Starting phenix.real_space_refine on Thu Mar 21 13:46:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6flq_4275/03_2024/6flq_4275_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6flq_4275/03_2024/6flq_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6flq_4275/03_2024/6flq_4275.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6flq_4275/03_2024/6flq_4275.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6flq_4275/03_2024/6flq_4275_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6flq_4275/03_2024/6flq_4275_neut.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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 Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 156": "NH1" <-> "NH2" Residue "D ARG 860": "NH1" <-> "NH2" Residue "D ARG 905": "NH1" <-> "NH2" Residue "D ARG 1123": "NH1" <-> "NH2" Residue "D ARG 1194": "NH1" <-> "NH2" Residue "D ARG 1284": "NH1" <-> "NH2" Residue "D TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: {'GLN:plan1': 1, 'ASP:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} 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: {'GLN:plan1': 1, 'ASP:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} 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: {'GLN:plan1': 19, 'HIS:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 19, 'TRP:plan': 4, 'ASP:plan': 42, 'PHE:plan': 14, 'GLU:plan': 56, 'ARG:plan': 33} 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: 16.05, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 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: 12.48 Conformation dependent library (CDL) restraints added in 5.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7172 Finding SS restraints... Secondary structure from input PDB file: 134 helices and 52 sheets defined 38.7% alpha, 13.5% beta 37 base pairs and 68 stacking pairs defined. Time for finding SS restraints: 10.43 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: 14.42 Time building geometry restraints manager: 13.47 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: 93.94 - 103.50: 623 103.50 - 113.07: 17177 113.07 - 122.63: 20653 122.63 - 132.19: 3624 132.19 - 141.75: 37 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 2.520 nonbonded pdb=" OD2 ASP D 129 " pdb=" NH1 ARG D 220 " model vdw 1.976 2.520 nonbonded pdb=" NH1 ARG D1341 " pdb=" OE2 GLU D1343 " model vdw 1.980 2.520 nonbonded pdb=" NH1 ARG A 33 " pdb=" OD2 ASP A 199 " model vdw 2.024 2.520 nonbonded pdb=" OH TYR D 68 " pdb=" NH1 ARG D 81 " model vdw 2.046 2.520 ... (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 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 6.640 Check model and map are aligned: 0.520 Set scattering table: 0.320 Process input model: 93.220 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.120 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.020 ------------------------------------------------------------------------------- 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 30786 Z= 1.018 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 : 5.97 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.039 0.005 TRP C1276 HIS 0.019 0.005 HIS D 545 PHE 0.061 0.005 PHE D 620 TYR 0.055 0.005 TYR C1229 ARG 0.018 0.002 ARG D 352 *********************** 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 fitting. rotamer outliers: 38 poor density : 296 time to evaluate : 3.348 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: 0.4324 time to fit residues: 223.1619 Evaluate side-chains 213 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 200 time to evaluate : 2.805 ------------------------------------------------------------------------------- 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 331 optimal weight: 8.9990 chunk 297 optimal weight: 0.0570 chunk 165 optimal weight: 0.7980 chunk 101 optimal weight: 7.9990 chunk 200 optimal weight: 5.9990 chunk 159 optimal weight: 8.9990 chunk 308 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 chunk 356 optimal weight: 30.0000 overall best weight: 1.5704 ------------------------------------------------------------------------------- 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 273 HIS C 387 ASN C 513 GLN C 551 HIS C 628 HIS ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN C1038 GLN C1146 GLN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1299 ASN D 113 HIS D 232 ASN D 365 GLN D 424 ASN D 665 GLN ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN D1098 GLN ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0721 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 30786 Z= 0.206 Angle : 0.668 10.252 42114 Z= 0.353 Chirality : 0.045 0.180 4931 Planarity : 0.006 0.097 5260 Dihedral : 16.331 148.924 5279 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.55 % Favored : 93.40 % Rotamer: Outliers : 2.35 % Allowed : 9.15 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.08 % Twisted Proline : 3.90 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.12), residues: 3846 helix: -0.87 (0.13), residues: 1372 sheet: -2.00 (0.21), residues: 488 loop : -2.64 (0.12), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D1193 HIS 0.008 0.001 HIS D 419 PHE 0.019 0.002 PHE D 437 TYR 0.026 0.002 TYR D 589 ARG 0.008 0.001 ARG C 175 *********************** 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 294 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 230 time to evaluate : 3.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.2984 (pp) cc_final: 0.2645 (pt) REVERT: B 37 HIS cc_start: 0.0094 (m90) cc_final: -0.0476 (m-70) REVERT: C 429 MET cc_start: -0.3489 (mtp) cc_final: -0.4121 (ptp) REVERT: C 653 MET cc_start: 0.1883 (ttp) cc_final: 0.1462 (mtp) REVERT: C 667 LEU cc_start: -0.1056 (OUTLIER) cc_final: -0.1796 (tt) REVERT: C 711 ASP cc_start: 0.2529 (m-30) cc_final: 0.1990 (m-30) REVERT: C 741 MET cc_start: -0.0367 (mmm) cc_final: -0.0766 (mmm) REVERT: C 799 ASN cc_start: 0.0070 (OUTLIER) cc_final: -0.0392 (p0) REVERT: C 1066 MET cc_start: 0.2294 (mmm) cc_final: 0.1908 (mmt) REVERT: C 1170 MET cc_start: -0.1229 (mmm) cc_final: -0.1806 (mmm) REVERT: C 1253 LEU cc_start: 0.4808 (OUTLIER) cc_final: 0.4397 (mt) REVERT: D 372 MET cc_start: 0.1686 (mmp) cc_final: -0.0159 (mmm) REVERT: D 772 TYR cc_start: 0.0329 (t80) cc_final: -0.0807 (t80) REVERT: D 1370 MET cc_start: -0.0444 (tpt) cc_final: -0.0968 (ppp) REVERT: E 7 GLN cc_start: -0.0197 (tp40) cc_final: -0.2647 (pm20) outliers start: 64 outliers final: 30 residues processed: 287 average time/residue: 0.4284 time to fit residues: 199.6155 Evaluate side-chains 227 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 194 time to evaluate : 3.