Starting phenix.real_space_refine (version: dev) on Sat Jun 4 03:15:01 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhg_26514/06_2022/7uhg_26514_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhg_26514/06_2022/7uhg_26514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhg_26514/06_2022/7uhg_26514.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhg_26514/06_2022/7uhg_26514.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhg_26514/06_2022/7uhg_26514_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhg_26514/06_2022/7uhg_26514_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.005 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "C GLU 343": "OE1" <-> "OE2" Residue "A TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "A GLU 543": "OE1" <-> "OE2" Residue "A PHE 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 914": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 941": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 959": "OD1" <-> "OD2" Residue "A PHE 1150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 129": "OD1" <-> "OD2" Residue "D GLU 191": "OE1" <-> "OE2" Residue "D GLU 278": "OE1" <-> "OE2" Residue "D ASP 300": "OD1" <-> "OD2" Residue "D ASP 320": "OD1" <-> "OD2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "D ASP 439": "OD1" <-> "OD2" Residue "D TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 555": "OE1" <-> "OE2" Residue "D ASP 569": "OD1" <-> "OD2" Residue "D ASP 616": "OD1" <-> "OD2" Residue "D TYR 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4617/modules/chem_data/mon_lib" Total number of atoms: 20414 Number of models: 1 Model: "" Number of chains: 11 Chain: "C" Number of atoms: 2575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2575 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 18, 'TRANS': 304, 'PCIS': 1} Chain: "A" Number of atoms: 9900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1230, 9900 Classifications: {'peptide': 1230} Link IDs: {'PTRANS': 36, 'TRANS': 1193} Chain breaks: 7 Chain: "D" Number of atoms: 7570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7570 Classifications: {'peptide': 948} Link IDs: {'PTRANS': 38, 'TRANS': 907, 'PCIS': 2} Chain breaks: 5 Chain: "B" 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 chiralities: 2 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" 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 chiralities: 2 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "H" 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 chiralities: 2 Chain: "I" 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 chiralities: 2 Chain: "A" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 130 Unusual residues: {' CA': 1, '3PE': 1, 'CLR': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 11.96, per 1000 atoms: 0.59 Number of scatterers: 20414 At special positions: 0 Unit cell: (172.67, 170.442, 182.696, 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) Ca 2 19.99 S 112 16.00 P 1 15.00 O 3757 8.00 N 3351 7.00 C 13191 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 326 " distance=2.04 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A1044 " - pdb=" SG CYS A1055 " distance=2.03 Simple disulfide: pdb=" SG CYS A1421 " - pdb=" SG CYS A1435 " distance=2.03 Simple disulfide: pdb=" SG CYS D 303 " - pdb=" SG CYS D1044 " distance=2.03 Simple disulfide: pdb=" SG CYS D 404 " - pdb=" SG CYS D1071 " distance=2.03 Simple disulfide: pdb=" SG CYS D 667 " - pdb=" SG CYS D 697 " distance=2.03 Simple disulfide: pdb=" SG CYS D 904 " - pdb=" SG CYS D 974 " distance=2.03 Simple disulfide: pdb=" SG CYS D 996 " - pdb=" SG CYS D1026 " distance=2.03 Simple disulfide: pdb=" SG CYS D 999 " - pdb=" SG CYS D1024 " distance=2.03 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 B 1 " - " NAG B 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " NAG E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " NAG G 3 " " NAG G 3 " - " NAG G 4 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG B 1 " - " ASN A 329 " " NAG D1201 " - " ASN D 92 " " NAG E 1 " - " ASN D 184 " " NAG F 1 " - " ASN D 348 " " NAG G 1 " - " ASN D 468 " " NAG H 1 " - " ASN D 613 " " NAG I 1 " - " ASN D 895 " Time building additional restraints: 8.22 Conformation dependent library (CDL) restraints added in 2.8 seconds 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4736 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 14 sheets defined 49.2% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.08 Creating SS restraints... Processing helix chain 'C' and resid 39 through 55 Processing helix chain 'C' and resid 121 through 132 removed outlier: 3.760A pdb=" N GLU C 132 " --> pdb=" O ARG C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 158 No H-bonds generated for 'chain 'C' and resid 156 through 158' Processing helix chain 'C' and resid 191 through 207 removed outlier: 4.415A pdb=" N LEU C 200 " --> pdb=" O MET C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 263 Processing helix chain 'C' and resid 297 through 307 Processing helix chain 'C' and resid 309 through 313 Processing helix chain 'C' and resid 315 through 327 Processing helix chain 'C' and resid 330 through 332 No H-bonds generated for 'chain 'C' and resid 330 through 332' Processing helix chain 'C' and resid 342 through 360 Processing helix chain 'A' and resid 129 through 144 Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 156 through 179 removed outlier: 3.817A pdb=" N LYS A 163 " --> pdb=" O HIS A 159 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 176 " --> pdb=" O PHE A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 216 removed outlier: 3.530A pdb=" N VAL A 205 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 245 removed outlier: 