Starting phenix.real_space_refine on Sat Feb 17 15:56:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qen_13934/02_2024/7qen_13934_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qen_13934/02_2024/7qen_13934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qen_13934/02_2024/7qen_13934.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qen_13934/02_2024/7qen_13934.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qen_13934/02_2024/7qen_13934_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qen_13934/02_2024/7qen_13934_updated.pdb" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 76 5.49 5 Mg 2 5.21 5 S 91 5.16 5 C 11965 2.51 5 N 3245 2.21 5 O 3826 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 162": "OE1" <-> "OE2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 242": "OE1" <-> "OE2" Residue "B GLU 251": "OE1" <-> "OE2" Residue "B GLU 252": "OE1" <-> "OE2" Residue "B ARG 260": "NH1" <-> "NH2" Residue "B PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B GLU 306": "OE1" <-> "OE2" Residue "B GLU 316": "OE1" <-> "OE2" Residue "B ASP 321": "OD1" <-> "OD2" Residue "B GLU 348": "OE1" <-> "OE2" Residue "B GLU 356": "OE1" <-> "OE2" Residue "B ASP 365": "OD1" <-> "OD2" Residue "B GLU 1251": "OE1" <-> "OE2" Residue "B GLU 1254": "OE1" <-> "OE2" Residue "B PHE 1264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1266": "OE1" <-> "OE2" Residue "B GLU 1280": "OE1" <-> "OE2" Residue "B TYR 1282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1294": "OE1" <-> "OE2" Residue "B GLU 1304": "OE1" <-> "OE2" Residue "B ARG 1318": "NH1" <-> "NH2" Residue "B GLU 1371": "OE1" <-> "OE2" Residue "B GLU 1389": "OE1" <-> "OE2" Residue "A GLU 4": "OE1" <-> "OE2" Residue "A ASP 22": "OD1" <-> "OD2" Residue "A ASP 24": "OD1" <-> "OD2" Residue "A ASP 43": "OD1" <-> "OD2" Residue "A ARG 58": "NH1" <-> "NH2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A GLU 201": "OE1" <-> "OE2" Residue "A GLU 202": "OE1" <-> "OE2" Residue "A GLU 204": "OE1" <-> "OE2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 946": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 957": "OE1" <-> "OE2" Residue "A ASP 962": "OD1" <-> "OD2" Residue "A GLU 991": "OE1" <-> "OE2" Residue "A GLU 1023": "OE1" <-> "OE2" Residue "A TYR 1024": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1059": "OE1" <-> "OE2" Residue "A ASP 1115": "OD1" <-> "OD2" Residue "A ARG 1133": "NH1" <-> "NH2" Residue "A PHE 1139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1154": "NH1" <-> "NH2" Residue "C ASP 59": "OD1" <-> "OD2" Residue "C ASP 91": "OD1" <-> "OD2" Residue "C ARG 107": "NH1" <-> "NH2" Residue "C GLU 164": "OE1" <-> "OE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "C GLU 177": "OE1" <-> "OE2" Residue "C GLU 197": "OE1" <-> "OE2" Residue "C ASP 211": "OD1" <-> "OD2" Residue "C PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 277": "OE1" <-> "OE2" Residue "C PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 291": "OD1" <-> "OD2" Residue "C GLU 297": "OE1" <-> "OE2" Residue "C ASP 317": "OD1" <-> "OD2" Residue "C GLU 320": "OE1" <-> "OE2" Residue "C ARG 648": "NH1" <-> "NH2" Residue "C GLU 689": "OE1" <-> "OE2" Residue "C ASP 705": "OD1" <-> "OD2" Residue "C ASP 706": "OD1" <-> "OD2" Residue "C GLU 726": "OE1" <-> "OE2" Residue "C TYR 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 746": "OD1" <-> "OD2" Residue "D GLU 8": "OE1" <-> "OE2" Residue "D ASP 26": "OD1" <-> "OD2" Residue "D ASP 36": "OD1" <-> "OD2" Residue "D GLU 43": "OE1" <-> "OE2" Residue "D ASP 46": "OD1" <-> "OD2" Residue "D ASP 50": "OD1" <-> "OD2" Residue "D GLU 53": "OE1" <-> "OE2" Residue "D TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 87": "OD1" <-> "OD2" Residue "D PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 114": "OE1" <-> "OE2" Residue "D ASP 128": "OD1" <-> "OD2" Residue "D ASP 150": "OD1" <-> "OD2" Residue "D PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 160": "OD1" <-> "OD2" Residue "D GLU 169": "OE1" <-> "OE2" Residue "D GLU 176": "OE1" <-> "OE2" Residue "D PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "D GLU 264": "OE1" <-> "OE2" Residue "D TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 273": "OD1" <-> "OD2" Residue "D ASP 345": "OD1" <-> "OD2" Residue "D GLU 350": "OE1" <-> "OE2" Residue "D GLU 364": "OE1" <-> "OE2" Residue "D GLU 365": "OE1" <-> "OE2" Residue "D ARG 366": "NH1" <-> "NH2" Residue "D ASP 369": "OD1" <-> "OD2" Residue "D GLU 446": "OE1" <-> "OE2" Residue "D ASP 532": "OD1" <-> "OD2" Residue "D GLU 539": "OE1" <-> "OE2" Residue "D ARG 556": "NH1" <-> "NH2" Residue "D GLU 558": "OE1" <-> "OE2" Residue "D GLU 578": "OE1" <-> "OE2" Residue "D ASP 595": "OD1" <-> "OD2" Residue "D GLU 623": "OE1" <-> "OE2" Residue "D ASP 643": "OD1" <-> "OD2" Residue "D ASP 661": "OD1" <-> "OD2" Residue "D GLU 698": "OE1" <-> "OE2" Residue "D GLU 716": "OE1" <-> "OE2" Residue "D ASP 737": "OD1" <-> "OD2" Residue "D ARG 742": "NH1" <-> "NH2" Residue "D GLU 749": "OE1" <-> "OE2" Residue "D ARG 750": "NH1" <-> "NH2" Residue "D GLU 766": "OE1" <-> "OE2" Residue "D ASP 769": "OD1" <-> "OD2" Residue "D ASP 785": "OD1" <-> "OD2" Residue "D GLU 787": "OE1" <-> "OE2" Residue "D ASP 812": "OD1" <-> "OD2" Residue "D GLU 862": "OE1" <-> "OE2" Residue "D GLU 910": "OE1" <-> "OE2" Residue "D ASP 912": "OD1" <-> "OD2" Residue "D PHE 913": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 915": "OD1" <-> "OD2" Residue "D GLU 929": "OE1" <-> "OE2" Residue "D ASP 952": "OD1" <-> "OD2" Residue "D GLU 986": "OE1" <-> "OE2" Residue "D ASP 990": "OD1" <-> "OD2" Residue "D ASP 1003": "OD1" <-> "OD2" Residue "D TYR 1020": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1026": "OE1" <-> "OE2" Residue "D ARG 1032": "NH1" <-> "NH2" Residue "D ASP 1061": "OD1" <-> "OD2" Residue "D ASP 1069": "OD1" <-> "OD2" Residue "D ASP 1091": "OD1" <-> "OD2" Residue "D PHE 1093": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1099": "OD1" <-> "OD2" Residue "D ASP 1100": "OD1" <-> "OD2" Residue "D GLU 1105": "OE1" <-> "OE2" Residue "D GLU 1121": "OE1" <-> "OE2" Residue "D ASP 1145": "OD1" <-> "OD2" Residue "D ASP 1146": "OD1" <-> "OD2" Residue "D GLU 1159": "OE1" <-> "OE2" Residue "D ASP 1160": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19205 Number of models: 1 Model: "" Number of chains: 8 Chain: "F" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 735 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "G" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 700 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "B" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3318 Classifications: {'peptide': 419} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 11, 'TRANS': 407} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 3709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3709 Classifications: {'peptide': 465} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 452} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2345 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 1, 'TRANS': 289} Chain breaks: 5 Chain: "D" Number of atoms: 8334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1050, 8334 Classifications: {'peptide': 1050} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 1021} Chain breaks: 5 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.97, per 1000 atoms: 0.52 Number of scatterers: 19205 At special positions: 0 Unit cell: (135.2, 147.68, 166.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 91 16.00 P 76 15.00 Mg 2 11.99 O 3826 8.00 N 3245 7.00 C 11965 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 7.94 Conformation dependent library (CDL) restraints added in 3.4 seconds 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4264 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 90 helices and 7 sheets defined 58.5% alpha, 6.8% beta 35 base pairs and 68 stacking pairs defined. Time for finding SS restraints: 9.30 Creating SS restraints... Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 191 through 202 removed outlier: 4.075A pdb=" N ILE B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 209 No H-bonds generated for 'chain 'B' and resid 207 through 209' Processing helix chain 'B' and resid 214 through 216 No H-bonds generated for 'chain 'B' and resid 214 through 216' Processing helix chain 'B' and resid 279 through 288 Processing helix chain 'B' and resid 323 through 330 Processing helix chain 'B' and resid 337 through 365 Processing helix chain 'B' and resid 1234 through 1285 Processing helix chain 'B' and resid 1301 through 1304 No H-bonds generated for 'chain 'B' and resid 1301 through 1304' Processing helix chain 'B' and resid 1320 through 1322 No H-bonds generated for 'chain 'B' and resid 1320 through 1322' Processing helix chain 'B' and resid 1325 through 1342 Processing helix chain 'B' and resid 1359 through 1370 Processing helix chain 'B' and resid 1385 through 1389 Processing helix chain 'A' and resid 38 through 49 Processing helix chain 'A' and resid 67 through 70 Processing helix chain 'A' and resid 124 through 131 Processing helix chain 'A' and resid 158 through 169 removed outlier: 3.618A pdb=" N ILE A 165 " --> pdb=" O ILE A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 202 removed outlier: 3.750A pdb=" N ARG A 177 " --> pdb=" O MET A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 239 removed outlier: 4.603A pdb=" N ARG A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 953 Processing helix chain 'A' and resid 961 through 981 removed outlier: 3.796A pdb=" N LYS A 974 " --> pdb=" O GLN A 970 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS A 980 " --> pdb=" O GLN A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1047 removed outlier: 4.240A pdb=" N GLU A1023 " --> pdb=" O SER A1019 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N TYR A1024 " --> pdb=" O LYS A1020 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS A1035 " --> pdb=" O LYS A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1065 No H-bonds generated for 'chain 'A' and resid 1063 through 1065' Processing helix chain 'A' and resid 1081 through 1083 No H-bonds generated for 'chain 'A' and resid 1081 through 1083' Processing helix chain 'A' and resid 1086 through 1103 Processing helix chain 'A' and resid 1120 through 1131 removed outlier: 3.864A pdb=" N GLN A1124 " --> pdb=" O LEU A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1151 removed outlier: 4.439A pdb=" N ASN A1151 " --> pdb=" O GLY A1147 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 39 Processing helix chain 'C' and resid 54 through 57 No H-bonds generated for 'chain 'C' and resid 54 through 57' Processing helix chain 'C' and resid 72 through 107 removed outlier: 5.133A pdb=" N ARG C 107 " --> pdb=" O GLY C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 196 Processing helix chain 'C' and resid 277 through 286 removed outlier: 3.638A pdb=" N LEU C 283 " --> pdb=" O GLU C 279 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 295 removed outlier: 3.711A pdb=" N ALA C 294 " --> pdb=" O PHE C 290 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL C 295 " --> pdb=" O ASP C 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 290 through 295' Processing helix chain 'C' and resid 302 through 310 Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 647 through 671 Processing helix chain 'C' and resid 693 through 701 removed outlier: 4.007A pdb=" N LYS C 701 " --> pdb=" O GLN C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 726 Processing helix chain 'D' and resid 7 through 14 Processing helix chain 'D' and resid 27 through 38 Processing helix chain 'D' and resid 49 through 58 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 67 through 93 Processing helix chain 'D' and resid 98 through 135 Proline residue: D 106 - end of helix Processing helix chain 'D' and resid 148 through 174 removed outlier: 3.911A pdb=" N ALA D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 182 No H-bonds generated for 'chain 'D' and resid 179 through 182' Processing helix chain 'D' and resid 186 through 205 Proline residue: D 199 - end of helix removed outlier: 4.411A pdb=" N GLU D 205 " --> pdb=" O PHE D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 228 Processing helix chain 'D' and resid 233 through 246 Processing helix chain 'D' and resid 251 through 263 Processing helix chain 'D' and resid 269 through 279 Processing helix chain 'D' and resid 290 through 304 Processing helix chain 'D' and resid 306 through 321 removed outlier: 4.131A pdb=" N ARG D 311 " --> pdb=" O GLY D 307 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLN D 312 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET D 313 " --> pdb=" O MET D 309 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ASN D 314 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU D 315 " --> pdb=" O ARG D 311 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR D 318 " --> pdb=" O ASN D 314 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LEU D 319 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N LEU D 320 " --> pdb=" O VAL D 316 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ASN D 321 " --> pdb=" O ILE D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 341 Processing helix chain 'D' and resid 345 through 347 No H-bonds generated for 'chain 'D' and