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1117 LEU Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain D residue 44 ILE 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 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 1272 SER Chi-restraints excluded: chain D residue 1310 THR 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 198 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 297 optimal weight: 3.9990 chunk 243 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 357 optimal weight: 1.9990 chunk 386 optimal weight: 8.9990 chunk 318 optimal weight: 3.9990 chunk 354 optimal weight: 4.9990 chunk 121 optimal weight: 30.0000 chunk 286 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 462 ASN C 513 GLN C 526 HIS ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 GLN C 688 GLN ** C 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1111 GLN C1116 HIS ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN D 206 ASN D 469 HIS D 594 GLN ** D 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 7 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1235 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 30786 Z= 0.259 Angle : 0.744 20.132 42114 Z= 0.388 Chirality : 0.046 0.203 4931 Planarity : 0.006 0.085 5260 Dihedral : 16.257 152.480 5271 Min Nonbonded Distance : 1.680 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.98 % Favored : 91.97 % Rotamer: Outliers : 2.94 % Allowed : 11.80 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.08 % Twisted Proline : 3.90 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.13), residues: 3846 helix: -0.22 (0.14), residues: 1395 sheet: -1.64 (0.22), residues: 490 loop : -2.59 (0.12), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D1193 HIS 0.009 0.002 HIS C 526 PHE 0.031 0.003 PHE D 141 TYR 0.026 0.002 TYR C1281 ARG 0.015 0.001 ARG C 801 *********************** 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 301 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 221 time to evaluate : 3.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 ARG cc_start: 0.4099 (mtm-85) cc_final: 0.2734 (mtm180) REVERT: A 152 TYR cc_start: 0.0513 (p90) cc_final: 0.0018 (p90) REVERT: A 173 VAL cc_start: 0.0481 (t) cc_final: -0.1400 (p) REVERT: B 177 TYR cc_start: -0.1468 (OUTLIER) cc_final: -0.2800 (p90) REVERT: B 203 ILE cc_start: -0.1298 (OUTLIER) cc_final: -0.1806 (tt) REVERT: C 27 LEU cc_start: -0.1345 (OUTLIER) cc_final: -0.3003 (mt) REVERT: C 156 PHE cc_start: -0.1431 (OUTLIER) cc_final: -0.1817 (m-10) REVERT: C 429 MET cc_start: -0.2737 (mtp) cc_final: -0.3399 (ttt) REVERT: C 488 MET cc_start: 0.1466 (ttp) cc_final: 0.1162 (ttt) REVERT: C 653 MET cc_start: 0.2152 (ttp) cc_final: 0.0852 (mmp) REVERT: C 667 LEU cc_start: 0.1277 (OUTLIER) cc_final: -0.0080 (tt) REVERT: C 680 LEU cc_start: -0.1536 (OUTLIER) cc_final: -0.1743 (mp) REVERT: C 711 ASP cc_start: 0.3967 (m-30) cc_final: 0.3681 (m-30) REVERT: C 741 MET cc_start: -0.0399 (mmm) cc_final: -0.1675 (mmm) REVERT: C 799 ASN cc_start: 0.0549 (OUTLIER) cc_final: -0.0723 (p0) REVERT: C 1066 MET cc_start: 0.2593 (mmm) cc_final: 0.1707 (mmt) REVERT: C 1170 MET cc_start: -0.1124 (mmm) cc_final: -0.1631 (mmm) REVERT: C 1253 LEU cc_start: 0.4475 (OUTLIER) cc_final: 0.4199 (mm) REVERT: C 1337 ILE cc_start: 0.1322 (OUTLIER) cc_final: 0.1103 (tt) REVERT: D 402 GLU cc_start: -0.0510 (tt0) cc_final: -0.1417 (mt-10) REVERT: D 485 MET cc_start: 0.3584 (ttm) cc_final: 0.2666 (ttm) REVERT: D 697 MET cc_start: -0.0876 (tmm) cc_final: -0.1512 (ttt) REVERT: D 698 MET cc_start: -0.2916 (tpt) cc_final: -0.3322 (ttp) REVERT: D 1326 GLN cc_start: 0.3311 (OUTLIER) cc_final: 0.3039 (mm-40) REVERT: E 30 MET cc_start: -0.2255 (tpt) cc_final: -0.2478 (tpt) outliers start: 80 outliers final: 37 residues processed: 288 average time/residue: 0.4024 time to fit residues: 188.1234 Evaluate side-chains 243 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 196 time to evaluate : 3.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 177 TYR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 688 GLN Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1287 LEU Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 809 VAL 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 1260 MET Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1326 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 353 optimal weight: 30.0000 chunk 268 optimal weight: 10.0000 chunk 185 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 170 optimal weight: 6.9990 chunk 240 optimal weight: 3.9990 chunk 358 optimal weight: 40.0000 chunk 379 optimal weight: 10.0000 chunk 187 optimal weight: 2.9990 chunk 340 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 HIS B 37 HIS C 86 GLN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 HIS ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 462 ASN ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1136 GLN ** C1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1220 GLN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 921 GLN D1279 GLN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 7 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1829 moved from start: 0.7157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 30786 Z= 0.385 Angle : 0.963 19.326 42114 Z= 0.501 Chirality : 0.052 0.284 4931 Planarity : 0.008 0.094 5260 Dihedral : 16.766 166.771 5268 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.65 % Favored : 90.28 % Rotamer: Outliers : 5.26 % Allowed : 13.35 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.08 % Twisted Proline : 3.25 % Twisted General : 0.