : 20.40 % Favored : 76.76 % 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 aren not related in a simple way. whole: -1.79 (0.13), residues: 3846 helix: 0.33 (0.15), residues: 1367 sheet: -1.06 (0.23), residues: 459 loop : -2.40 (0.13), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1262 TYR 0.025 0.001 TYR C1231 PHE 0.027 0.001 PHE D 377 TRP 0.017 0.001 TRP D1193 HIS 0.006 0.001 HIS D 777 Details of bonding type rmsd covalent geometry : bond 0.00270 (30786) covalent geometry : angle 0.65651 (42114) hydrogen bonds : bond 0.04206 ( 1208) hydrogen bonds : angle 5.16309 ( 3363) metal coordination : bond 0.00987 ( 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 268 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 191 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.3380 (tpt-90) cc_final: 0.2829 (mtm180) REVERT: A 31 LEU cc_start: 0.2416 (pp) cc_final: 0.1602 (tp) REVERT: A 160 HIS cc_start: 0.2061 (OUTLIER) cc_final: -0.2999 (t70) REVERT: A 188 GLU cc_start: 0.0535 (OUTLIER) cc_final: -0.0275 (tm-30) REVERT: A 205 MET cc_start: 0.2015 (mmm) cc_final: 0.1745 (mmt) REVERT: C 239 MET cc_start: -0.0063 (ptt) cc_final: -0.0548 (ptt) REVERT: C 265 LYS cc_start: 0.1503 (OUTLIER) cc_final: 0.0782 (ttmp) REVERT: C 429 MET cc_start: -0.2088 (mtp) cc_final: -0.4572 (ptp) REVERT: C 447 HIS cc_start: 0.0416 (OUTLIER) cc_final: -0.1513 (m170) REVERT: C 522 SER cc_start: 0.4502 (OUTLIER) cc_final: 0.3038 (p) REVERT: C 667 LEU cc_start: 0.0161 (OUTLIER) cc_final: -0.0158 (mt) REVERT: C 685 MET cc_start: 0.3447 (mtm) cc_final: 0.3070 (mtt) REVERT: C 741 MET cc_start: 0.0124 (mmm) cc_final: -0.0736 (mmm) REVERT: C 867 GLU cc_start: 0.1424 (OUTLIER) cc_final: 0.0136 (tt0) REVERT: C 943 LYS cc_start: 0.0788 (OUTLIER) cc_final: 0.0171 (mmtt) REVERT: C 1107 MET cc_start: 0.3103 (tpp) cc_final: 0.1659 (mmp) REVERT: C 1170 MET cc_start: 0.0597 (mmm) cc_final: -0.0235 (mmm) REVERT: C 1304 MET cc_start: 0.2233 (tpt) cc_final: 0.1988 (tpt) REVERT: C 1321 GLU cc_start: 0.0117 (OUTLIER) cc_final: -0.1251 (tt0) REVERT: D 29 MET cc_start: 0.2184 (tpt) cc_final: 0.1358 (tmm) REVERT: D 400 MET cc_start: -0.0729 (ttp) cc_final: -0.1493 (tpp) REVERT: D 475 GLU cc_start: 0.0685 (OUTLIER) cc_final: -0.0048 (mt-10) REVERT: D 484 MET cc_start: 0.6166 (ttt) cc_final: 0.5839 (ttp) REVERT: D 581 MET cc_start: 0.3815 (tmm) cc_final: 0.2826 (ttp) REVERT: D 609 TYR cc_start: 0.1451 (t80) cc_final: 0.0425 (t80) REVERT: D 624 ILE cc_start: -0.2494 (OUTLIER) cc_final: -0.3145 (pt) REVERT: D 698 MET cc_start: -0.3373 (tpt) cc_final: -0.3982 (tmm) REVERT: D 725 MET cc_start: 0.3501 (mmt) cc_final: 0.2429 (tmm) REVERT: D 892 PHE cc_start: 0.2706 (OUTLIER) cc_final: -0.1232 (p90) REVERT: D 905 ARG cc_start: 0.0787 (OUTLIER) cc_final: -0.4164 (ptm160) REVERT: D 1025 MET cc_start: -0.2773 (ptp) cc_final: -0.4886 (mtt) REVERT: D 1370 MET cc_start: 0.0048 (tpt) cc_final: -0.1323 (tmm) outliers start: 77 outliers final: 55 residues processed: 255 average time/residue: 0.1722 time to fit residues: 70.4807 Evaluate side-chains 252 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 184 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 98 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 35 PHE 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 192 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 518 ASN Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 820 GLU Chi-restraints excluded: chain C residue 867 GLU Chi-restraints excluded: chain C residue 908 GLU Chi-restraints excluded: chain C residue 943 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 1229 TYR Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1246 ARG Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1321 GLU 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 195 GLU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 447 ILE 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 545 HIS Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 809 VAL Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 892 PHE 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 1279 GLN Chi-restraints excluded: chain D residue 1302 