resid 345 through 347' Processing helix chain 'D' and resid 354 through 368 removed outlier: 3.580A pdb=" N LEU D 359 " --> pdb=" O GLN D 355 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE D 367 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N GLN D 368 " --> pdb=" O GLU D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 385 Processing helix chain 'D' and resid 393 through 408 removed outlier: 4.426A pdb=" N ALA D 397 " --> pdb=" O ASN D 393 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N GLN D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 427 Processing helix chain 'D' and resid 441 through 454 removed outlier: 4.029A pdb=" N SER D 451 " --> pdb=" O TYR D 447 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLU D 452 " --> pdb=" O LEU D 448 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N SER D 453 " --> pdb=" O LYS D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 552 removed outlier: 3.778A pdb=" N ASN D 549 " --> pdb=" O GLU D 545 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N PHE D 552 " --> pdb=" O SER D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 571 Processing helix chain 'D' and resid 577 through 588 removed outlier: 3.968A pdb=" N HIS D 586 " --> pdb=" O LYS D 582 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU D 587 " --> pdb=" O LYS D 583 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL D 588 " --> pdb=" O MET D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 612 removed outlier: 3.581A pdb=" N GLU D 606 " --> pdb=" O VAL D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 636 removed outlier: 3.910A pdb=" N SER D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 656 removed outlier: 4.005A pdb=" N GLN D 649 " --> pdb=" O ALA D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 677 removed outlier: 3.794A pdb=" N ALA D 675 " --> pdb=" O ILE D 671 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER D 676 " --> pdb=" O TYR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 712 removed outlier: 3.769A pdb=" N LEU D 712 " --> pdb=" O GLY D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 716 through 719 No H-bonds generated for 'chain 'D' and resid 716 through 719' Processing helix chain 'D' and resid 722 through 728 removed outlier: 3.799A pdb=" N ASN D 727 " --> pdb=" O GLU D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 751 removed outlier: 3.732A pdb=" N ARG D 750 " --> pdb=" O LEU D 746 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET D 751 " --> pdb=" O ALA D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 765 through 779 removed outlier: 4.704A pdb=" N VAL D 770 " --> pdb=" O GLU D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 786 through 802 Proline residue: D 790 - end of helix removed outlier: 3.897A pdb=" N GLU D 793 " --> pdb=" O PRO D 790 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU D 796 " --> pdb=" O GLU D 793 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N PHE D 800 " --> pdb=" O SER D 797 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR D 801 " --> pdb=" O ALA D 798 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE D 802 " --> pdb=" O LEU D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 806 through 821 Processing helix chain 'D' and resid 839 through 879 removed outlier: 3.880A pdb=" N THR D 877 " --> pdb=" O ILE D 873 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG D 878 " --> pdb=" O GLU D 874 " (cutoff:3.500A) Processing helix chain 'D' and resid 910 through 922 Processing helix chain 'D' and resid 933 through 943 Proline residue: D 938 - end of helix removed outlier: 3.714A pdb=" N GLU D 941 " --> pdb=" O CYS D 937 " (cutoff:3.500A) Processing helix chain 'D' and resid 953 through 967 Processing helix chain 'D' and resid 971 through 987 removed outlier: 3.865A pdb=" N LYS D 976 " --> pdb=" O LYS D 972 " (cutoff:3.500A) Proline residue: D 979 - end of helix Processing helix chain 'D' and resid 991 through 995 Processing helix chain 'D' and resid 998 through 1007 removed outlier: 3.729A pdb=" N VAL D1006 " --> pdb=" O GLY D1002 " (cutoff:3.500A) Processing helix chain 'D' and resid 1015 through 1021 Processing helix chain 'D' and resid 1028 through 1041 Processing helix chain 'D' and resid 1053 through 1061 removed outlier: 4.136A pdb=" N CYS D1059 " --> pdb=" O GLU D1055 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU D1060 " --> pdb=" O MET D1056 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP D1061 " --> pdb=" O ALA D1057 " (cutoff:3.500A) Processing helix chain 'D' and resid 1065 through 1080 removed outlier: 3.961A pdb=" N SER D1080 " --> pdb=" O THR D1076 " (cutoff:3.500A) Processing helix chain 'D' and resid 1084 through 1096 removed outlier: 4.942A pdb=" N ILE D1090 " --> pdb=" O TYR D1086 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ASP D1091 " --> pdb=" O ASN D1087 " (cutoff:3.500A) Processing helix chain 'D' and resid 1104 through 1116 removed outlier: 4.118A pdb=" N LYS D1109 " --> pdb=" O GLU D1105 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N THR D1116 " --> pdb=" O LYS D1112 " (cutoff:3.500A) Processing helix chain 'D' and resid 1121 through 1135 Processing helix chain 'D' and resid 1141 through 1152 Processing helix chain 'D' and resid 1159 through 1166 Processing sheet with id= A, first strand: chain 'B' and resid 170 through 172 removed outlier: 6.906A pdb=" N HIS B 235 " --> pdb=" O ASN B 157 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU B 159 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA B 233 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU B 161 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N SER B 231 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N TYR B 270 " --> pdb=" O SER B 277 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 1403 through 1410 removed outlier: 7.431A pdb=" N PHE B 180 " --> pdb=" O GLN B1393 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N VAL B1395 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA B 182 " --> pdb=" O VAL B1395 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL B1397 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL B 184 " --> pdb=" O VAL B1397 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N LYS B1399 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE B1378 " --> pdb=" O SER B 181 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL B 183 " --> pdb=" O PHE B1378 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL B1380 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N GLY B 185 " --> pdb=" O VAL B1380 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 1290 through 1295 Processing sheet with id= D, first strand: chain 'A' and resid 17 through 20 removed outlier: 3.787A pdb=" N LYS A 2 " --> pdb=" O ASP A 84 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL A 82 " --> pdb=" O GLU A 4 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU A 6 " --> pdb=" O THR A 80 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR A 80 " --> pdb=" O LEU A 6 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ILE A 8 " --> pdb=" O SER A 78 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N SER A 78 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR A 115 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1164 through 1170 removed outlier: 4.566A pdb=" N VAL A1155 " --> pdb=" O MET A1170 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N PHE A1139 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ILE A 30 " --> pdb=" O PHE A1139 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL A1141 " --> pdb=" O ILE A 30 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N GLY A 32 " --> pdb=" O VAL A1141 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1051 through 1057 Processing sheet with id= G, first strand: chain 'C' and resid 689 through 691 951 hydrogen bonds defined for protein. 2793 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 68 stacking parallelities Total time for adding SS restraints: 7.86 Time building geometry restraints manager: 8.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5472 1.34 - 1.46: 3450 1.46 - 1.57: 10420 1.57 - 1.69: 132 1.69 - 1.81: 152 Bond restraints: 19626 Sorted by residual: bond pdb=" C4 ATP B2000 " pdb=" C5 ATP B2000 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.02e+01 bond pdb=" C4 ATP A2000 " pdb=" C5 ATP A2000 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.68e+01 bond pdb=" C5 ATP B2000 " pdb=" C6 ATP B2000 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.31e+01 bond pdb=" C5 ATP A2000 " pdb=" C6 ATP A2000 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 4.03e+01 bond pdb=" C5 ATP A2000 " pdb=" N7 ATP A2000 " ideal model delta sigma weight residual 1.387 1.340 0.047 1.00e-02 1.00e+04 2.19e+01 ... (remaining 19621 not shown) Histogram of bond angle deviations from ideal: 97.91 - 105.54: 639 105.54 - 113.16: 10653 113.16 - 120.79: 9546 120.79 - 128.42: 5756 128.42 - 136.05: 146 Bond angle restraints: 26740 Sorted by residual: angle pdb=" PB ATP B2000 " pdb=" O3B ATP B2000 " pdb=" PG ATP B2000 " ideal model delta sigma weight residual 139.87 120.93 18.94 1.00e+00 1.00e+00 3.59e+02 angle pdb=" PB ATP A2000 " pdb=" O3B ATP A2000 " pdb=" PG ATP A2000 " ideal model delta sigma weight residual 139.87 122.06 17.81 1.00e+00 1.00e+00 3.17e+02 angle pdb=" PA ATP B2000 " pdb=" O3A ATP B2000 " pdb=" PB ATP B2000 " ideal model delta sigma weight residual 136.83 120.98 15.85 1.00e+00 1.00e+00 2.51e+02 angle pdb=" PA ATP A2000 " pdb=" O3A ATP A2000 " pdb=" PB ATP A2000 " ideal model delta sigma weight residual 136.83 121.64 15.19 1.00e+00 1.00e+00 2.31e+02 angle pdb=" C5 ATP B2000 " pdb=" C4 ATP B2000 " pdb=" N3 ATP B2000 " ideal model delta sigma weight residual 126.80 118.82 7.98 1.00e+00 1.00e+00 6.37e+01 ... (remaining 26735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 10033 17.99 - 35.98: 1341 35.98 - 53.98: 432 53.98 - 71.97: 181 71.97 - 89.96: 20 Dihedral angle restraints: 12007 sinusoidal: 5480 harmonic: 6527 Sorted by residual: dihedral pdb=" CA ASP D 345 " pdb=" C ASP D 345 " pdb=" N PRO D 346 " pdb=" CA PRO D 346 " ideal model delta harmonic sigma weight residual 180.00 -150.12 -29.88 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA GLN D 344 " pdb=" C GLN D 344 " pdb=" N ASP D 345 " pdb=" CA ASP D 345 " ideal model delta harmonic sigma weight residual 180.00 -152.56 -27.44 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA VAL B 173 " pdb=" C VAL B 173 " pdb=" N GLY B 174 " pdb=" CA GLY B 174 " ideal model delta harmonic sigma weight residual 180.00 155.34 24.66 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 12004 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2569 0.072 - 0.143: 481 0.143 - 0.215: 43 0.215 - 0.286: 7 0.286 - 0.358: 1 Chirality restraints: 3101 Sorted by residual: chirality pdb=" CB VAL D1049 " pdb=" CA VAL D1049 " pdb=" CG1 VAL D1049 " pdb=" CG2 VAL D1049 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" CA THR D 186 " pdb=" N THR D 186 " pdb=" C THR D 186 " pdb=" CB THR D 186 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA ASN D 266 " pdb=" N ASN D 266 " pdb=" C ASN D 266 " pdb=" CB ASN D 266 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 3098 not shown) Planarity restraints: 3141 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 290 " -0.062 5.00e-02 4.00e+02 9.31e-02 1.39e+01 pdb=" N PRO D 291 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO D 291 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO D 291 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 66 " -0.046 5.00e-02 4.00e+02 6.94e-02 7.70e+00 pdb=" N PRO D 67 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO D 67 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 67 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 186 " 0.044 5.00e-02 4.00e+02 6.53e-02 6.82e+00 pdb=" N PRO D 187 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 187 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 187 " 0.037 5.00e-02 4.00e+02 ... (remaining 3138 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 202 2.63 - 3.20: 16255 3.20 - 3.77: 31153 3.77 - 4.33: 41961 4.33 - 4.90: 65960 Nonbonded interactions: 155531 Sorted by model distance: nonbonded pdb=" OE1 GLN A 147 " pdb="MG MG A2001 " model vdw 2.068 2.170 nonbonded pdb=" O2B ATP A2000 " pdb="MG MG A2001 " model vdw 2.080 2.170 nonbonded pdb=" OE1 GLN B 302 " pdb="MG MG B2001 " model vdw 2.085 2.170 nonbonded pdb=" O2B ATP B2000 " pdb="MG MG B2001 " model vdw 2.089 2.170 nonbonded pdb=" OG SER B 192 " pdb="MG MG B2001 " model vdw 2.139 2.170 ... (remaining 155526 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.690 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 60.430 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 19626 Z= 0.342 Angle : 0.963 18.938 26740 Z= 0.576 Chirality : 0.055 0.358 3101 Planarity : 0.007 0.093 3141 Dihedral : 19.011 89.959 7743 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.20 % Allowed : 6.39 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.14), residues: 2177 helix: -2.38 (0.10), residues: 1295 sheet: -0.38 (0.40), residues: 166 loop : -2.66 (0.19), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 669 HIS 0.009 0.001 HIS D 435 PHE 0.032 0.002 PHE A 27 TYR 0.024 0.002 TYR D 529 ARG 0.012 0.001 ARG