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.12), residues: 3846 helix: -0.48 (0.14), residues: 1364 sheet: -1.53 (0.22), residues: 481 loop : -2.74 (0.12), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D1020 HIS 0.012 0.002 HIS C 165 PHE 0.050 0.003 PHE B 8 TYR 0.044 0.003 TYR D 349 ARG 0.016 0.001 ARG C 758 *********************** 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 358 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 215 time to evaluate : 3.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.3806 (tpt-90) cc_final: 0.2101 (tpm170) REVERT: A 143 ARG cc_start: 0.4892 (mtm-85) cc_final: 0.3558 (mtp180) REVERT: A 152 TYR cc_start: 0.3092 (p90) cc_final: 0.0684 (m-80) REVERT: A 205 MET cc_start: 0.1544 (mmm) cc_final: 0.0875 (ttm) REVERT: B 203 ILE cc_start: -0.1239 (OUTLIER) cc_final: -0.1710 (tt) REVERT: C 27 LEU cc_start: -0.0605 (OUTLIER) cc_final: -0.1634 (mt) REVERT: C 136 PHE cc_start: 0.3685 (m-10) cc_final: 0.3480 (m-10) REVERT: C 425 ILE cc_start: -0.2830 (OUTLIER) cc_final: -0.3265 (pt) REVERT: C 429 MET cc_start: -0.2329 (mtp) cc_final: -0.4660 (ptt) REVERT: C 447 HIS cc_start: 0.1413 (OUTLIER) cc_final: -0.1246 (t-90) REVERT: C 653 MET cc_start: 0.2042 (ttp) cc_final: 0.1124 (mmp) REVERT: C 667 LEU cc_start: 0.1912 (OUTLIER) cc_final: 0.0871 (mt) REVERT: C 681 MET cc_start: 0.1285 (tpp) cc_final: 0.1053 (mmt) REVERT: C 757 THR cc_start: 0.1652 (OUTLIER) cc_final: 0.0300 (p) REVERT: C 941 LYS cc_start: 0.3691 (mttp) cc_final: 0.2699 (mttp) REVERT: C 1038 GLN cc_start: -0.0900 (OUTLIER) cc_final: -0.1623 (tm-30) REVERT: C 1064 ASP cc_start: 0.1485 (OUTLIER) cc_final: 0.1002 (t0) REVERT: C 1170 MET cc_start: -0.0222 (mmm) cc_final: -0.0870 (mmm) REVERT: D 141 PHE cc_start: 0.7112 (OUTLIER) cc_final: 0.6578 (t80) REVERT: D 363 LEU cc_start: -0.0945 (OUTLIER) cc_final: -0.1395 (pp) REVERT: D 582 ILE cc_start: 0.2260 (OUTLIER) cc_final: 0.1729 (pt) REVERT: D 609 TYR cc_start: 0.0506 (t80) cc_final: -0.1171 (t80) REVERT: D 644 MET cc_start: 0.3754 (mmp) cc_final: 0.3482 (mmt) REVERT: D 789 LYS cc_start: 0.2882 (ttpt) cc_final: 0.1507 (mmpt) REVERT: D 905 ARG cc_start: 0.0724 (OUTLIER) cc_final: -0.4294 (ptm160) REVERT: D 1025 MET cc_start: -0.3799 (ptp) cc_final: -0.4876 (tpp) REVERT: D 1370 MET cc_start: 0.1866 (ppp) cc_final: 0.1461 (tmm) REVERT: E 30 MET cc_start: -0.1563 (tpt) cc_final: -0.1789 (tpt) outliers start: 143 outliers final: 76 residues processed: 333 average time/residue: 0.4189 time to fit residues: 222.6529 Evaluate side-chains 292 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 204 time to evaluate : 3.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 153 VAL 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 201 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 85 CYS Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 188 PHE 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 425 ILE Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 553 THR 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 748 ILE Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 820 GLU Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 1038 GLN 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 1160 ASP 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 1254 VAL Chi-restraints excluded: chain C residue 1287 LEU Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 141 PHE 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 338 PHE Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 474 LEU 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 582 ILE Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 806 ASP Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 892 PHE Chi-restraints excluded: chain D residue 897 HIS Chi-restraints excluded: chain D residue 898 CYS Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 950 ILE Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1279 GLN Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain E residue 21 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 316 optimal weight: 7.9990 chunk 215 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 282 optimal weight: 3.9990 chunk 156 optimal weight: 20.0000 chunk 324 optimal weight: 0.5980 chunk 262 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 193 optimal weight: 1.9990 chunk 340 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 447 HIS C 450 ASN ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 808 ASN C1146 GLN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 907 HIS ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1687 moved from start: 0.7323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 30786 Z= 0.197 Angle : 0.674 12.815 42114 Z= 0.351 Chirality : 0.044 0.211 4931 Planarity : 0.005 0.078 5260 Dihedral : 16.157 156.551 5264 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.51 % Favored : 92.43 % Rotamer: Outliers : 3.90 % Allowed : 15.66 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.08 % Twisted Proline : 1.95 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.13), residues: 3846 helix: 0.11 (0.14), residues: 1381 sheet: -1.31 (0.22), residues: 498 loop : -2.58 (0.13), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D1193 HIS 0.007 0.001 HIS D 817 PHE 0.025 0.002 PHE B 8 TYR 0.021 0.002 TYR C1281 ARG 0.010 0.001 ARG C 936 *********************** 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 309 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 203 time to evaluate : 2.