Starting phenix.real_space_refine on Mon Dec 11 21:12:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qen_13934/12_2023/7qen_13934_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qen_13934/12_2023/7qen_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_13934/12_2023/7qen_13934.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qen_13934/12_2023/7qen_13934.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qen_13934/12_2023/7qen_13934_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qen_13934/12_2023/7qen_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 10.61, per 1000 atoms: 0.55 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: 7.26 Conformation dependent library (CDL) restraints added in 3.3 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: 9.23 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: 8.92 Time building geometry restraints manager: 7.84 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: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.680 Check model and map are aligned: 0.300 Set scattering table: 0.170 Process input model: 59.720 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.730 ------------------------------------------------------------------------------- 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 : 2.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 591 average time/residue: 0.3538 time to fit residues: 306.3826 Evaluate side-chains 511 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 509 time to evaluate : 2.030 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1720 time to fit residues: 3.5575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 58 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 177 optimal weight: 0.3980 chunk 68 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 206 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 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 653 ASN C 659 ASN C 725 ASN C 738 ASN D 70 GLN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 GLN D 269 GLN D 351 HIS ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 GLN D 657 GLN D1031 GLN D1158 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19626 Z= 0.198 Angle : 0.573 8.368 26740 Z= 0.310 Chirality : 0.040 0.345 3101 Planarity : 0.004 0.077 3141 Dihedral : 17.922 82.102 3257 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.65 % Allowed : 15.73 % Favored : 82.62 % 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: -1.48 (0.16), residues: 2177 helix: -0.42 (0.13), residues: 1295 sheet: 0.36 (0.41), residues: 161 loop : -2.21 (0.20), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1033 HIS 0.006 0.001 HIS D 541 PHE 0.023 0.001 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 553 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 520 time to evaluate : 2.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 18 residues processed: 532 average time/residue: 0.3642 time to fit residues: 283.7762 Evaluate side-chains 508 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 490 time to evaluate : 2.026 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1780 time to fit residues: 9.0199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 171 optimal weight: 1.9990 chunk 140 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 206 optimal weight: 0.8980 chunk 223 optimal weight: 7.9990 chunk 183 optimal weight: 0.7980 chunk 204 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 ASN D 72 GLN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN D 269 GLN ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 ASN D 657 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.1984 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= 0.251 Angle : 0.571 7.666 26740 Z= 0.309 Chirality : 0.041 0.304 3101 Planarity : 0.004 0.076 3141 Dihedral : 18.110 83.612 3257 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.30 % Allowed : 18.68 % Favored : 80.02 % 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: -0.51 (0.17), residues: 2177 helix: 0.42 (0.14), residues: 1292 sheet: 0.69 (0.41), residues: 161 loop : -1.91 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1033 HIS 0.007 0.001 HIS D 541 PHE 0.029 0.002 PHE B 155 TYR 0.018 0.002 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 555 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 529 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 539 average time/residue: 0.2786 time to fit residues: 220.8883 Evaluate side-chains 514 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 503 time to evaluate : 2.277 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2100 time to fit residues: 7.1403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 204 optimal weight: 0.3980 chunk 155 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 chunk 138 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 196 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 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 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS B1283 GLN B1340 HIS A 28 ASN C 725 ASN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN D 269 GLN ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1158 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2248 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= 0.217 Angle : 0.551 8.925 26740 Z= 0.298 Chirality : 0.041 0.286 3101 Planarity : 0.004 0.072 3141 Dihedral : 17.837 83.629 3257 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.55 % Allowed : 20.13 % 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: 0.02 (0.18), residues: 2177 helix: 0.86 (0.14), residues: 1290 sheet: 0.82 (0.41), residues: 161 loop : -1.71 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1033 HIS 0.005 0.001 HIS D 541 PHE 0.021 0.002 PHE D 579 TYR 0.019 0.002 TYR D1086 ARG 0.004 0.000 ARG D 198 *********************** 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 535 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 504 time to evaluate : 1.