A 965 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 590 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 252 GLU cc_start: 0.7172 (pm20) cc_final: 0.6939 (pm20) REVERT: B 263 PHE cc_start: 0.8545 (m-80) cc_final: 0.8105 (m-80) REVERT: B 264 LYS cc_start: 0.8760 (mmtt) cc_final: 0.8289 (tppt) REVERT: B 269 LYS cc_start: 0.8014 (mtpt) cc_final: 0.7710 (mtpt) REVERT: B 288 ASN cc_start: 0.8162 (t0) cc_final: 0.7746 (t0) REVERT: B 289 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7830 (mm-30) REVERT: B 307 ASN cc_start: 0.8136 (m-40) cc_final: 0.7934 (m110) REVERT: B 312 LYS cc_start: 0.8404 (mptt) cc_final: 0.8082 (mptt) REVERT: B 325 GLU cc_start: 0.7679 (mp0) cc_final: 0.7327 (mp0) REVERT: B 336 TYR cc_start: 0.8548 (m-80) cc_final: 0.8312 (m-10) REVERT: B 1260 LYS cc_start: 0.7892 (mttt) cc_final: 0.7572 (mtpp) REVERT: B 1265 ASP cc_start: 0.7792 (t0) cc_final: 0.7588 (t0) REVERT: B 1267 PHE cc_start: 0.8130 (t80) cc_final: 0.7919 (t80) REVERT: B 1271 PHE cc_start: 0.8171 (t80) cc_final: 0.7927 (t80) REVERT: B 1343 LYS cc_start: 0.8084 (tttt) cc_final: 0.7829 (ttmt) REVERT: B 1405 LYS cc_start: 0.8633 (mttt) cc_final: 0.8267 (mttm) REVERT: B 1412 ILE cc_start: 0.8289 (pt) cc_final: 0.8059 (pt) REVERT: A 19 VAL cc_start: 0.8581 (t) cc_final: 0.8274 (p) REVERT: A 28 ASN cc_start: 0.7403 (m-40) cc_final: 0.7181 (m-40) REVERT: A 54 MET cc_start: 0.7482 (mmt) cc_final: 0.7125 (mmt) REVERT: A 81 ILE cc_start: 0.7845 (tt) cc_final: 0.7592 (tt) REVERT: A 109 LEU cc_start: 0.8640 (mt) cc_final: 0.8406 (mp) REVERT: A 129 GLN cc_start: 0.7396 (tm-30) cc_final: 0.6866 (tm-30) REVERT: A 135 GLN cc_start: 0.8065 (pt0) cc_final: 0.7784 (pt0) REVERT: A 157 LYS cc_start: 0.7749 (mptt) cc_final: 0.7495 (mptt) REVERT: A 160 GLU cc_start: 0.6971 (mp0) cc_final: 0.6546 (mp0) REVERT: A 178 ARG cc_start: 0.7242 (tmm160) cc_final: 0.6734 (ttp-110) REVERT: A 187 LYS cc_start: 0.8521 (tppt) cc_final: 0.8203 (tppt) REVERT: A 188 LYS cc_start: 0.8565 (mmtt) cc_final: 0.8328 (mmtm) REVERT: A 189 GLU cc_start: 0.7881 (tp30) cc_final: 0.7666 (tp30) REVERT: A 198 LEU cc_start: 0.8303 (tt) cc_final: 0.8056 (tp) REVERT: A 217 PHE cc_start: 0.7205 (t80) cc_final: 0.6759 (t80) REVERT: A 985 ASN cc_start: 0.7891 (p0) cc_final: 0.7442 (p0) REVERT: A 994 GLU cc_start: 0.7450 (mm-30) cc_final: 0.6994 (mm-30) REVERT: A 997 GLU cc_start: 0.6888 (tp30) cc_final: 0.6601 (tp30) REVERT: A 1005 LYS cc_start: 0.8048 (mttt) cc_final: 0.7662 (mttp) REVERT: A 1009 LYS cc_start: 0.7790 (tttt) cc_final: 0.7396 (ttmm) REVERT: A 1016 GLU cc_start: 0.7310 (tt0) cc_final: 0.6934 (tt0) REVERT: A 1018 ILE cc_start: 0.8128 (pt) cc_final: 0.7841 (mt) REVERT: A 1023 GLU cc_start: 0.6961 (tp30) cc_final: 0.6639 (tp30) REVERT: A 1029 LEU cc_start: 0.7455 (tp) cc_final: 0.7015 (mm) REVERT: A 1082 ILE cc_start: 0.8646 (tp) cc_final: 0.8008 (pt) REVERT: A 1146 GLU cc_start: 0.7326 (tt0) cc_final: 0.6903 (tt0) REVERT: C 32 GLU cc_start: 0.7973 (tp30) cc_final: 0.7703 (mm-30) REVERT: C 42 LYS cc_start: 0.7501 (mmmt) cc_final: 0.7184 (mmmt) REVERT: C 64 LYS cc_start: 0.8324 (mtmt) cc_final: 0.7827 (mmmm) REVERT: C 84 LYS cc_start: 0.7987 (mmtp) cc_final: 0.7698 (mmtp) REVERT: C 99 LYS cc_start: 0.8109 (mtpt) cc_final: 0.7888 (mtmt) REVERT: C 189 LYS cc_start: 0.8089 (mmtt) cc_final: 0.7713 (mmmm) REVERT: C 196 ASP cc_start: 0.7537 (t0) cc_final: 0.7143 (t0) REVERT: C 197 GLU cc_start: 0.7412 (pp20) cc_final: 0.6948 (pp20) REVERT: C 211 ASP cc_start: 0.7507 (OUTLIER) cc_final: 0.7232 (m-30) REVERT: C 277 GLU cc_start: 0.7204 (mp0) cc_final: 0.6714 (mp0) REVERT: C 279 GLU cc_start: 0.6803 (tp30) cc_final: 0.6540 (tp30) REVERT: C 288 ILE cc_start: 0.8248 (pt) cc_final: 0.8022 (pt) REVERT: C 297 GLU cc_start: 0.6896 (pm20) cc_final: 0.6459 (pm20) REVERT: C 643 LYS cc_start: 0.7438 (mtmm) cc_final: 0.7121 (mtmm) REVERT: C 653 ASN cc_start: 0.7850 (m-40) cc_final: 0.7618 (m110) REVERT: C 659 ASN cc_start: 0.8098 (m-40) cc_final: 0.7882 (m110) REVERT: C 691 LYS cc_start: 0.8031 (mtpp) cc_final: 0.7777 (mtpp) REVERT: C 705 ASP cc_start: 0.7724 (t0) cc_final: 0.7421 (t0) REVERT: C 709 LYS cc_start: 0.8144 (ttpt) cc_final: 0.7832 (ttpt) REVERT: C 718 ILE cc_start: 0.6892 (pt) cc_final: 0.6686 (mt) REVERT: C 743 ASN cc_start: 0.7829 (t0) cc_final: 0.6466 (t0) REVERT: D 6 LEU cc_start: 0.7779 (tp) cc_final: 0.7533 (tt) REVERT: D 62 PHE cc_start: 0.7767 (t80) cc_final: 0.7559 (t80) REVERT: D 78 SER cc_start: 0.7302 (t) cc_final: 0.6966 (t) REVERT: D 89 LYS cc_start: 0.8300 (tptm) cc_final: 0.7856 (tptm) REVERT: D 105 ILE cc_start: 0.8160 (tt) cc_final: 0.7772 (pt) REVERT: D 165 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7478 (tm-30) REVERT: D 167 LEU cc_start: 0.7981 (mt) cc_final: 0.7768 (mt) REVERT: D 169 GLU cc_start: 0.7125 (mm-30) cc_final: 0.6632 (mm-30) REVERT: D 173 LYS cc_start: 0.7910 (tppt) cc_final: 0.7669 (tppt) REVERT: D 202 VAL cc_start: 0.8549 (p) cc_final: 0.8307 (m) REVERT: D 205 GLU cc_start: 0.7006 (tm-30) cc_final: 0.6781 (tm-30) REVERT: D 213 SER cc_start: 0.8616 (t) cc_final: 0.7794 (t) REVERT: D 217 MET cc_start: 0.6884 (mpp) cc_final: 0.6484 (mpp) REVERT: D 260 LEU cc_start: 0.8797 (tp) cc_final: 0.8465 (tt) REVERT: D 269 GLN cc_start: 0.7900 (tp-100) cc_final: 0.7562 (tp-100) REVERT: D 277 GLU cc_start: 0.7367 (tt0) cc_final: 0.7035 (pt0) REVERT: D 287 ASP cc_start: 0.7632 (t70) cc_final: 0.7431 (t0) REVERT: D 303 GLU cc_start: 0.7548 (tm-30) cc_final: 0.7347 (tm-30) REVERT: D 322 ASN cc_start: 0.8178 (t0) cc_final: 0.7928 (t0) REVERT: D 341 GLU cc_start: 0.7381 (tp30) cc_final: 0.6941 (tp30) REVERT: D 364 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6824 (mt-10) REVERT: D 365 GLU cc_start: 0.6644 (mt-10) cc_final: 0.6420 (mt-10) REVERT: D 385 ILE cc_start: 0.8850 (mt) cc_final: 0.8609 (mt) REVERT: D 542 LYS cc_start: 0.7797 (tttt) cc_final: 0.7516 (ttpp) REVERT: D 554 LYS cc_start: 0.8348 (mttt) cc_final: 0.8027 (mtpp) REVERT: D 606 GLU cc_start: 0.7607 (tp30) cc_final: 0.7267 (tp30) REVERT: D 698 GLU cc_start: 0.6589 (mp0) cc_final: 0.6263 (mp0) REVERT: D 722 LEU cc_start: 0.8664 (tp) cc_final: 0.8285 (tt) REVERT: D 749 GLU cc_start: 0.7497 (tm-30) cc_final: 0.7197 (tm-30) REVERT: D 773 LYS cc_start: 0.8054 (tptt) cc_final: 0.7803 (tptt) REVERT: D 815 ARG cc_start: 0.7859 (ttm170) cc_final: 0.7305 (mtm-85) REVERT: D 819 MET cc_start: 0.7145 (mmt) cc_final: 0.6925 (mmt) REVERT: D 921 LYS cc_start: 0.8205 (mtpt) cc_final: 0.7995 (mtmt) REVERT: D 952 ASP cc_start: 0.7468 (t0) cc_final: 0.7243 (t0) REVERT: D 970 SER cc_start: 0.8222 (t) cc_final: 0.7666 (p) REVERT: D 990 ASP cc_start: 0.7624 (t0) cc_final: 0.7416 (t0) REVERT: D 993 ILE cc_start: 0.8244 (mt) cc_final: 0.8025 (mt) REVERT: D 1017 ASP cc_start: 0.7789 (t70) cc_final: 0.7392 (t0) REVERT: D 1027 ASN cc_start: 0.7649 (t0) cc_final: 0.7263 (t0) REVERT: D 1048 LYS cc_start: 0.7871 (mtpt) cc_final: 0.6040 (mtpt) REVERT: D 1055 GLU cc_start: 0.7116 (tp30) cc_final: 0.6750 (tp30) REVERT: D 1058 LYS cc_start: 0.8392 (mttt) cc_final: 0.8179 (mttp) REVERT: D 1105 GLU cc_start: 0.7704 (pm20) cc_final: 0.7415 (pm20) REVERT: D 1109 LYS cc_start: 0.8210 (tptm) cc_final: 0.7934 (tppp) REVERT: D 1139 GLU cc_start: 0.7021 (tm-30) cc_final: 0.6523 (tm-30) outliers start: 4 outliers final: 2 residues processed: 591 average time/residue: 0.3525 time to fit residues: 304.1145 Evaluate side-chains 529 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 526 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain C residue 211 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 191 optimal weight: 0.6980 chunk 172 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 177 optimal weight: 0.3980 chunk 68 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 206 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 GLN ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 ASN B 235 HIS B 237 GLN B 307 ASN B 359 ASN B1243 ASN B1247 GLN B1283 GLN B1361 ASN A 34 ASN A 135 GLN A 212 ASN A1151 ASN C 68 ASN C 71 ASN C 313 ASN C 725 ASN C 738 ASN D 70 GLN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 GLN D 351 HIS ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 ASN D 610 GLN D 657 GLN D1031 GLN D1158 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19626 Z= 0.217 Angle : 0.560 8.487 26740 Z= 0.303 Chirality : 0.040 0.172 3101 Planarity : 0.004 0.078 3141 Dihedral : 17.939 82.192 3261 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.70 % Allowed : 14.24 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.16), residues: 2177 helix: -0.42 (0.13), residues: 1296 sheet: 0.29 (0.41), residues: 161 loop : -2.19 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1033 HIS 0.006 0.001 HIS D 541 PHE 0.023 0.002 PHE B1264 TYR 0.019 0.001 TYR D 529 ARG 0.009 0.000 ARG D 198 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 544 time to evaluate : 2.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 VAL cc_start: 0.8168 (m) cc_final: 0.7671 (t) REVERT: B 252 GLU cc_start: 0.7100 (pm20) cc_final: 0.6741 (pm20) REVERT: B 263 PHE cc_start: 0.8553 (m-80) cc_final: 0.7951 (m-80) REVERT: B 264 LYS cc_start: 0.8749 (mmtt) cc_final: 0.8387 (tppt) REVERT: B 269 LYS cc_start: 0.8050 (mtpt) cc_final: 0.7538 (mtpt) REVERT: B 288 ASN cc_start: 0.8118 (t0) cc_final: 0.7720 (t0) REVERT: B 289 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7710 (mm-30) REVERT: B 307 ASN cc_start: 0.8179 (m110) cc_final: 0.7956 (m110) REVERT: B 312 LYS cc_start: 0.8494 (mptt) cc_final: 0.8156 (mptt) REVERT: B 325 GLU cc_start: 0.7754 (mp0) cc_final: 0.7366 (mp0) REVERT: B 336 TYR cc_start: 0.8484 (m-80) cc_final: 0.8252 (m-10) REVERT: B 1249 ARG cc_start: 0.6934 (tmm-80) cc_final: 0.6720 (tmm-80) REVERT: B 1260 LYS cc_start: 0.7790 (mttt) cc_final: 0.7516 (mtpp) REVERT: B 1265 ASP cc_start: 0.7757 (t0) cc_final: 0.7542 (t0) REVERT: B 1281 MET cc_start: 0.7393 (mmt) cc_final: 0.6988 (mpp) REVERT: B 1282 TYR cc_start: 0.7973 (t80) cc_final: 0.7447 (t80) REVERT: B 1342 TYR cc_start: 0.8662 (t80) cc_final: 0.8278 (t80) REVERT: B 1373 THR cc_start: 0.8447 (m) cc_final: 0.8191 (t) REVERT: B 1405 LYS cc_start: 0.8506 (mttt) cc_final: 0.8193 (mttm) REVERT: B 1412 ILE cc_start: 0.8269 (pt) cc_final: 0.8002 (pt) REVERT: A 28 ASN cc_start: 0.7332 (m-40) cc_final: 0.7103 (m-40) REVERT: A 54 MET cc_start: 0.7368 (mmt) cc_final: 0.6942 (mmt) REVERT: A 109 LEU cc_start: 0.8689 (mt) cc_final: 0.8414 (mp) REVERT: A 129 GLN cc_start: 0.7496 (tm-30) cc_final: 0.6871 (tm-30) REVERT: A 160 GLU cc_start: 0.7013 (mp0) cc_final: 0.6717 (mp0) REVERT: A 178 ARG cc_start: 0.7244 (tmm160) cc_final: 0.6672 (ttp-110) REVERT: A 182 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7530 (mm-30) REVERT: A 187 LYS cc_start: 0.8543 (tppt) cc_final: 0.8179 (tppt) REVERT: A 189 GLU cc_start: 0.7820 (tp30) cc_final: 0.7606 (tp30) REVERT: A 209 LYS cc_start: 0.7287 (mmtm) cc_final: 0.6902 (mmtm) REVERT: A 217 PHE cc_start: 0.7150 (t80) cc_final: 0.6930 (t80) REVERT: A 985 ASN cc_start: 0.7917 (p0) cc_final: 0.7412 (p0) REVERT: A 994 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7108 (mm-30) REVERT: A 1005 LYS cc_start: 0.7975 (mttt) cc_final: 0.7643 (mttp) REVERT: A 1008 GLU cc_start: 0.6918 (tp30) cc_final: 0.6641 (tp30) REVERT: A 1009 LYS cc_start: 0.7690 (tttt) cc_final: 0.7359 (ttmm) REVERT: A 1016 GLU cc_start: 0.7281 (tt0) cc_final: 0.6900 (tt0) REVERT: A 1018 ILE cc_start: 0.7932 (pt) cc_final: 0.7668 (mt) REVERT: A 1023 GLU cc_start: 0.7040 (tp30) cc_final: 0.6749 (tp30) REVERT: A 1082 ILE cc_start: 0.8578 (tp) cc_final: 0.8041 (pt) REVERT: A 1146 GLU cc_start: 0.7306 (tt0) cc_final: 0.6726 (tt0) REVERT: C 42 LYS cc_start: 0.7453 (mmmt) cc_final: 0.7135 (mmmt) REVERT: C 64 LYS cc_start: 0.8342 (mtmt) cc_final: 0.7835 (mmmm) REVERT: C 189 LYS cc_start: 0.8055 (mmtt) cc_final: 0.7710 (mmmm) REVERT: C 196 ASP cc_start: 0.7455 (t0) cc_final: 0.7043 (t0) REVERT: C 197 GLU cc_start: 0.7346 (pp20) cc_final: 0.6907 (pp20) REVERT: C 211 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7281 (m-30) REVERT: C 277 GLU cc_start: 0.7206 (mp0) cc_final: 0.6697 (mp0) REVERT: C 293 ILE cc_start: 0.8034 (mm) cc_final: 0.7757 (tp) REVERT: C 297 GLU cc_start: 0.6901 (pm20) cc_final: 0.6388 (pm20) REVERT: C 643 LYS cc_start: 0.7429 (mtmm) cc_final: 0.7158 (mtmm) REVERT: C 664 GLU cc_start: 0.7299 (mp0) cc_final: 0.6592 (mp0) REVERT: C 691 LYS cc_start: 0.8050 (mtpp) cc_final: 0.7820 (mtpp) REVERT: C 705 ASP cc_start: 0.7722 (t0) cc_final: 0.7382 (t0) REVERT: C 709 LYS cc_start: 0.8148 (ttpt) cc_final: 0.7800 (ttpt) REVERT: C 730 GLN cc_start: 0.7491 (mt0) cc_final: 0.7279 (mt0) REVERT: D 89 LYS cc_start: 0.8321 (tptm) cc_final: 0.7909 (mmtt) REVERT: D 105 ILE cc_start: 0.8220 (tt) cc_final: 0.7783 (pt) REVERT: D 117 TYR cc_start: 0.7591 (t80) cc_final: 0.7286 (t80) REVERT: D 169 GLU cc_start: 0.7173 (mm-30) cc_final: 0.6707 (mm-30) REVERT: D 173 LYS cc_start: 0.7957 (tppt) cc_final: 0.7717 (tppt) REVERT: D 202 VAL cc_start: 0.8581 (p) cc_final: 0.8323 (m) REVERT: D 205 GLU cc_start: 0.7043 (tm-30) cc_final: 0.6644 (tm-30) REVERT: D 213 SER cc_start: 0.8569 (t) cc_final: 0.8110 (t) REVERT: D 260 LEU cc_start: 0.8756 (tp) cc_final: 0.8488 (tt) REVERT: D 269 GLN cc_start: 0.7859 (tp-100) cc_final: 0.7535 (tp-100) REVERT: D 287 ASP cc_start: 0.7576 (t70) cc_final: 0.7208 (t0) REVERT: D 303 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7306 (tm-30) REVERT: D 333 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7414 (mt-10) REVERT: D 341 GLU cc_start: 0.7398 (tp30) cc_final: 0.7028 (tp30) REVERT: D 363 LEU cc_start: 0.7846 (mt) cc_final: 0.7508 (mp) REVERT: D 364 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7011 (mt-10) REVERT: D 385 ILE cc_start: 0.8881 (mt) cc_final: 0.8653 (mt) REVERT: D 420 LYS cc_start: 0.8479 (tttt) cc_final: 0.8211 (ttpt) REVERT: D 554 LYS cc_start: 0.8367 (mttt) cc_final: 0.8031 (mtpp) REVERT: D 570 ASP cc_start: 0.7112 (t0) cc_final: 0.6669 (t0) REVERT: D 606 GLU cc_start: 0.7682 (tp30) cc_final: 0.7370 (tp30) REVERT: D 662 GLN cc_start: 0.7044 (tp-100) cc_final: 0.6748 (tm-30) REVERT: D 677 LYS cc_start: 0.8003 (mmtm) cc_final: 0.7800 (mmtm) REVERT: D 722 LEU cc_start: 0.8660 (tp) cc_final: 0.8429 (tp) REVERT: D 726 LEU cc_start: 0.8331 (mp) cc_final: 0.8069 (mt) REVERT: D 749 GLU cc_start: 0.7491 (tm-30) cc_final: 0.7154 (tm-30) REVERT: D 815 ARG cc_start: 0.7786 (ttm170) cc_final: 0.7386 (mtm-85) REVERT: D 867 GLU cc_start: 0.7811 (tp30) cc_final: 0.7458 (tp30) REVERT: D 921 LYS cc_start: 0.8199 (mtpt) cc_final: 0.7945 (mtmt) REVERT: D 942 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6838 (mm-30) REVERT: D 970 SER cc_start: 0.8219 (t) cc_final: 0.7738 (p) REVERT: D 1017 ASP cc_start: 0.7960 (t70) cc_final: 0.7552 (t0) REVERT: D 1046 GLN cc_start: 0.7489 (mm-40) cc_final: 0.7156 (mm-40) REVERT: D 1055 GLU cc_start: 0.7147 (tp30) cc_final: 0.6946 (tp30) REVERT: D 1058 LYS cc_start: 0.8386 (mttt) cc_final: 0.8101 (mttp) REVERT: D 1072 ARG cc_start: 0.7611 (ttm110) cc_final: 0.7352 (ttm110) REVERT: D 1105 GLU cc_start: 0.7680 (pm20) cc_final: 0.7430 (mp0) REVERT: D 1109 LYS cc_start: 0.8212 (tptm) cc_final: 0.7946 (tppp) REVERT: D 1139 GLU cc_start: 0.7046 (tm-30) cc_final: 0.6501 (tm-30) outliers start: 34 outliers final: 18 residues processed: 557 average time/residue: 0.3796 time to fit residues: 312.9930 Evaluate side-chains 535 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 516 time to evaluate : 2.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 1354 ASP Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 983 ASN Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 946 ASN Chi-restraints excluded: chain D residue 1047 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 114 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 171 optimal weight: 0.5980 chunk 140 optimal weight: 0.6980 chunk 56 optimal weight: 0.0040 chunk 206 optimal weight: 0.8980 chunk 223 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 204 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS B1283 GLN B1340 HIS B1386 ASN C 653 ASN C 659 ASN C 725 ASN D 72 GLN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19626 Z= 0.192 Angle : 0.525 7.550 26740 Z= 0.286 Chirality : 0.039 0.180 3101 Planarity : 0.004 0.072 3141 Dihedral : 18.051 82.568 3259 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.30 % Allowed : 16.83 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.17), residues: 2177 helix: 0.52 (0.14), residues: 1292 sheet: 0.60 (0.41), residues: 161 loop : -1.87 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1033 HIS 0.006 0.001 HIS D 541 PHE 0.029 0.002 PHE B 155 TYR 0.016 0.001 TYR D 529 ARG 0.006 0.000 ARG D 198 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 530 time to evaluate : 2.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 173 VAL cc_start: 0.8070 (m) cc_final: 0.7522 (t) REVERT: B 252 GLU cc_start: 0.7059 (pm20) cc_final: 0.6817 (pm20) REVERT: B 263 PHE cc_start: 0.8564 (m-80) cc_final: 0.7887 (m-80) REVERT: B 264 LYS cc_start: 0.8769 (mmtt) cc_final: 0.8405 (tppt) REVERT: B 269 LYS cc_start: 0.8032 (mtpt) cc_final: 0.7637 (mtpt) REVERT: B 288 ASN cc_start: 0.8061 (t0) cc_final: 0.7643 (t0) REVERT: B 289 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7692 (mm-30) REVERT: B 307 ASN cc_start: 0.8169 (m110) cc_final: 0.7947 (m110) REVERT: B 312 LYS cc_start: 0.8397 (mptt) cc_final: 0.8105 (mptt) REVERT: B 325 GLU cc_start: 0.7754 (mp0) cc_final: 0.7309 (mp0) REVERT: B 336 TYR cc_start: 0.8499 (m-80) cc_final: 0.8276 (m-10) REVERT: B 1249 ARG cc_start: 0.6993 (tmm-80) cc_final: 0.6731 (tmm-80) REVERT: B 1260 LYS cc_start: 0.7747 (mttt) cc_final: 0.7484 (mtpp) REVERT: B 1265 ASP cc_start: 0.7719 (t0) cc_final: 0.7487 (t0) REVERT: B 1292 GLU cc_start: 0.7013 (tp30) cc_final: 0.6787 (tp30) REVERT: B 1405 LYS cc_start: 0.8536 (mttt) cc_final: 0.8206 (mttm) REVERT: B 1412 ILE cc_start: 0.8243 (pt) cc_final: 0.7953 (pt) REVERT: A 28 ASN cc_start: 0.7279 (m-40) cc_final: 0.7042 (m-40) REVERT: A 54 MET cc_start: 0.7208 (mmt) cc_final: 0.6838 (mmt) REVERT: A 109 LEU cc_start: 0.8687 (mt) cc_final: 0.8403 (mp) REVERT: A 129 GLN cc_start: 0.7482 (tm-30) cc_final: 0.6912 (tm-30) REVERT: A 160 GLU cc_start: 0.7044 (mp0) cc_final: 0.6543 (mp0) REVERT: A 178 ARG cc_start: 0.7242 (tmm160) cc_final: 0.6655 (ttp-110) REVERT: A 182 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7454 (mm-30) REVERT: A 187 LYS cc_start: 0.8551 (tppt) cc_final: 0.8187 (tppt) REVERT: A 189 GLU cc_start: 0.7756 (tp30) cc_final: 0.7479 (tp30) REVERT: A 209 LYS cc_start: 0.7309 (mmtm) cc_final: 0.6970 (mmtm) REVERT: A 985 ASN cc_start: 0.7950 (p0) cc_final: 0.7452 (p0) REVERT: A 994 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7097 (mm-30) REVERT: A 1005 LYS cc_start: 0.7923 (mttt) cc_final: 0.7613 (mttp) REVERT: A 1009 LYS cc_start: 0.7673 (tttt) cc_final: 0.7348 (ttmm) REVERT: A 1016 GLU cc_start: 0.7277 (tt0) cc_final: 0.6905 (tt0) REVERT: A 1023 GLU cc_start: 0.6991 (tp30) cc_final: 0.6701 (tp30) REVERT: A 1082 ILE cc_start: 0.8582 (tp) cc_final: 0.8025 (pt) REVERT: A 1146 GLU cc_start: 0.7314 (tt0) cc_final: 0.6661 (tt0) REVERT: C 42 LYS cc_start: 0.7427 (mmmt) cc_final: 0.7106 (mmmt) REVERT: C 64 LYS cc_start: 0.8296 (mtmt) cc_final: 0.7824 (mmmm) REVERT: C 99 LYS cc_start: 0.7947 (mttp) cc_final: 0.7640 (mtmm) REVERT: C 170 PHE cc_start: 0.7972 (t80) cc_final: 0.7592 (t80) REVERT: C 174 LYS cc_start: 0.7940 (ttmm) cc_final: 0.7569 (ttmm) REVERT: C 189 LYS cc_start: 0.8037 (mmtt) cc_final: 0.7723 (mmmm) REVERT: C 196 ASP cc_start: 0.7438 (t0) cc_final: 0.7060 (t0) REVERT: C 197 GLU cc_start: 0.7381 (pp20) cc_final: 0.6924 (pp20) REVERT: C 211 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7254 (m-30) REVERT: C 277 GLU cc_start: 0.7158 (mp0) cc_final: 0.6679 (mp0) REVERT: C 293 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7593 (tp) REVERT: C 297 GLU cc_start: 0.6883 (pm20) cc_final: 0.6321 (pm20) REVERT: C 643 LYS cc_start: 0.7461 (mtmm) cc_final: 0.7141 (mtmm) REVERT: C 664 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6666 (mp0) REVERT: C 705 ASP cc_start: 0.7683 (t0) cc_final: 0.7371 (t0) REVERT: C 709 LYS cc_start: 0.8119 (ttpt) cc_final: 0.7775 (ttpt) REVERT: C 730 GLN cc_start: 0.7468 (mt0) cc_final: 0.7242 (mt0) REVERT: D 89 LYS cc_start: 0.8321 (tptm) cc_final: 0.7912 (mmtt) REVERT: D 105 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7778 (pt) REVERT: D 117 TYR cc_start: 0.7600 (t80) cc_final: 0.7238 (t80) REVERT: D 169 GLU cc_start: 0.7122 (mm-30) cc_final: 0.6788 (mm-30) REVERT: D 173 LYS cc_start: 0.7949 (tppt) cc_final: 0.7693 (tppt) REVERT: D 202 VAL cc_start: 0.8592 (p) cc_final: 0.8324 (m) REVERT: D 205 GLU cc_start: 0.7036 (tm-30) cc_final: 0.6587 (tm-30) REVERT: D 213 SER cc_start: 0.8773 (t) cc_final: 0.8379 (p) REVERT: D 260 LEU cc_start: 0.8747 (tp) cc_final: 0.8458 (tt) REVERT: D 269 GLN cc_start: 0.7825 (tp-100) cc_final: 0.7525 (tp-100) REVERT: D 341 GLU cc_start: 0.7437 (tp30) cc_final: 0.7078 (tp30) REVERT: D 363 LEU cc_start: 0.7835 (mt) cc_final: 0.7472 (mp) REVERT: D 364 GLU cc_start: 0.7427 (mt-10) cc_final: 0.6868 (mt-10) REVERT: D 394 LYS cc_start: 0.7801 (tptp) cc_final: 0.7574 (tptp) REVERT: D 420 LYS cc_start: 0.8458 (tttt) cc_final: 0.8211 (ttpt) REVERT: D 554 LYS cc_start: 0.8366 (mttt) cc_final: 0.8029 (mtpp) REVERT: D 570 ASP cc_start: 0.7202 (t0) cc_final: 0.6841 (t0) REVERT: D 606 GLU cc_start: 0.7677 (tp30) cc_final: 0.7233 (tp30) REVERT: D 662 GLN cc_start: 0.7101 (tp-100) cc_final: 0.6641 (tm-30) REVERT: D 698 GLU cc_start: 0.6651 (mp0) cc_final: 0.6207 (mp0) REVERT: D 722 LEU cc_start: 0.8720 (tp) cc_final: 0.8499 (tp) REVERT: D 726 LEU cc_start: 0.8349 (mp) cc_final: 0.8066 (mt) REVERT: D 749 GLU cc_start: 0.7514 (tm-30) cc_final: 0.7086 (tm-30) REVERT: D 776 TYR cc_start: 0.8022 (t80) cc_final: 0.7058 (t80) REVERT: D 791 MET cc_start: 0.7948 (tmm) cc_final: 0.7743 (tmm) REVERT: D 815 ARG cc_start: 0.7776 (ttm170) cc_final: 0.7439 (mtt90) REVERT: D 860 TYR cc_start: 0.7646 (t80) cc_final: 0.7290 (t80) REVERT: D 867 GLU cc_start: 0.7841 (tp30) cc_final: 0.7490 (tp30) REVERT: D 921 LYS cc_start: 0.8186 (mtpt) cc_final: 0.7943 (mtmt) REVERT: D 970 SER cc_start: 0.8224 (t) cc_final: 0.7662 (p) REVERT: D 1004 MET cc_start: 0.7145 (mmm) cc_final: 0.6589 (mmm) REVERT: D 1017 ASP cc_start: 0.7969 (t70) cc_final: 0.7576 (t0) REVERT: D 1046 GLN cc_start: 0.7387 (mm-40) cc_final: 0.7117 (mm-40) REVERT: D 1055 GLU cc_start: 0.7147 (tp30) cc_final: 0.6843 (tp30) REVERT: D 1058 LYS cc_start: 0.8324 (mttt) cc_final: 0.8022 (mtmm) REVERT: D 1077 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7269 (mm-30) REVERT: D 1105 GLU cc_start: 0.7613 (pm20) cc_final: 0.7316 (mp0) REVERT: D 1107 PHE cc_start: 0.8048 (t80) cc_final: 0.7846 (t80) REVERT: D 1109 LYS cc_start: 0.8196 (tptm) cc_final: 0.7934 (tppp) REVERT: D 1139 GLU cc_start: 0.7045 (tm-30) cc_final: 0.6520 (tm-30) REVERT: D 1143 GLN cc_start: 0.7591 (mp10) cc_final: 0.7115 (mp10) outliers start: 46 outliers final: 23 residues processed: 550 average time/residue: 0.3505 time to fit residues: 280.3220 Evaluate side-chains 541 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 514 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 1307 THR Chi-restraints excluded: chain B residue 1314 LYS Chi-restraints excluded: chain B residue 1319 ASN Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 983 ASN Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1019 SER Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 664 GLU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 946 ASN Chi-restraints excluded: chain D residue 988 SER Chi-restraints excluded: chain D residue 1047 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 204 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 chunk 207 optimal weight: 0.2980 chunk 219 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 ASN B 235 HIS B 266 ASN B1386 ASN ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 ASN D1158 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19626 Z= 0.264 Angle : 0.556 8.270 26740 Z= 0.298 Chirality : 0.041 0.180 3101 Planarity : 0.004 0.075 3141 Dihedral : 17.822 88.034 3259 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.80 % Allowed : 17.53 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.18), residues: 2177 helix: 0.83 (0.14), residues: 1297 sheet: 0.66 (0.41), residues: 166 loop : -1.66 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1033 HIS 0.006 0.001 HIS D 541 PHE 0.022 0.002 PHE B1302 TYR 0.019 0.002 TYR D1086 ARG 0.005 0.000 ARG D1022 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 527 time to evaluate : 2.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 VAL cc_start: 0.8078 (m) cc_final: 0.7600 (t) REVERT: B 213 ARG cc_start: 0.8106 (mtm110) cc_final: 0.7861 (mtp-110) REVERT: B 252 GLU cc_start: 0.7053 (pm20) cc_final: 0.6786 (pm20) REVERT: B 264 LYS cc_start: 0.8801 (mmtt) cc_final: 0.8438 (tppt) REVERT: B 288 ASN cc_start: 0.8012 (t0) cc_final: 0.7610 (t0) REVERT: B 289 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7710 (mm-30) REVERT: B 307 ASN cc_start: 0.8123 (m110) cc_final: 0.7871 (m110) REVERT: B 312 LYS cc_start: 0.8480 (mptt) cc_final: 0.8155 (mptt) REVERT: B 325 GLU cc_start: 0.7759 (mp0) cc_final: 0.7286 (mp0) REVERT: B 336 TYR cc_start: 0.8482 (m-80) cc_final: 0.8265 (m-10) REVERT: B 1260 LYS cc_start: 0.7777 (mttt) cc_final: 0.7515 (mtpp) REVERT: B 1265 ASP cc_start: 0.7787 (t0) cc_final: 0.7548 (t0) REVERT: B 1281 MET cc_start: 0.7146 (mmt) cc_final: 0.6697 (mpp) REVERT: B 1322 ASN cc_start: 0.7990 (p0) cc_final: 0.7574 (t0) REVERT: B 1373 THR cc_start: 0.8516 (m) cc_final: 0.8302 (t) REVERT: B 1405 LYS cc_start: 0.8598 (mttt) cc_final: 0.8233 (mttm) REVERT: B 1412 ILE cc_start: 0.8202 (pt) cc_final: 0.7931 (pt) REVERT: A 19 VAL cc_start: 0.8548 (t) cc_final: 0.8282 (p) REVERT: A 28 ASN cc_start: 0.7272 (m-40) cc_final: 0.7016 (m-40) REVERT: A 54 MET cc_start: 0.7156 (mmt) cc_final: 0.6817 (mmt) REVERT: A 109 LEU cc_start: 0.8710 (mt) cc_final: 0.8402 (mp) REVERT: A 129 GLN cc_start: 0.7508 (tm-30) cc_final: 0.7134 (tm-30) REVERT: A 160 GLU cc_start: 0.7036 (mp0) cc_final: 0.6570 (mp0) REVERT: A 178 ARG cc_start: 0.7063 (tmm160) cc_final: 0.6763 (ttp-110) REVERT: A 187 LYS cc_start: 0.8579 (tppt) cc_final: 0.8231 (tppt) REVERT: A 209 LYS cc_start: 0.7369 (mmtm) cc_final: 0.7066 (mmtm) REVERT: A 985 ASN cc_start: 0.8010 (p0) cc_final: 0.7484 (p0) REVERT: A 994 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7145 (mm-30) REVERT: A 1001 LYS cc_start: 0.7659 (mmmm) cc_final: 0.7333 (mmmm) REVERT: A 1005 LYS cc_start: 0.7901 (mttt) cc_final: 0.7496 (mttp) REVERT: A 1009 LYS cc_start: 0.7663 (tttt) cc_final: 