Starting phenix.real_space_refine on Fri Mar 15 16:35:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsi_30834/03_2024/7dsi_30834_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsi_30834/03_2024/7dsi_30834.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsi_30834/03_2024/7dsi_30834.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsi_30834/03_2024/7dsi_30834.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsi_30834/03_2024/7dsi_30834_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsi_30834/03_2024/7dsi_30834_updated.pdb" } resolution = 3.21 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= -0.000 sd= 1.000 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 3 5.49 5 Mg 1 5.21 5 S 60 5.16 5 C 7826 2.51 5 N 2015 2.21 5 O 2280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 168": "NH1" <-> "NH2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 447": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A ARG 544": "NH1" <-> "NH2" Residue "A ARG 547": "NH1" <-> "NH2" Residue "A ARG 580": "NH1" <-> "NH2" Residue "A TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 703": "NH1" <-> "NH2" Residue "A ARG 713": "NH1" <-> "NH2" Residue "A TYR 740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 765": "NH1" <-> "NH2" Residue "A ARG 809": "NH1" <-> "NH2" Residue "A ARG 848": "NH1" <-> "NH2" Residue "A ARG 865": "NH1" <-> "NH2" Residue "A ARG 880": "NH1" <-> "NH2" Residue "A ARG 883": "NH1" <-> "NH2" Residue "A ARG 916": "NH1" <-> "NH2" Residue "A ARG 953": "NH1" <-> "NH2" Residue "A ARG 966": "NH1" <-> "NH2" Residue "A ARG 1088": "NH1" <-> "NH2" Residue "A ARG 1104": "NH1" <-> "NH2" Residue "A ARG 1153": "NH1" <-> "NH2" Residue "A ARG 1167": "NH1" <-> "NH2" Residue "A ARG 1178": "NH1" <-> "NH2" Residue "A ARG 1257": "NH1" <-> "NH2" Residue "A ARG 1268": "NH1" <-> "NH2" Residue "A TYR 1273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1308": "NH1" <-> "NH2" Residue "A TYR 1314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1371": "NH1" <-> "NH2" Residue "A ARG 1393": "NH1" <-> "NH2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 143": "NH1" <-> "NH2" Residue "B ARG 162": "NH1" <-> "NH2" Residue "B TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "B PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 199": "NH1" <-> "NH2" Residue "B TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12185 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1145, 9124 Classifications: {'peptide': 1145} Link IDs: {'PTRANS': 36, 'TRANS': 1108} Chain breaks: 2 Chain: "B" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2934 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ACP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.72, per 1000 atoms: 0.55 Number of scatterers: 12185 At special positions: 0 Unit cell: (141.37, 109.72, 130.82, 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 60 16.00 P 3 15.00 Mg 1 11.99 O 2280 8.00 N 2015 7.00 C 7826 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 777 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 231 " distance=2.04 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " BETA1-6 " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG C 1 " - " ASN B 298 " " NAG D 1 " - " ASN B 240 " " NAG E 1 " - " ASN B 256 " Time building additional restraints: 4.31 Conformation dependent library (CDL) restraints added in 2.2 seconds 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2816 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 6 sheets defined 30.0% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.94 Creating SS restraints... Processing helix chain 'A' and resid 221 through 231 Processing helix chain 'A' and resid 249 through 252 No H-bonds generated for 'chain 'A' and resid 249 through 252' Processing helix chain 'A' and resid 255 through 258 No H-bonds generated for 'chain 'A' and resid 255 through 258' Processing helix chain 'A' and resid 263 through 272 removed outlier: 3.574A pdb=" N VAL A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 549 through 575 removed outlier: 3.881A pdb=" N GLY A 568 " --> pdb=" O CYS A 564 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY A 572 " --> pdb=" O GLY A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 621 removed outlier: 3.543A pdb=" N ALA A 605 " --> pdb=" O SER A 601 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU A 612 " --> pdb=" O LEU A 608 