3.535A pdb=" N ARG A 240 " --> pdb=" O LYS A 237 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A 242 " --> pdb=" O LEU A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 Processing helix chain 'A' and resid 255 through 267 removed outlier: 3.649A pdb=" N VAL A 259 " --> pdb=" O PRO A 255 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N VAL A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 292 removed outlier: 4.342A pdb=" N HIS A 273 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE A 274 " --> pdb=" O PRO A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 361 Processing helix chain 'A' and resid 366 through 376 removed outlier: 3.564A pdb=" N ASP A 375 " --> pdb=" O TYR A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 393 Processing helix chain 'A' and resid 395 through 419 removed outlier: 3.545A pdb=" N GLU A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 413 " --> pdb=" O PHE A 409 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU A 414 " --> pdb=" O SER A 410 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG A 419 " --> pdb=" O LYS A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 430 Processing helix chain 'A' and resid 432 through 439 removed outlier: 4.293A pdb=" N LYS A 436 " --> pdb=" O GLU A 432 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 521 No H-bonds generated for 'chain 'A' and resid 518 through 521' Processing helix chain 'A' and resid 523 through 541 removed outlier: 3.582A pdb=" N ILE A 540 " --> pdb=" O ASN A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 577 removed outlier: 3.670A pdb=" N SER A 576 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU A 577 " --> pdb=" O LYS A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 584 removed outlier: 3.549A pdb=" N VAL A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 606 removed outlier: 3.640A pdb=" N THR A 602 " --> pdb=" O GLY A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 619 Processing helix chain 'A' and resid 622 through 628 removed outlier: 3.907A pdb=" N ARG A 625 " --> pdb=" O ARG A 622 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 626 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE A 627 " --> pdb=" O LEU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 632 No H-bonds generated for 'chain 'A' and resid 630 through 632' Processing helix chain 'A' and resid 637 through 644 Processing helix chain 'A' and resid 647 through 672 removed outlier: 3.612A pdb=" N SER A 652 " --> pdb=" O LYS A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 703 Processing helix chain 'A' and resid 707 through 718 removed outlier: 3.727A pdb=" N TYR A 718 " --> pdb=" O GLY A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 746 removed outlier: 3.601A pdb=" N ILE A 734 " --> pdb=" O TYR A 731 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 735 " --> pdb=" O PHE A 732 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N CYS A 738 " --> pdb=" O LEU A 735 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN A 740 " --> pdb=" O ILE A 737 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR A 741 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 753 removed outlier: 3.551A pdb=" N VAL A 752 " --> pdb=" O LEU A 748 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP A 753 " --> pdb=" O ALA A 749 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 748 through 753' Processing helix chain 'A' and resid 755 through 771 removed outlier: 3.620A pdb=" N GLU A 767 " --> pdb=" O THR A 763 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A 771 " --> pdb=" O GLU A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 883 removed outlier: 3.673A pdb=" N LEU A 882 " --> pdb=" O GLY A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 904 removed outlier: 4.035A pdb=" N ALA A 901 " --> pdb=" O MET A 897 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 902 " --> pdb=" O LEU A 898 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 903 " --> pdb=" O SER A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 940 removed outlier: 3.579A pdb=" N LEU A 935 " --> pdb=" O THR A 931 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 936 " --> pdb=" O VAL A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 969 removed outlier: 3.508A pdb=" N ASP A 959 " --> pdb=" O PHE A 955 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET A 960 " --> pdb=" O ASN A 956 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A 966 " --> pdb=" O VAL A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 997 removed outlier: 4.769A pdb=" N VAL A 988 " --> pdb=" O ARG A 984 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LEU A 989 " --> pdb=" O VAL A 985 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ARG A 990 " --> pdb=" O LEU A 986 " (cutoff:3.500A) Proline residue: A 991 - end of helix removed outlier: 4.391A pdb=" N ALA A 994 " --> pdb=" O ARG A 990 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ILE A 995 " --> pdb=" O PRO A 991 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ASN A 996 " --> pdb=" O LEU A 992 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ARG A 997 " --> pdb=" O ARG A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1016 removed outlier: 3.648A pdb=" N HIS A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1037 removed outlier: 3.515A pdb=" N THR A1023 " --> pdb=" O MET A1019 " (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 1087 through 1098 Processing helix chain 'A' and resid 1103 through 1111 Processing helix chain 'A' and resid 1126 through 1138 removed outlier: 3.738A pdb=" N ILE A1134 " --> pdb=" O PHE A1131 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR A1135 " --> pdb=" O PHE A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1161 