0.7340 (ttmm) REVERT: A 1016 GLU cc_start: 0.7197 (tt0) cc_final: 0.6875 (tt0) REVERT: A 1082 ILE cc_start: 0.8685 (tp) cc_final: 0.8326 (tp) REVERT: A 1146 GLU cc_start: 0.7286 (tt0) cc_final: 0.6786 (tt0) REVERT: A 1157 ARG cc_start: 0.7658 (mtp85) cc_final: 0.7081 (mtp85) REVERT: C 42 LYS cc_start: 0.7361 (mmmt) cc_final: 0.7040 (mmmt) REVERT: C 64 LYS cc_start: 0.8461 (mtmt) cc_final: 0.7933 (mmmm) REVERT: C 170 PHE cc_start: 0.8130 (t80) cc_final: 0.7579 (t80) REVERT: C 174 LYS cc_start: 0.8032 (ttmm) cc_final: 0.7723 (ttmm) REVERT: C 189 LYS cc_start: 0.8110 (mmtt) cc_final: 0.7739 (mmmm) REVERT: C 197 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6995 (pp20) REVERT: C 293 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7593 (tp) REVERT: C 297 GLU cc_start: 0.6966 (pm20) cc_final: 0.6439 (pm20) REVERT: C 643 LYS cc_start: 0.7449 (mtmm) cc_final: 0.7222 (mtmm) REVERT: C 664 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6562 (mp0) REVERT: C 705 ASP cc_start: 0.7658 (t0) cc_final: 0.7354 (t0) REVERT: C 709 LYS cc_start: 0.8112 (ttpt) cc_final: 0.7779 (ttpt) REVERT: C 730 GLN cc_start: 0.7529 (mt0) cc_final: 0.7285 (mt0) REVERT: D 89 LYS cc_start: 0.8377 (tptm) cc_final: 0.7955 (mmtt) REVERT: D 105 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7741 (pt) REVERT: D 117 TYR cc_start: 0.7600 (t80) cc_final: 0.7282 (t80) REVERT: D 127 GLN cc_start: 0.7870 (pp30) cc_final: 0.7297 (tm-30) REVERT: D 173 LYS cc_start: 0.7953 (tppt) cc_final: 0.7689 (tppt) REVERT: D 202 VAL cc_start: 0.8632 (p) cc_final: 0.8294 (m) REVERT: D 205 GLU cc_start: 0.7100 (tm-30) cc_final: 0.6615 (tm-30) REVERT: D 241 MET cc_start: 0.7690 (tpt) cc_final: 0.7418 (tpt) REVERT: D 260 LEU cc_start: 0.8771 (tp) cc_final: 0.8477 (tt) REVERT: D 269 GLN cc_start: 0.7872 (tp-100) cc_final: 0.7593 (tp-100) REVERT: D 303 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7194 (tm-30) REVERT: D 333 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7129 (mm-30) REVERT: D 341 GLU cc_start: 0.7503 (tp30) cc_final: 0.7143 (tp30) REVERT: D 363 LEU cc_start: 0.7897 (mt) cc_final: 0.7508 (mp) REVERT: D 394 LYS cc_start: 0.7854 (tptp) cc_final: 0.7621 (tptp) REVERT: D 420 LYS cc_start: 0.8503 (tttt) cc_final: 0.8257 (ttpt) REVERT: D 554 LYS cc_start: 0.8366 (mttt) cc_final: 0.8027 (mtpp) REVERT: D 570 ASP cc_start: 0.7245 (t0) cc_final: 0.6928 (t0) REVERT: D 606 GLU cc_start: 0.7671 (tp30) cc_final: 0.7227 (tp30) REVERT: D 662 GLN cc_start: 0.7075 (tp-100) cc_final: 0.6616 (tm-30) REVERT: D 722 LEU cc_start: 0.8727 (tp) cc_final: 0.8519 (tp) REVERT: D 726 LEU cc_start: 0.8433 (mp) cc_final: 0.8167 (mt) REVERT: D 749 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7072 (tm-30) REVERT: D 815 ARG cc_start: 0.7761 (ttm170) cc_final: 0.7460 (mtt90) REVERT: D 867 GLU cc_start: 0.7901 (tp30) cc_final: 0.7608 (tp30) REVERT: D 921 LYS cc_start: 0.8177 (mtpt) cc_final: 0.7970 (mtmt) REVERT: D 970 SER cc_start: 0.8281 (t) cc_final: 0.7679 (p) REVERT: D 1004 MET cc_start: 0.7191 (mmm) cc_final: 0.6711 (mmm) REVERT: D 1017 ASP cc_start: 0.7984 (t70) cc_final: 0.7587 (t0) REVERT: D 1027 ASN cc_start: 0.7618 (t0) cc_final: 0.7297 (t0) REVERT: D 1055 GLU cc_start: 0.7191 (tp30) cc_final: 0.6973 (tp30) REVERT: D 1058 LYS cc_start: 0.8397 (mttt) cc_final: 0.8156 (mttp) REVERT: D 1109 LYS cc_start: 0.8246 (tptm) cc_final: 0.7986 (tppp) REVERT: D 1139 GLU cc_start: 0.7067 (tm-30) cc_final: 0.6519 (tm-30) outliers start: 56 outliers final: 33 residues processed: 554 average time/residue: 0.3455 time to fit residues: 281.9035 Evaluate side-chains 556 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 519 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 1319 ASN Chi-restraints excluded: chain B residue 1375 ASN Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 983 ASN Chi-restraints excluded: chain A residue 1019 SER Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 209 ASN Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 664 GLU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 368 GLN Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 946 ASN Chi-restraints excluded: chain D residue 988 SER Chi-restraints excluded: chain D residue 1047 VAL Chi-restraints excluded: chain D residue 1056 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 182 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 163 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 187 optimal weight: 0.8980 chunk 151 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 ASN B 235 HIS B 266 ASN A 195 ASN A1151 ASN C 321 ASN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 19626 Z= 0.310 Angle : 0.573 6.943 26740 Z= 0.309 Chirality : 0.042 0.176 3101 Planarity : 0.004 0.075 3141 Dihedral : 17.659 87.079 3257 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.15 % Allowed : 18.53 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.18), residues: 2177 helix: 0.96 (0.14), residues: 1290 sheet: 0.65 (0.41), residues: 166 loop : -1.55 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1033 HIS 0.007 0.001 HIS D 541 PHE 0.023 0.002 PHE B1302 TYR 0.019 0.002 TYR D 789 ARG 0.003 0.000 ARG B 297 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 527 time to evaluate : 2.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 VAL cc_start: 0.8113 (m) cc_final: 0.7675 (t) REVERT: B 252 GLU cc_start: 0.7069 (pm20) cc_final: 0.6823 (pm20) REVERT: B 264 LYS cc_start: 0.8792 (mmtt) cc_final: 0.8421 (tppt) REVERT: B 288 ASN cc_start: 0.8014 (t0) cc_final: 0.7599 (t0) REVERT: B 289 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7874 (mm-30) REVERT: B 307 ASN cc_start: 0.8145 (m110) cc_final: 0.7892 (m110) REVERT: B 312 LYS cc_start: 0.8485 (mptt) cc_final: 0.8163 (mptt) REVERT: B 325 GLU cc_start: 0.7757 (mp0) cc_final: 0.7295 (mp0) REVERT: B 1260 LYS cc_start: 0.7833 (mttt) cc_final: 0.7556 (mtpp) REVERT: B 1265 ASP cc_start: 0.7804 (t0) cc_final: 0.7543 (t0) REVERT: B 1271 PHE cc_start: 0.7943 (t80) cc_final: 0.7618 (t80) REVERT: B 1281 MET cc_start: 0.7275 (mmt) cc_final: 0.6867 (mpp) REVERT: B 1322 ASN cc_start: 0.7900 (p0) cc_final: 0.7567 (t0) REVERT: B 1367 ASN cc_start: 0.7834 (m-40) cc_final: 0.7562 (m-40) REVERT: B 1373 THR cc_start: 0.8383 (m) cc_final: 0.8120 (t) REVERT: B 1405 LYS cc_start: 0.8614 (mttt) cc_final: 0.8233 (mttm) REVERT: B 1412 ILE cc_start: 0.8120 (pt) cc_final: 0.7889 (pt) REVERT: A 19 VAL cc_start: 0.8588 (t) cc_final: 0.8302 (p) REVERT: A 28 ASN cc_start: 0.7282 (m-40) cc_final: 0.6995 (m-40) REVERT: A 54 MET cc_start: 0.7075 (mmt) cc_final: 0.6499 (mmp) REVERT: A 109 LEU cc_start: 0.8711 (mt) cc_final: 0.8393 (mp) REVERT: A 129 GLN cc_start: 0.7540 (tm-30) cc_final: 0.7155 (tm-30) REVERT: A 160 GLU cc_start: 0.7049 (mp0) cc_final: 0.6622 (mp0) REVERT: A 178 ARG cc_start: 0.7169 (tmm160) cc_final: 0.6786 (ttp-110) REVERT: A 187 LYS cc_start: 0.8573 (tppt) cc_final: 0.8230 (tppt) REVERT: A 191 LYS cc_start: 0.8423 (tppt) cc_final: 0.8097 (ttmm) REVERT: A 209 LYS cc_start: 0.7381 (mmtm) cc_final: 0.7144 (mmtm) REVERT: A 985 ASN cc_start: 0.8068 (p0) cc_final: 0.7536 (p0) REVERT: A 994 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7167 (mm-30) REVERT: A 1005 LYS cc_start: 0.7894 (mttt) cc_final: 0.7594 (mttp) REVERT: A 1008 GLU cc_start: 0.6800 (tp30) cc_final: 0.6599 (tp30) REVERT: A 1009 LYS cc_start: 0.7687 (tttt) cc_final: 0.7370 (ttmm) REVERT: A 1011 LYS cc_start: 0.8243 (tttt) cc_final: 0.7989 (tttt) REVERT: A 1016 GLU cc_start: 0.7242 (tt0) cc_final: 0.6902 (tt0) REVERT: A 1082 ILE cc_start: 0.8689 (tp) cc_final: 0.8345 (tp) REVERT: A 1146 GLU cc_start: 0.7290 (tt0) cc_final: 0.6810 (tt0) REVERT: C 32 GLU cc_start: 0.7930 (tp30) cc_final: 0.7588 (mm-30) REVERT: C 42 LYS cc_start: 0.7387 (mmmt) cc_final: 0.7064 (mmmt) REVERT: C 64 LYS cc_start: 0.8495 (mtmt) cc_final: 0.7958 (mmmm) REVERT: C 84 LYS cc_start: 0.8065 (mmtp) cc_final: 0.7836 (mmtp) REVERT: C 170 PHE cc_start: 0.8120 (t80) cc_final: 0.7563 (t80) REVERT: C 174 LYS cc_start: 0.8071 (ttmm) cc_final: 0.7700 (ttmm) REVERT: C 189 LYS cc_start: 0.8120 (mmtt) cc_final: 0.7748 (mmmm) REVERT: C 197 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6998 (pp20) REVERT: C 293 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7591 (tp) REVERT: C 297 GLU cc_start: 0.6993 (pm20) cc_final: 0.6470 (pm20) REVERT: C 705 ASP cc_start: 0.7681 (t0) cc_final: 0.7382 (t0) REVERT: C 709 LYS cc_start: 0.8105 (ttpt) cc_final: 0.7771 (ttpt) REVERT: C 730 GLN cc_start: 0.7487 (mt0) cc_final: 0.7191 (mt0) REVERT: D 89 LYS cc_start: 0.8384 (tptm) cc_final: 0.7986 (mmtt) REVERT: D 105 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7740 (pt) REVERT: D 117 TYR cc_start: 0.7630 (t80) cc_final: 0.7328 (t80) REVERT: D 127 GLN cc_start: 0.7863 (pp30) cc_final: 0.7258 (tm-30) REVERT: D 173 LYS cc_start: 0.7992 (tppt) cc_final: 0.7440 (tppt) REVERT: D 202 VAL cc_start: 0.8653 (p) cc_final: 0.8287 (m) REVERT: D 205 GLU cc_start: 0.7121 (tm-30) cc_final: 0.6635 (tm-30) REVERT: D 269 GLN cc_start: 0.7900 (tp-100) cc_final: 0.7604 (tp-100) REVERT: D 303 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7189 (tm-30) REVERT: D 341 GLU cc_start: 0.7549 (tp30) cc_final: 0.7175 (tp30) REVERT: D 363 LEU cc_start: 0.7909 (mt) cc_final: 0.7452 (mp) REVERT: D 394 LYS cc_start: 0.7819 (tptp) cc_final: 0.7553 (tptp) REVERT: D 420 LYS cc_start: 0.8513 (tttt) cc_final: 0.8281 (ttpt) REVERT: D 554 LYS cc_start: 0.8365 (mttt) cc_final: 0.8028 (mtpp) REVERT: D 570 ASP cc_start: 0.7288 (t0) cc_final: 0.6984 (t0) REVERT: D 606 GLU cc_start: 0.7735 (tp30) cc_final: 0.7196 (tp30) REVERT: D 662 GLN cc_start: 0.7085 (tp-100) cc_final: 0.6607 (tm-30) REVERT: D 698 GLU cc_start: 0.6669 (mp0) cc_final: 0.6169 (mp0) REVERT: D 722 LEU cc_start: 0.8668 (tp) cc_final: 0.8307 (tt) REVERT: D 749 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7048 (tm-30) REVERT: D 791 MET cc_start: 0.7975 (tmm) cc_final: 0.7678 (tmm) REVERT: D 815 ARG cc_start: 0.7785 (ttm170) cc_final: 0.7473 (mtt90) REVERT: D 921 LYS cc_start: 0.8184 (mtpt) cc_final: 0.7938 (mtmt) REVERT: D 970 SER cc_start: 0.8326 (t) cc_final: 0.7687 (p) REVERT: D 1004 MET cc_start: 0.7160 (mmm) cc_final: 0.6698 (mmm) REVERT: D 1017 ASP cc_start: 0.7993 (t70) cc_final: 0.7620 (t0) REVERT: D 1055 GLU cc_start: 0.7300 (tp30) cc_final: 0.7084 (tp30) REVERT: D 1058 LYS cc_start: 0.8414 (mttt) cc_final: 0.8185 (mttp) REVERT: D 1109 LYS cc_start: 0.8233 (tptm) cc_final: 0.7975 (tppp) REVERT: D 1139 GLU cc_start: 0.7090 (tm-30) cc_final: 0.6524 (tm-30) outliers start: 63 outliers final: 40 residues processed: 556 average time/residue: 0.3898 time to fit residues: 321.2933 Evaluate side-chains 563 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 520 time to evaluate : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 1295 LEU Chi-restraints excluded: chain B residue 1319 ASN Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 983 ASN Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 946 ASN Chi-restraints excluded: chain D residue 988 SER Chi-restraints excluded: chain D residue 1047 VAL Chi-restraints excluded: chain D residue 1056 MET Chi-restraints excluded: chain D residue 1060 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 73 optimal weight: 2.9990 chunk 197 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 219 optimal weight: 0.9980 chunk 182 optimal weight: 0.9980 chunk 101 optimal weight: 0.0470 chunk 18 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS B 266 ASN A 195 ASN D 37 GLN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19626 Z= 0.208 Angle : 0.542 10.085 26740 Z= 0.290 Chirality : 0.040 0.170 3101 Planarity : 0.003 0.071 3141 Dihedral : 17.491 88.310 3257 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.95 % Allowed : 19.43 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.18), residues: 2177 helix: 1.22 (0.14), residues: 1291 sheet: 0.89 (0.41), residues: 161 loop : -1.42 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1033 HIS 0.006 0.001 HIS D 541 PHE 0.027 0.002 PHE A 217 TYR 0.021 0.001 TYR D1086 ARG 0.006 0.000 ARG D 198 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 537 time to evaluate : 1.