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL A 613 " --> pdb=" O TYR A 609 " (cutoff:3.500A) Proline residue: A 614 - end of helix Processing helix chain 'A' and resid 625 through 633 removed outlier: 3.697A pdb=" N TYR A 633 " --> pdb=" O ALA A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 638 No H-bonds generated for 'chain 'A' and resid 636 through 638' Processing helix chain 'A' and resid 696 through 698 No H-bonds generated for 'chain 'A' and resid 696 through 698' Processing helix chain 'A' and resid 709 through 721 removed outlier: 3.933A pdb=" N ARG A 713 " --> pdb=" O GLU A 709 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 721 " --> pdb=" O ALA A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 776 Processing helix chain 'A' and resid 799 through 808 removed outlier: 3.512A pdb=" N ALA A 806 " --> pdb=" O ALA A 802 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR A 807 " --> pdb=" O ALA A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 829 No H-bonds generated for 'chain 'A' and resid 827 through 829' Processing helix chain 'A' and resid 874 through 877 No H-bonds generated for 'chain 'A' and resid 874 through 877' Processing helix chain 'A' and resid 891 through 906 removed outlier: 4.675A pdb=" N THR A 896 " --> pdb=" O ILE A 892 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A 897 " --> pdb=" O LEU A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 925 No H-bonds generated for 'chain 'A' and resid 923 through 925' Processing helix chain 'A' and resid 942 through 949 Processing helix chain 'A' and resid 971 through 980 removed outlier: 3.917A pdb=" N GLU A 976 " --> pdb=" O PRO A 972 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU A 980 " --> pdb=" O GLU A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1002 removed outlier: 3.535A pdb=" N ASN A 998 " --> pdb=" O GLU A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1042 removed outlier: 3.526A pdb=" N TYR A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1078 No H-bonds generated for 'chain 'A' and resid 1075 through 1078' Processing helix chain 'A' and resid 1087 through 1094 Processing helix chain 'A' and resid 1107 through 1120 removed outlier: 3.584A pdb=" N ALA A1111 " --> pdb=" O PRO A1107 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A1117 " --> pdb=" O VAL A1113 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP A1119 " --> pdb=" O LYS A1115 " (cutoff:3.500A) Processing helix chain 'A' and resid 1136 through 1139 No H-bonds generated for 'chain 'A' and resid 1136 through 1139' Processing helix chain 'A' and resid 1168 through 1174 Processing helix chain 'A' and resid 1178 through 1187 removed outlier: 3.562A pdb=" N LYS A1182 " --> pdb=" O ARG A1178 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU A1184 " --> pdb=" O SER A1180 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU A1186 " --> pdb=" O LYS A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1199 removed outlier: 4.210A pdb=" N LYS A1194 " --> pdb=" O GLU A1190 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN A1195 " --> pdb=" O PHE A1191 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET A1196 " --> pdb=" O PHE A1192 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE A1198 " --> pdb=" O LYS A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1204 No H-bonds generated for 'chain 'A' and resid 1201 through 1204' Processing helix chain 'A' and resid 1232 through 1240 Processing helix chain 'A' and resid 1248 through 1251 No H-bonds generated for 'chain 'A' and resid 1248 through 1251' Processing helix chain 'A' and resid 1253 through 1260 removed outlier: 3.936A pdb=" N VAL A1258 " --> pdb=" O LEU A1255 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE A1260 " --> pdb=" O ARG A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1292 removed outlier: 3.733A pdb=" N LEU A1271 " --> pdb=" O GLN A1267 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A1273 " --> pdb=" O LYS A1269 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE A1282 " --> pdb=" O LEU A1278 " (cutoff:3.500A) Proline residue: A1288 - end of helix removed outlier: 3.608A pdb=" N VAL A1291 " --> pdb=" O PHE A1287 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR A1292 " --> pdb=" O PRO A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1330 removed outlier: 4.037A pdb=" N VAL A1313 " --> pdb=" O TYR A1309 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR A1314 " --> pdb=" O PHE A1310 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR A1316 " --> pdb=" O GLY A1312 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A1318 " --> pdb=" O TYR A1314 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER A1322 " --> pdb=" O ILE A1318 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR A1326 " --> pdb=" O SER A1322 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL A1327 " --> pdb=" O CYS A1323 " (cutoff:3.500A) Processing helix chain 'A' and resid 1336 through 1346 removed outlier: 3.563A pdb=" N PHE A1341 " --> pdb=" O PHE A1337 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A1345 " --> pdb=" O PHE A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1356 Processing helix chain 'A' and resid 1368 through 1372 Processing helix chain 'A' and resid 1378 through 1403 removed outlier: 4.713A pdb=" N PHE A1383 " --> pdb=" O TRP A1379 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL A1384 " --> pdb=" O ALA A1380 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU A1387 " --> pdb=" O PHE A1383 " (cutoff:3.500A) Proline residue: A1392 - end of helix removed outlier: 3.684A pdb=" N PHE A1403 " --> pdb=" O PHE A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1416 removed outlier: 3.846A pdb=" N GLN A1416 " --> pdb=" O ARG A1412 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 94 removed outlier: 4.297A pdb=" N ILE B 88 " --> pdb=" O VAL B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 198 No H-bonds generated for 'chain 'B' and resid 195 through 198' Processing helix chain 'B' and resid 205 through 208 No H-bonds generated for 'chain 'B' and resid 205 through 208' Processing helix chain 'B' and resid 233 through 237 removed outlier: 3.514A pdb=" N SER B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 233 through 237' Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'B' and resid 373 through 387 removed outlier: 4.184A pdb=" N TYR B 378 " --> pdb=" O LEU B 374 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU B 379 " --> pdb=" O GLY B 375 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N CYS B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 397 removed outlier: 4.424A pdb=" N TRP B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 485 through 488 removed outlier: 3.592A pdb=" N MET A 485 " --> pdb=" O GLU A 498 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1143 through 1145 removed outlier: 6.357A pdb=" N TYR A 663 " --> pdb=" O LEU A1126 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ILE A1128 " --> pdb=" O TYR A 663 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE A 665 " --> pdb=" O ILE A1128 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LYS A 984 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N SER A 666 " --> pdb=" O LYS A 984 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N TRP A 986 " --> pdb=" O SER A 666 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A1100 " --> pdb=" O LEU A 985 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 687 through 689 removed outlier: 3.508A pdb=" N VAL A 687 " --> pdb=" O ILE A 684 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N CYS A 682 " --> pdb=" O TYR A 689 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ALA A 962 " --> pdb=" O LYS A 680 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N CYS A 682 " --> pdb=" O GLY A 960 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLY A 960 " --> pdb=" O CYS A 682 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ILE A 684 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 9.124A pdb=" N LEU A 958 " --> pdb=" O ILE A 684 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE A 913 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLY A 960 " --> pdb=" O LEU A 911 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU A 911 " --> pdb=" O GLY A 960 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA A 962 " --> pdb=" O ARG A 909 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ARG A 909 " --> pdb=" O ALA A 962 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 830 through 833 removed outlier: 3.629A pdb=" N ILE A 825 " --> pdb=" O LYS A 832 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY A 817 " --> pdb=" O ILE A 824 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLU A 826 " --> pdb=" O PHE A 815 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N PHE A 815 " --> pdb=" O GLU A 826 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 127 through 129 removed outlier: 3.549A pdb=" N VAL B 178 " --> pdb=" O GLY B 358 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR B 360 " --> pdb=" O ASN B 176 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TYR B 177 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU B 326 " --> pdb=" O TYR B 177 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU B 179 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N THR B 324 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 141 through 144 273 hydrogen bonds defined for protein. 