TYR Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain E residue 16 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 70 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 194 optimal weight: 0.9980 chunk 296 optimal weight: 20.0000 chunk 233 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 336 optimal weight: 0.0870 chunk 46 optimal weight: 7.9990 chunk 208 optimal weight: 3.9990 chunk 37 optimal weight: 0.0570 chunk 106 optimal weight: 0.8980 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 HIS ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 688 GLN ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5621 r_free = 0.5621 target = 0.352455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5620 r_free = 0.5620 target = 0.342677 restraints weight = 84436.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.5627 r_free = 0.5627 target = 0.343706 restraints weight = 61916.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.5627 r_free = 0.5627 target = 0.343737 restraints weight = 40055.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.5627 r_free = 0.5627 target = 0.343739 restraints weight = 38763.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5627 r_free = 0.5627 target = 0.343741 restraints weight = 38718.479| |-----------------------------------------------------------------------------| r_work (final): 0.5486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1770 moved from start: 1.0178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30792 Z= 0.117 Angle : 0.630 10.601 42114 Z= 0.327 Chirality : 0.043 0.236 4931 Planarity : 0.005 0.092 5260 Dihedral : 15.926 154.496 5260 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.67 % Favored : 92.28 % Rotamer: Outliers : 2.61 % Allowed : 20.77 % Favored : 76.62 % 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 aren not related in a simple way. whole: -1.56 (0.13), residues: 3846 helix: 0.55 (0.15), residues: 1380 sheet: -0.98 (0.23), residues: 476 loop : -2.30 (0.13), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 403 TYR 0.022 0.001 TYR C1231 PHE 0.019 0.001 PHE D 377 TRP 0.013 0.001 TRP D1193 HIS 0.005 0.001 HIS D 777 Details of bonding type rmsd covalent geometry : bond 0.00250 (30786) covalent geometry : angle 0.63020 (42114) hydrogen bonds : bond 0.03891 ( 1208) hydrogen bonds : angle 4.88978 ( 3363) metal coordination : bond 0.01292 ( 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 269 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 198 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.2792 (pp) cc_final: 0.2267 (tp) REVERT: A 160 HIS cc_start: 0.3047 (OUTLIER) cc_final: -0.1836 (t70) REVERT: A 188 GLU cc_start: 0.0724 (OUTLIER) cc_final: -0.0319 (tm-30) REVERT: A 205 MET cc_start: 0.1727 (mmm) cc_final: 0.1418 (mmm) REVERT: B 203 ILE cc_start: -0.0630 (OUTLIER) cc_final: -0.1159 (tt) REVERT: C 90 VAL cc_start: -0.3420 (OUTLIER) cc_final: -0.3856 (p) REVERT: C 161 LYS cc_start: 0.1685 (OUTLIER) cc_final: 0.1232 (mttm) REVERT: C 239 MET cc_start: 0.0578 (ptt) cc_final: 0.0129 (ptt) REVERT: C 447 HIS cc_start: 0.0412 (OUTLIER) cc_final: -0.1358 (m170) REVERT: C 522 SER cc_start: 0.4416 (OUTLIER) cc_final: 0.2740 (m) REVERT: C 667 LEU cc_start: 0.0297 (OUTLIER) cc_final: 0.0083 (mt) REVERT: C 741 MET cc_start: 0.0078 (mmm) cc_final: -0.0759 (mmm) REVERT: C 867 GLU cc_start: 0.1573 (OUTLIER) cc_final: -0.0023 (tt0) REVERT: C 943 LYS cc_start: 0.1185 (OUTLIER) cc_final: 0.0590 (mmtt) REVERT: C 1107 MET cc_start: 0.2813 (tpp) cc_final: 0.1562 (mmp) REVERT: C 1170 MET cc_start: 0.0766 (mmm) cc_final: -0.0062 (mmm) REVERT: C 1321 GLU cc_start: -0.0717 (OUTLIER) cc_final: -0.2054 (tt0) REVERT: D 29 MET cc_start: 0.2709 (tpt) cc_final: 0.1848 (tmm) REVERT: D 400 MET cc_start: -0.1271 (ttp) cc_final: -0.2175 (mmt) REVERT: D 475 GLU cc_start: 0.1116 (OUTLIER) cc_final: 0.0353 (mt-10) REVERT: D 484 MET cc_start: 0.5898 (ttt) cc_final: 0.5572 (ttp) REVERT: D 581 MET cc_start: 0.3616 (tmm) cc_final: 0.2587 (ttp) REVERT: D 609 TYR cc_start: 0.1584 (t80) cc_final: 0.0738 (t80) REVERT: D 698 MET cc_start: -0.3193 (tpt) cc_final: -0.3825 (tmm) REVERT: D 725 MET cc_start: 0.3292 (mmt) cc_final: 