removed outlier: 3.607A pdb=" N VAL A1148 " --> pdb=" O MET A1144 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS A1161 " --> pdb=" O GLU A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1180 removed outlier: 3.840A pdb=" N GLN A1174 " --> pdb=" O LYS A1170 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS A1175 " --> pdb=" O ASN A1171 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLU A1177 " --> pdb=" O ARG A1173 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR A1178 " --> pdb=" O GLN A1174 " (cutoff:3.500A) Processing helix chain 'A' and resid 1193 through 1202 removed outlier: 4.514A pdb=" N PHE A1198 " --> pdb=" O TYR A1194 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TRP A1199 " --> pdb=" O GLN A1195 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR A1200 " --> pdb=" O TYR A1196 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL A1201 " --> pdb=" O LYS A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1223 Processing helix chain 'A' and resid 1231 through 1259 removed outlier: 4.164A pdb=" N ALA A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1264 No H-bonds generated for 'chain 'A' and resid 1261 through 1264' Processing helix chain 'A' and resid 1268 through 1287 removed outlier: 3.819A pdb=" N PHE A1272 " --> pdb=" O ALA A1268 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU A1275 " --> pdb=" O THR A1271 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A1276 " --> pdb=" O PHE A1272 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A1277 " --> pdb=" O ASP A1273 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP A1283 " --> pdb=" O GLY A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1330 removed outlier: 3.509A pdb=" N LEU A1320 " --> pdb=" O THR A1316 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHE A1321 " --> pdb=" O PHE A1317 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG A1322 " --> pdb=" O PHE A1318 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N VAL A1323 " --> pdb=" O ARG A1319 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N MET A1324 " --> pdb=" O LEU A1320 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG A1325 " --> pdb=" O PHE A1321 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N LEU A1326 " --> pdb=" O ARG A1322 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N VAL A1327 " --> pdb=" O VAL A1323 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS A1328 " --> pdb=" O MET A1324 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A1329 " --> pdb=" O ARG A1325 " (cutoff:3.500A) Processing helix chain 'A' and resid 1337 through 1349 Processing helix chain 'A' and resid 1353 through 1372 removed outlier: 3.944A pdb=" N ILE A1357 " --> pdb=" O VAL A1353 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN A1370 " --> pdb=" O VAL A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1392 through 1403 Processing helix chain 'A' and resid 1408 through 1415 Processing helix chain 'A' and resid 1438 through 1470 removed outlier: 3.681A pdb=" N ILE A1441 " --> pdb=" O ASN A1438 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE A1444 " --> pdb=" O ILE A1441 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE A1445 " --> pdb=" O VAL A1442 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER A1446 " --> pdb=" O TYR A1443 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET A1449 " --> pdb=" O SER A1446 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS A1451 " --> pdb=" O TYR A1448 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A1452 " --> pdb=" O MET A1449 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A1454 " --> pdb=" O CYS A1451 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A1455 " --> pdb=" O ALA A1452 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A1456 " --> pdb=" O PHE A1453 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL A1460 " --> pdb=" O ASN A1457 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE A1467 " --> pdb=" O MET A1464 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ASP A1468 " --> pdb=" O ASP A1465 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A1470 " --> pdb=" O PHE A1467 " (cutoff:3.500A) Processing helix chain 'A' and resid 1479 through 1491 Processing helix chain 'A' and resid 1502 through 1510 removed outlier: 4.441A pdb=" N VAL A1506 " --> pdb=" O LEU A1503 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG A1510 " --> pdb=" O THR A1507 " (cutoff:3.500A) Processing helix chain 'A' and resid 1527 through 1533 removed outlier: 4.255A pdb=" N VAL A1532 " --> pdb=" O CYS A1528 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA A1533 " --> pdb=" O LYS A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1546 through 1557 removed outlier: 4.423A pdb=" N LEU A1550 " --> pdb=" O ASN A1547 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N PHE A1551 " --> pdb=" O ALA A1548 " (cutoff:3.500A) Processing helix chain 'A' and resid 1566 through 1575 removed outlier: 3.937A pdb=" N ASN A1570 " --> pdb=" O LEU A1566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1585 through 1588 No H-bonds generated for 'chain 'A' and resid 1585 through 1588' Processing helix chain 'D' and resid 30 through 51 removed outlier: 3.855A pdb=" N GLU D 42 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU D 47 " --> pdb=" O ASP D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 64 removed outlier: 3.509A pdb=" N VAL D 58 " --> pdb=" O VAL D 54 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR D 64 " --> pdb=" O ILE D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 110 removed outlier: 3.905A pdb=" N VAL D 79 " --> pdb=" O ALA D 75 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU D 103 