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.3860 (tpt-90) cc_final: 0.2106 (tpm170) REVERT: A 143 ARG cc_start: 0.4281 (mtm-85) cc_final: 0.3359 (mtm180) REVERT: A 162 GLU cc_start: -0.2176 (OUTLIER) cc_final: -0.5260 (tt0) REVERT: B 203 ILE cc_start: -0.1252 (OUTLIER) cc_final: -0.1755 (tt) REVERT: C 429 MET cc_start: -0.2403 (mtp) cc_final: -0.4593 (ptp) REVERT: C 447 HIS cc_start: 0.0774 (OUTLIER) cc_final: -0.1491 (t-90) REVERT: C 653 MET cc_start: 0.1998 (ttp) cc_final: 0.1289 (mmp) REVERT: C 667 LEU cc_start: 0.1006 (OUTLIER) cc_final: 0.0088 (mt) REVERT: C 741 MET cc_start: 0.0018 (mmm) cc_final: -0.1043 (mmm) REVERT: C 757 THR cc_start: 0.1743 (OUTLIER) cc_final: 0.0248 (m) REVERT: C 867 GLU cc_start: 0.0177 (OUTLIER) cc_final: -0.0541 (tt0) REVERT: C 936 ARG cc_start: 0.5720 (tpm170) cc_final: 0.4777 (ttp-170) REVERT: C 941 LYS cc_start: 0.3416 (mttp) cc_final: 0.2675 (mttp) REVERT: C 1066 MET cc_start: 0.1640 (mmt) cc_final: 0.1293 (mmt) REVERT: C 1170 MET cc_start: -0.0202 (mmm) cc_final: -0.0795 (mmm) REVERT: D 20 ILE cc_start: 0.0710 (OUTLIER) cc_final: 0.0445 (tt) REVERT: D 200 GLN cc_start: 0.5833 (mm-40) cc_final: 0.5514 (mm-40) REVERT: D 644 MET cc_start: 0.3260 (mmp) cc_final: 0.2939 (mmt) REVERT: D 789 LYS cc_start: 0.2863 (ttpt) cc_final: 0.1429 (mmpt) REVERT: D 897 HIS cc_start: 0.5763 (OUTLIER) cc_final: 0.5557 (m170) REVERT: D 905 ARG cc_start: 0.0791 (OUTLIER) cc_final: -0.4051 (ptm160) REVERT: D 1025 MET cc_start: -0.3927 (ptp) cc_final: -0.5001 (tpp) REVERT: D 1193 TRP cc_start: 0.0829 (OUTLIER) cc_final: -0.3321 (m100) REVERT: D 1282 TYR cc_start: 0.4162 (m-80) cc_final: 0.2458 (m-80) outliers start: 106 outliers final: 67 residues processed: 289 average time/residue: 0.4182 time to fit residues: 192.3382 Evaluate side-chains 269 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 192 time to evaluate : 3.080 ------------------------------------------------------------------------------- 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 98 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 37 HIS 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 84 GLU Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 867 GLU Chi-restraints excluded: chain C residue 908 GLU 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 1117 LEU Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1226 THR Chi-restraints excluded: chain C residue 1239 VAL 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 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 154 LEU Chi-restraints excluded: chain D residue 165 TYR Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 366 CYS Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 457 TYR Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 809 VAL Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 882 VAL 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 1189 MET Chi-restraints excluded: chain D residue 1193 TRP Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain D residue 1361 THR Chi-restraints excluded: chain E residue 36 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 127 optimal weight: 7.9990 chunk 342 optimal weight: 30.0000 chunk 75 optimal weight: 8.9990 chunk 223 optimal weight: 8.9990 chunk 93 optimal weight: 9.9990 chunk 380 optimal weight: 50.0000 chunk 315 optimal weight: 6.9990 chunk 176 optimal weight: 20.0000 chunk 31 optimal weight: 0.3980 chunk 125 optimal weight: 9.9990 chunk 199 optimal weight: 6.9990 overall best weight: 6.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 HIS ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 ASN C 258 ASN ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 GLN ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 GLN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1288 GLN ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 594 GLN D 665 GLN D 792 ASN D1244 GLN D1279 GLN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2248 moved from start: 0.9594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.114 30786 Z= 0.493 Angle : 1.105 21.788 42114 Z= 0.575 Chirality : 0.057 0.327 4931 Planarity : 0.009 0.176 5260 Dihedral : 17.133 171.870 5263 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 26.08 Ramachandran Plot: Outliers : 0.26 % Allowed : 11.99 % Favored : 87.75 % Rotamer: Outliers : 5.70 % Allowed : 16.25 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.08 % Twisted Proline : 2.60 % Twisted General : 0.70 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.13), residues: 3846 helix: -0.50 (0.14), residues: 1311 sheet: -1.36 (0.23), residues: 463 loop : -2.86 (0.12), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP D1193 HIS 0.026 0.003 HIS C 447 PHE 0.072 0.004 PHE B 8 TYR 0.037 0.004 TYR C1305 ARG 0.021 0.002 ARG C1216 *********************** 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 372 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 217 time to evaluate : 3.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.2155 (tp) cc_final: 0.1935 (pp) REVERT: A 137 ASN cc_start: 0.1233 (OUTLIER) cc_final: 0.0314 (t0) REVERT: A 162 GLU cc_start: -0.2420 (OUTLIER) cc_final: -0.2864 (mm-30) REVERT: B 203 ILE cc_start: -0.0319 (OUTLIER) cc_final: -0.0777 (tt) REVERT: C 41 GLN cc_start: 0.2930 (OUTLIER) cc_final: 0.2249 (tm-30) REVERT: C 84 GLU cc_start: 0.5882 (OUTLIER) cc_final: 0.4781 (pm20) REVERT: C 384 LEU cc_start: 0.3423 (OUTLIER) cc_final: 0.2575 (tp) REVERT: C 429 MET cc_start: -0.1583 (mtp) cc_final: -0.4313 (ppp) REVERT: C 572 ILE cc_start: 0.0718 (OUTLIER) cc_final: 0.0231 (mm) REVERT: C 653 MET cc_start: 0.2387 (ttp) cc_final: 0.1383 (mmp) REVERT: C 757 THR cc_start: 0.2703 (OUTLIER) cc_final: 0.1630 (p) REVERT: C 867 GLU cc_start: 0.0384 (OUTLIER) cc_final: -0.0810 (tt0) REVERT: C 1170 MET cc_start: 0.0570 (mmm) cc_final: -0.0254 (mmm) REVERT: C 1195 ILE cc_start: 0.6211 (mt) cc_final: 0.5870 (tp) REVERT: C 1321 GLU cc_start: 0.1210 (OUTLIER) cc_final: 0.0337 (tp30) REVERT: D 20 ILE cc_start: 0.0684 (OUTLIER) cc_final: 0.0071 (tt) REVERT: D 29 MET cc_start: 0.2786 (tpt) cc_final: 0.1508 (tmm) REVERT: D 102 MET cc_start: 0.3570 (tpt) cc_final: 0.3236 (tpt) REVERT: D 363 LEU cc_start: 0.0501 (OUTLIER) cc_final: 0.0224 (pp) REVERT: D 400 MET cc_start: -0.0595 (ttt) cc_final: -0.2527 (mpp) REVERT: D 582 ILE cc_start: 0.2320 (OUTLIER) cc_final: 0.1920 (pt) REVERT: D 897 HIS cc_start: 0.6467 (OUTLIER) cc_final: 0.6033 (t70) REVERT: D 905 ARG cc_start: 0.1113 (OUTLIER) cc_final: -0.4306 (ptm160) REVERT: D 1193 TRP cc_start: 0.1190 (OUTLIER) cc_final: -0.2020 (m100) REVERT: D 1284 ARG cc_start: 0.1636 (ttt90) cc_final: -0.0257 (ttt90) REVERT: D 1370 MET cc_start: 0.0941 (tmm) cc_final: 0.0424 (ttp) outliers start: 155 outliers final: 98 residues processed: 351 average time/residue: 0.3999 time to fit residues: 227.0363 Evaluate side-chains 316 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 202 time to evaluate : 2.