777 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.81 Time building geometry restraints manager: 4.76 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: 3837 1.34 - 1.46: 2992 1.46 - 1.58: 5538 1.58 - 1.70: 8 1.70 - 1.83: 91 Bond restraints: 12466 Sorted by residual: bond pdb=" O3A ACP A1601 " pdb=" PB ACP A1601 " ideal model delta sigma weight residual 1.698 1.597 0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" O2B ACP A1601 " pdb=" PB ACP A1601 " ideal model delta sigma weight residual 1.507 1.607 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" C4 ACP A1601 " pdb=" C5 ACP A1601 " ideal model delta sigma weight residual 1.386 1.467 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" O3G ACP A1601 " pdb=" PG ACP A1601 " ideal model delta sigma weight residual 1.532 1.608 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C5 ACP A1601 " pdb=" C6 ACP A1601 " ideal model delta sigma weight residual 1.407 1.482 -0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 12461 not shown) Histogram of bond angle deviations from ideal: 97.60 - 105.43: 223 105.43 - 113.26: 6612 113.26 - 121.09: 6465 121.09 - 128.92: 3509 128.92 - 136.75: 103 Bond angle restraints: 16912 Sorted by residual: angle pdb=" C LYS A1294 " pdb=" N ASN A1295 " pdb=" CA ASN A1295 " ideal model delta sigma weight residual 122.46 131.31 -8.85 1.41e+00 5.03e-01 3.94e+01 angle pdb=" C GLU A1084 " pdb=" N ASP A1085 " pdb=" CA ASP A1085 " ideal model delta sigma weight residual 125.66 135.67 -10.01 1.85e+00 2.92e-01 2.93e+01 angle pdb=" C ARG A1363 " pdb=" N GLU A1364 " pdb=" CA GLU A1364 " ideal model delta sigma weight residual 121.54 130.24 -8.70 1.91e+00 2.74e-01 2.07e+01 angle pdb=" N LEU B 393 " pdb=" CA LEU B 393 " pdb=" C LEU B 393 " ideal model delta sigma weight residual 114.56 108.96 5.60 1.27e+00 6.20e-01 1.95e+01 angle pdb=" C PHE A 232 " pdb=" N GLN A 233 " pdb=" CA GLN A 233 " ideal model delta sigma weight residual 121.54 129.90 -8.36 1.91e+00 2.74e-01 1.92e+01 ... (remaining 16907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.35: 7151 22.35 - 44.70: 291 44.70 - 67.05: 26 67.05 - 89.39: 13 89.39 - 111.74: 20 Dihedral angle restraints: 7501 sinusoidal: 3108 harmonic: 4393 Sorted by residual: dihedral pdb=" CA PHE A1045 " pdb=" C PHE A1045 " pdb=" N ASN A1046 " pdb=" CA ASN A1046 " ideal model delta harmonic sigma weight residual 180.00 146.55 33.45 0 5.00e+00 4.00e-02 4.48e+01 dihedral pdb=" CA GLU A1218 " pdb=" C GLU A1218 " pdb=" N TYR A1219 " pdb=" CA TYR A1219 " ideal model delta harmonic sigma weight residual 180.00 147.41 32.59 0 5.00e+00 4.00e-02 4.25e+01 dihedral pdb=" CA MET B 169 " pdb=" C MET B 169 " pdb=" N LYS B 170 " pdb=" CA LYS B 170 " ideal model delta harmonic sigma weight residual -180.00 -147.54 -32.46 0 5.00e+00 4.00e-02 4.21e+01 ... (remaining 7498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1307 0.055 - 0.111: 450 0.111 - 0.166: 103 0.166 - 0.222: 20 0.222 - 0.277: 8 Chirality restraints: 1888 Sorted by residual: chirality pdb=" CB ILE B 403 " pdb=" CA ILE B 403 " pdb=" CG1 ILE B 403 " pdb=" CG2 ILE B 403 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C4 NAG D 2 " pdb=" C3 NAG D 2 " pdb=" C5 NAG D 2 " pdb=" O4 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.53 -2.27 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB ILE B 327 " pdb=" CA ILE B 327 " pdb=" CG1 ILE B 327 " pdb=" CG2 ILE B 327 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 1885 not shown) Planarity restraints: 2142 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 398 " -0.032 2.00e-02 2.50e+03 6.42e-02 4.13e+01 pdb=" C PHE B 398 " 0.111 2.00e-02 2.50e+03 pdb=" O PHE B 398 " -0.043 2.00e-02 2.50e+03 pdb=" N GLY B 399 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1408 " 0.032 2.00e-02 2.50e+03 6.20e-02 3.85e+01 