Starting phenix.real_space_refine on Thu Mar 5 09:05:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uhg_26514/03_2026/7uhg_26514.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uhg_26514/03_2026/7uhg_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 { model { file = "/net/cci-nas-00/data/ceres_data/7uhg_26514/03_2026/7uhg_26514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uhg_26514/03_2026/7uhg_26514.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uhg_26514/03_2026/7uhg_26514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uhg_26514/03_2026/7uhg_26514.map" } 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 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= 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 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. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 304} 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: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 907} 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.40, per 1000 atoms: 0.22 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 - 3.00 Amino acid : True - 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: 1.69 Conformation dependent library (CDL) restraints added in 889.9 milliseconds 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... Secondary structure from input PDB file: 109 helices and 17 sheets defined 55.4% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'C' and resid 38 through 56 removed outlier: 4.277A pdb=" N ARG C 42 " --> pdb=" O GLU C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 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 155 through 159 Processing helix chain 'C' and resid 190 through 208 removed outlier: 4.415A pdb=" N LEU C 200 " --> pdb=" O MET C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 263 Processing helix chain 'C' and resid 296 through 308 removed outlier: 3.831A pdb=" N LEU C 300 " --> pdb=" O SER C 296 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY C 308 " --> pdb=" O ILE C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 314 removed outlier: 3.944A pdb=" N HIS C 314 " --> pdb=" O SER C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 328 removed outlier: 3.840A pdb=" N CYS C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 333 Processing helix chain 'C' and resid 341 through 361 removed outlier: 3.635A pdb=" N ALA C 345 " --> pdb=" O GLN C 341 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS C 361 " --> pdb=" O TRP C 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 145 Processing helix chain 'A' and resid 155 through 180 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) removed outlier: 3.608A pdb=" N ILE A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 217 removed outlier: 3.530A pdb=" N VAL A 205 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 247 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) Proline residue: A 247 - end of helix Processing helix chain 'A' and resid 248 through 253 removed outlier: 4.389A pdb=" N SER A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 248 through 253' Processing helix chain 'A' and resid 254 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 268 through 293 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 349 through 362 removed outlier: 3.591A pdb=" N THR A 362 " --> pdb=" O PHE A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 377 removed outlier: 4.098A pdb=" N VAL A 369 " --> pdb=" O GLY A 365 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP A 375 " --> pdb=" O TYR A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 394 removed outlier: 3.663A pdb=" N TYR A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 416 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) Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'A' and resid 420 through 431 Processing helix chain 'A' and resid 431 through 440 removed outlier: 4.020A pdb=" N LEU A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) 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) removed outlier: 3.994A pdb=" N ASP A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 522 Processing helix chain 'A' and resid 522 through 542 removed outlier: 3.582A pdb=" N ILE A 540 " --> pdb=" O ASN A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 578 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) removed outlier: 4.027A pdb=" N GLY A 578 " --> pdb=" O MET A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 585 removed outlier: 3.549A pdb=" N VAL A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 607 removed outlier: 3.660A pdb=" N ARG A 589 " --> pdb=" O SER A 585 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR A 602 " --> pdb=" O GLY A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 620 Processing helix chain 'A' and resid 621 through 633 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) removed outlier: 4.371A pdb=" N ARG A 631 " --> pdb=" O LYS A 628 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N HIS A 632 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TRP A 633 " --> pdb=" O THR A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 645 removed outlier: 3.601A pdb=" N ASN A 645 " --> pdb=" O ALA A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 673 removed outlier: 3.612A pdb=" N SER A 652 " --> pdb=" O LYS A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 704 Processing helix chain 'A' and resid 706 through 717 Processing helix chain 'A' and resid 726 through 728 No H-bonds generated for 'chain 'A' and resid 726 through 728' Processing helix chain 'A' and resid 729 through 747 removed outlier: 3.846A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 754 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) Processing helix chain 'A' and resid 754 through 772 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) removed outlier: 3.672A pdb=" N LYS A 772 " --> pdb=" O GLU A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 884 removed outlier: 3.673A pdb=" N LEU A 882 " --> pdb=" O GLY A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 905 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 913 through 941 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 970 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 987 Processing helix chain 'A' and resid 988 through 997 Proline residue: A 991 - end of helix removed outlier: 3.614A pdb=" N ILE A 995 " --> pdb=" O LEU A 992 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN A 996 " --> pdb=" O ARG A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1015 removed outlier: 3.648A pdb=" N HIS A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1038 removed outlier: 3.560A pdb=" N VAL A1021 " --> pdb=" O ASN A1017 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A1023 " --> pdb=" O MET A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1066 No H-bonds generated for 'chain 'A' and resid 1064 through 1066' Processing helix chain 'A' and resid 1086 through 1099 Processing helix chain 'A' and resid 1102 through 1112 removed outlier: 3.556A pdb=" N ASP A1112 " --> pdb=" O TYR A1108 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1127 No H-bonds generated for 'chain 'A' and resid 1125 through 1127' Processing helix chain 'A' and resid 1128 through 1139 removed outlier: 4.301A pdb=" N PHE A1132 " --> pdb=" O ILE A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1159 removed outlier: 3.607A pdb=" N VAL A1148 " --> pdb=" O MET A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1162 No H-bonds generated for 'chain 'A' and resid 1160 through 1162' Processing helix chain 'A' and resid 1169 through 1181 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 1192 