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 246 LEU 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 479 LEU Chi-restraints excluded: chain C residue 554 HIS Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 686 GLN Chi-restraints excluded: chain C residue 728 ASP Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 820 GLU Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 867 GLU Chi-restraints excluded: chain C residue 908 GLU Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1064 ASP Chi-restraints excluded: chain C residue 1116 HIS Chi-restraints excluded: chain C residue 1117 LEU Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1188 ASP Chi-restraints excluded: chain C residue 1226 THR 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 1287 LEU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1321 GLU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 62 PHE 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 338 PHE Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 365 GLN Chi-restraints excluded: chain D residue 366 CYS Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 506 VAL 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 746 LEU Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 806 ASP Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 892 PHE Chi-restraints excluded: chain D residue 897 HIS Chi-restraints excluded: chain D residue 898 CYS Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1193 TRP Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1272 SER 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 1344 LEU Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain E residue 36 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 366 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 216 optimal weight: 0.0070 chunk 277 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 320 optimal weight: 0.9980 chunk 212 optimal weight: 4.9990 chunk 378 optimal weight: 6.9990 chunk 237 optimal weight: 2.9990 chunk 230 optimal weight: 0.9990 chunk 174 optimal weight: 30.0000 overall best weight: 2.0004 ------------------------------------------------------------------------------- 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 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN C 659 GLN ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 GLN ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1991 moved from start: 0.9493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 30786 Z= 0.216 Angle : 0.729 12.544 42114 Z= 0.380 Chirality : 0.046 0.204 4931 Planarity : 0.005 0.077 5260 Dihedral : 16.484 164.017 5261 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.07 % Favored : 90.87 % Rotamer: Outliers : 4.49 % Allowed : 18.42 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.08 % Twisted Proline : 1.30 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.13), residues: 3846 helix: 0.06 (0.14), residues: 1339 sheet: -1.17 (0.22), residues: 478 loop : -2.69 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D1193 HIS 0.009 0.001 HIS D 907 PHE 0.036 0.002 PHE B 8 TYR 0.020 0.002 TYR C1281 ARG 0.010 0.001 ARG C 540 *********************** 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 326 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 204 time to evaluate : 3.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.3877 (tpt-90) cc_final: 0.3362 (mtt90) REVERT: A 162 GLU cc_start: -0.2507 (OUTLIER) cc_final: -0.2768 (mm-30) REVERT: A 205 MET cc_start: 0.1497 (mmm) cc_final: 0.1256 (mmm) REVERT: B 51 MET cc_start: 0.1441 (tpp) cc_final: 0.1170 (tpp) REVERT: B 203 ILE cc_start: -0.0471 (OUTLIER) cc_final: -0.0963 (tt) REVERT: C 27 LEU cc_start: -0.1216 (OUTLIER) cc_final: -0.2324 (mt) REVERT: C 84 GLU cc_start: 0.5001 (OUTLIER) cc_final: 0.4420 (pm20) REVERT: C 384 LEU cc_start: 0.3304 (OUTLIER) cc_final: 0.2699 (tt) REVERT: C 488 MET cc_start: 0.1364 (ttt) cc_final: 0.1083 (ptt) REVERT: C 653 MET cc_start: 0.2077 (ttp) cc_final: 0.1524 (mmp) REVERT: C 663 VAL cc_start: 0.5551 (m) cc_final: 0.4446 (p) REVERT: C 867 GLU cc_start: 0.1103 (OUTLIER) cc_final: -0.0151 (tt0) REVERT: C 941 LYS cc_start: 0.3398 (OUTLIER) cc_final: 0.3071 (tttp) REVERT: C 1170 MET cc_start: 0.0343 (mmm) cc_final: -0.0434 (mmm) REVERT: C 1195 ILE cc_start: 0.6126 (mt) cc_final: 0.5866 (tp) REVERT: D 363 LEU cc_start: -0.0548 (OUTLIER) cc_final: -0.0794 (pp) REVERT: D 400 MET cc_start: 0.0219 (ttt) cc_final: -0.2222 (mpp) REVERT: D 484 MET cc_start: 0.6419 (ttt) cc_final: 0.6027 (ttp) REVERT: D 725 MET cc_start: 0.3036 (mmt) cc_final: 0.2184 (ppp) REVERT: D 892 PHE cc_start: 0.2924 (OUTLIER) cc_final: -0.0755 (p90) REVERT: D 897 HIS cc_start: 0.6306 (OUTLIER) cc_final: 0.5799 (t70) REVERT: D 905 ARG cc_start: 0.0846 (OUTLIER) cc_final: -0.3966 (ptm160) REVERT: D 1025 MET cc_start: -0.4299 (ptp) cc_final: -0.5155 (tpp) REVERT: D 1193 TRP cc_start: 0.0987 (OUTLIER) cc_final: -0.2549 (m100) outliers start: 122 outliers final: 84 residues processed: 306 average time/residue: 0.4280 time to fit residues: 209.4615 Evaluate side-chains 293 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 197 time to evaluate : 3.