pdb=" C VAL A1408 " -0.107 2.00e-02 2.50e+03 pdb=" O VAL A1408 " 0.040 2.00e-02 2.50e+03 pdb=" N GLU A1409 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 142 " -0.025 2.00e-02 2.50e+03 2.42e-02 1.46e+01 pdb=" CG TRP B 142 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP B 142 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP B 142 " 0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP B 142 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP B 142 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 142 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 142 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 142 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP B 142 " -0.002 2.00e-02 2.50e+03 ... (remaining 2139 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1503 2.75 - 3.29: 11363 3.29 - 3.83: 20010 3.83 - 4.36: 24065 4.36 - 4.90: 40427 Nonbonded interactions: 97368 Sorted by model distance: nonbonded pdb=" OH TYR A1193 " pdb=" OE1 GLN A1280 " model vdw 2.215 2.440 nonbonded pdb=" OE1 GLU B 102 " pdb=" OH TYR B 360 " model vdw 2.257 2.440 nonbonded pdb=" O THR A1353 " pdb=" OG SER A1357 " model vdw 2.266 2.440 nonbonded pdb=" OH TYR A 609 " pdb=" O MET A1222 " model vdw 2.307 2.440 nonbonded pdb=" O LEU A 658 " pdb=" OH TYR A1256 " model vdw 2.319 2.440 ... (remaining 97363 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' } 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: 1.840 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: 7.330 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 34.310 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 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 0.101 12466 Z= 0.373 Angle : 1.049 11.668 16912 Z= 0.552 Chirality : 0.060 0.277 1888 Planarity : 0.006 0.073 2139 Dihedral : 14.174 111.741 4676 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.27 % Favored : 91.66 % Rotamer: Outliers : 0.15 % Allowed : 4.89 % Favored : 94.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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: -5.64 (0.15), residues: 1499 helix: -4.64 (0.09), residues: 556 sheet: -2.68 (0.34), residues: 159 loop : -3.31 (0.17), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.004 TRP B 142 HIS 0.011 0.002 HIS A 778 PHE 0.039 0.003 PHE A1287 TYR 0.035 0.003 TYR B 228 ARG 0.011 0.001 ARG A 508 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 181 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 778 HIS cc_start: 0.7671 (p-80) cc_final: 0.7450 (p-80) REVERT: A 827 MET cc_start: 0.8150 (mpp) cc_final: 0.7925 (mpp) outliers start: 2 outliers final: 0 residues processed: 183 average time/residue: 0.2861 time to fit residues: 72.7137 Evaluate side-chains 102 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 45 optimal weight: 0.4980 chunk 71 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 194 ASN A 278 HIS A 412 ASN A 550 ASN A 556 ASN ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 GLN A 738 GLN A 769 HIS ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1139 GLN A1176 HIS A1307 HIS B 50 ASN B 125 HIS B 171 ASN B 172 ASN B 186 HIS B 313 ASN B 347 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12466 Z= 0.235 Angle : 0.700 9.033 16912 Z= 0.362 Chirality : 0.046 0.294 1888 Planarity : 0.004 0.039 2139 Dihedral : 12.900 87.618 1824 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.87 % Favored : 93.06 % Rotamer: Outliers : 1.53 % Allowed : 9.94 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.59 (0.17), residues: 1499 helix: -3.44 (0.14), residues: 566 sheet: -2.11 (0.35), residues: 167 loop : -2.95 (0.19), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 142 HIS 0.005 0.001 HIS A 778 PHE 0.017 0.002 PHE B 128 TYR 0.019 0.002 TYR A1292 ARG 0.004 0.000 ARG A 916 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 778 HIS cc_start: 0.7624 (p-80) cc_final: 0.7416 (p-80) REVERT: A 827 MET cc_start: 0.8329 (mpp) cc_final: 0.8107 (mpp) REVERT: A 1305 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7956 (pp) REVERT: B 403 ILE cc_start: 0.6971 (mm) cc_final: 0.6741 (mm) outliers start: 20 outliers final: 9 residues processed: 132 average time/residue: 0.2456 time to fit residues: 47.6134 Evaluate side-chains 106 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1406 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 280 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 