through 1203 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 1204 through 1224 Processing helix chain 'A' and resid 1230 through 1260 removed outlier: 4.164A pdb=" N ALA A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1265 removed outlier: 4.036A pdb=" N PHE A1265 " --> pdb=" O PRO A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1288 removed outlier: 3.707A pdb=" N THR A1271 " --> pdb=" O ASP A1267 " (cutoff:3.500A) 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) removed outlier: 4.227A pdb=" N GLU A1288 " --> pdb=" O VAL A1284 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1320 removed outlier: 3.799A pdb=" N ARG A1319 " --> pdb=" O ILE A1315 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A1320 " --> pdb=" O THR A1316 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1315 through 1320' Processing helix chain 'A' and resid 1321 through 1323 No H-bonds generated for 'chain 'A' and resid 1321 through 1323' Processing helix chain 'A' and resid 1324 through 1331 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) removed outlier: 3.942A pdb=" N SER A1331 " --> pdb=" O VAL A1327 " (cutoff:3.500A) Processing helix chain 'A' and resid 1336 through 1350 Processing helix chain 'A' and resid 1352 through 1373 removed outlier: 3.593A pdb=" N LEU A1356 " --> pdb=" O TYR A1352 " (cutoff:3.500A) 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 1391 through 1404 Processing helix chain 'A' and resid 1407 through 1414 Processing helix chain 'A' and resid 1439 through 1465 Processing helix chain 'A' and resid 1466 through 1471 Processing helix chain 'A' and resid 1478 through 1492 removed outlier: 3.908A pdb=" N LEU A1482 " --> pdb=" O GLY A1478 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR A1492 " --> pdb=" O ILE A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1501 through 1503 No H-bonds generated for 'chain 'A' and resid 1501 through 1503' Processing helix chain 'A' and resid 1504 through 1511 removed outlier: 3.882A pdb=" N ARG A1511 " --> pdb=" O THR A1507 " (cutoff:3.500A) Processing helix chain 'A' and resid 1526 through 1534 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) removed outlier: 3.887A pdb=" N MET A1534 " --> pdb=" O ARG A1530 " (cutoff:3.500A) Processing helix chain 'A' and resid 1546 through 1558 removed outlier: 3.525A pdb=" N LEU A1550 " --> pdb=" O PHE A1546 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE A1551 " --> pdb=" O ASN A1547 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ALA A1552 " --> pdb=" O ALA A1548 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A1553 " --> pdb=" O THR A1549 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1576 removed outlier: 3.818A pdb=" N ALA A1569 " --> pdb=" O ASN A1565 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN A1570 " --> pdb=" O LEU A1566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1584 through 1589 removed outlier: 4.094A pdb=" N LEU A1589 " --> pdb=" O SER A1585 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 52 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) removed outlier: 3.704A pdb=" N SER D 52 " --> pdb=" O ALA D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 65 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) removed outlier: 3.945A pdb=" N GLN D 65 " --> pdb=" O TYR D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 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 176 through 186 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 188 through 200 removed outlier: 4.141A pdb=" N VAL D 192 " --> pdb=" O ALA D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 240 Processing helix chain 'D' and resid 241 through 249 removed outlier: 3.867A pdb=" N GLY D 247 " --> pdb=" O TRP D 243 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA D 249 " --> pdb=" O ILE D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 265 Processing helix chain 'D' and resid 266 through 280 Processing helix chain 'D' and resid 281 through 283 No H-bonds generated for 'chain 'D' and resid 281 through 283' Processing helix chain 'D' and resid 311 through 323 removed outlier: 3.557A pdb=" N LYS D 316 " --> pdb=" O VAL D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 344 Processing helix chain 'D' and resid 369 through 377 Processing helix chain 'D' and resid 396 through 406 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) removed outlier: 3.745A pdb=" N ASN D 406 " --> pdb=" O MET D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 417 No H-bonds generated for 'chain 'D' and resid 415 through 417' Processing helix chain 'D' and resid 418 through 423 Processing helix chain 'D' and resid 425 through 431 removed outlier: 4.248A pdb=" N VAL D 429 " --> pdb=" O GLU D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 438 removed outlier: 4.192A pdb=" N GLY D 438 " --> pdb=" O MET D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 442 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 560 through 565 removed outlier: 3.665A pdb=" N GLU D 565 " --> pdb=" O PHE D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 580 removed outlier: 4.111A pdb=" N GLU D 573 " --> pdb=" O ASP D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 647 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) Processing helix chain 'D' and resid 648 through 651 removed outlier: 6.131A pdb=" N ASP D 651 " --> pdb=" O LEU D 648 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 648 through 651' Processing helix chain 'D' and resid 652 through 657 Processing helix chain 'D' and resid 678 through 688 removed outlier: 3.834A pdb=" N ASP D 688 " --> pdb=" O ASN D 684 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 719 removed outlier: 3.844A pdb=" N VAL D 705 " --> pdb=" O LEU D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 745 through 752 removed outlier: 3.632A pdb=" N GLU D 750 " --> pdb=" O GLU D 747 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP D 752 " --> pdb=" O GLY D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 760 Processing helix chain 'D' and resid 761 through 770 removed outlier: 3.641A pdb=" N ASP D 769 " --> pdb=" O LYS D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 827 removed outlier: 3.588A pdb=" N GLU D 823 " --> pdb=" O ASN D 819 " (cutoff:3.500A) Processing helix chain 'D' and resid 874 through 878 Processing helix chain 'D' and resid 879 through 889 Processing sheet with id=AA1, first strand: chain 'C' and resid 115 through 119 removed outlier: 8.779A pdb=" N TRP C 103 " --> pdb=" O LYS C 98 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LYS C 98 " --> pdb=" O TRP C 103 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE C 105 " --> pdb=" O LYS C 96 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG C 65 " --> pdb=" O ASP C 172 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP C 172 " --> pdb=" O ARG C 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 180 through 183 removed outlier: 6.622A pdb=" N ILE C 289 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N LEU C 337 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N PHE C 291 " --> pdb=" O LEU C 337 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 212 through 215 removed outlier: 3.715A pdb=" N THR C 215 " --> pdb=" O VAL C 268 " (cutoff:3.500A) Processing sheet with id=AA4, 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=AA5, first strand: chain 'A' and resid 1058 through 1062 Processing sheet with id=AA6, first strand: chain 'A' and resid 1499 through 1500 removed outlier: 3.555A pdb=" N ILE A1500 " --> pdb=" O VAL A1544 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL A1544 " --> pdb=" O ILE A1500 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 68 through 72 Processing sheet