0.2467 (tmm) REVERT: D 892 PHE cc_start: 0.2288 (OUTLIER) cc_final: -0.1830 (p90) REVERT: D 905 ARG cc_start: 0.0747 (OUTLIER) cc_final: -0.4006 (ptm160) REVERT: D 1025 MET cc_start: -0.2186 (ptp) cc_final: -0.4281 (mtt) REVERT: D 1370 MET cc_start: 0.0243 (tpt) cc_final: -0.0902 (tmm) outliers start: 71 outliers final: 54 residues processed: 255 average time/residue: 0.1578 time to fit residues: 64.8515 Evaluate side-chains 262 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 194 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU 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 98 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 35 PHE 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 192 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 246 LEU 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 575 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 820 GLU Chi-restraints excluded: chain C residue 867 GLU Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 908 GLU Chi-restraints excluded: chain C residue 943 LYS Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1116 HIS Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1229 TYR Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1243 MET Chi-restraints excluded: chain C residue 1246 ARG Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain C residue 1321 GLU 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 317 THR Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 474 LEU 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 545 HIS Chi-restraints excluded: chain D residue 809 VAL Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 877 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 1279 GLN Chi-restraints excluded: chain E residue 16 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 367 optimal weight: 8.9990 chunk 246 optimal weight: 9.9990 chunk 331 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 192 optimal weight: 1.9990 chunk 370 optimal weight: 40.0000 chunk 352 optimal weight: 20.0000 chunk 272 optimal weight: 0.8980 chunk 100 optimal weight: 20.0000 chunk 125 optimal weight: 20.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 688 GLN ** 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 = 0.5594 r_free = 0.5594 target = 0.349007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5589 r_free = 0.5589 target = 0.338522 restraints weight = 84405.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5593 r_free = 0.5593 target = 0.339225 restraints weight = 67994.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.5598 r_free = 0.5598 target = 0.339983 restraints weight = 44942.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.5598 r_free = 0.5598 target = 0.340002 restraints weight = 34045.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.5599 r_free = 0.5599 target = 0.340142 restraints weight = 31799.538| |-----------------------------------------------------------------------------| r_work (final): 0.5400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1996 moved from start: 1.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 30792 Z= 0.174 Angle : 0.744 15.627 42114 Z= 0.385 Chirality : 0.046 0.269 4931 Planarity : 0.006 0.090 5260 Dihedral : 16.261 164.879 5260 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.72 % Favored : 90.22 % Rotamer: Outliers : 3.16 % Allowed : 20.04 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.08 % Twisted Proline : 1.30 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -1.75 (0.13), residues: 3846 helix: 0.38 (0.14), residues: 1376 sheet: -1.05 (0.23), residues: 467 loop : -2.39 (0.13), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 101 TYR 0.026 0.002 TYR C1281 PHE 0.036 0.002 PHE C 389 TRP 0.015 0.001 TRP D1193 HIS 0.009 0.001 HIS C 447 Details of bonding type rmsd covalent geometry : bond 0.00381 (30786) covalent geometry : angle 0.74432 (42114) hydrogen bonds : bond 0.04913 ( 1208) hydrogen bonds : angle 5.35239 ( 3363) metal coordination : bond 0.01573 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3714.94 seconds wall clock time: 65 minutes 11.65 seconds (3911.65 seconds total)