147 optimal weight: 0.0670 chunk 121 optimal weight: 0.1980 chunk 135 optimal weight: 1.9990 chunk 46 optimal weight: 20.0000 chunk 109 optimal weight: 0.3980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1139 GLN B 282 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12466 Z= 0.173 Angle : 0.636 10.208 16912 Z= 0.320 Chirality : 0.044 0.273 1888 Planarity : 0.003 0.033 2139 Dihedral : 10.254 86.091 1824 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.14 % Favored : 92.80 % Rotamer: Outliers : 1.83 % Allowed : 12.54 % Favored : 85.63 % 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: -3.75 (0.19), residues: 1499 helix: -2.47 (0.18), residues: 566 sheet: -1.66 (0.39), residues: 155 loop : -2.70 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1415 HIS 0.004 0.001 HIS A 778 PHE 0.015 0.001 PHE B 128 TYR 0.019 0.001 TYR A1082 ARG 0.005 0.000 ARG A 966 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 111 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 778 HIS cc_start: 0.7599 (p-80) cc_final: 0.7347 (p-80) REVERT: A 1305 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7976 (pp) outliers start: 24 outliers final: 11 residues processed: 128 average time/residue: 0.2622 time to fit residues: 48.6011 Evaluate side-chains 105 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1196 MET Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 377 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 4.9990 chunk 102 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 chunk 15 optimal weight: 50.0000 chunk 65 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 ASN ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1139 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12466 Z= 0.339 Angle : 0.677 9.272 16912 Z= 0.343 Chirality : 0.048 0.327 1888 Planarity : 0.004 0.037 2139 Dihedral : 9.150 84.776 1824 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.81 % Favored : 92.13 % Rotamer: Outliers : 2.60 % Allowed : 12.84 % Favored : 84.56 % 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: -3.44 (0.19), residues: 1499 helix: -2.07 (0.19), residues: 571 sheet: -1.65 (0.38), residues: 165 loop : -2.61 (0.20), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 308 HIS 0.005 0.001 HIS A1293 PHE 0.019 0.002 PHE B 353 TYR 0.024 0.002 TYR A1292 ARG 0.007 0.000 ARG A 714 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 103 time to evaluate : 1.269 Fit side-chains revert: symmetry clash REVERT: A 677 MET cc_start: 0.8763 (mmm) cc_final: 0.8205 (mmt) REVERT: A 778 HIS cc_start: 0.7785 (p-80) cc_final: 0.7506 (p-80) REVERT: A 1305 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8140 (pp) outliers start: 34 outliers final: 23 residues processed: 126 average time/residue: 0.2379 time to fit residues: 44.3399 Evaluate side-chains 111 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 87 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 766 CYS Chi-restraints excluded: chain A residue 1008 ASN Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1196 MET Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1437 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 2 optimal weight: 40.0000 chunk 107 optimal weight: 0.8980 chunk 59 optimal weight: 8.9990 chunk 123 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 0 optimal weight: 40.0000 chunk 74 optimal weight: 3.9990 chunk 130 optimal weight: 0.0870 chunk 36 optimal weight: 0.0670 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1139 GLN B 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12466 Z= 0.183 Angle : 0.616 9.479 16912 Z= 0.307 Chirality : 0.044 0.302 1888 Planarity : 0.003 0.031 2139 Dihedral : 8.312 81.730 1824 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.94 % Favored : 93.00 % Rotamer: Outliers : 2.45 % Allowed : 13.99 % Favored : 83.56 % 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: -3.02 (0.20), residues: 1499 helix: -1.71 (0.20), residues: 564 sheet: -1.39 (0.40), residues: 154 loop : -2.37 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 603 HIS 0.006 0.001 HIS A 778 PHE 0.016 0.001 PHE A1365 TYR 0.017 0.001 TYR A 740 ARG 0.005 0.000 ARG A 966 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 103 time to evaluate : 1.333 Fit side-chains revert: symmetry clash REVERT: A 836 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8182 (pp) outliers start: 32 outliers final: 23 residues processed: 126 average