with id=AA8, first strand: chain 'D' and resid 142 through 144 removed outlier: 6.359A pdb=" N VAL D 122 " --> pdb=" O GLN D 143 " (cutoff:3.500A) removed outlier: 9.285A pdb=" N VAL D 166 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR D 125 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 142 through 144 removed outlier: 6.359A pdb=" N VAL D 122 " --> pdb=" O GLN D 143 " (cutoff:3.500A) removed outlier: 9.285A pdb=" N VAL D 166 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR D 125 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing sheet with id=AB1, 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) Processing sheet with id=AB2, first strand: chain 'D' and resid 298 through 300 removed outlier: 8.137A pdb=" N ALA D 292 " --> pdb=" O MET D 254 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ILE D 256 " --> pdb=" O ALA D 292 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N PHE D 294 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL D 258 " --> pdb=" O PHE D 294 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LYS D 356 " --> pdb=" O ARG D 383 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N PHE D 385 " --> pdb=" O LYS D 356 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE D 358 " --> pdb=" O PHE D 385 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N PHE D 387 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU D 360 " --> pdb=" O PHE D 387 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N VAL D 389 " --> pdb=" O LEU D 360 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N THR D 362 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N TYR D 411 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR D 386 " --> pdb=" O TYR D 411 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ILE D 413 " --> pdb=" O THR D 386 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N SER D 388 " --> pdb=" O ILE D 413 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 521 through 523 removed outlier: 3.595A pdb=" N LEU D 523 " --> pdb=" O ALA D 514 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 658 through 659 removed outlier: 3.687A pdb=" N ALA D 731 " --> pdb=" O LYS D 815 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET D 793 " --> pdb=" O THR D 776 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 800 through 801 Processing sheet with id=AB6, first strand: chain 'D' and resid 859 through 861 removed outlier: 6.584A pdb=" N ILE D 852 " --> pdb=" O LEU D 860 " (cutoff:3.500A) 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=AB7, 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=AB8, first strand: chain 'D' and resid 903 through 904 981 hydrogen bonds defined for protein. 2799 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: 4.25 Time building geometry restraints manager: 2.27 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=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.492 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C1 NAG G 3 " pdb=" O5 NAG G 3 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.78e+00 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 ... (remaining 20849 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 27648 1.75 - 3.50: 508 3.50 - 5.25: 64 5.25 - 6.99: 27 6.99 - 8.74: 6 Bond angle restraints: 28253 Sorted by residual: 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 angle pdb=" N CYS A 333 " pdb=" CA CYS A 333 " pdb=" C CYS A 333 " ideal model delta sigma weight residual 109.40 116.35 -6.95 1.63e+00 3.76e-01 1.82e+01 angle pdb=" N THR A 331 " pdb=" CA THR A 331 " pdb=" C THR A 331 " ideal model delta sigma weight residual 109.50 115.57 -6.07 1.58e+00 4.01e-01 1.47e+01 angle pdb=" C ALA C 350 " pdb=" N GLU C 351 " pdb=" CA GLU C 351 " ideal model delta sigma weight residual 120.31 115.10 5.21 1.52e+00 4.33e-01 1.18e+01 angle pdb=" CA GLU C 351 " pdb=" CB GLU C 351 " pdb=" CG GLU C 351 " ideal model delta sigma weight residual 114.10 120.38 -6.28 2.00e+00 2.50e-01 9.85e+00 ... (remaining 28248 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.76: 11900 22.76 - 45.53: 784 45.53 - 68.29: 123 68.29 - 91.05: 31 91.05 - 113.81: 35 Dihedral angle restraints: 12873 sinusoidal: 5556 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=" CB CYS D 404 " pdb=" SG CYS D 404 " pdb=" SG CYS D1071 " pdb=" CB CYS D1071 " ideal model delta sinusoidal sigma weight residual 93.00 49.80 43.20 1 1.00e+01 1.00e-02 2.60e+01 dihedral pdb=" CB CYS A 317 " pdb=" SG CYS A 317 " pdb=" SG CYS A 333 " pdb=" CB CYS A 333 " ideal model delta sinusoidal sigma weight residual -86.00 -125.52 39.52 1 1.00e+01 1.00e-02 2.19e+01 ... (remaining 12870 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: 565 2.71 - 3.26: 20678 3.26 - 3.81: 31095 3.81 - 4.35: 40874 4.35 - 4.90: 67404 Nonbonded interactions: 160616 Sorted by model distance: nonbonded pdb=" O4 NAG F 2 " pdb=" O7 NAG F 2 " model vdw 2.167 3.040 nonbonded pdb=" O VAL A 390 " pdb=" OG SER A 394 " model vdw 2.169 3.040 nonbonded pdb=" OG SER C 186 " pdb=" OG1 THR C 193 " model vdw 2.208 3.040 nonbonded pdb=" O TYR A1364 " pdb=" OH TYR A1443 " model vdw 2.242 3.040 nonbonded pdb=" OG SER C 69 " pdb=" OE1 GLU C 88 " model vdw 2.256 3.040 ... (remaining 160611 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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 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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.510 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:6.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 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 : 0.004 0.086 20880 Z= 0.164 Angle : 0.619 19.596 28321 Z= 0.291 Chirality : 0.049 0.642 3234 Planarity : 0.004 0.112 3554 Dihedral : 16.292 113.814 8107 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.41 % Favored : 95.51 % Rotamer: Outliers : 0.09 % Allowed : 0.36 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1319 TYR 0.012 0.001 TYR D 512 PHE 0.028 0.001 PHE A 293 TRP 0.009 0.001 TRP A1103 HIS 0.003 0.001 HIS A 632 Details of bonding type rmsd covalent geometry : bond 0.00361 (20854) covalent geometry : angle 0.57880 (28253) SS BOND : bond 0.00236 ( 10) SS BOND : angle 2.04617 ( 20) hydrogen bonds : bond 0.25600 ( 961) hydrogen bonds : angle 7.85158 ( 2799) link_BETA1-4 : bond 0.00844 ( 9) link_BETA1-4 : angle 3.38168 ( 27) link_NAG-ASN : bond 0.01174 ( 7) link_NAG-ASN : angle 6.90832 ( 21) *********************** 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 to be fit. rotamer outliers: 2 poor density : 317 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 107 ARG cc_start: 0.1531 (mtt-85) cc_final: 0.0762 (mtp180) REVERT: C 196 MET cc_start: 0.4327 (ttt) cc_final: 0.4009 (pp-130) REVERT: A 332 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7253 (pt0) REVERT: A 1210 MET cc_start: 0.5928 (tpt) cc_final: 0.4454 (tmt) REVERT: A 1449 MET cc_start: 0.8405 (mtm) cc_final: 0.8170 (mtm) REVERT: A 1545 MET cc_start: 0.3788 (mmt) cc_final: 0.3301 (ppp) outliers start: 2 outliers final: 1 residues processed: 319 average time/residue: 0.5832 time to fit residues: 213.0814 Evaluate side-chains 241 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 239 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 334 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.0770 chunk 66 optimal weight: 4.9990 chunk 247 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 GLN A 754 ASN A1145 ASN A1172 GLN D 41 GLN D 422 ASN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 694 ASN D 824 ASN D 972 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.197044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.128986 restraints weight = 25368.639| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.18 