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 185 removed outlier: 3.670A pdb=" N ASN D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TRP D 185 " --> pdb=" O ASN D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 199 removed outlier: 3.620A pdb=" N ASP D 190 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU D 191 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN D 196 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 240 No H-bonds generated for 'chain 'D' and resid 238 through 240' Processing helix chain 'D' and resid 242 through 248 removed outlier: 3.867A pdb=" N GLY D 247 " --> pdb=" O TRP D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 264 No H-bonds generated for 'chain 'D' and resid 262 through 264' Processing helix chain 'D' and resid 267 through 282 removed outlier: 3.645A pdb=" N GLU D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR D 282 " --> pdb=" O GLU D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 324 removed outlier: 3.557A pdb=" N LYS D 316 " --> pdb=" O VAL D 312 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN D 324 " --> pdb=" O ASP D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 345 removed outlier: 3.715A pdb=" N LEU D 345 " --> pdb=" O PHE D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 376 Processing helix chain 'D' and resid 397 through 405 removed outlier: 3.552A pdb=" N ALA D 403 " --> pdb=" O ILE D 399 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N CYS D 404 " --> pdb=" O GLN D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 removed outlier: 4.340A pdb=" N ARG D 420 " --> pdb=" O GLY D 417 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE D 421 " --> pdb=" O ALA D 418 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN D 422 " --> pdb=" O ILE D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 430 removed outlier: 3.617A pdb=" N LEU D 430 " --> pdb=" O LEU D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 437 Processing helix chain 'D' and resid 439 through 441 No H-bonds generated for 'chain 'D' and resid 439 through 441' Processing helix chain 'D' and resid 494 through 500 removed outlier: 3.787A pdb=" N LEU D 500 " --> pdb=" O ASP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 564 No H-bonds generated for 'chain 'D' and resid 561 through 564' Processing helix chain 'D' and resid 569 through 579 removed outlier: 4.111A pdb=" N GLU D 573 " --> pdb=" O ASP D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 639 through 648 removed outlier: 4.325A pdb=" N TYR D 644 " --> pdb=" O THR D 640 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR D 647 " --> pdb=" O ARG D 643 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU D 648 " --> pdb=" O TYR D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 656 removed outlier: 4.618A pdb=" N GLU D 654 " --> pdb=" O ASP D 651 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU D 655 " --> pdb=" O ASN D 652 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER D 656 " --> pdb=" O PHE D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 687 Processing helix chain 'D' and resid 700 through 718 removed outlier: 3.844A pdb=" N VAL D 705 " --> pdb=" O LEU D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 751 removed outlier: 3.632A pdb=" N GLU D 750 " --> pdb=" O GLU D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 760 No H-bonds generated for 'chain 'D' and resid 758 through 760' Processing helix chain 'D' and resid 762 through 769 removed outlier: 3.641A pdb=" N ASP D 769 " --> pdb=" O LYS D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 826 removed outlier: 3.588A pdb=" N GLU D 823 " --> pdb=" O ASN D 819 " (cutoff:3.500A) Processing helix chain 'D' and resid 875 through 877 No H-bonds generated for 'chain 'D' and resid 875 through 877' Processing helix chain 'D' and resid 880 through 888 Processing helix chain 'D' and resid 1047 through 1049 No H-bonds generated for 'chain 'D' and resid 1047 through 1049' Processing sheet with id= A, first strand: chain 'C' and resid 171 through 173 removed outlier: 3.877A pdb=" N ASP C 172 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG C 65 " --> pdb=" O ASP C 172 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE C 105 " --> pdb=" O LYS C 96 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LYS C 98 " --> pdb=" O TRP C 103 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N TRP C 103 " --> pdb=" O LYS C 98 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 180 through 183 removed outlier: 6.103A pdb=" N ILE C 288 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL C 183 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL C 290 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL C 335 " --> pdb=" O PHE C 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'C' and resid 212 through 215 removed outlier: 6.610A pdb=" N LEU C 266 " --> pdb=" O SER C 213 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N THR C 215 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL C 268 " --> pdb=" O THR C 215 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 299 through 303 removed outlier: 3.869A pdb=" N THR A 300 " --> pdb=" O ARG A 334 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG A 334 " --> pdb=" O THR A 300 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1058 through 1062 Processing sheet with id= F, first strand: chain 'D' and resid 68 through 72 Processing sheet with id= G, first strand: chain 'D' and resid 122 through 124 Processing sheet with id= H, first strand: chain 'D' and resid 165 through 167 removed outlier: 6.652A pdb=" N VAL D 466 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N VAL D 487 " --> pdb=" O LEU D 464 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU D 464 " --> pdb=" O VAL D 487 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY D 489 " --> pdb=" O GLY D 462 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLY D 462 " --> pdb=" O GLY D 489 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ASP D 491 " --> pdb=" O ILE D 460 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE D 460 " --> pdb=" O ASP D 491 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 298 through 300 removed outlier: 6.851A pdb=" N ASN D 355 " --> pdb=" O ASP D 253 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N LEU D 255 " --> pdb=" O ASN D 355 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE D 357 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LEU D 257 " --> pdb=" O ILE D 357 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N MET D 359 " --> pdb=" O LEU D 257 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ASP D 259 " --> pdb=" O MET D 359 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N PHE D 361 " --> pdb=" O ASP D 259 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ARG D 383 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LEU D 360 " --> pdb=" O ARG D 383 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE D 385 " --> pdb=" O LEU D 360 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N THR D 362 " --> pdb=" O PHE D 385 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N PHE D 387 " --> pdb=" O THR D 362 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 511 through 515 Processing sheet with id= K, first strand: chain 'D' and resid 741 through 743 removed outlier: 6.297A pdb=" N LYS D 815 " --> pdb=" O LYS D 730 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ARG D 732 " --> pdb=" O GLY D 813 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLY D 813 " --> pdb=" O ARG D 732 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL D 734 " --> pdb=" O VAL D 811 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL D 811 " --> pdb=" O VAL D 734 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET D 793 " --> pdb=" O THR D 776 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 848 through 854 removed outlier: 4.249A pdb=" N GLU D1019 " --> pdb=" O ILE D1002 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE D1002 " --> pdb=" O GLU D1019 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 892 through 899 removed outlier: 4.000A pdb=" N ILE D 975 " --> pdb=" O SER D1038 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 150 through 152 removed outlier: 4.151A pdb=" N ASP D 152 " --> pdb=" O ARG D 157 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ARG D 157 " --> pdb=" O ASP D 152 " (cutoff:3.500A) 819 hydrogen bonds defined for protein. 2208 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: 7.28 Time building geometry restraints manager: 8.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3596 1.33 - 1.45: 5346 1.45 - 1.57: 11719 1.57 - 1.69: 17 1.69 - 1.82: 176 Bond restraints: 20854 Sorted by residual: bond pdb=" C6 CLR A2203 " pdb=" C7 CLR A2203 " ideal model delta sigma weight residual 1.492 1.540 -0.048 2.00e-02 2.50e+03 5.67e+00 bond pdb=" C6 CLR A2205 " pdb=" C7 CLR A2205 " ideal model delta sigma weight residual 1.492 1.539 -0.047 2.00e-02 2.50e+03 5.50e+00 bond pdb=" C20 CLR A2203 " pdb=" C22 CLR A2203 " ideal model delta sigma weight residual 1.535 1.579 -0.044 2.00e-02 2.50e+03 4.87e+00 bond pdb=" C20 CLR A2202 " pdb=" C22 CLR A2202 " ideal model delta sigma weight residual 1.535 1.579 -0.044 2.00e-02 2.50e+03 4.81e+00 bond pdb=" C6 CLR A2202 " pdb=" C7 CLR A2202 " ideal model delta sigma weight residual 1.492 1.534 -0.042 2.00e-02 2.50e+03 4.40e+00 ... (remaining 20849 not shown) Histogram of bond angle deviations from ideal: 97.69 - 104.96: 334 104.96 - 112.23: 10369 112.23 - 119.51: 7087 119.51 - 126.78: 10213 126.78 - 134.05: 250 Bond angle restraints: 28253 Sorted by residual: angle pdb=" C2 NAG G 4 " pdb=" N2 NAG G 4 " pdb=" C7 NAG G 4 " ideal model delta sigma weight residual 123.12 129.07 -5.95 1.28e+00 6.08e-01 2.15e+01 angle pdb=" C2 NAG E 2 " pdb=" N2 NAG E 2 " pdb=" C7 NAG E 2 " ideal model delta sigma weight residual 123.12 129.06 -5.94 1.28e+00 6.08e-01 2.14e+01 angle pdb=" C2 NAG G 3 " pdb=" N2 NAG G 3 " pdb=" C7 NAG G 3 " ideal model delta sigma weight residual 123.12 129.05 -5.93 1.28e+00 6.08e-01 2.14e+01 angle pdb=" C2 NAG B 2 " pdb=" N2 NAG B 2 " pdb=" C7 NAG B 2 " ideal model delta sigma weight residual 123.12 129.02 -5.90 1.28e+00 6.08e-01 2.12e+01 angle pdb=" N GLU C 351 " pdb=" CA GLU C 351 " pdb=" CB GLU C 351 " ideal model delta sigma weight residual 110.28 117.24 -6.96 1.55e+00 4.16e-01 2.02e+01 ... (remaining 28248 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.43: 11466 21.43 - 42.85: 845 42.85 - 64.28: 83 64.28 - 85.70: 29 85.70 - 107.13: 15 Dihedral angle restraints: 12438 sinusoidal: 5121 harmonic: 7317 Sorted by residual: dihedral pdb=" CB CYS D 667 " pdb=" SG CYS D 667 " pdb=" SG CYS D 697 " pdb=" CB CYS D 697 " ideal model delta sinusoidal sigma weight residual -86.00 -21.20 -64.80 1 1.00e+01 1.00e-02 5.51e+01 dihedral pdb=" C1 NAG I 1 " pdb=" C2 NAG I 1 " pdb=" C3 NAG I 1 " pdb=" C4 NAG I 1 " ideal model delta sinusoidal sigma weight residual -50.00 57.13 -107.13 1 2.00e+01 2.50e-03 3.11e+01 dihedral pdb=" C3 NAG I 1 " pdb=" C1 NAG I 1 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sinusoidal sigma weight residual -50.00 54.44 -104.44 1 2.00e+01 2.50e-03 3.00e+01 ... (remaining 12435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 3198 0.128 - 0.257: 21 0.257 - 0.385: 12 0.385 - 0.514: 2 0.514 - 0.642: 1 Chirality restraints: 3234 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN D 348 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN D 895 