time/residue: 0.2426 time to fit residues: 45.3969 Evaluate side-chains 112 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 88 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 929 LYS Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 1008 ASN Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1196 MET Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1406 THR Chi-restraints excluded: chain A residue 1437 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 274 ASN ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 GLN A 763 GLN A1139 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 12466 Z= 0.481 Angle : 0.741 9.422 16912 Z= 0.374 Chirality : 0.050 0.392 1888 Planarity : 0.004 0.036 2139 Dihedral : 8.367 81.703 1824 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.74 % Favored : 91.19 % Rotamer: Outliers : 3.59 % Allowed : 14.45 % Favored : 81.96 % 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: -3.13 (0.20), residues: 1499 helix: -1.79 (0.20), residues: 572 sheet: -1.56 (0.39), residues: 156 loop : -2.42 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 603 HIS 0.008 0.002 HIS A 778 PHE 0.028 0.002 PHE A1045 TYR 0.029 0.002 TYR A1221 ARG 0.005 0.001 ARG A1171 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 100 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 31 residues processed: 134 average time/residue: 0.2587 time to fit residues: 52.2224 Evaluate side-chains 116 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 85 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 929 LYS Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1008 ASN Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1196 MET Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1406 THR Chi-restraints excluded: chain A residue 1437 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 9.9990 chunk 82 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 chunk 90 optimal weight: 0.3980 chunk 88 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12466 Z= 0.213 Angle : 0.630 8.888 16912 Z= 0.318 Chirality : 0.045 0.333 1888 Planarity : 0.003 0.032 2139 Dihedral : 8.048 80.499 1824 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.27 % Favored : 92.66 % Rotamer: Outliers : 2.60 % Allowed : 15.60 % Favored : 81.80 % 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: -2.78 (0.20), residues: 1499 helix: -1.48 (0.21), residues: 558 sheet: -1.30 (0.40), residues: 154 loop : -2.25 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 603 HIS 0.006 0.001 HIS A 278 PHE 0.019 0.001 PHE B 152 TYR 0.017 0.001 TYR A 740 ARG 0.005 0.000 ARG A 966 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 88 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 930 TYR cc_start: 0.7464 (m-80) cc_final: 0.7101 (m-80) outliers start: 34 outliers final: 27 residues processed: 112 average time/residue: 0.2024 time to fit residues: 35.4733 Evaluate side-chains 110 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 83 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 929 LYS Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1008 ASN Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1196 MET Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1406 THR Chi-restraints excluded: chain A residue 1437 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 0.2980 chunk 91 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 13 optimal weight: 40.0000 chunk 113 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 138 optimal weight: 0.7980 chunk 126 optimal weight: 0.6980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 ASN ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12466 Z= 0.303 Angle : 0.653 9.654 16912 Z= 0.329 Chirality : 0.046 0.354 1888 Planarity : 0.004 0.040 2139 Dihedral : 7.956 79.763 1824 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.81 % Favored : 92.13 % Rotamer: Outliers : 2.75 % Allowed : 15.52 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.20), residues: 1499 helix: -1.43 (0.21), residues: 572 sheet: -1.24 (0.40), residues: 152 loop : -2.32 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 603 HIS 0.006 0.001 HIS A 778 PHE 0.020 0.002 PHE B 152 TYR 0.018 0.002 TYR A 740 ARG 0.008 0.000 ARG A 966 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 88 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 930 TYR cc_start: 0.7560 (m-80) cc_final: 0.7044 (m-80) REVERT: B 388 MET