r_work: 0.3123 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20880 Z= 0.139 Angle : 0.648 17.289 28321 Z= 0.315 Chirality : 0.045 0.417 3234 Planarity : 0.004 0.079 3554 Dihedral : 11.993 105.073 3299 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.21 % Favored : 95.71 % Rotamer: Outliers : 1.76 % Allowed : 10.45 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.17), residues: 2472 helix: 0.47 (0.15), residues: 1229 sheet: -0.44 (0.31), residues: 284 loop : -1.19 (0.20), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 157 TYR 0.012 0.001 TYR D 764 PHE 0.015 0.001 PHE D 686 TRP 0.011 0.001 TRP C 357 HIS 0.006 0.001 HIS D1004 Details of bonding type rmsd covalent geometry : bond 0.00288 (20854) covalent geometry : angle 0.62122 (28253) SS BOND : bond 0.00270 ( 10) SS BOND : angle 1.68832 ( 20) hydrogen bonds : bond 0.05595 ( 961) hydrogen bonds : angle 5.03347 ( 2799) link_BETA1-4 : bond 0.00900 ( 9) link_BETA1-4 : angle 2.84726 ( 27) link_NAG-ASN : bond 0.01147 ( 7) link_NAG-ASN : angle 5.76344 ( 21) *********************** 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 302 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 263 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 107 ARG cc_start: 0.1012 (mtt-85) cc_final: 0.0510 (mtp-110) REVERT: C 177 MET cc_start: -0.0186 (pp-130) cc_final: -0.0478 (ppp) REVERT: C 344 ASP cc_start: 0.4530 (t0) cc_final: 0.4301 (t0) REVERT: A 165 GLU cc_start: 0.8143 (tp30) cc_final: 0.7867 (pt0) REVERT: A 209 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7813 (mm) REVERT: A 266 LYS cc_start: 0.7260 (pptt) cc_final: 0.7049 (pttt) REVERT: A 1012 ILE cc_start: 0.8370 (mt) cc_final: 0.8165 (mt) REVERT: A 1208 GLU cc_start: 0.6794 (pp20) cc_final: 0.6575 (pp20) REVERT: A 1210 MET cc_start: 0.5602 (tpt) cc_final: 0.4337 (tmt) REVERT: A 1262 LYS cc_start: 0.6602 (pptt) cc_final: 0.6024 (mmtt) REVERT: A 1269 TRP cc_start: 0.7614 (OUTLIER) cc_final: 0.5504 (m-90) REVERT: A 1370 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7251 (mt0) REVERT: D 794 VAL cc_start: 0.8849 (t) cc_final: 0.8642 (p) REVERT: D 803 GLN cc_start: 0.7664 (mp-120) cc_final: 0.7318 (mm-40) REVERT: D 806 LEU cc_start: 0.8847 (tp) cc_final: 0.8438 (tm) REVERT: D 848 MET cc_start: 0.7055 (mmt) cc_final: 0.6846 (mmt) REVERT: D 883 MET cc_start: 0.8388 (tpt) cc_final: 0.8081 (tpt) REVERT: D 985 ASN cc_start: 0.7537 (OUTLIER) cc_final: 0.7010 (m-40) outliers start: 39 outliers final: 13 residues processed: 286 average time/residue: 0.5482 time to fit residues: 179.8371 Evaluate side-chains 253 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 236 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 1028 MET Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1269 TRP Chi-restraints excluded: chain A residue 1370 GLN Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain D residue 673 SER Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain D residue 851 VAL Chi-restraints excluded: chain D residue 881 SER Chi-restraints excluded: chain D residue 985 ASN Chi-restraints excluded: chain D residue 1009 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 215 optimal weight: 1.9990 chunk 152 optimal weight: 10.0000 chunk 170 optimal weight: 3.9990 chunk 85 optimal weight: 0.3980 chunk 91 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 156 optimal weight: 9.9990 chunk 149 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 84 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 972 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.196755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.125746 restraints weight = 25487.369| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.09 r_work: 0.3097 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20880 Z= 0.126 Angle : 0.609 16.474 28321 Z= 0.291 Chirality : 0.044 0.273 3234 Planarity : 0.004 0.064 3554 Dihedral : 10.689 105.701 3292 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.37 % Favored : 95.55 % Rotamer: Outliers : 2.35 % Allowed : 13.21 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.17), residues: 2472 helix: 0.78 (0.15), residues: 1232 sheet: -0.32 (0.31), residues: 283 loop : -1.16 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 419 TYR 0.010 0.001 TYR D1068 PHE 0.029 0.001 PHE A1147 TRP 0.009 0.001 TRP D 205 HIS 0.005 0.001 HIS D1004 Details of bonding type rmsd covalent geometry : bond 0.00272 (20854) covalent geometry : angle 0.58071 (28253) SS BOND : bond 0.00276 ( 10) SS BOND : angle 1.54613 ( 20) hydrogen bonds : bond 0.04643 ( 961) hydrogen bonds : angle 4.68680 ( 2799) link_BETA1-4 : bond 0.00908 ( 9) link_BETA1-4 : angle 2.79943 ( 27) link_NAG-ASN : bond 0.00883 ( 7) link_NAG-ASN : angle 5.80538 ( 21) *********************** 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 313 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 261 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 107 ARG cc_start: 0.1110 (mtt-85) cc_final: 0.0593 (mtp-110) REVERT: C 304 ILE cc_start: 0.5291 (mm) cc_final: 0.5081 (tt) REVERT: A 134 LEU cc_start: 0.8565 (mt) cc_final: 0.8326 (mt) REVERT: A 165 GLU cc_start: 0.8051 (tp30) cc_final: 0.7804 (pt0) REVERT: A 209 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7774 (mm) REVERT: A 291 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8076 (mp0) REVERT: A 293 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.6198 (p90) REVERT: A 373 MET cc_start: 0.8615 (mmm) cc_final: 0.8373 (mmp) REVERT: A 402 LEU cc_start: 0.8449 (tp) cc_final: 0.8137 (mm) REVERT: A 1012 ILE cc_start: 0.8308 (mt) cc_final: 0.8091 (mt) REVERT: A 1018 ILE cc_start: 0.8255 (mm) cc_final: 0.7808 (mp) REVERT: A 1053 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7964 (mt-10) REVERT: A 1208 GLU cc_start: 0.6819 (pp20) cc_final: 0.6603 (pp20) REVERT: A 1210 MET cc_start: 0.5551 (tpt) cc_final: 0.4293 (tmt) REVERT: A 1260 LYS cc_start: 0.6302 (OUTLIER) cc_final: 0.5412 (tttp) REVERT: A 1269 TRP cc_start: 0.7555 (OUTLIER) cc_final: 0.5373 (m-90) REVERT: A 1534 MET cc_start: 0.5556 (mpp) cc_final: 0.4252 (pmt) REVERT: D 678 GLU cc_start: 0.8097 (pt0) cc_final: 0.6536 (mm-30) REVERT: D 803 GLN cc_start: 0.7680 (mp-120) cc_final: 0.7313 (mm-40) REVERT: D 883 MET cc_start: 0.8346 (tpt) cc_final: 0.8047 (tpt) REVERT: D 985 ASN cc_start: 0.7501 (OUTLIER) cc_final: 0.6852 (m-40) REVERT: D 1017 MET cc_start: 0.7864 (ttm) cc_final: 0.7557 (ttm) outliers start: 52 outliers final: 17 residues processed: 294 average time/residue: 0.5559 time to fit residues: 189.2075 Evaluate side-chains 266 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 242 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 923 ASP Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 1053 GLU Chi-restraints excluded: chain A residue 1156 GLN Chi-restraints excluded: chain A residue 1260 LYS Chi-restraints excluded: chain A residue 1269 TRP Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain D residue 673 SER Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 851 VAL Chi-restraints excluded: chain D residue 881 SER Chi-restraints excluded: chain D residue 985 ASN Chi-restraints excluded: chain D residue 1009 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 232 optimal weight: 9.9990 chunk 246 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 224 optimal weight: 0.0030 chunk 199 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 17 optimal weight: 0.0670 chunk 110 optimal weight: 0.8980 chunk 210 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 overall best weight: 0.4928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 972 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.198161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.128288 