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.66e+00 chirality pdb=" C17 CLR A2203 " pdb=" C13 CLR A2203 " pdb=" C16 CLR A2203 " pdb=" C20 CLR A2203 " both_signs ideal model delta sigma weight residual False 2.55 2.94 -0.39 2.00e-01 2.50e+01 3.75e+00 ... (remaining 3231 not shown) Planarity restraints: 3561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS C 328 " -0.075 5.00e-02 4.00e+02 1.12e-01 2.02e+01 pdb=" N PRO C 329 " 0.194 5.00e-02 4.00e+02 pdb=" CA PRO C 329 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO C 329 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 254 " -0.070 5.00e-02 4.00e+02 1.05e-01 1.78e+01 pdb=" N PRO A 255 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO A 255 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 255 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 613 " -0.024 2.00e-02 2.50e+03 2.24e-02 6.29e+00 pdb=" CG ASN D 613 " 0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN D 613 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN D 613 " 0.028 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " -0.027 2.00e-02 2.50e+03 ... (remaining 3558 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 571 2.71 - 3.26: 20798 3.26 - 3.81: 31205 3.81 - 4.35: 41142 4.35 - 4.90: 67468 Nonbonded interactions: 161184 Sorted by model distance: nonbonded pdb=" O4 NAG F 2 " pdb=" O7 NAG F 2 " model vdw 2.167 2.440 nonbonded pdb=" O VAL A 390 " pdb=" OG SER A 394 " model vdw 2.169 2.440 nonbonded pdb=" OG SER C 186 " pdb=" OG1 THR C 193 " model vdw 2.208 2.440 nonbonded pdb=" O TYR A1364 " pdb=" OH TYR A1443 " model vdw 2.242 2.440 nonbonded pdb=" OG SER C 69 " pdb=" OE1 GLU C 88 " model vdw 2.256 2.440 ... (remaining 161179 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 'B' selection = chain 'F' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 1 5.49 5 S 112 5.16 5 C 13191 2.51 5 N 3351 2.21 5 O 3757 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.830 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: 7.030 Check model and map are aligned: 0.320 Convert atoms to be neutral: 0.190 Process input model: 53.810 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:13.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 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 : 0.003 0.070 20854 Z= 0.215 Angle : 0.561 8.743 28253 Z= 0.290 Chirality : 0.048 0.642 3234 Planarity : 0.004 0.112 3554 Dihedral : 14.803 107.126 7672 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.41 % Favored : 95.51 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -1.09 (0.16), residues: 2472 helix: -0.30 (0.15), residues: 1198 sheet: -0.55 (0.32), residues: 258 loop : -1.14 (0.19), residues: 1016 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 317 time to evaluate : 2.420 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 319 average time/residue: 1.0761 time to fit residues: 397.7221 Evaluate side-chains 239 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 238 time to evaluate : 2.396 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 3.3465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 210 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 100 optimal weight: 0.4980 chunk 195 optimal weight: 0.0070 chunk 75 optimal weight: 4.9990 chunk 118 optimal weight: 7.9990 chunk 145 optimal weight: 20.0000 chunk 226 optimal weight: 0.9990 overall best weight: 0.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1172 GLN ** A1466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN D 111 HIS ** D 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 824 ASN D 972 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 20854 Z= 0.182 Angle : 0.553 10.562 28253 Z= 0.294 Chirality : 0.044 0.512 3234 Planarity : 0.005 0.099 3554 Dihedral : 8.778 106.796 2857 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.45 % Favored : 95.47 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.58 (0.17), residues: 2472 helix: 0.31 (0.15), residues: 1209 sheet: -0.37 (0.31), residues: 271 loop : -1.17 (0.20), residues: 992 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 256 time to evaluate : 2.344 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 15 residues processed: 280 average time/residue: 1.1073 time to fit residues: 359.8312 Evaluate side-chains 251 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 236 time to evaluate : 2.492 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 11 residues processed: 5 average time/residue: 0.9031 time to fit residues: 8.6988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 125 optimal weight: 0.0040 chunk 70 optimal weight: 0.9990 chunk 188 optimal weight: 4.9990 chunk 153 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 226 optimal weight: 0.0980 chunk 244 optimal weight: 0.9980 chunk 201 optimal weight: 5.9990 chunk 224 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 181 optimal weight: 0.6980 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 953 ASN A1035 GLN A1466 ASN ** D 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 972 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.063 20854 Z= 0.141 Angle : 0.494 9.560 28253 Z= 0.263 Chirality : 0.042 0.475 3234 Planarity : 0.004 0.095 3554 Dihedral : 8.693 106.742 2857 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.33 % Favored : 95.59 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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 (0.17), residues: 2472 helix: 0.58 (0.15), residues: 1206 sheet: -0.28 (0.31), residues: 277 loop : -1.14 (0.20), residues: 989 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 255 time to evaluate : 2.