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 VAL cc_start: 0.7941 (m) cc_final: 0.7440 (t) REVERT: B 213 ARG cc_start: 0.8129 (mtm110) cc_final: 0.7538 (mtm110) REVERT: B 224 PHE cc_start: 0.8641 (m-80) cc_final: 0.8244 (m-80) REVERT: B 252 GLU cc_start: 0.7087 (pm20) cc_final: 0.6794 (pm20) REVERT: B 264 LYS cc_start: 0.8783 (mmtt) cc_final: 0.8398 (tppt) REVERT: B 269 LYS cc_start: 0.8000 (mtpt) cc_final: 0.7521 (mtpt) REVERT: B 289 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7848 (mm-30) REVERT: B 307 ASN cc_start: 0.8144 (m110) cc_final: 0.7896 (m110) REVERT: B 312 LYS cc_start: 0.8463 (mptt) cc_final: 0.8173 (mptt) REVERT: B 325 GLU cc_start: 0.7753 (mp0) cc_final: 0.7294 (mp0) REVERT: B 1260 LYS cc_start: 0.7780 (mttt) cc_final: 0.7498 (mtpp) REVERT: B 1265 ASP cc_start: 0.7741 (t0) cc_final: 0.7511 (t0) REVERT: B 1271 PHE cc_start: 0.7918 (t80) cc_final: 0.7604 (t80) REVERT: B 1281 MET cc_start: 0.7278 (mmt) cc_final: 0.6804 (mpp) REVERT: B 1317 TRP cc_start: 0.8395 (m100) cc_final: 0.8195 (m100) REVERT: B 1322 ASN cc_start: 0.7914 (p0) cc_final: 0.7657 (t0) REVERT: B 1367 ASN cc_start: 0.7767 (m-40) cc_final: 0.7486 (m-40) REVERT: B 1374 LYS cc_start: 0.8247 (mtpt) cc_final: 0.7936 (mtpt) REVERT: B 1405 LYS cc_start: 0.8592 (mttt) cc_final: 0.8217 (mttm) REVERT: B 1412 ILE cc_start: 0.8218 (pt) cc_final: 0.7943 (pt) REVERT: A 19 VAL cc_start: 0.8547 (t) cc_final: 0.8255 (p) REVERT: A 28 ASN cc_start: 0.7204 (m-40) cc_final: 0.6948 (m-40) REVERT: A 54 MET cc_start: 0.7039 (mmt) cc_final: 0.6461 (mmm) REVERT: A 109 LEU cc_start: 0.8684 (mt) cc_final: 0.8386 (mp) REVERT: A 129 GLN cc_start: 0.7535 (tm-30) cc_final: 0.7146 (tm-30) REVERT: A 160 GLU cc_start: 0.7092 (mp0) cc_final: 0.6683 (mp0) REVERT: A 178 ARG cc_start: 0.7157 (tmm160) cc_final: 0.6840 (ttp-170) REVERT: A 180 LYS cc_start: 0.8325 (mttm) cc_final: 0.8116 (mtpp) REVERT: A 187 LYS cc_start: 0.8573 (tppt) cc_final: 0.8230 (tppt) REVERT: A 191 LYS cc_start: 0.8402 (tppt) cc_final: 0.8157 (ttmm) REVERT: A 208 GLU cc_start: 0.5818 (OUTLIER) cc_final: 0.5594 (pp20) REVERT: A 209 LYS cc_start: 0.7323 (mmtm) cc_final: 0.6886 (mmtm) REVERT: A 985 ASN cc_start: 0.8086 (p0) cc_final: 0.7339 (p0) REVERT: A 994 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7118 (mm-30) REVERT: A 1005 LYS cc_start: 0.7903 (mttt) cc_final: 0.7596 (mttp) REVERT: A 1008 GLU cc_start: 0.6807 (tp30) cc_final: 0.6586 (tp30) REVERT: A 1009 LYS cc_start: 0.7665 (tttt) cc_final: 0.7352 (ttmm) REVERT: A 1016 GLU cc_start: 0.7229 (tt0) cc_final: 0.6873 (tt0) REVERT: A 1082 ILE cc_start: 0.8718 (tp) cc_final: 0.8372 (tp) REVERT: A 1146 GLU cc_start: 0.7310 (tt0) cc_final: 0.6841 (tt0) REVERT: C 33 GLU cc_start: 0.6419 (pp20) cc_final: 0.5939 (pp20) REVERT: C 42 LYS cc_start: 0.7382 (mmmt) cc_final: 0.7017 (mmmt) REVERT: C 64 LYS cc_start: 0.8458 (mtmt) cc_final: 0.7939 (mmmm) REVERT: C 84 LYS cc_start: 0.7968 (mmtp) cc_final: 0.7719 (mmtp) REVERT: C 170 PHE cc_start: 0.8060 (t80) cc_final: 0.7515 (t80) REVERT: C 174 LYS cc_start: 0.8057 (ttmm) cc_final: 0.7734 (ttmm) REVERT: C 189 LYS cc_start: 0.8098 (mmtt) cc_final: 0.7760 (mmmm) REVERT: C 196 ASP cc_start: 0.7464 (t0) cc_final: 0.7058 (t0) REVERT: C 197 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7008 (pp20) REVERT: C 293 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7599 (tp) REVERT: C 297 GLU cc_start: 0.7080 (pm20) cc_final: 0.6513 (pm20) REVERT: C 705 ASP cc_start: 0.7672 (t0) cc_final: 0.7379 (t0) REVERT: C 709 LYS cc_start: 0.8084 (ttpt) cc_final: 0.7760 (ttpt) REVERT: C 730 GLN cc_start: 0.7524 (mt0) cc_final: 0.7272 (mt0) REVERT: D 8 GLU cc_start: 0.7764 (pm20) cc_final: 0.7558 (pm20) REVERT: D 68 LYS cc_start: 0.7411 (tptp) cc_final: 0.7205 (tptp) REVERT: D 89 LYS cc_start: 0.8344 (tptm) cc_final: 0.7904 (mmtt) REVERT: D 105 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7702 (pt) REVERT: D 117 TYR cc_start: 0.7657 (t80) cc_final: 0.7307 (t80) REVERT: D 127 GLN cc_start: 0.7900 (pp30) cc_final: 0.7348 (tm-30) REVERT: D 173 LYS cc_start: 0.7921 (tppt) cc_final: 0.7348 (tppt) REVERT: D 198 ARG cc_start: 0.8221 (ttp-110) cc_final: 0.7773 (mtp85) REVERT: D 202 VAL cc_start: 0.8624 (p) cc_final: 0.8297 (m) REVERT: D 205 GLU cc_start: 0.7099 (tm-30) cc_final: 0.6583 (tm-30) REVERT: D 213 SER cc_start: 0.8776 (OUTLIER) cc_final: 0.8501 (p) REVERT: D 241 MET cc_start: 0.7671 (tpt) cc_final: 0.7335 (tpt) REVERT: D 260 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8522 (tt) REVERT: D 269 GLN cc_start: 0.7879 (tp-100) cc_final: 0.7569 (tp-100) REVERT: D 303 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7179 (tm-30) REVERT: D 312 GLN cc_start: 0.7778 (mm-40) cc_final: 0.7480 (tp-100) REVERT: D 333 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7113 (mm-30) REVERT: D 341 GLU cc_start: 0.7508 (tp30) cc_final: 0.7131 (tp30) REVERT: D 363 LEU cc_start: 0.7891 (mt) cc_final: 0.7464 (mp) REVERT: D 420 LYS cc_start: 0.8477 (tttt) cc_final: 0.8234 (ttpt) REVERT: D 554 LYS cc_start: 0.8360 (mttt) cc_final: 0.8015 (mtpp) REVERT: D 570 ASP cc_start: 0.7176 (t0) cc_final: 0.6881 (t0) REVERT: D 606 GLU cc_start: 0.7646 (tp30) cc_final: 0.7122 (tp30) REVERT: D 662 GLN cc_start: 0.7034 (tp-100) cc_final: 0.6536 (tm-30) REVERT: D 698 GLU cc_start: 0.6672 (mp0) cc_final: 0.6160 (mp0) REVERT: D 722 LEU cc_start: 0.8657 (tp) cc_final: 0.8092 (tt) REVERT: D 749 GLU cc_start: 0.7579 (tm-30) cc_final: 0.7022 (tm-30) REVERT: D 791 MET cc_start: 0.7954 (tmm) cc_final: 0.7720 (tmm) REVERT: D 815 ARG cc_start: 0.7738 (ttm170) cc_final: 0.7449 (mtt90) REVERT: D 867 GLU cc_start: 0.7874 (tp30) cc_final: 0.7439 (tp30) REVERT: D 921 LYS cc_start: 0.8190 (mtpt) cc_final: 0.7912 (mtmt) REVERT: D 924 GLU cc_start: 0.7128 (tt0) cc_final: 0.6748 (tt0) REVERT: D 970 SER cc_start: 0.8262 (t) cc_final: 0.7673 (p) REVERT: D 980 LEU cc_start: 0.8225 (tp) cc_final: 0.7767 (mt) REVERT: D 1004 MET cc_start: 0.7153 (mmm) cc_final: 0.6712 (mmm) REVERT: D 1017 ASP cc_start: 0.7967 (t70) cc_final: 0.7600 (t0) REVERT: D 1027 ASN cc_start: 0.7630 (t0) cc_final: 0.7194 (t0) REVERT: D 1055 GLU cc_start: 0.7244 (tp30) cc_final: 0.7007 (tp30) REVERT: D 1058 LYS cc_start: 0.8387 (mttt) cc_final: 0.8154 (mttp) REVERT: D 1077 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7281 (mm-30) REVERT: D 1109 LYS cc_start: 0.8240 (tptm) cc_final: 0.7966 (tppp) REVERT: D 1139 GLU cc_start: 0.7111 (tm-30) cc_final: 0.6540 (tm-30) outliers start: 59 outliers final: 32 residues processed: 567 average time/residue: 0.3505 time to fit residues: 290.3642 Evaluate side-chains 560 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 522 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 1319 ASN Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 983 ASN Chi-restraints excluded: chain A residue 1019 SER Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 857 THR Chi-restraints excluded: chain D residue 988 SER Chi-restraints excluded: chain D residue 1029 MET Chi-restraints excluded: chain D residue 1047 VAL Chi-restraints excluded: chain D residue 1056 MET Chi-restraints excluded: chain D residue 1127 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 211 optimal weight: 0.4980 chunk 24 optimal weight: 0.0980 chunk 125 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 184 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 218 optimal weight: 0.9980 chunk 136 optimal weight: 9.9990 chunk 133 optimal weight: 0.8980 chunk 101 optimal weight: 0.0570 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS B 266 ASN B1386 ASN A1151 ASN D 37 GLN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19626 Z= 0.178 Angle : 0.531 9.091 26740 Z= 0.285 Chirality : 0.039 0.171 3101 Planarity : 0.003 0.068 3141 Dihedral : 17.389 88.193 3257 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.05 % Allowed : 20.08 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.18), residues: 2177 helix: 1.41 (0.14), residues: 1293 sheet: 0.92 (0.41), residues: 166 loop : -1.32 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 23 HIS 0.005 0.001 HIS D 541 PHE 0.031 0.001 PHE A 217 TYR 0.018 0.001 TYR D1086 ARG 0.007 0.000 ARG A1157 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 525 time to evaluate : 2.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 VAL cc_start: 0.7852 (m) cc_final: 0.7309 (t) REVERT: B 213 ARG cc_start: 0.8121 (mtm110) cc_final: 0.7702 (mtp-110) REVERT: B 224 PHE cc_start: 0.8663 (m-80) cc_final: 0.8239 (m-80) REVERT: B 242 GLU cc_start: 0.6959 (pm20) cc_final: 0.6684 (pm20) REVERT: B 252 GLU cc_start: 0.7045 (pm20) cc_final: 0.6739 (pm20) REVERT: B 264 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8416 (tppt) REVERT: B 269 LYS cc_start: 0.7998 (mtpt) cc_final: 0.7502 (mtpt) REVERT: B 289 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7504 (mm-30) REVERT: B 307 ASN cc_start: 0.8131 (m110) cc_final: 0.7880 (m110) REVERT: B 312 LYS cc_start: 0.8389 (mptt) cc_final: 0.8101 (mptt) REVERT: B 325 GLU cc_start: 0.7767 (mp0) cc_final: 0.7296 (mp0) REVERT: B 1260 LYS cc_start: 0.7752 (mttt) cc_final: 0.7468 (mtpp) REVERT: B 1265 ASP cc_start: 0.7709 (t0) cc_final: 0.7491 (t0) REVERT: B 1271 PHE cc_start: 0.7933 (t80) cc_final: 0.7602 (t80) REVERT: B 1317 TRP cc_start: 0.8400 (m100) cc_final: 0.8188 (m100) REVERT: B 1322 ASN cc_start: 0.7905 (p0) cc_final: 0.7637 (t0) REVERT: B 1367 ASN cc_start: 0.7774 (m-40) cc_final: 0.7561 (m-40) REVERT: B 1374 LYS cc_start: 0.8260 (mtpt) cc_final: 0.7900 (mtpt) REVERT: B 1405 LYS cc_start: 0.8587 (mttt) cc_final: 0.8202 (mttm) REVERT: B 1412 ILE cc_start: 0.8217 (pt) cc_final: 0.7962 (pt) REVERT: A 28 ASN cc_start: 0.7138 (m-40) cc_final: 0.6884 (m-40) REVERT: A 54 MET cc_start: 0.7087 (mmt) cc_final: 0.6483 (mmm) REVERT: A 109 LEU cc_start: 0.8663 (mt) cc_final: 0.8375 (mp) REVERT: A 129 GLN cc_start: 0.7509 (tm-30) cc_final: 0.6896 (tm-30) REVERT: A 157 LYS cc_start: 0.7710 (mptt) cc_final: 0.7425 (mptt) REVERT: A 160 GLU cc_start: 0.7056 (mp0) cc_final: 0.6670 (mp0) REVERT: A 178 ARG cc_start: 0.7157 (tmm160) cc_final: 0.6699 (ttp-110) REVERT: A 180 LYS cc_start: 0.8307 (mttm) cc_final: 0.8079 (mtpp) REVERT: A 187 LYS cc_start: 0.8572 (tppt) cc_final: 0.8208 (tppt) REVERT: A 208 GLU cc_start: 0.5789 (OUTLIER) cc_final: 0.5570 (pp20) REVERT: A 209 LYS cc_start: 0.7309 (mmtm) cc_final: 0.6846 (mmtm) REVERT: A 985 ASN cc_start: 0.8179 (p0) cc_final: 0.7425 (p0) REVERT: A 994 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7105 (mm-30) REVERT: A 1005 LYS cc_start: 0.7900 (mttt) cc_final: 0.7572 (mttp) REVERT: A 1008 GLU cc_start: 0.6764 (tp30) cc_final: 0.6563 (tp30) REVERT: A 1009 LYS cc_start: 0.7643 (tttt) cc_final: 0.7399 (ttmm) REVERT: A 1016 GLU cc_start: 0.7207 (tt0) cc_final: 0.6847 (tt0) REVERT: A 1082 ILE cc_start: 0.8713 (tp) cc_final: 0.8376 (tp) REVERT: A 1146 GLU cc_start: 0.7297 (tt0) cc_final: 0.6877 (tt0) REVERT: A 1157 ARG cc_start: 0.7630 (mtp85) cc_final: 0.7160 (mtp85) REVERT: C 33 GLU cc_start: 0.6421 (pp20) cc_final: 0.5957 (pp20) REVERT: C 42 LYS cc_start: 0.7400 (mmmt) cc_final: 0.7058 (mmmt) REVERT: C 64 LYS cc_start: 0.8309 (mtmt) cc_final: 0.7824 (mmmm) REVERT: C 84 LYS cc_start: 0.7926 (mmtp) cc_final: 0.7713 (mmtp) REVERT: C 170 PHE cc_start: 0.7972 (t80) cc_final: 0.7406 (t80) REVERT: C 174 LYS cc_start: 0.8040 (ttmm) cc_final: 0.7705 (ttmm) REVERT: C 189 LYS cc_start: 0.8092 (mmtt) cc_final: 0.7756 (mmmm) REVERT: C 196 ASP cc_start: 0.7447 (t0) cc_final: 0.7086 (t0) REVERT: C 197 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6851 (pp20) REVERT: C 293 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7569 (tp) REVERT: C 297 GLU cc_start: 0.7015 (pm20) cc_final: 0.6477 (pm20) REVERT: C 705 ASP cc_start: 0.7665 (t0) cc_final: 0.7373 (t0) REVERT: C 709 LYS cc_start: 0.8085 (ttpt) cc_final: 0.7749 (ttpt) REVERT: C 730 GLN cc_start: 0.7502 (mt0) cc_final: 0.7252 (mt0) REVERT: D 6 LEU cc_start: 0.8052 (tp) cc_final: 0.7810 (tp) REVERT: D 65 LEU cc_start: 0.7400 (mt) cc_final: 0.7156 (mp) REVERT: D 68 LYS cc_start: 0.7416 (tptp) cc_final: 0.6946 (tptp) REVERT: D 89 LYS cc_start: 0.8324 (tptm) cc_final: 0.7913 (mmtt) REVERT: D 105 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7662 (pt) REVERT: D 117 TYR cc_start: 0.7620 (t80) cc_final: 0.7268 (t80) REVERT: D 173 LYS cc_start: 0.7897 (tppt) cc_final: 0.7332 (tppt) REVERT: D 202 VAL cc_start: 0.8595 (p) cc_final: 0.8257 (m) REVERT: D 205 GLU cc_start: 0.7085 (tm-30) cc_final: 0.6568 (tm-30) REVERT: D 213 SER cc_start: 0.8770 (OUTLIER) cc_final: 0.8484 (p) REVERT: D 241 MET cc_start: 0.7575 (tpt) cc_final: 0.7343 (tpt) REVERT: D 260 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8525 (tt) REVERT: D 269 GLN cc_start: 0.7868 (tp-100) cc_final: 0.7552 (tp-100) REVERT: D 303 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7193 (tm-30) REVERT: D 312 GLN cc_start: 0.7761 (mm-40) cc_final: 0.7451 (tp-100) REVERT: D 333 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7292 (mt-10) REVERT: D 341 GLU cc_start: 0.7493 (tp30) cc_final: 0.7126 (tp30) REVERT: D 420 LYS cc_start: 0.8473 (tttt) cc_final: 0.8244 (ttpt) REVERT: D 554 LYS cc_start: 0.8353 (mttt) cc_final: 0.8007 (mtpp) REVERT: D 570 ASP cc_start: 0.7124 (t0) cc_final: 0.6921 (t0) REVERT: D 606 GLU cc_start: 0.7585 (tp30) cc_final: 0.7207 (tp30) REVERT: D 662 GLN cc_start: 0.7002 (tp-100) cc_final: 0.6616 (tm-30) REVERT: D 698 GLU cc_start: 0.6668 (mp0) cc_final: 0.6163 (mp0) REVERT: D 726 LEU cc_start: 0.8374 (mp) cc_final: 0.8163 (mt) REVERT: D 749 GLU cc_start: 0.7548 (tm-30) cc_final: 0.7004 (tm-30) REVERT: D 776 TYR cc_start: 0.8053 (t80) cc_final: 0.7043 (t80) REVERT: D 791 MET cc_start: 0.7941 (tmm) cc_final: 0.7708 (tmm) REVERT: D 815 ARG cc_start: 0.7685 (ttm170) cc_final: 0.7418 (mtt90) REVERT: D 867 GLU cc_start: 0.7920 (tp30) cc_final: 0.7436 (tp30) REVERT: D 921 LYS cc_start: 0.8146 (mtpt) cc_final: 0.7917 (mtmt) REVERT: D 924 GLU cc_start: 0.7158 (tt0) cc_final: 0.6769 (tt0) REVERT: D 970 SER cc_start: 0.8270 (t) cc_final: 0.7701 (p) REVERT: D 1003 ASP cc_start: 0.6607 (m-30) cc_final: 0.6315 (m-30) REVERT: D 1012 VAL cc_start: 0.8058 (m) cc_final: 0.7676 (p) REVERT: D 1017 ASP cc_start: 0.7951 (t70) cc_final: 0.7633 (t0) REVERT: D 1027 ASN cc_start: 0.7620 (t0) cc_final: 0.7217 (t0) REVERT: D 1055 GLU cc_start: 0.7311 (tp30) cc_final: 0.7075 (tp30) REVERT: D 1058 LYS cc_start: 0.8401 (mttt) cc_final: 0.8158 (mttp) REVERT: D 1077 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7251 (mm-30) REVERT: D 1109 LYS cc_start: 0.8238 (tptm) cc_final: 0.7972 (tppp) REVERT: D 1139 GLU cc_start: 0.7120 (tm-30) cc_final: 0.6550 (tm-30) outliers start: 61 outliers final: 44 residues processed: 554 average time/residue: 0.3442 time to fit residues: 279.6699 Evaluate side-chains 567 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 517 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 1319 ASN Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 983 ASN Chi-restraints excluded: chain A residue 1019 SER Chi-restraints excluded: chain A residue 1168 SER Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 398 LYS Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 988 SER Chi-restraints excluded: chain D residue 999 LEU Chi-restraints excluded: chain D residue 1029 MET Chi-restraints excluded: chain D residue 1032 ARG Chi-restraints excluded: chain D residue 1047 VAL Chi-restraints excluded: chain D residue 1056 MET Chi-restraints excluded: chain D residue 1127 LEU Chi-restraints excluded: chain D residue 1171 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 135 optimal weight: 0.3980 chunk 87 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 149 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 171 optimal weight: 0.5980 chunk 199 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 ASN B 235 HIS B 266 ASN B1386 ASN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19626 Z= 0.204 Angle : 0.549 9.965 26740 Z= 0.292 Chirality : 0.040 0.210 3101 Planarity : 0.003 0.068 3141 Dihedral : 17.348 87.642 3257 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.00 % Allowed : 20.38 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.18), residues: 2177 helix: 1.42 (0.14), residues: 1299 sheet: 0.99 (0.42), residues: 166 loop : -1.28 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1033 HIS 0.006 0.001 HIS D 541 PHE 0.027 0.002 PHE D 579 TYR 0.024 0.001 TYR D1086 ARG 0.007 0.000 ARG D 198 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 521 time to evaluate : 2.348 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 VAL cc_start: 0.7947 (m) cc_final: 0.7438 (t) REVERT: B 213 ARG cc_start: 0.8130 (mtm110) cc_final: 0.7782 (mtm-85) REVERT: B 224 PHE cc_start: 0.8719 (m-80) cc_final: 0.8230 (m-80) REVERT: B 242 GLU cc_start: 0.6927 (pm20) cc_final: 0.6672 (pm20) REVERT: B 252 GLU cc_start: 0.7056 (pm20) cc_final: 0.6801 (pm20) REVERT: B 264 LYS cc_start: 0.8784 (mmtt) cc_final: 0.8420 (tppt) REVERT: B 269 LYS cc_start: 0.7996 (mtpt) cc_final: 0.7590 (mtpt) REVERT: B 289 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7506 (mm-30) REVERT: B 307 ASN cc_start: 0.8149 (m110) cc_final: 0.7911 (m110) REVERT: B 312 LYS cc_start: 0.8396 (mptt) cc_final: 0.8126 (mptt) REVERT: B 325 GLU cc_start: 0.7754 (mp0) cc_final: 0.7290 (mp0) REVERT: B 1260 LYS cc_start: 0.7749 (mttt) cc_final: 0.7475 (mtpp) REVERT: B 1265 ASP cc_start: 0.7736 (t0) cc_final: 0.7508 (t0) REVERT: B 1271 PHE cc_start: 0.7926 (t80) cc_final: 0.7606 (t80) REVERT: B 1317 TRP cc_start: 0.8381 (m100) cc_final: 0.8159 (m100) REVERT: B 1322 ASN cc_start: 0.7895 (p0) cc_final: 0.7654 (t0) REVERT: B 1367 ASN cc_start: 0.7743 (m-40) cc_final: 0.7492 (m-40) REVERT: B 1373 THR cc_start: 0.8352 (t) cc_final: 0.8112 (t) REVERT: B 1405 LYS cc_start: 0.8558 (mttt) cc_final: 0.8180 (mttm) REVERT: B 1412 ILE cc_start: 0.8185 (pt) cc_final: 0.7927 (pt) REVERT: A 28 ASN cc_start: 0.7164 (m-40) cc_final: 0.6929 (m-40) REVERT: A 54 MET cc_start: 0.7074 (mmt) cc_final: 0.6476 (mmm) REVERT: A 109 LEU cc_start: 0.8669 (mt) cc_final: 0.8385 (mp) REVERT: A 129 GLN cc_start: 0.7520 (tm-30) cc_final: 0.6898 (tm-30) REVERT: A 157 LYS cc_start: 0.7718 (mptt) cc_final: 0.7424 (mptt) REVERT: A 160 GLU cc_start: 0.7055 (mp0) cc_final: 0.6694 (mp0) REVERT: A 178 ARG cc_start: 0.7155 (tmm160) cc_final: 0.6697 (ttp-110) REVERT: A 180 LYS cc_start: 0.8312 (mttm) cc_final: 0.8089 (mtpp) REVERT: A 187 LYS cc_start: 0.8569 (tppt) cc_final: 0.8211 (tppt) REVERT: A 208 GLU cc_start: 0.5805 (OUTLIER) cc_final: 0.5584 (pp20) REVERT: A 209 LYS cc_start: 0.7358 (mmtm) cc_final: 0.6846 (mmtm) REVERT: A 994 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7122 (mm-30) REVERT: A 1005 LYS cc_start: 0.7898 (mttt) cc_final: 0.7569 (mttp) REVERT: A 1009 LYS cc_start: 0.7635 (tttt) cc_final: 0.7396 (ttmm) REVERT: A 1016 GLU cc_start: 0.7213 (tt0) cc_final: 0.6843 (tt0) REVERT: A 1082 ILE cc_start: 0.8718 (tp) cc_final: 0.8399 (tp) REVERT: A 1146 GLU cc_start: 0.7264 (tt0) cc_final: 0.6899 (tt0) REVERT: C 42 LYS cc_start: 0.7419 (mmmt) cc_final: 0.7082 (mmmt) REVERT: C 64 LYS cc_start: 0.8335 (mtmt) cc_final: 0.7991 (mtpt) REVERT: C 84 LYS cc_start: 0.7934 (mmtp) cc_final: 0.7710 (mmtp) REVERT: C 170 PHE cc_start: 0.7987 (t80) cc_final: 0.7395 (t80) REVERT: C 174 LYS cc_start: 0.8056 (ttmm) cc_final: 0.7679 (ttmm) REVERT: C 189 LYS cc_start: 0.8115 (mmtt) cc_final: 0.7765 (mmmm) REVERT: C 196 ASP cc_start: 0.7439 (t0) cc_final: 0.7030 (t0) REVERT: C 197 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6861 (pp20) REVERT: C 293 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7578 (tp) REVERT: C 297 GLU cc_start: 0.7052 (pm20) cc_final: 0.6503 (pm20) REVERT: C 646 ASP cc_start: 0.7125 (OUTLIER) cc_final: 0.6788 (p0) REVERT: C 705 ASP cc_start: 0.7658 (t0) cc_final: 0.7375 (t0) REVERT: C 709 LYS cc_start: 0.8118 (ttpt) cc_final: 0.7780 (ttpt) REVERT: C 730 GLN cc_start: 0.7512 (mt0) cc_final: 0.7262 (mt0) REVERT: D 65 LEU cc_start: 0.7371 (mt) cc_final: 0.7137 (mp) REVERT: D 68 LYS cc_start: 0.7443 (tptp) cc_final: 0.6998 (tptp) REVERT: D 89 LYS cc_start: 0.8333 (tptm) cc_final: 0.7912 (mmtt) REVERT: D 105 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7688 (pt) REVERT: D 117 TYR cc_start: 0.7635 (t80) cc_final: 0.7284 (t80) REVERT: D 173 LYS cc_start: 0.7917 (tppt) cc_final: 0.7339 (tppt) REVERT: D 202 VAL cc_start: 0.8609 (p) cc_final: 0.8264 (m) REVERT: D 205 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6607 (tm-30) REVERT: D 213 SER cc_start: 0.8789 (OUTLIER) cc_final: 0.8497 (p) REVERT: D 241 MET cc_start: 0.7618 (tpt) cc_final: 0.7362 (tpt) REVERT: D 260 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8527 (tt) REVERT: D 269 GLN cc_start: 0.7889 (tp-100) cc_final: 0.7572 (tp-100) REVERT: D 303 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7203 (tm-30) REVERT: D 312 GLN cc_start: 0.7760 (mm-40) cc_final: 0.7558 (tp-100) REVERT: D 333 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7330 (mt-10) REVERT: D 341 GLU cc_start: 0.7504 (tp30) cc_final: 0.7136 (tp30) REVERT: D 420 LYS cc_start: 0.8479 (tttt) cc_final: 0.8246 (ttpt) REVERT: D 554 LYS cc_start: 0.8352 (mttt) cc_final: 0.8006 (mtpp) REVERT: D 570 ASP cc_start: 0.7148 (t0) cc_final: 0.6930 (t0) REVERT: D 606 GLU cc_start: 0.7534 (tp30) cc_final: 0.7157 (tp30) REVERT: D 662 GLN cc_start: 0.7006 (tp-100) cc_final: 0.6618 (tm-30) REVERT: D 749 GLU cc_start: 0.7567 (tm-30) cc_final: 0.6958 (tm-30) REVERT: D 776 TYR cc_start: 0.8066 (t80) cc_final: 0.7110 (t80) REVERT: D 791 MET cc_start: 0.7946 (tmm) cc_final: 0.7711 (tmm) REVERT: D 815 ARG cc_start: 0.7691 (ttm170) cc_final: 0.7395 (mtt90) REVERT: D 867 GLU cc_start: 0.7902 (tp30) cc_final: 0.7428 (tp30) REVERT: D 921 LYS cc_start: 0.8165 (mtpt) cc_final: 0.7927 (mtmt) REVERT: D 970 SER cc_start: 0.8294 (t) cc_final: 0.7729 (p) REVERT: D 1003 ASP cc_start: 0.6570 (m-30) cc_final: 0.6349 (m-30) REVERT: D 1017 ASP cc_start: 0.7969 (t70) cc_final: 0.7647 (t0) REVERT: D 1055 GLU cc_start: 0.7327 (tp30) cc_final: 0.7104 (tp30) REVERT: D 1058 LYS cc_start: 0.8408 (mttt) cc_final: 0.8172 (mttp) REVERT: D 1077 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7266 (mm-30) REVERT: D 1107 PHE cc_start: 0.7952 (t80) cc_final: 0.7735 (t80) REVERT: D 1109 LYS cc_start: 0.8284 (tptm) cc_final: 0.8011 (tppp) REVERT: D 1139 GLU cc_start: 0.7153 (tm-30) cc_final: 0.6580 (tm-30) outliers start: 60 outliers final: 45 residues processed: 554 average time/residue: 0.3636 time to fit residues: 296.9042 Evaluate side-chains 566 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 514 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 1314 LYS Chi-restraints excluded: chain B residue 1319 ASN Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 983 ASN Chi-restraints excluded: chain A residue 1168 SER Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 646 ASP Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 368 GLN Chi-restraints excluded: chain D residue 398 LYS Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 857 THR Chi-restraints excluded: chain D residue 988 SER Chi-restraints excluded: chain D residue 999 LEU Chi-restraints excluded: chain D residue 1029 MET Chi-restraints excluded: chain D residue 1032 ARG Chi-restraints excluded: chain D residue 1047 VAL Chi-restraints excluded: chain D residue 1056 MET Chi-restraints excluded: chain D residue 1127 LEU Chi-restraints excluded: chain D residue 1171 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 209 optimal weight: 0.5980 chunk 191 optimal weight: 1.9990 chunk 203 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 62 optimal weight: 0.2980 chunk 184 optimal weight: 1.9990 chunk 192 optimal weight: 0.6980 chunk 133 optimal weight: 0.5980 chunk 215 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 ASN B 235 HIS A 970 GLN A1151 ASN D 37 GLN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19626 Z= 0.199 Angle : 0.552 9.066 26740 Z= 0.294 Chirality : 0.040 0.207 3101 Planarity : 0.003 0.068 3141 Dihedral : 17.301 87.869 3257 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.00 % Allowed : 21.08 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.18), residues: 2177 helix: 1.48 (0.14), residues: 1300 sheet: 1.03 (0.42), residues: 161 loop : -1.31 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 669 HIS 0.006 0.001 HIS D 541 PHE 0.022 0.001 PHE B1302 TYR 0.022 0.001 TYR D1086 ARG 0.008 0.000 ARG D 198 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 519 time to evaluate : 2.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 VAL cc_start: 0.7962 (m) cc_final: 0.7429 (t) REVERT: B 213 ARG cc_start: 0.8167 (mtm110) cc_final: 0.7839 (mtm-85) REVERT: B 224 PHE cc_start: 0.8719 (m-80) cc_final: 0.8224 (m-80) REVERT: B 242 GLU cc_start: 0.6910 (pm20) cc_final: 0.6661 (pm20) REVERT: B 252 GLU cc_start: 0.7085 (pm20) cc_final: 0.6733 (pm20) REVERT: B 264 LYS cc_start: 0.8767 (mmtt) cc_final: 0.8423 (tppt) REVERT: B 269 LYS cc_start: 0.7961 (mtpt) cc_final: 0.7516 (mtpt) REVERT: B 289 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7509 (mm-30) REVERT: B 307 ASN cc_start: 0.8143 (m110) cc_final: 0.7899 (m110) REVERT: B 312 LYS cc_start: 0.8399 (mptt) cc_final: 0.8148 (mptt) REVERT: B 325 GLU cc_start: 0.7762 (mp0) cc_final: 0.7288 (mp0) REVERT: B 1260 LYS cc_start: 0.7746 (mttt) cc_final: 0.7475 (mtpp) REVERT: B 1265 ASP cc_start: 0.7749 (t0) cc_final: 0.7518 (t0) REVERT: B 1271 PHE cc_start: 0.7922 (t80) cc_final: 0.7598 (t80) REVERT: B 1317 TRP cc_start: 0.8394 (m100) cc_final: 0.8189 (m100) REVERT: B 1322 ASN cc_start: 0.7892 (p0) cc_final: 0.7647 (t0) REVERT: B 1350 MET cc_start: 0.8357 (mtp) cc_final: 0.8146 (mtm) REVERT: B 1367 ASN cc_start: 0.7773 (m-40) cc_final: 0.7562 (m-40) REVERT: B 1373 THR cc_start: 0.8337 (t) cc_final: 0.8096 (t) REVERT: B 1405 LYS cc_start: 0.8531 (mttt) cc_final: 0.8090 (mttm) REVERT: B 1412 ILE cc_start: 0.8192 (pt) cc_final: 0.7935 (pt) REVERT: A 28 ASN cc_start: 0.7038 (m-40) cc_final: 0.6804 (m-40) REVERT: A 54 MET cc_start: 0.7151 (mmt) cc_final: 0.6661 (mmm) REVERT: A 109 LEU cc_start: 0.8665 (mt) cc_final: 0.8381 (mp) REVERT: A 129 GLN cc_start: 0.7516 (tm-30) cc_final: 0.6892 (tm-30) REVERT: A 157 LYS cc_start: 0.7719 (mptt) cc_final: 0.7442 (mptt) REVERT: A 160 GLU cc_start: 0.7061 (mp0) cc_final: 0.6719 (mp0) REVERT: A 178 ARG cc_start: 0.7164 (tmm160) cc_final: 0.6706 (ttp-110) REVERT: A 180 LYS cc_start: 0.8312 (mttm) cc_final: 0.8087 (mtpp) REVERT: A 187 LYS cc_start: 0.8533 (tppt) cc_final: 0.8174 (tppt) REVERT: A 189 GLU cc_start: 0.7867 (tp30) cc_final: 0.7607 (tp30) REVERT: A 208 GLU cc_start: 0.5795 (OUTLIER) cc_final: 0.5577 (pp20) REVERT: A 209 LYS cc_start: 0.7329 (mmtm) cc_final: 0.6836 (mmtm) REVERT: A 970 GLN cc_start: 0.5329 (OUTLIER) cc_final: 0.5123 (pp30) REVERT: A 994 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7119 (mm-30) REVERT: A 1001 LYS cc_start: 0.7619 (mmmm) cc_final: 0.7288 (mmmm) REVERT: A 1005 LYS cc_start: 0.7891 (mttt) cc_final: 0.7446 (mttp) REVERT: A 1009 LYS cc_start: 0.7598 (tttt) cc_final: 0.7361 (ttmm) REVERT: A 1016 GLU cc_start: 0.7192 (tt0) cc_final: 0.6824 (tt0) REVERT: A 1061 LYS cc_start: 0.7225 (mmmm) cc_final: 0.6990 (mmmm) REVERT: A 1082 ILE cc_start: 0.8736 (tp) cc_final: 0.8408 (tp) REVERT: A 1146 GLU cc_start: 0.7265 (tt0) cc_final: 0.6879 (tt0) REVERT: C 42 LYS cc_start: 0.7387 (mmmt) cc_final: 0.7050 (mmmt) REVERT: C 64 LYS cc_start: 0.8310 (mtmt) cc_final: 0.7965 (mtpt) REVERT: C 84 LYS cc_start: 0.7933 (mmtp) cc_final: 0.7713 (mmtp) REVERT: C 170 PHE cc_start: 0.7977 (t80) cc_final: 0.7414 (t80) REVERT: C 174 LYS cc_start: 0.8057 (ttmm) cc_final: 0.7701 (ttmm) REVERT: C 189 LYS cc_start: 0.8110 (mmtt) cc_final: 0.7761 (mmmm) REVERT: C 196 ASP cc_start: 0.7447 (t0) cc_final: 0.7066 (t0) REVERT: C 197 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7114 (pp20) REVERT: C 293 