restraints weight = 25538.571| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.09 r_work: 0.3183 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20880 Z= 0.107 Angle : 0.585 16.526 28321 Z= 0.278 Chirality : 0.042 0.265 3234 Planarity : 0.004 0.058 3554 Dihedral : 9.752 105.548 3292 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.57 % Favored : 95.35 % Rotamer: Outliers : 2.49 % Allowed : 15.43 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.17), residues: 2472 helix: 0.91 (0.15), residues: 1239 sheet: -0.28 (0.31), residues: 283 loop : -1.16 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 499 TYR 0.007 0.001 TYR A1178 PHE 0.031 0.001 PHE A1212 TRP 0.009 0.001 TRP D 205 HIS 0.003 0.000 HIS A 885 Details of bonding type rmsd covalent geometry : bond 0.00221 (20854) covalent geometry : angle 0.55803 (28253) SS BOND : bond 0.00230 ( 10) SS BOND : angle 1.28943 ( 20) hydrogen bonds : bond 0.03823 ( 961) hydrogen bonds : angle 4.45376 ( 2799) link_BETA1-4 : bond 0.00932 ( 9) link_BETA1-4 : angle 2.75667 ( 27) link_NAG-ASN : bond 0.00928 ( 7) link_NAG-ASN : angle 5.61553 ( 21) *********************** 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 308 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 253 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 ARG cc_start: 0.1074 (mtt-85) cc_final: 0.0658 (mtp-110) REVERT: C 255 GLU cc_start: 0.3378 (OUTLIER) cc_final: 0.2555 (tt0) REVERT: C 304 ILE cc_start: 0.5176 (mm) cc_final: 0.4927 (tt) REVERT: C 343 GLU cc_start: 0.6492 (mm-30) cc_final: 0.5809 (pt0) REVERT: A 165 GLU cc_start: 0.8114 (tp30) cc_final: 0.7848 (pt0) REVERT: A 209 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7711 (mm) REVERT: A 293 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.6177 (p90) REVERT: A 402 LEU cc_start: 0.8402 (tp) cc_final: 0.8149 (mm) REVERT: A 984 ARG cc_start: 0.8257 (ttp80) cc_final: 0.8043 (ttp-110) REVERT: A 1012 ILE cc_start: 0.8284 (mt) cc_final: 0.8078 (mt) REVERT: A 1018 ILE cc_start: 0.8229 (mm) cc_final: 0.7782 (mp) REVERT: A 1053 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8070 (mt-10) REVERT: A 1208 GLU cc_start: 0.6896 (pp20) cc_final: 0.6640 (pp20) REVERT: A 1269 TRP cc_start: 0.7565 (OUTLIER) cc_final: 0.5369 (m-90) REVERT: A 1534 MET cc_start: 0.5549 (mpp) cc_final: 0.4209 (pmm) REVERT: A 1536 MET cc_start: 0.3547 (mpp) cc_final: 0.3157 (mpp) REVERT: D 667 CYS cc_start: 0.2440 (OUTLIER) cc_final: 0.2053 (t) REVERT: D 678 GLU cc_start: 0.8089 (pt0) cc_final: 0.6558 (mm-30) REVERT: D 803 GLN cc_start: 0.7756 (mp-120) cc_final: 0.7292 (mm-40) REVERT: D 883 MET cc_start: 0.8380 (tpt) cc_final: 0.8107 (tpt) REVERT: D 1017 MET cc_start: 0.7836 (ttm) cc_final: 0.7532 (ttm) outliers start: 55 outliers final: 18 residues processed: 287 average time/residue: 0.5733 time to fit residues: 189.8947 Evaluate side-chains 257 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 233 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1053 GLU Chi-restraints excluded: chain A residue 1156 GLN Chi-restraints excluded: chain A residue 1269 TRP Chi-restraints excluded: chain A residue 1370 GLN Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 667 CYS Chi-restraints excluded: chain D residue 673 SER Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 851 VAL Chi-restraints excluded: chain D residue 881 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 238 optimal weight: 0.8980 chunk 172 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 216 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 136 optimal weight: 0.6980 chunk 163 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 972 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.197288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 109)---------------| | r_work = 0.3431 r_free = 0.3431 target = 0.129153 restraints weight = 25357.255| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 3.31 r_work: 0.3159 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20880 Z= 0.115 Angle : 0.574 15.213 28321 Z= 0.276 Chirality : 0.043 0.268 3234 Planarity : 0.004 0.055 3554 Dihedral : 9.452 105.351 3292 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.61 % Favored : 95.31 % Rotamer: Outliers : 2.49 % Allowed : 16.38 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.17), residues: 2472 helix: 1.05 (0.15), residues: 1230 sheet: -0.32 (0.31), residues: 285 loop : -1.13 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 499 TYR 0.009 0.001 TYR D1068 PHE 0.028 0.001 PHE A1212 TRP 0.010 0.001 TRP A1103 HIS 0.002 0.000 HIS A 912 Details of bonding type rmsd covalent geometry : bond 0.00255 (20854) covalent geometry : angle 0.55022 (28253) SS BOND : bond 0.00250 ( 10) SS BOND : angle 1.41100 ( 20) hydrogen bonds : bond 0.03751 ( 961) hydrogen bonds : angle 4.37455 ( 2799) link_BETA1-4 : bond 0.00918 ( 9) link_BETA1-4 : angle 2.76632 ( 27) link_NAG-ASN : bond 0.00733 ( 7) link_NAG-ASN : angle 5.00455 ( 21) *********************** 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 306 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 251 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 107 ARG cc_start: 0.1109 (mtt-85) cc_final: 0.0587 (mtm110) REVERT: C 177 MET cc_start: -0.0455 (pp-130) cc_final: -0.0796 (ppp) REVERT: C 255 GLU cc_start: 0.3257 (OUTLIER) cc_final: 0.2536 (tt0) REVERT: C 304 ILE cc_start: 0.5020 (mm) cc_final: 0.4799 (tt) REVERT: C 343 GLU cc_start: 0.6529 (mm-30) cc_final: 0.5836 (pt0) REVERT: A 165 GLU cc_start: 0.7972 (tp30) cc_final: 0.7690 (pt0) REVERT: A 209 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7709 (mm) REVERT: A 293 PHE cc_start: 0.8701 (OUTLIER) cc_final: 0.6156 (p90) REVERT: A 402 LEU cc_start: 0.8380 (tp) cc_final: 0.8109 (mm) REVERT: A 984 ARG cc_start: 0.8224 (ttp80) cc_final: 0.8006 (ttp-110) REVERT: A 1012 ILE cc_start: 0.8231 (mt) cc_final: 0.8025 (mt) REVERT: A 1018 ILE cc_start: 0.8262 (mm) cc_final: 0.7816 (mp) REVERT: A 1053 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8056 (mt-10) REVERT: A 1212 PHE cc_start: 0.7489 (t80) cc_final: 0.7279 (t80) REVERT: A 1269 TRP cc_start: 0.7502 (OUTLIER) cc_final: 0.5289 (m-90) REVERT: A 1534 MET cc_start: 0.5547 (mpp) cc_final: 0.4212 (pmm) REVERT: A 1536 MET cc_start: 0.3197 (mpp) cc_final: 0.2842 (mpp) REVERT: D 157 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8424 (mtp85) REVERT: D 279 MET cc_start: 0.9149 (ttm) cc_final: 0.8921 (ttp) REVERT: D 667 CYS cc_start: 0.2410 (OUTLIER) cc_final: 0.2066 (t) REVERT: D 678 GLU cc_start: 0.8042 (pt0) cc_final: 0.6498 (mm-30) REVERT: D 803 GLN cc_start: 0.7686 (mp-120) cc_final: 0.7324 (mm-40) REVERT: D 883 MET cc_start: 0.8291 (tpt) cc_final: 0.8001 (tpt) REVERT: D 985 ASN cc_start: 0.7433 (OUTLIER) cc_final: 0.6874 (m-40) REVERT: D 1017 MET cc_start: 0.7914 (ttm) cc_final: 0.7607 (ttm) outliers start: 55 outliers final: 19 residues processed: 289 average time/residue: 0.5685 time to fit residues: 189.1199 Evaluate side-chains 259 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 232 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1053 GLU Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1269 TRP Chi-restraints excluded: chain A residue 1370 GLN Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 667 CYS Chi-restraints excluded: chain D residue 673 SER Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 851 VAL Chi-restraints excluded: chain D residue 881 SER Chi-restraints excluded: chain D residue 985 ASN Chi-restraints excluded: chain D residue 1064 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 196 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 228 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 247 optimal weight: 3.9990 chunk 22 optimal weight: 