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 14 residues processed: 281 average time/residue: 1.0539 time to fit residues: 346.9508 Evaluate side-chains 248 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 234 time to evaluate : 2.535 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 10 residues processed: 4 average time/residue: 0.7645 time to fit residues: 6.7275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 223 optimal weight: 0.6980 chunk 170 optimal weight: 3.9990 chunk 117 optimal weight: 0.0470 chunk 25 optimal weight: 0.0970 chunk 108 optimal weight: 0.7980 chunk 152 optimal weight: 8.9990 chunk 227 optimal weight: 3.9990 chunk 240 optimal weight: 0.0060 chunk 118 optimal weight: 5.9990 chunk 215 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 overall best weight: 0.3292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 140 ASN A 953 ASN ** D 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 717 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.085 20854 Z= 0.141 Angle : 0.484 12.718 28253 Z= 0.257 Chirality : 0.041 0.459 3234 Planarity : 0.004 0.103 3554 Dihedral : 8.640 106.854 2857 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.33 % Favored : 95.59 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.16 (0.17), residues: 2472 helix: 0.77 (0.15), residues: 1197 sheet: -0.25 (0.32), residues: 273 loop : -1.09 (0.20), residues: 1002 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 256 time to evaluate : 2.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 16 residues processed: 280 average time/residue: 1.0927 time to fit residues: 358.6248 Evaluate side-chains 248 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 232 time to evaluate : 2.550 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 13 residues processed: 3 average time/residue: 0.5604 time to fit residues: 5.5912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 200 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 3 optimal weight: 30.0000 chunk 179 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 122 optimal weight: 7.9990 chunk 216 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 972 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.083 20854 Z= 0.299 Angle : 0.574 11.127 28253 Z= 0.302 Chirality : 0.045 0.490 3234 Planarity : 0.005 0.096 3554 Dihedral : 8.867 108.814 2857 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.69 % Favored : 95.23 % Rotamer Outliers : 2.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.37 (0.17), residues: 2472 helix: 0.59 (0.15), residues: 1211 sheet: -0.31 (0.31), residues: 273 loop : -1.21 (0.20), residues: 988 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 248 time to evaluate : 2.530 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 30 residues processed: 285 average time/residue: 1.1119 time to fit residues: 368.0553 Evaluate side-chains 266 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 236 time to evaluate : 2.468 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 23 residues processed: 7 average time/residue: 0.6904 time to fit residues: 9.4549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 80 optimal weight: 0.7980 chunk 216 optimal weight: 0.4980 chunk 47 optimal weight: 7.9990 chunk 141 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 240 optimal weight: 0.9990 chunk 199 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 20 optimal weight: 20.0000 chunk 79 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 GLN A 690 ASN ** A 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 996 ASN ** D 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 20854 Z= 0.163 Angle : 0.508 9.955 28253 Z= 0.270 Chirality : 0.042 0.468 3234 Planarity : 0.004 0.102 3554 Dihedral : 8.760 107.633 2857 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.37 % Favored : 95.55 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.14 (0.17), residues: 2472 helix: 0.81 (0.15), residues: 1197 sheet: -0.31 (0.31), residues: 276 loop : -1.10 (0.20), residues: 999 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 240 time to evaluate : 2.379 Fit side-chains revert: symmetry clash outliers start: 48 outliers final: 26 residues processed: 277 average time/residue: 1.0826 time to fit residues: 350.8481 Evaluate side-chains 256 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 230 time to evaluate : 2.438 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 22 residues processed: 4 average time/residue: 0.4452 time to fit residues: 5.8089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 232 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 137 optimal weight: 0.5980 chunk 175 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 202 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 239 optimal weight: 10.0000 chunk 150 optimal weight: 20.0000 chunk 146 optimal weight: 10.0000 chunk 110 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.091 20854 Z= 0.211 Angle : 0.529 9.380 28253 Z= 0.280 Chirality : 0.043 0.477 3234 Planarity : 0.004 0.104 3554 Dihedral : 8.782 108.092 2857 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.49 % Favored : 95.43 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.16 (0.17), residues: 2472 helix: 0.82 (0.15), residues: 1196 sheet: -0.35 (0.31), residues: 266 loop : -1.11 (0.19), residues: 1010 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 238 time to evaluate : 2.