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 13 residues processed: 517 average time/residue: 0.3439 time to fit residues: 263.5271 Evaluate side-chains 505 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 492 time to evaluate : 2.050 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2378 time to fit residues: 8.1642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 3 optimal weight: 3.9990 chunk 163 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 187 optimal weight: 0.8980 chunk 151 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 196 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1151 ASN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 GLN ** 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: 0.7200 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19626 Z= 0.233 Angle : 0.553 7.380 26740 Z= 0.298 Chirality : 0.041 0.276 3101 Planarity : 0.004 0.071 3141 Dihedral : 17.700 86.275 3257 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.70 % Allowed : 20.93 % Favored : 77.37 % 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: 0.31 (0.18), residues: 2177 helix: 1.04 (0.14), residues: 1292 sheet: 0.89 (0.41), residues: 161 loop : -1.49 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1033 HIS 0.006 0.001 HIS D 541 PHE 0.026 0.002 PHE C 170 TYR 0.016 0.001 TYR D 529 ARG 0.004 0.000 ARG D 311 *********************** 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 534 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 500 time to evaluate : 2.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 17 residues processed: 515 average time/residue: 0.3493 time to fit residues: 267.1956 Evaluate side-chains 511 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 494 time to evaluate : 1.982 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1825 time to fit residues: 8.6106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 43 optimal weight: 0.0770 chunk 128 optimal weight: 0.0040 chunk 54 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 overall best weight: 0.9954 ------------------------------------------------------------------------------- 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 ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 ASN C 321 ASN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN D 269 GLN ** 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: 0.7217 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 19626 Z= 0.286 Angle : 0.589 11.233 26740 Z= 0.315 Chirality : 0.042 0.275 3101 Planarity : 0.004 0.072 3141 Dihedral : 17.581 86.867 3257 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.40 % Allowed : 21.48 % Favored : 77.12 % 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: 0.34 (0.18), residues: 2177 helix: 1.05 (0.14), residues: 1291 sheet: 0.91 (0.40), residues: 161 loop : -1.42 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1033 HIS 0.007 0.001 HIS D 541 PHE 0.027 0.002 PHE A 217 TYR 0.028 0.002 TYR D 776 ARG 0.003 0.000 ARG C 215 *********************** 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 551 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 523 time to evaluate : 2.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 12 residues processed: 535 average time/residue: 0.3534 time to fit residues: 279.6283 Evaluate side-chains 516 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 504 time to evaluate : 2.058 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2139 time to fit residues: 7.4509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 211 optimal weight: 0.7980 chunk 24 optimal weight: 0.0040 chunk 125 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 124 optimal weight: 0.2980 chunk 184 optimal weight: 0.9990 chunk 122 optimal weight: 0.5980 chunk 218 optimal weight: 2.9990 chunk 136 optimal weight: 8.9990 chunk 133 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- 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 B1386 ASN ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN C 725 ASN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN D 269 GLN ** D 347 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: 0.7182 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19626 Z= 0.185 Angle : 0.566 9.117 26740 Z= 0.301 Chirality : 0.040 0.271 3101 Planarity : 0.003 0.068 3141 Dihedral : 17.410 89.225 3257 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.85 % Allowed : 22.93 % Favored : 76.22 % 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: 0.61 (0.18), residues: 2177 helix: 1.28 (0.14), residues: 1295 sheet: 0.95 (0.40), residues: 161 loop : -1.32 (0.23), residues: 721 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 0.033 0.002 PHE C 170 TYR 0.024 0.001 TYR B 279 ARG 0.005 0.000 ARG D 366 *********************** 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 524 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 507 time to evaluate : 2.