0.0980 chunk 75 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 996 ASN D 972 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.195790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.127034 restraints weight = 25286.552| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.91 r_work: 0.3105 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20880 Z= 0.129 Angle : 0.593 14.959 28321 Z= 0.285 Chirality : 0.043 0.316 3234 Planarity : 0.004 0.053 3554 Dihedral : 9.232 105.079 3292 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.65 % Favored : 95.27 % Rotamer: Outliers : 2.31 % Allowed : 17.42 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.17), residues: 2472 helix: 1.09 (0.15), residues: 1231 sheet: -0.35 (0.31), residues: 285 loop : -1.15 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 499 TYR 0.011 0.001 TYR D1068 PHE 0.025 0.001 PHE A1212 TRP 0.010 0.001 TRP A1103 HIS 0.002 0.000 HIS A 912 Details of bonding type rmsd covalent geometry : bond 0.00296 (20854) covalent geometry : angle 0.56939 (28253) SS BOND : bond 0.00268 ( 10) SS BOND : angle 1.62703 ( 20) hydrogen bonds : bond 0.03772 ( 961) hydrogen bonds : angle 4.35753 ( 2799) link_BETA1-4 : bond 0.00926 ( 9) link_BETA1-4 : angle 2.84127 ( 27) link_NAG-ASN : bond 0.00682 ( 7) link_NAG-ASN : angle 5.01595 ( 21) *********************** 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 284 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 233 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 177 MET cc_start: -0.0491 (pp-130) cc_final: -0.0807 (ppp) REVERT: C 255 GLU cc_start: 0.3429 (OUTLIER) cc_final: 0.2710 (tt0) REVERT: C 343 GLU cc_start: 0.6552 (mm-30) cc_final: 0.5864 (pt0) REVERT: A 165 GLU cc_start: 0.8007 (tp30) cc_final: 0.7655 (pt0) REVERT: A 209 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7580 (mm) REVERT: A 291 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8153 (tp30) REVERT: A 293 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.6274 (p90) REVERT: A 402 LEU cc_start: 0.8398 (tp) cc_final: 0.8118 (mm) REVERT: A 1012 ILE cc_start: 0.8231 (mt) cc_final: 0.8020 (mt) REVERT: A 1018 ILE cc_start: 0.8179 (mm) cc_final: 0.7741 (mp) REVERT: A 1053 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8104 (mt-10) REVERT: A 1269 TRP cc_start: 0.7526 (OUTLIER) cc_final: 0.5255 (m-90) REVERT: A 1534 MET cc_start: 0.5553 (mpp) cc_final: 0.4108 (pmm) REVERT: A 1536 MET cc_start: 0.3107 (mpp) cc_final: 0.2740 (mpp) REVERT: D 157 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8512 (mtp85) REVERT: D 604 ASN cc_start: 0.8237 (m-40) cc_final: 0.7937 (m-40) REVERT: D 667 CYS cc_start: 0.2805 (OUTLIER) cc_final: 0.2494 (t) REVERT: D 678 GLU cc_start: 0.8044 (pt0) cc_final: 0.6432 (mm-30) REVERT: D 803 GLN cc_start: 0.7711 (mp-120) cc_final: 0.7319 (mm-40) REVERT: D 883 MET cc_start: 0.8207 (tpt) cc_final: 0.7899 (tpt) REVERT: D 985 ASN cc_start: 0.7446 (OUTLIER) cc_final: 0.6885 (m-40) REVERT: D 1017 MET cc_start: 0.7861 (ttm) cc_final: 0.7518 (ttm) outliers start: 51 outliers final: 26 residues processed: 266 average time/residue: 0.5798 time to fit residues: 178.0735 Evaluate side-chains 264 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 229 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1028 MET Chi-restraints excluded: chain A residue 1053 GLU Chi-restraints excluded: chain A residue 1269 TRP Chi-restraints excluded: chain A residue 1370 GLN Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 667 CYS Chi-restraints excluded: chain D residue 673 SER Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 851 VAL Chi-restraints excluded: chain D residue 881 SER Chi-restraints excluded: chain D residue 985 ASN Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1064 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 20 optimal weight: 30.0000 chunk 152 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 219 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 236 optimal weight: 0.8980 chunk 173 optimal weight: 3.9990 chunk 186 optimal weight: 0.7980 chunk 189 optimal weight: 0.9990 chunk 227 optimal weight: 5.9990 chunk 230 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 108 GLN D 972 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.195271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.3343 r_free = 0.3343 target = 0.124345 restraints weight = 25293.951| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.58 r_work: 0.3121 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20880 Z= 0.136 Angle : 0.600 14.530 28321 Z= 0.290 Chirality : 0.044 0.266 3234 Planarity : 0.004 0.052 3554 Dihedral : 9.015 105.253 3292 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.65 % Favored : 95.27 % Rotamer: Outliers : 2.76 % Allowed : 17.47 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.17), residues: 2472 helix: 1.10 (0.15), residues: 1226 sheet: -0.35 (0.31), residues: 285 loop : -1.18 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 499 TYR 0.013 0.001 TYR D1068 PHE 0.034 0.001 PHE A1147 TRP 0.010 0.001 TRP A1199 HIS 0.002 0.001 HIS A 544 Details of bonding type rmsd covalent geometry : bond 0.00314 (20854) covalent geometry : angle 0.57636 (28253) SS BOND : bond 0.00269 ( 10) SS BOND : angle 1.74986 ( 20) hydrogen bonds : bond 0.03811 ( 961) hydrogen bonds : angle 4.34623 ( 2799) link_BETA1-4 : bond 0.00934 ( 9) link_BETA1-4 : angle 2.91948 ( 27) link_NAG-ASN : bond 0.00867 ( 7) link_NAG-ASN : angle 4.97829 ( 21) *********************** 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 302 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 241 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 177 MET cc_start: -0.0528 (pp-130) cc_final: -0.0829 (ppp) REVERT: C 255 GLU cc_start: 0.3419 (OUTLIER) cc_final: 0.2656 (tt0) REVERT: C 343 GLU cc_start: 0.6540 (mm-30) cc_final: 0.5885 (pt0) REVERT: A 165 GLU cc_start: 0.7967 (tp30) cc_final: 0.7703 (pt0) REVERT: A 209 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7423 (mm) REVERT: A 266 LYS cc_start: 0.7352 (pttt) cc_final: 0.7080 (pptt) REVERT: A 291 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8170 (tp30) REVERT: A 293 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.6338 (p90) REVERT: A 312 GLU cc_start: 0.6927 (pm20) cc_final: 0.6628 (pt0) REVERT: A 402 LEU cc_start: 0.8387 (tp) cc_final: 0.8112 (mm) REVERT: A 1012 ILE cc_start: 0.8238 (mt) cc_final: 0.8026 (mt) REVERT: A 1018 ILE cc_start: 0.8178 (mm) cc_final: 0.7740 (mp) REVERT: A 1053 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8067 (mt-10) REVERT: A 1269 TRP cc_start: 0.7527 (OUTLIER) cc_final: 0.5247 (m-90) REVERT: A 1324 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7599 (tpp) REVERT: A 1534 MET cc_start: 0.5598 (mpp) cc_final: 0.4344 (pmm) REVERT: D 157 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8544 (mtp85) REVERT: D 604 ASN cc_start: 0.8197 (m-40) cc_final: 0.7895 (m-40) REVERT: D 667 CYS cc_start: 0.2683 (OUTLIER) cc_final: 0.2466 (t) REVERT: D 678 GLU cc_start: 0.8019 (pt0) cc_final: 0.6420 (mm-30) REVERT: D 803 GLN cc_start: 0.7696 (mp-120) cc_final: 0.7268 (mm-40) REVERT: D 883 MET cc_start: 0.8171 (tpt) cc_final: 0.7880 (tpt) REVERT: D 985 ASN cc_start: 0.7660 (OUTLIER) cc_final: 0.7123 (m-40) REVERT: D 1017 MET cc_start: 0.7918 (ttm) cc_final: 0.7573 (ttm) outliers start: 61 outliers final: 30 residues processed: 283 average time/residue: 0.5503 time to fit residues: 180.7263 Evaluate side-chains 266 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 226 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1028 MET Chi-restraints excluded: chain A residue 1053 GLU Chi-restraints excluded: chain A residue 1269 TRP Chi-restraints excluded: chain A residue 1324 MET Chi-restraints excluded: chain A residue 1370 GLN Chi-restraints excluded: chain A residue 1391 THR Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 667 CYS Chi-restraints excluded: chain D residue 673 SER Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 851 VAL Chi-restraints excluded: chain D residue 881 SER Chi-restraints excluded: chain D residue 985 ASN Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1064 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 47 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 78 optimal weight: 0.0870 chunk 31 optimal weight: 4.9990 chunk 176 optimal weight: 0.8980 chunk 164 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 197 optimal weight: 0.4980 chunk 8 optimal weight: 5.