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 29 residues processed: 271 average time/residue: 1.0903 time to fit residues: 346.2315 Evaluate side-chains 260 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 231 time to evaluate : 2.575 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 24 residues processed: 5 average time/residue: 0.6608 time to fit residues: 7.5515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 148 optimal weight: 0.0980 chunk 95 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 72 optimal weight: 0.0170 chunk 47 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 152 optimal weight: 10.0000 chunk 163 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 188 optimal weight: 1.9990 overall best weight: 0.8022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 ASN ** A 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.103 20854 Z= 0.167 Angle : 0.504 9.217 28253 Z= 0.268 Chirality : 0.042 0.463 3234 Planarity : 0.004 0.109 3554 Dihedral : 8.733 107.531 2857 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.33 % Favored : 95.59 % Rotamer Outliers : 2.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.10 (0.17), residues: 2472 helix: 0.88 (0.15), residues: 1200 sheet: -0.32 (0.31), residues: 265 loop : -1.11 (0.19), residues: 1007 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 235 time to evaluate : 2.370 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 26 residues processed: 269 average time/residue: 1.0731 time to fit residues: 339.1846 Evaluate side-chains 251 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 225 time to evaluate : 2.405 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 24 residues processed: 2 average time/residue: 0.2211 time to fit residues: 4.1545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 218 optimal weight: 0.9980 chunk 229 optimal weight: 4.9990 chunk 209 optimal weight: 9.9990 chunk 223 optimal weight: 1.9990 chunk 134 optimal weight: 0.2980 chunk 97 optimal weight: 0.4980 chunk 175 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 202 optimal weight: 2.9990 chunk 211 optimal weight: 0.9980 chunk 222 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 ASN A 745 ASN ** D 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 972 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.126 20854 Z= 0.170 Angle : 0.517 11.514 28253 Z= 0.273 Chirality : 0.042 0.459 3234 Planarity : 0.004 0.121 3554 Dihedral : 8.702 107.456 2857 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.49 % Favored : 95.43 % Rotamer Outliers : 1.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.06 (0.17), residues: 2472 helix: 0.89 (0.15), residues: 1206 sheet: -0.28 (0.31), residues: 275 loop : -1.09 (0.20), residues: 991 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 240 time to evaluate : 2.518 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 26 residues processed: 272 average time/residue: 1.0830 time to fit residues: 346.7275 Evaluate side-chains 255 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 229 time to evaluate : 2.179 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 23 residues processed: 3 average time/residue: 0.5774 time to fit residues: 5.4169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 146 optimal weight: 8.9990 chunk 236 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 228 optimal weight: 8.9990 chunk 197 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 121 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 ASN ** A 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.147 20854 Z= 0.255 Angle : 0.563 14.056 28253 Z= 0.298 Chirality : 0.044 0.480 3234 Planarity : 0.005 0.138 3554 Dihedral : 8.814 108.288 2857 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.98 % Favored : 94.94 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.20 (0.17), residues: 2472 helix: 0.76 (0.15), residues: 1216 sheet: -0.31 (0.31), residues: 269 loop : -1.16 (0.20), residues: 987 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 231 time to evaluate : 2.542 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 24 residues processed: 260 average time/residue: 1.1077 time to fit residues: 337.2442 Evaluate side-chains 246 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 222 time to evaluate : 2.314 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 22 residues processed: 2 average time/residue: 0.2129 time to fit residues: 4.0516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 156 optimal weight: 0.9990 chunk 210 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 182 optimal weight: 0.9990 chunk 29 optimal weight: 0.0020 chunk 54 optimal weight: 0.4980 chunk 197 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 203 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 ASN ** A 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1042 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.196384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.130246 restraints weight = 25250.248| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.37 r_work: 0.3295 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work: 0.3253 rms_B_bonded: 2.21 restraints_weight: 0.1250 r_work: 0.3228 rms_B_bonded: 2.39 restraints_weight: 0.0625 r_work: 0.3198 rms_B_bonded: 2.69 restraints_weight: 0.0312 r_work: 0.3159 rms_B_bonded: 3.15 restraints_weight: 0.0156 r_work: 0.3110 rms_B_bonded: 3.84 restraints_weight: 0.0078 r_work: 0.3042 rms_B_bonded: 4.93 restraints_weight: 0.0039 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.129 20854 Z= 0.169 Angle : 0.519 10.773 28253 Z= 0.276 Chirality : 0.042 0.453 3234 Planarity : 0.004 0.120 3554 Dihedral : 8.721 107.166 2857 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.33 % Favored : 95.59 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.06 (0.17), residues: 2472 helix: 0.89 (0.15), residues: 1217 sheet: -0.31 (0.31), residues: 275 loop : -1.10 (0.20), residues: 980 =============================================================================== Job complete usr+sys time: 6036.45 seconds wall clock time: 108 minutes 52.34 seconds (6532.34 seconds total)