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7594 (tp) REVERT: C 297 GLU cc_start: 0.7018 (pm20) cc_final: 0.6455 (pm20) REVERT: C 646 ASP cc_start: 0.7113 (OUTLIER) cc_final: 0.6792 (p0) REVERT: C 705 ASP cc_start: 0.7655 (t0) cc_final: 0.7375 (t0) REVERT: C 709 LYS cc_start: 0.8128 (ttpt) cc_final: 0.7791 (ttpt) REVERT: C 730 GLN cc_start: 0.7514 (mt0) cc_final: 0.7276 (mt0) REVERT: D 65 LEU cc_start: 0.7342 (mt) cc_final: 0.7122 (mp) REVERT: D 68 LYS cc_start: 0.7447 (tptp) cc_final: 0.7163 (tptp) REVERT: D 89 LYS cc_start: 0.8294 (tptm) cc_final: 0.7872 (mmtt) REVERT: D 105 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7681 (pt) REVERT: D 117 TYR cc_start: 0.7640 (t80) cc_final: 0.7297 (t80) REVERT: D 173 LYS cc_start: 0.7902 (tppt) cc_final: 0.7323 (tppt) REVERT: D 202 VAL cc_start: 0.8600 (p) cc_final: 0.8254 (m) REVERT: D 205 GLU cc_start: 0.7111 (tm-30) cc_final: 0.6614 (tm-30) REVERT: D 213 SER cc_start: 0.8789 (OUTLIER) cc_final: 0.8483 (p) REVERT: D 241 MET cc_start: 0.7614 (tpt) cc_final: 0.7365 (tpt) REVERT: D 260 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8522 (tt) REVERT: D 269 GLN cc_start: 0.7890 (tp-100) cc_final: 0.7567 (tp-100) REVERT: D 303 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7203 (tm-30) REVERT: D 333 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7311 (mt-10) REVERT: D 341 GLU cc_start: 0.7496 (tp30) cc_final: 0.7137 (tp30) REVERT: D 420 LYS cc_start: 0.8501 (tttt) cc_final: 0.8275 (ttpt) REVERT: D 554 LYS cc_start: 0.8351 (mttt) cc_final: 0.8009 (mtpp) REVERT: D 570 ASP cc_start: 0.7134 (t0) cc_final: 0.6924 (t0) REVERT: D 606 GLU cc_start: 0.7523 (tp30) cc_final: 0.7147 (tp30) REVERT: D 662 GLN cc_start: 0.7016 (tp-100) cc_final: 0.6626 (tm-30) REVERT: D 698 GLU cc_start: 0.6755 (mp0) cc_final: 0.6258 (mp0) REVERT: D 749 GLU cc_start: 0.7579 (tm-30) cc_final: 0.6970 (tm-30) REVERT: D 776 TYR cc_start: 0.8065 (t80) cc_final: 0.7131 (t80) REVERT: D 791 MET cc_start: 0.7969 (tmm) cc_final: 0.7710 (tmm) REVERT: D 815 ARG cc_start: 0.7649 (ttm170) cc_final: 0.7390 (mtt90) REVERT: D 867 GLU cc_start: 0.7924 (tp30) cc_final: 0.7464 (tp30) REVERT: D 921 LYS cc_start: 0.8157 (mtpt) cc_final: 0.7928 (mtmt) REVERT: D 970 SER cc_start: 0.8297 (t) cc_final: 0.7757 (p) REVERT: D 1003 ASP cc_start: 0.6648 (m-30) cc_final: 0.6323 (m-30) REVERT: D 1012 VAL cc_start: 0.8069 (m) cc_final: 0.7694 (p) REVERT: D 1027 ASN cc_start: 0.7635 (t0) cc_final: 0.7248 (t0) REVERT: D 1055 GLU cc_start: 0.7336 (tp30) cc_final: 0.7099 (tp30) REVERT: D 1058 LYS cc_start: 0.8411 (mttt) cc_final: 0.8183 (mttp) REVERT: D 1077 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7280 (mm-30) REVERT: D 1109 LYS cc_start: 0.8260 (tptm) cc_final: 0.7994 (tppp) REVERT: D 1117 PHE cc_start: 0.8208 (m-80) cc_final: 0.7864 (t80) REVERT: D 1139 GLU cc_start: 0.7178 (tm-30) cc_final: 0.6637 (tm-30) outliers start: 60 outliers final: 43 residues processed: 554 average time/residue: 0.3448 time to fit residues: 281.3396 Evaluate side-chains 565 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 514 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 1314 LYS Chi-restraints excluded: chain B residue 1319 ASN Chi-restraints excluded: chain B residue 1354 ASP Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 970 GLN Chi-restraints excluded: chain A residue 983 ASN Chi-restraints excluded: chain A residue 1019 SER Chi-restraints excluded: chain A residue 1168 SER Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 646 ASP Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 368 GLN Chi-restraints excluded: chain D residue 398 LYS Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 857 THR Chi-restraints excluded: chain D residue 988 SER Chi-restraints excluded: chain D residue 999 LEU Chi-restraints excluded: chain D residue 1029 MET Chi-restraints excluded: chain D residue 1032 ARG Chi-restraints excluded: chain D residue 1047 VAL Chi-restraints excluded: chain D residue 1056 MET Chi-restraints excluded: chain D residue 1127 LEU Chi-restraints excluded: chain D residue 1171 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 131 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 149 optimal weight: 0.5980 chunk 226 optimal weight: 0.7980 chunk 208 optimal weight: 0.4980 chunk 180 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 143 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 ASN B 235 HIS A 970 GLN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19626 Z= 0.239 Angle : 0.569 9.574 26740 Z= 0.303 Chirality : 0.041 0.195 3101 Planarity : 0.003 0.068 3141 Dihedral : 17.320 88.290 3257 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.65 % Allowed : 21.58 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.18), residues: 2177 helix: 1.45 (0.14), residues: 1293 sheet: 0.99 (0.41), residues: 161 loop : -1.32 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1033 HIS 0.006 0.001 HIS D 541 PHE 0.022 0.002 PHE B1302 TYR 0.021 0.001 TYR D1086 ARG 0.008 0.000 ARG D 198 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 517 time to evaluate : 2.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 VAL cc_start: 0.7977 (m) cc_final: 0.7492 (t) REVERT: B 213 ARG cc_start: 0.8155 (mtm110) cc_final: 0.7794 (mtm-85) REVERT: B 224 PHE cc_start: 0.8721 (m-80) cc_final: 0.8214 (m-80) REVERT: B 252 GLU cc_start: 0.7036 (pm20) cc_final: 0.6748 (pm20) REVERT: B 264 LYS cc_start: 0.8787 (mmtt) cc_final: 0.8483 (tppt) REVERT: B 289 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7607 (mm-30) REVERT: B 307 ASN cc_start: 0.8143 (m110) cc_final: 0.7908 (m110) REVERT: B 312 LYS cc_start: 0.8462 (mptt) cc_final: 0.8183 (mptt) REVERT: B 325 GLU cc_start: 0.7758 (mp0) cc_final: 0.7285 (mp0) REVERT: B 1260 LYS cc_start: 0.7763 (mttt) cc_final: 0.7495 (mtpp) REVERT: B 1265 ASP cc_start: 0.7752 (t0) cc_final: 0.7525 (t0) REVERT: B 1267 PHE cc_start: 0.7942 (t80) cc_final: 0.7695 (t80) REVERT: B 1271 PHE cc_start: 0.7934 (t80) cc_final: 0.7599 (t80) REVERT: B 1317 TRP cc_start: 0.8402 (m100) cc_final: 0.8189 (m100) REVERT: B 1322 ASN cc_start: 0.7875 (p0) cc_final: 0.7646 (t0) REVERT: B 1367 ASN cc_start: 0.7736 (m-40) cc_final: 0.7535 (m-40) REVERT: B 1373 THR cc_start: 0.8315 (t) cc_final: 0.8088 (t) REVERT: B 1405 LYS cc_start: 0.8503 (mttt) cc_final: 0.8054 (mttm) REVERT: B 1412 ILE cc_start: 0.8159 (pt) cc_final: 0.7886 (pt) REVERT: A 54 MET cc_start: 0.7177 (mmt) cc_final: 0.6641 (mmm) REVERT: A 109 LEU cc_start: 0.8687 (mt) cc_final: 0.8386 (mp) REVERT: A 129 GLN cc_start: 0.7544 (tm-30) cc_final: 0.6921 (tm-30) REVERT: A 157 LYS cc_start: 0.7698 (mptt) cc_final: 0.7416 (mptt) REVERT: A 160 GLU cc_start: 0.7067 (mp0) cc_final: 0.6726 (mp0) REVERT: A 178 ARG cc_start: 0.7184 (tmm160) cc_final: 0.6739 (ttp-110) REVERT: A 180 LYS cc_start: 0.8312 (mttm) cc_final: 0.8088 (mtpp) REVERT: A 187 LYS cc_start: 0.8558 (tppt) cc_final: 0.8208 (tppt) REVERT: A 189 GLU cc_start: 0.7889 (tp30) cc_final: 0.7547 (tp30) REVERT: A 208 GLU cc_start: 0.5820 (OUTLIER) cc_final: 0.5612 (pp20) REVERT: A 209 LYS cc_start: 0.7356 (mmtm) cc_final: 0.6856 (mmtm) REVERT: A 994 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7131 (mm-30) REVERT: A 1001 LYS cc_start: 0.7636 (mmmm) cc_final: 0.7290 (mmmm) REVERT: A 1005 LYS cc_start: 0.7881 (mttt) cc_final: 0.7448 (mttp) REVERT: A 1009 LYS cc_start: 0.7615 (tttt) cc_final: 0.7368 (ttmm) REVERT: A 1016 GLU cc_start: 0.7209 (tt0) cc_final: 0.6836 (tt0) REVERT: A 1061 LYS cc_start: 0.7246 (mmmm) cc_final: 0.7009 (mmmm) REVERT: A 1082 ILE cc_start: 0.8734 (tp) cc_final: 0.8410 (tp) REVERT: A 1146 GLU cc_start: 0.7273 (tt0) cc_final: 0.6892 (tt0) REVERT: C 42 LYS cc_start: 0.7397 (mmmt) cc_final: 0.7071 (mmmt) REVERT: C 64 LYS cc_start: 0.8333 (mtmt) cc_final: 0.7995 (mtpt) REVERT: C 84 LYS cc_start: 0.7946 (mmtp) cc_final: 0.7714 (mmtp) REVERT: C 170 PHE cc_start: 0.8015 (t80) cc_final: 0.7480 (t80) REVERT: C 174 LYS cc_start: 0.8089 (ttmm) cc_final: 0.7754 (ttmm) REVERT: C 189 LYS cc_start: 0.8128 (mmtt) cc_final: 0.7776 (mmmm) REVERT: C 197 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7122 (pp20) REVERT: C 293 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7597 (tp) REVERT: C 297 GLU cc_start: 0.7003 (pm20) cc_final: 0.6439 (pm20) REVERT: C 646 ASP cc_start: 0.7122 (OUTLIER) cc_final: 0.6788 (p0) REVERT: C 705 ASP cc_start: 0.7653 (t0) cc_final: 0.7376 (t0) REVERT: C 709 LYS cc_start: 0.8177 (ttpt) cc_final: 0.7839 (ttpt) REVERT: C 730 GLN cc_start: 0.7435 (mt0) cc_final: 0.7185 (mt0) REVERT: D 65 LEU cc_start: 0.7347 (mt) cc_final: 0.7113 (mp) REVERT: D 68 LYS cc_start: 0.7451 (tptp) cc_final: 0.7157 (tptp) REVERT: D 89 LYS cc_start: 0.8325 (tptm) cc_final: 0.7899 (mmtt) REVERT: D 105 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7688 (pt) REVERT: D 117 TYR cc_start: 0.7639 (t80) cc_final: 0.7266 (t80) REVERT: D 173 LYS cc_start: 0.7955 (tppt) cc_final: 0.7736 (tppt) REVERT: D 202 VAL cc_start: 0.8614 (p) cc_final: 0.8262 (m) REVERT: D 205 GLU cc_start: 0.7126 (tm-30) cc_final: 0.6632 (tm-30) REVERT: D 213 SER cc_start: 0.8793 (OUTLIER) cc_final: 0.8494 (p) REVERT: D 241 MET cc_start: 0.7666 (tpt) cc_final: 0.7401 (tpt) REVERT: D 260 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8528 (tt) REVERT: D 269 GLN cc_start: 0.7898 (tp-100) cc_final: 0.7584 (tp-100) REVERT: D 303 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7203 (tm-30) REVERT: D 333 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7393 (mt-10) REVERT: D 341 GLU cc_start: 0.7523 (tp30) cc_final: 0.7149 (tp30) REVERT: D 364 GLU cc_start: 0.7490 (mt-10) cc_final: 0.6910 (mp0) REVERT: D 420 LYS cc_start: 0.8503 (tttt) cc_final: 0.8275 (ttpt) REVERT: D 554 LYS cc_start: 0.8352 (mttt) cc_final: 0.8006 (mtpp) REVERT: D 570 ASP cc_start: 0.7147 (t0) cc_final: 0.6924 (t0) REVERT: D 606 GLU cc_start: 0.7515 (tp30) cc_final: 0.7007 (tp30) REVERT: D 662 GLN cc_start: 0.7039 (tp-100) cc_final: 0.6661 (tm-30) REVERT: D 749 GLU cc_start: 0.7594 (tm-30) cc_final: 0.6986 (tm-30) REVERT: D 776 TYR cc_start: 0.8077 (t80) cc_final: 0.7122 (t80) REVERT: D 791 MET cc_start: 0.7953 (tmm) cc_final: 0.7727 (tmm) REVERT: D 815 ARG cc_start: 0.7671 (ttm170) cc_final: 0.7404 (mtt90) REVERT: D 867 GLU cc_start: 0.7921 (tp30) cc_final: 0.7461 (tp30) REVERT: D 921 LYS cc_start: 0.8155 (mtpt) cc_final: 0.7927 (mtmt) REVERT: D 924 GLU cc_start: 0.7182 (tt0) cc_final: 0.6848 (tt0) REVERT: D 970 SER cc_start: 0.8343 (t) cc_final: 0.7849 (p) REVERT: D 1003 ASP cc_start: 0.6740 (m-30) cc_final: 0.6301 (m-30) REVERT: D 1012 VAL cc_start: 0.8067 (m) cc_final: 0.7692 (p) REVERT: D 1055 GLU cc_start: 0.7376 (tp30) cc_final: 0.7138 (tp30) REVERT: D 1058 LYS cc_start: 0.8421 (mttt) cc_final: 0.8191 (mttp) REVERT: D 1077 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7302 (mm-30) REVERT: D 1109 LYS cc_start: 0.8299 (tptm) cc_final: 0.8030 (tppp) REVERT: D 1117 PHE cc_start: 0.8203 (m-80) cc_final: 0.7901 (t80) REVERT: D 1137 LYS cc_start: 0.7999 (tptp) cc_final: 0.7691 (tptp) REVERT: D 1139 GLU cc_start: 0.7198 (tm-30) cc_final: 0.6648 (tm-30) outliers start: 53 outliers final: 43 residues processed: 548 average time/residue: 0.3466 time to fit residues: 280.4192 Evaluate side-chains 566 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 516 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 1319 ASN Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 970 GLN Chi-restraints excluded: chain A residue 983 ASN Chi-restraints excluded: chain A residue 1168 SER Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 646 ASP Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 368 GLN Chi-restraints excluded: chain D residue 398 LYS Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 857 THR Chi-restraints excluded: chain D residue 988 SER Chi-restraints excluded: chain D residue 999 LEU Chi-restraints excluded: chain D residue 1029 MET Chi-restraints excluded: chain D residue 1047 VAL Chi-restraints excluded: chain D residue 1056 MET Chi-restraints excluded: chain D residue 1127 LEU Chi-restraints excluded: chain D residue 1171 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 55 optimal weight: 0.8980 chunk 166 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 180 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 185 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 158 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 ASN B 235 HIS B 266 ASN A 970 GLN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.147684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.122064 restraints weight = 29168.004| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.07 r_work: 0.3378 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19626 Z= 0.222 Angle : 0.564 9.643 26740 Z= 0.301 Chirality : 0.041 0.189 3101 Planarity : 0.003 0.068 3141 Dihedral : 17.296 88.701 3257 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.90 % Allowed : 21.43 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.18), residues: 2177 helix: 1.49 (0.14), residues: 1288 sheet: 0.99 (0.41), residues: 161 loop : -1.28 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 23 HIS 0.006 0.001 HIS D 541 PHE 0.023 0.001 PHE D1107 TYR 0.021 0.001 TYR D1086 ARG 0.008 0.000 ARG D 198 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5691.94 seconds wall clock time: 103 minutes 34.68 seconds (6214.68 seconds total)