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 645 ASN A 745 ASN A 996 ASN D 972 GLN D1042 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.197017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.3370 r_free = 0.3370 target = 0.126154 restraints weight = 25372.762| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.83 r_work: 0.3127 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20880 Z= 0.105 Angle : 0.582 13.968 28321 Z= 0.279 Chirality : 0.043 0.268 3234 Planarity : 0.004 0.051 3554 Dihedral : 8.675 105.375 3292 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.61 % Favored : 95.31 % Rotamer: Outliers : 2.22 % Allowed : 18.33 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.17), residues: 2472 helix: 1.17 (0.15), residues: 1234 sheet: -0.30 (0.31), residues: 285 loop : -1.15 (0.20), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1029 TYR 0.011 0.001 TYR D 719 PHE 0.027 0.001 PHE D 686 TRP 0.011 0.001 TRP A1199 HIS 0.002 0.000 HIS D 885 Details of bonding type rmsd covalent geometry : bond 0.00226 (20854) covalent geometry : angle 0.56063 (28253) SS BOND : bond 0.00223 ( 10) SS BOND : angle 1.46362 ( 20) hydrogen bonds : bond 0.03423 ( 961) hydrogen bonds : angle 4.24375 ( 2799) link_BETA1-4 : bond 0.00923 ( 9) link_BETA1-4 : angle 2.86932 ( 27) link_NAG-ASN : bond 0.00766 ( 7) link_NAG-ASN : angle 4.59868 ( 21) *********************** 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 292 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 243 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 107 ARG cc_start: 0.1335 (mtt-85) cc_final: 0.0788 (mpt90) REVERT: C 177 MET cc_start: -0.0436 (pp-130) cc_final: -0.0665 (ppp) REVERT: C 255 GLU cc_start: 0.3431 (OUTLIER) cc_final: 0.2642 (tt0) REVERT: C 343 GLU cc_start: 0.6264 (mm-30) cc_final: 0.5514 (pt0) REVERT: A 165 GLU cc_start: 0.7952 (tp30) cc_final: 0.7663 (pt0) REVERT: A 209 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7441 (mm) REVERT: A 261 LEU cc_start: 0.8493 (tp) cc_final: 0.8270 (tm) REVERT: A 266 LYS cc_start: 0.7356 (pttt) cc_final: 0.7124 (pptt) REVERT: A 293 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.6325 (p90) REVERT: A 312 GLU cc_start: 0.6903 (pm20) cc_final: 0.6636 (pt0) REVERT: A 402 LEU cc_start: 0.8365 (tp) cc_final: 0.8124 (mm) REVERT: A 1012 ILE cc_start: 0.8200 (mt) cc_final: 0.7991 (mt) REVERT: A 1018 ILE cc_start: 0.8182 (mm) cc_final: 0.7747 (mp) REVERT: A 1047 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8119 (pt0) REVERT: A 1053 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8063 (mt-10) REVERT: A 1210 MET cc_start: 0.5223 (tpt) cc_final: 0.3951 (OUTLIER) REVERT: A 1269 TRP cc_start: 0.7565 (OUTLIER) cc_final: 0.5295 (m-90) REVERT: A 1324 MET cc_start: 0.7935 (mmt) cc_final: 0.7585 (tpp) REVERT: A 1534 MET cc_start: 0.5566 (mpp) cc_final: 0.4349 (pmm) REVERT: D 157 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8444 (mtp85) REVERT: D 268 THR cc_start: 0.9106 (OUTLIER) cc_final: 0.8803 (t) REVERT: D 604 ASN cc_start: 0.8224 (m-40) cc_final: 0.7922 (m-40) REVERT: D 667 CYS cc_start: 0.2624 (OUTLIER) cc_final: 0.2393 (t) REVERT: D 678 GLU cc_start: 0.7972 (pt0) cc_final: 0.6345 (mm-30) REVERT: D 803 GLN cc_start: 0.7627 (mp-120) cc_final: 0.7192 (mm-40) REVERT: D 883 MET cc_start: 0.8206 (tpt) cc_final: 0.7934 (tpt) REVERT: D 985 ASN cc_start: 0.7656 (OUTLIER) cc_final: 0.7109 (m-40) REVERT: D 1017 MET cc_start: 0.7906 (ttm) cc_final: 0.7696 (ttm) outliers start: 49 outliers final: 28 residues processed: 279 average time/residue: 0.5463 time to fit residues: 176.4910 Evaluate side-chains 267 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 230 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 1047 GLU Chi-restraints excluded: chain A residue 1053 GLU Chi-restraints excluded: chain A residue 1269 TRP Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1370 GLN Chi-restraints excluded: chain A residue 1391 THR Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1466 ASN Chi-restraints excluded: chain A residue 1532 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 667 CYS Chi-restraints excluded: chain D residue 673 SER Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 851 VAL Chi-restraints excluded: chain D residue 881 SER Chi-restraints excluded: chain D residue 985 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 246 optimal weight: 3.9990 chunk 220 optimal weight: 3.9990 chunk 205 optimal weight: 7.9990 chunk 189 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 178 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 215 optimal weight: 0.0980 chunk 247 optimal weight: 0.6980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 645 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.195901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.3438 r_free = 0.3438 target = 0.128148 restraints weight = 25262.551| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.17 r_work: 0.3165 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20880 Z= 0.125 Angle : 0.598 13.785 28321 Z= 0.286 Chirality : 0.043 0.270 3234 Planarity : 0.004 0.051 3554 Dihedral : 8.521 105.066 3292 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.45 % Favored : 95.47 % Rotamer: Outliers : 1.90 % Allowed : 19.10 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.17), residues: 2472 helix: 1.19 (0.15), residues: 1226 sheet: -0.31 (0.31), residues: 285 loop : -1.17 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 984 TYR 0.012 0.001 TYR D 719 PHE 0.033 0.001 PHE A1147 TRP 0.010 0.001 TRP A1103 HIS 0.002 0.000 HIS D 306 Details of bonding type rmsd covalent geometry : bond 0.00288 (20854) covalent geometry : angle 0.57591 (28253) SS BOND : bond 0.00258 ( 10) SS BOND : angle 1.61934 ( 20) hydrogen bonds : bond 0.03579 ( 961) hydrogen bonds : angle 4.27055 ( 2799) link_BETA1-4 : bond 0.00902 ( 9) link_BETA1-4 : angle 2.96493 ( 27) link_NAG-ASN : bond 0.00687 ( 7) link_NAG-ASN : angle 4.63742 ( 21) *********************** 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 274 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 232 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 107 ARG cc_start: 0.1532 (mtt-85) cc_final: 0.0820 (mpt90) REVERT: C 115 ILE cc_start: 0.1868 (tt) cc_final: 0.1285 (tp) REVERT: C 177 MET cc_start: -0.0367 (pp-130) cc_final: -0.0590 (ppp) REVERT: C 255 GLU cc_start: 0.3432 (OUTLIER) cc_final: 0.2585 (tt0) REVERT: C 343 GLU cc_start: 0.6499 (mm-30) cc_final: 0.5586 (pt0) REVERT: A 209 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7537 (mm) REVERT: A 293 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.6445 (p90) REVERT: A 312 GLU cc_start: 0.6890 (pm20) cc_final: 0.6643 (pt0) REVERT: A 402 LEU cc_start: 0.8369 (tp) cc_final: 0.8158 (mm) REVERT: A 521 LYS cc_start: 0.7971 (mtmt) cc_final: 0.7214 (tptp) REVERT: A 999 LYS cc_start: 0.7596 (ttmt) cc_final: 0.6812 (mptt) REVERT: A 1012 ILE cc_start: 0.8320 (mt) cc_final: 0.8112 (mt) REVERT: A 1053 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8018 (mt-10) REVERT: A 1199 TRP cc_start: 0.6270 (OUTLIER) cc_final: 0.4899 (t60) REVERT: A 1210 MET cc_start: 0.5431 (tpt) cc_final: 0.4030 (OUTLIER) REVERT: A 1269 TRP cc_start: 0.7597 (OUTLIER) cc_final: 0.5346 (m-90) REVERT: A 1534 MET cc_start: 0.5579 (mpp) cc_final: 0.4346 (pmm) REVERT: D 157 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8485 (mtp85) REVERT: D 604 ASN cc_start: 0.8167 (m-40) cc_final: 0.7886 (m-40) REVERT: D 678 GLU cc_start: 0.7984 (pt0) cc_final: 0.6458 (mm-30) REVERT: D 803 GLN cc_start: 0.7644 (mp-120) cc_final: 0.7213 (mm-40) REVERT: D 883 MET cc_start: 0.8247 (tpt) cc_final: 0.7969 (tpt) REVERT: D 985 ASN cc_start: 0.7672 (OUTLIER) cc_final: 0.7126 (m-40) outliers start: 42 outliers final: 29 residues processed: 266 average time/residue: 0.5228 time to fit residues: 161.3149 Evaluate side-chains 263 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 227 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 1053 GLU Chi-restraints excluded: chain A residue 1199 TRP Chi-restraints excluded: chain A residue 1269 TRP Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1370 GLN Chi-restraints excluded: chain A residue 1391 THR Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1466 ASN Chi-restraints excluded: chain A residue 1532 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 673 SER Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 851 VAL Chi-restraints excluded: chain D residue 881 SER Chi-restraints excluded: chain D residue 985 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 220 optimal weight: 0.8980 chunk 192 optimal weight: 1.9990 chunk 235 optimal weight: 0.9980 chunk 212 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 41 optimal weight: 0.3980 chunk 228 optimal weight: 0.0020 chunk 231 optimal weight: 4.9990 chunk 177 optimal weight: 0.6980 chunk 234 optimal weight: 0.6980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 645 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.197286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3423 r_free = 0.3423 target = 0.129100 restraints weight = 25371.741| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 3.24 r_work: 0.3144 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 20880 Z= 0.106 Angle : 0.590 13.171 28321 Z= 0.281 Chirality : 0.043 0.267 3234 Planarity : 0.004 0.051 3554 Dihedral : 8.230 105.201 3292 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.37 % Favored : 95.55 % Rotamer: Outliers : 1.81 % Allowed : 19.37 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.17), residues: 2472 helix: 1.26 (0.15), residues: 1232 sheet: -0.28 (0.31), residues: 285 loop : -1.15 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1378 TYR 0.011 0.001 TYR D 719 PHE 0.027 0.001 PHE D 686 TRP 0.011 0.001 TRP D 205 HIS 0.001 0.000 HIS A 632 Details of bonding type rmsd covalent geometry : bond 0.00229 (20854) covalent geometry : angle 0.56863 (28253) SS BOND : bond 0.00219 ( 10) SS BOND : angle 2.26275 ( 20) hydrogen bonds : bond 0.03343 ( 961) hydrogen bonds : angle 4.17886 ( 2799) link_BETA1-4 : bond 0.00890 ( 9) link_BETA1-4 : angle 2.96307 ( 27) link_NAG-ASN : bond 0.00742 ( 7) link_NAG-ASN : angle 4.34461 ( 21) ********************** 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 274 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 234 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 107 ARG cc_start: 0.1461 (mtt-85) cc_final: 0.0794 (mpt90) REVERT: C 115 ILE cc_start: 0.1848 (tt) cc_final: 0.1251 (tp) REVERT: C 177 MET cc_start: -0.0445 (pp-130) cc_final: -0.0659 (ppp) REVERT: C 255 GLU cc_start: 0.3419 (OUTLIER) cc_final: 0.2596 (tt0) REVERT: C 343 GLU cc_start: 0.6327 (mm-30) cc_final: 0.5505 (pt0) REVERT: A 165 GLU cc_start: 0.7889 (pt0) cc_final: 0.7661 (pt0) REVERT: A 209 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7417 (mm) REVERT: A 293 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.6381 (p90) REVERT: A 312 GLU cc_start: 0.6817 (pm20) cc_final: 0.6603 (pt0) REVERT: A 402 LEU cc_start: 0.8307 (tp) cc_final: 0.8095 (mm) REVERT: A 521 LYS cc_start: 0.7992 (mtmt) cc_final: 0.7229 (tptp) REVERT: A 926 PHE cc_start: 0.7636 (m-80) cc_final: 0.7244 (m-80) REVERT: A 999 LYS cc_start: 0.7411 (ttmt) cc_final: 0.6603 (mptt) REVERT: A 1012 ILE cc_start: 0.8208 (mt) cc_final: 0.8007 (mt) REVERT: A 1019 MET cc_start: 0.7756 (mtp) cc_final: 0.7406 (mtt) REVERT: A 1047 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8118 (pt0) REVERT: A 1053 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8061 (mt-10) REVERT: A 1210 MET cc_start: 0.5208 (tpt) cc_final: 0.3836 (OUTLIER) REVERT: A 1269 TRP cc_start: 0.7563 (OUTLIER) cc_final: 0.5284 (m-90) REVERT: A 1324 MET cc_start: 0.7955 (mmt) cc_final: 0.7606 (tpp) REVERT: A 1467 PHE cc_start: 0.7868 (t80) cc_final: 0.7570 (t80) REVERT: A 1534 MET cc_start: 0.5572 (mpp) cc_final: 0.4335 (pmm) REVERT: D 157 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8459 (ptm160) REVERT: D 268 THR cc_start: 0.9097 (OUTLIER) cc_final: 0.8797 (t) REVERT: D 604 ASN cc_start: 0.8198 (m-40) cc_final: 0.7887 (m-40) REVERT: D 803 GLN cc_start: 0.7608 (mp-120) cc_final: 0.7162 (mm-40) REVERT: D 883 MET cc_start: 0.8210 (tpt) cc_final: 0.7945 (tpt) REVERT: D 985 ASN cc_start: 0.7621 (OUTLIER) cc_final: 0.7062 (m-40) outliers start: 40 outliers final: 29 residues processed: 265 average time/residue: 0.5570 time to fit residues: 170.5801 Evaluate side-chains 263 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 226 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 1047 GLU Chi-restraints excluded: chain A residue 1053 GLU Chi-restraints excluded: chain A residue 1269 TRP Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1370 GLN Chi-restraints excluded: chain A residue 1391 THR Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1532 VAL Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 673 SER Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 851 VAL Chi-restraints excluded: chain D residue 881 SER Chi-restraints excluded: chain D residue 985 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 53 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 180 optimal weight: 0.9980 chunk 162 optimal weight: 5.9990 chunk 210 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 233 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.196573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 108)---------------| | r_work = 0.3363 r_free = 0.3363 target = 0.125602 restraints weight = 25340.762| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.62 r_work: 0.3125 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20880 Z= 0.116 Angle : 0.594 12.949 28321 Z= 0.283 Chirality : 0.043 0.270 3234 Planarity : 0.004 0.059 3554 Dihedral : 8.047 104.895 3292 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.45 % Favored : 95.47 % Rotamer: Outliers : 1.76 % Allowed : 19.50 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.17), residues: 2472 helix: 1.26 (0.15), residues: 1227 sheet: -0.30 (0.31), residues: 285 loop : -1.17 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A1378 TYR 0.013 0.001 TYR D 719 PHE 0.036 0.001 PHE A1147 TRP 0.011 0.001 TRP A1199 HIS 0.002 0.000 HIS D 306 Details of bonding type rmsd covalent geometry : bond 0.00263 (20854) covalent geometry : angle 0.57251 (28253) SS BOND : bond 0.00240 ( 10) SS BOND : angle 1.74555 ( 20) hydrogen bonds : bond 0.03423 ( 961) hydrogen bonds : angle 4.18864 ( 2799) link_BETA1-4 : bond 0.00872 ( 9) link_BETA1-4 : angle 3.15322 ( 27) link_NAG-ASN : bond 0.00657 ( 7) link_NAG-ASN : angle 4.36031 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10797.10 seconds wall clock time: 183 minutes 31.10 seconds (11011.10 seconds total)