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 8 PHE 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 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 27 LEU Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 188 PHE 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 479 LEU Chi-restraints excluded: chain C residue 554 HIS Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 686 GLN Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 820 GLU Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 867 GLU Chi-restraints excluded: chain C residue 893 THR Chi-restraints excluded: chain C residue 908 GLU Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 941 LYS Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1116 HIS Chi-restraints excluded: chain C residue 1117 LEU Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1188 ASP Chi-restraints excluded: chain C residue 1226 THR 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 1254 VAL Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain C residue 1292 THR 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 195 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 306 LEU 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 363 LEU Chi-restraints excluded: chain D residue 365 GLN Chi-restraints excluded: chain D residue 366 CYS Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 474 LEU 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 708 ASN Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 892 PHE Chi-restraints excluded: chain D residue 897 HIS Chi-restraints excluded: chain D residue 898 CYS Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1193 TRP Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1272 SER Chi-restraints excluded: chain D residue 1273 ASP Chi-restraints excluded: chain D residue 1287 ILE Chi-restraints excluded: chain D residue 1302 TYR Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 36 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 234 optimal weight: 4.9990 chunk 151 optimal weight: 0.7980 chunk 226 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 240 optimal weight: 2.9990 chunk 258 optimal weight: 8.9990 chunk 187 optimal weight: 6.9990 chunk 35 optimal weight: 30.0000 chunk 297 optimal weight: 30.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1256 GLN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1952 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 0.054 30786 Z= 0.197 Angle : 0.679 10.877 42114 Z= 0.352 Chirality : 0.044 0.209 4931 Planarity : 0.005 0.078 5260 Dihedral : 16.176 156.009 5261 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.91 % Favored : 90.04 % Rotamer: Outliers : 4.41 % Allowed : 18.60 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.08 % Twisted Proline : 1.30 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.13), residues: 3846 helix: 0.32 (0.14), residues: 1365 sheet: -1.18 (0.22), residues: 478 loop : -2.55 (0.13), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D1193 HIS 0.007 0.001 HIS D 907 PHE 0.028 0.002 PHE B 8 TYR 0.021 0.002 TYR C1231 ARG 0.009 0.001 ARG C 540 *********************** 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 325 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 205 time to evaluate : 2.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.4078 (tpt-90) cc_final: 0.3427 (mtt90) REVERT: A 137 ASN cc_start: -0.0429 (OUTLIER) cc_final: -0.0703 (t0) REVERT: A 172 LEU cc_start: 0.4988 (pt) cc_final: 0.4370 (tt) REVERT: A 188 GLU cc_start: 0.0643 (OUTLIER) cc_final: -0.0048 (tm-30) REVERT: A 205 MET cc_start: 0.1855 (mmm) cc_final: 0.1528 (mmm) REVERT: B 203 ILE cc_start: -0.0746 (OUTLIER) cc_final: -0.1328 (tt) REVERT: C 27 LEU cc_start: -0.1262 (OUTLIER) cc_final: -0.2397 (mt) REVERT: C 84 GLU cc_start: 0.4835 (OUTLIER) cc_final: 0.4109 (pm20) REVERT: C 239 MET cc_start: -0.0698 (ptt) cc_final: -0.1088 (ptt) REVERT: C 384 LEU cc_start: 0.3327 (OUTLIER) cc_final: 0.2791 (tt) REVERT: C 653 MET cc_start: 0.2036 (ttp) cc_final: 0.1380 (mmp) REVERT: C 867 GLU cc_start: 0.1046 (OUTLIER) cc_final: -0.0108 (tt0) REVERT: C 1066 MET cc_start: 0.1982 (mmt) cc_final: 0.1495 (mmt) REVERT: C 1170 MET cc_start: 0.0348 (mmm) cc_final: -0.0378 (mmm) REVERT: C 1195 ILE cc_start: 0.6104 (mt) cc_final: 0.5843 (tp) REVERT: C 1321 GLU cc_start: 0.0951 (OUTLIER) cc_final: -0.0110 (tp30) REVERT: D 400 MET cc_start: 0.0394 (ttt) cc_final: -0.1789 (mpp) REVERT: D 484 MET cc_start: 0.6375 (ttt) cc_final: 0.5931 (ttp) REVERT: D 582 ILE cc_start: 0.2192 (OUTLIER) cc_final: 0.1861 (pt) REVERT: D 609 TYR cc_start: 0.1424 (t80) cc_final: 0.0371 (t80) REVERT: D 698 MET cc_start: -0.2919 (tpt) cc_final: -0.3552 (tmm) REVERT: D 725 MET cc_start: 0.3484 (mmt) cc_final: 0.2652 (ppp) REVERT: D 892 PHE cc_start: 0.2928 (OUTLIER) cc_final: -0.1012 (p90) REVERT: D 897 HIS cc_start: 0.6343 (OUTLIER) cc_final: 0.5869 (t70) REVERT: D 905 ARG cc_start: 0.1012 (OUTLIER) cc_final: -0.3941 (ptm160) REVERT: D 911 LYS cc_start: 0.2286 (ttmt) cc_final: 0.1790 (pttt) REVERT: D 1025 MET cc_start: -0.4080 (ptp) cc_final: -0.4870 (tpp) REVERT: D 1193 TRP cc_start: 0.1032 (OUTLIER) cc_final: -0.3089 (m100) REVERT: D 1370 MET cc_start: 0.0986 (tmm) cc_final: 0.0533 (ttp) outliers start: 120 outliers final: 83 residues processed: 305 average time/residue: 0.4162 time to fit residues: 202.9178 Evaluate side-chains 291 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 195 time to evaluate : 3.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 137 ASN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 8 PHE 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 27 LEU Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 554 HIS Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 834 GLN 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 915 ASP 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 1160 ASP Chi-restraints excluded: chain C residue 1188 ASP Chi-restraints excluded: chain C residue 1226 THR 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 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 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 223 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 365 GLN Chi-restraints excluded: chain D residue 366 CYS Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 506 VAL 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 746 LEU Chi-restraints excluded: chain D residue 806 ASP Chi-restraints excluded: chain D residue 809 VAL Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 847 ASP 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 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 1193 TRP Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1272 SER Chi-restraints excluded: chain D residue 1273 ASP Chi-restraints excluded: chain D residue 1302 TYR Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain E residue 36 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 