cc_start: 0.6643 (OUTLIER) cc_final: 0.6229 (mpp) outliers start: 36 outliers final: 29 residues processed: 114 average time/residue: 0.2098 time to fit residues: 38.7588 Evaluate side-chains 116 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 86 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 929 LYS Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1008 ASN Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1196 MET Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1406 THR Chi-restraints excluded: chain A residue 1437 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.0980 chunk 138 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 41 optimal weight: 0.0170 chunk 121 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 142 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12466 Z= 0.161 Angle : 0.592 9.766 16912 Z= 0.298 Chirality : 0.043 0.293 1888 Planarity : 0.003 0.032 2139 Dihedral : 7.510 76.523 1824 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.47 % Favored : 93.46 % Rotamer: Outliers : 1.99 % Allowed : 16.67 % Favored : 81.35 % 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: -2.48 (0.21), residues: 1499 helix: -1.12 (0.22), residues: 559 sheet: -0.92 (0.41), residues: 150 loop : -2.23 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 603 HIS 0.005 0.001 HIS A 278 PHE 0.017 0.001 PHE B 152 TYR 0.016 0.001 TYR A 740 ARG 0.007 0.000 ARG A 966 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 96 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 603 TRP cc_start: 0.7144 (m100) cc_final: 0.6861 (m100) REVERT: A 930 TYR cc_start: 0.7529 (m-80) cc_final: 0.7007 (m-80) outliers start: 26 outliers final: 21 residues processed: 111 average time/residue: 0.1955 time to fit residues: 34.8230 Evaluate side-chains 113 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1008 ASN Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1196 MET Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1406 THR Chi-restraints excluded: chain A residue 1437 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 343 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 149 optimal weight: 0.1980 chunk 137 optimal weight: 0.0270 chunk 118 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 126 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12466 Z= 0.169 Angle : 0.597 10.085 16912 Z= 0.300 Chirality : 0.043 0.287 1888 Planarity : 0.003 0.031 2139 Dihedral : 7.304 74.235 1824 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.54 % Favored : 93.40 % Rotamer: Outliers : 1.68 % Allowed : 17.20 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.21), residues: 1499 helix: -1.00 (0.22), residues: 566 sheet: -0.80 (0.42), residues: 150 loop : -2.24 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 603 HIS 0.004 0.001 HIS A 278 PHE 0.017 0.001 PHE B 152 TYR 0.028 0.001 TYR A 639 ARG 0.007 0.000 ARG A 966 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 930 TYR cc_start: 0.7413 (m-80) cc_final: 0.6877 (m-80) outliers start: 22 outliers final: 21 residues processed: 114 average time/residue: 0.2199 time to fit residues: 39.6171 Evaluate side-chains 110 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 89 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1008 ASN Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1196 MET Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1437 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 343 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.172287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.102634 restraints weight = 17065.779| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.73 r_work: 0.3184 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12466 Z= 0.310 Angle : 0.655 9.799 16912 Z= 0.328 Chirality : 0.046 0.328 1888 Planarity : 0.004 0.032 2139 Dihedral : 7.483 74.145 1824 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.81 % Favored : 92.13 % Rotamer: Outliers : 1.91 % Allowed : 17.43 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.21), residues: 1499 helix: -1.00 (0.22), residues: 561 sheet: -1.17 (0.39), residues: 166 loop : -2.16 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 603 HIS 0.005 0.001 HIS A1417 PHE 0.019 0.002 PHE B 152 TYR 0.039 0.002 TYR A 639 ARG 0.007 0.000 ARG A 966 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2778.23 seconds wall clock time: 50 minutes 47.17 seconds (3047.17 seconds total)