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 514 average time/residue: 0.3549 time to fit residues: 269.2032 Evaluate side-chains 492 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 484 time to evaluate : 2.093 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2284 time to fit residues: 6.2757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 135 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 199 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 B 307 ASN B1247 GLN B1386 ASN ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1151 ASN D 262 ASN ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19626 Z= 0.264 Angle : 0.602 11.637 26740 Z= 0.319 Chirality : 0.042 0.280 3101 Planarity : 0.003 0.069 3141 Dihedral : 17.437 89.207 3257 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.00 % Allowed : 22.93 % Favored : 76.07 % 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: 0.59 (0.18), residues: 2177 helix: 1.23 (0.14), residues: 1293 sheet: 0.87 (0.40), residues: 166 loop : -1.26 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1033 HIS 0.007 0.001 HIS D 541 PHE 0.030 0.002 PHE B1271 TYR 0.024 0.002 TYR D1086 ARG 0.004 0.000 ARG D 366 *********************** 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 518 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 498 time to evaluate : 2.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 510 average time/residue: 0.3489 time to fit residues: 263.4156 Evaluate side-chains 497 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 486 time to evaluate : 2.074 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1827 time to fit residues: 6.6538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.1980 chunk 122 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 160 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 184 optimal weight: 0.9990 chunk 192 optimal weight: 0.5980 chunk 133 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 970 GLN D 269 GLN ** 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: 0.7183 moved from start: 0.2860 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= 0.206 Angle : 0.602 9.216 26740 Z= 0.316 Chirality : 0.041 0.279 3101 Planarity : 0.003 0.068 3141 Dihedral : 17.338 88.211 3257 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.60 % Allowed : 23.58 % Favored : 75.82 % 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: 0.70 (0.18), residues: 2177 helix: 1.33 (0.14), residues: 1281 sheet: 1.04 (0.40), residues: 161 loop : -1.21 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 23 HIS 0.005 0.001 HIS D 541 PHE 0.028 0.002 PHE B1271 TYR 0.023 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 510 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 498 time to evaluate : 2.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 504 average time/residue: 0.3546 time to fit residues: 263.3202 Evaluate side-chains 498 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 492 time to evaluate : 2.027 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3833 time to fit residues: 6.1636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 131 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 149 optimal weight: 0.7980 chunk 226 optimal weight: 0.7980 chunk 208 optimal weight: 0.9990 chunk 180 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 139 optimal weight: 0.0570 chunk 110 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 191 optimal weight: 1.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1151 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19626 Z= 0.235 Angle : 0.618 9.403 26740 Z= 0.324 Chirality : 0.042 0.278 3101 Planarity : 0.004 0.068 3141 Dihedral : 17.354 89.352 3257 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.20 % Allowed : 24.08 % Favored : 75.72 % 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: 0.68 (0.18), residues: 2177 helix: 1.30 (0.14), residues: 1292 sheet: 1.07 (0.40), residues: 161 loop : -1.24 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1033 HIS 0.006 0.001 HIS D 541 PHE 0.028 0.002 PHE B1271 TYR 0.022 0.002 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 497 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 493 time to evaluate : 1.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 495 average time/residue: 0.3541 time to fit residues: 259.2311 Evaluate side-chains 491 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 488 time to evaluate : 1.963 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1846 time to fit residues: 3.9320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 55 optimal weight: 0.9990 chunk 166 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 180 optimal weight: 0.8980 chunk 75 optimal weight: 0.0070 chunk 185 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 158 optimal weight: 0.3980 chunk 10 optimal weight: 0.5980 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 GLN D 262 ASN D 269 GLN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.148967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.124526 restraints weight = 29096.664| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.94 r_work: 0.3403 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19626 Z= 0.203 Angle : 0.621 9.455 26740 Z= 0.324 Chirality : 0.041 0.274 3101 Planarity : 0.004 0.067 3141 Dihedral : 17.279 88.766 3257 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.30 % Allowed : 24.48 % Favored : 75.22 % 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: 1.39 (0.14), residues: 1294 sheet: 0.97 (0.39), residues: 166 loop : -1.18 (0.23), residues: 717 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 0.027 0.002 PHE B1271 TYR 0.022 0.001 TYR D1086 ARG 0.009 0.000 ARG D 198 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5431.75 seconds wall clock time: 101 minutes 7.76 seconds (6067.76 seconds total)