344 optimal weight: 0.8980 chunk 362 optimal weight: 0.8980 chunk 331 optimal weight: 3.9990 chunk 352 optimal weight: 50.0000 chunk 212 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 chunk 277 optimal weight: 20.0000 chunk 108 optimal weight: 0.9990 chunk 318 optimal weight: 4.9990 chunk 333 optimal weight: 9.9990 chunk 351 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 447 HIS ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1307 ASN ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1880 moved from start: 0.9820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30786 Z= 0.172 Angle : 0.632 9.801 42114 Z= 0.329 Chirality : 0.043 0.207 4931 Planarity : 0.005 0.077 5260 Dihedral : 15.925 156.779 5260 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.59 % Favored : 92.36 % Rotamer: Outliers : 3.90 % Allowed : 18.82 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.08 % Twisted Proline : 1.30 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.13), residues: 3846 helix: 0.55 (0.15), residues: 1373 sheet: -1.13 (0.23), residues: 482 loop : -2.44 (0.13), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 580 HIS 0.007 0.001 HIS D 907 PHE 0.053 0.002 PHE C 812 TYR 0.023 0.001 TYR C1231 ARG 0.008 0.000 ARG D1262 *********************** 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 302 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 196 time to evaluate : 3.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 LEU cc_start: 0.5011 (pt) cc_final: 0.4324 (tt) REVERT: A 188 GLU cc_start: 0.0182 (OUTLIER) cc_final: -0.0694 (tm-30) REVERT: A 205 MET cc_start: 0.1925 (mmm) cc_final: 0.1625 (mmm) REVERT: C 27 LEU cc_start: -0.1414 (OUTLIER) cc_final: -0.2516 (mt) REVERT: C 84 GLU cc_start: 0.4772 (OUTLIER) cc_final: 0.4298 (pm20) REVERT: C 384 LEU cc_start: 0.3103 (OUTLIER) cc_final: 0.2679 (tt) REVERT: C 498 ILE cc_start: 0.0686 (mm) cc_final: -0.0705 (mt) REVERT: C 653 MET cc_start: 0.1948 (ttp) cc_final: 0.1384 (mmp) REVERT: C 663 VAL cc_start: 0.5336 (m) cc_final: 0.4048 (p) REVERT: C 867 GLU cc_start: 0.1150 (OUTLIER) cc_final: -0.0514 (tt0) REVERT: C 1066 MET cc_start: 0.1955 (mmt) cc_final: 0.1580 (mmt) REVERT: C 1170 MET cc_start: 0.0276 (mmm) cc_final: -0.0428 (mmm) REVERT: C 1195 ILE cc_start: 0.6126 (mt) cc_final: 0.5858 (tp) REVERT: C 1321 GLU cc_start: 0.0712 (OUTLIER) cc_final: -0.0831 (tt0) REVERT: D 29 MET cc_start: 0.2926 (tpt) cc_final: 0.1405 (tmm) REVERT: D 400 MET cc_start: 0.0364 (ttt) cc_final: -0.2139 (mpp) REVERT: D 484 MET cc_start: 0.6176 (ttt) cc_final: 0.5780 (ttp) REVERT: D 609 TYR cc_start: 0.1685 (t80) cc_final: 0.1130 (t80) REVERT: D 697 MET cc_start: -0.2937 (tpt) cc_final: -0.4338 (tpt) REVERT: D 698 MET cc_start: -0.2835 (tpt) cc_final: -0.3480 (tmm) REVERT: D 725 MET cc_start: 0.3061 (mmt) cc_final: 0.2760 (tmm) REVERT: D 892 PHE cc_start: 0.2546 (OUTLIER) cc_final: -0.1185 (p90) REVERT: D 905 ARG cc_start: 0.0941 (OUTLIER) cc_final: -0.3871 (ptm160) REVERT: D 911 LYS cc_start: 0.2132 (ttmt) cc_final: 0.1689 (pttt) REVERT: D 1025 MET cc_start: -0.3940 (ptp) cc_final: -0.4626 (tpp) REVERT: D 1193 TRP cc_start: 0.1212 (OUTLIER) cc_final: -0.2980 (m100) REVERT: D 1370 MET cc_start: 0.0881 (tmm) cc_final: 0.0466 (ttp) outliers start: 106 outliers final: 77 residues processed: 285 average time/residue: 0.4221 time to fit residues: 195.0271 Evaluate side-chains 276 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 190 time to evaluate : 3.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 8 PHE 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 C residue 27 LEU Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 820 GLU 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 915 ASP Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1116 HIS Chi-restraints excluded: chain C residue 1188 ASP Chi-restraints excluded: chain C residue 1226 THR 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 1292 THR Chi-restraints excluded: chain C residue 1321 GLU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 102 MET 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 223 LEU Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 365 GLN Chi-restraints excluded: chain D residue 366 CYS Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 474 LEU 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 708 ASN Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 806 ASP Chi-restraints excluded: chain D residue 809 VAL Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 847 ASP 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 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 1193 TRP Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1272 SER Chi-restraints excluded: chain D residue 1302 TYR Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain E residue 36 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 231 optimal weight: 3.9990 chunk 373 optimal weight: 40.0000 chunk 227 optimal weight: 6.9990 chunk 177 optimal weight: 2.9990 chunk 259 optimal weight: 20.0000 chunk 391 optimal weight: 6.9990 chunk 360 optimal weight: 40.0000 chunk 311 optimal weight: 0.1980 chunk 32 optimal weight: 6.9990 chunk 240 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- 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 84 ASN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN C 83 GLN C 688 GLN ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 HIS ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 ASN ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 768 ASN D1259 GLN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2170 moved from start: 1.0737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 30786 Z= 0.304 Angle : 0.823 18.807 42114 Z= 0.425 Chirality : 0.048 0.271 4931 Planarity : 0.006 0.084 5260 Dihedral : 16.429 170.291 5260 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.41 % Favored : 88.51 % Rotamer: Outliers : 3.86 % Allowed : 19.01 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.08 % Twisted Proline : 1.30 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.13), residues: 3846 helix: 0.36 (0.15), residues: 1333 sheet: -1.07 (0.24), residues: 440 loop : -2.55 (0.13), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D1193 HIS 0.010 0.002 HIS D 430 PHE 0.044 0.003 PHE C 812 TYR 0.025 0.002 TYR C 172 ARG 0.009 0.001 ARG D 101 ********************** 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 305 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 200 time to evaluate : 2.942 Fit side-chains REVERT: A 188 GLU cc_start: 0.0328 (OUTLIER) cc_final: -0.0492 (tm-30) REVERT: B 203 ILE cc_start: -0.0525 (OUTLIER) cc_final: -0.1069 (tt) REVERT: C 27 LEU cc_start: -0.1279 (OUTLIER) cc_final: -0.1748 (mt) REVERT: C 41 GLN cc_start: 0.2504 (OUTLIER) cc_final: 0.1968 (tm-30) REVERT: C 84 GLU cc_start: 0.5759 (OUTLIER) cc_final: 0.5084 (pm20) REVERT: C 384 LEU cc_start: 0.3395 (OUTLIER) cc_final: 0.2873 (tt) REVERT: C 653 MET cc_start: 0.2076 (ttp) cc_final: 0.1686 (mmp) REVERT: C 867 GLU cc_start: 0.1603 (OUTLIER) cc_final: 0.0733 (tt0) REVERT: C 893 THR cc_start: 0.2562 (OUTLIER) cc_final: 0.2074 (p) REVERT: C 1170 MET cc_start: 0.0338 (mmm) cc_final: -0.0439 (mmm) REVERT: C 1195 ILE cc_start: 0.6269 (mt) cc_final: 0.5947 (tp) REVERT: C 1304 MET cc_start: 0.1039 (tpt) cc_final: 0.0292 (mmm) REVERT: C 1321 GLU cc_start: 0.1286 (OUTLIER) cc_final: 0.0198 (tp30) REVERT: D 29 MET cc_start: 0.2879 (tpt) cc_final: 0.1435 (tmm) REVERT: D 400 MET cc_start: 0.0167 (ttt) cc_final: -0.1676 (mpp) REVERT: D 582 ILE cc_start: 0.2259 (OUTLIER) cc_final: 0.1988 (pt) REVERT: D 609 TYR cc_start: 0.1718 (t80) cc_final: 0.1198 (t80) REVERT: D 698 MET cc_start: -0.3134 (tpt) cc_final: -0.3949 (tmm) REVERT: D 863 LEU cc_start: 0.3239 (OUTLIER) cc_final: 0.2690 (pp) REVERT: D 892 PHE cc_start: 0.3018 (OUTLIER) cc_final: -0.0472 (p90) REVERT: D 897 HIS cc_start: 0.6672 (OUTLIER) cc_final: 0.6166 (t70) REVERT: D 905 ARG cc_start: 0.0771 (OUTLIER) cc_final: -0.4261 (ptm160) REVERT: D 911 LYS cc_start: 0.2217 (ttmt) cc_final: 0.1950 (pttt) REVERT: D 1025 MET cc_start: -0.4077 (ptp) cc_final: -0.4883 (tpp) REVERT: D 1193 TRP cc_start: 0.1306 (OUTLIER) cc_final: -0.2525 (m100) REVERT: D 1370 MET cc_start: 0.1198 (tmm) cc_final: 0.0971 (ttp) outliers start: 105 outliers final: 84 residues processed: 291 average time/residue: 0.4035 time to fit residues: 193.3892 Evaluate side-chains 294 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 195 time to evaluate : 2.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 59 VAL 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 168 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 8 PHE 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 201 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 41 GLN 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 84 GLU Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 686 GLN Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 820 GLU Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 867 GLU Chi-restraints excluded: chain C residue 893 THR Chi-restraints excluded: chain C residue 908 GLU Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1116 HIS Chi-restraints excluded: chain C residue 1117 LEU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1188 ASP Chi-restraints excluded: chain C residue 1226 THR 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 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 221 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 365 GLN Chi-restraints excluded: chain D residue 366 CYS Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 806 ASP Chi-restraints excluded: chain D residue 809 VAL Chi-restraints excluded: chain D residue 847 ASP 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 905 ARG Chi-restraints excluded: chain D residue 913 GLU 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 1193 TRP Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1302 TYR Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 36 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 247 optimal weight: 3.9990 chunk 332 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 287 optimal weight: 0.0570 chunk 46 optimal weight: 7.9990 chunk 86 optimal weight: 20.0000 chunk 312 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 320 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 57 optimal weight: 50.0000 overall best weight: 4.2104 ------------------------------------------------------------------------------- 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 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1072 ASN ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1366 HIS ** 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 = 0.5580 r_free = 0.5580 target = 0.347380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5567 r_free = 0.5567 target = 0.337195 restraints weight = 83478.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.5571 r_free = 0.5571 target = 0.337872 restraints weight = 74553.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5578 r_free = 0.5578 target = 0.338612 restraints weight = 54536.208| |-----------------------------------------------------------------------------| r_work (final): 0.5383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2121 moved from start: 1.0749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.334 30786 Z= 0.341 Angle : 0.905 65.900 42114 Z= 0.489 Chirality : 0.048 0.275 4931 Planarity : 0.007 0.266 5260 Dihedral : 16.429 170.285 5260 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 21.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.49 % Favored : 88.46 % Rotamer: Outliers : 3.93 % Allowed : 19.26 % Favored : 76.80 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.08 % Twisted Proline : 1.30 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.13), residues: 3846 helix: 0.34 (0.15), residues: 1333 sheet: -1.08 (0.24), residues: 440 loop : -2.56 (0.13), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D1193 HIS 0.011 0.002 HIS C 447 PHE 0.041 0.003 PHE C 389 TYR 0.024 0.002 TYR C 26 ARG 0.008 0.001 ARG D 322 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5380.94 seconds wall clock time: 98 minutes 21.94 seconds (5901.94 seconds total)