Starting phenix.real_space_refine on Sat Jul 4 12:54:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uhg_26514/07_2026/7uhg_26514.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uhg_26514/07_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_26514/07_2026/7uhg_26514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uhg_26514/07_2026/7uhg_26514.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7uhg_26514/07_2026/7uhg_26514.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uhg_26514/07_2026/7uhg_26514.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uhg_26514/07_2026/7uhg_26514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uhg_26514/07_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-6108/lib/python3.11/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 chiralities: 2 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 130 Unusual residues: {' CA': 1, '3PE': 1, 'CLR': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.33, per 1000 atoms: 0.21 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: 2.04 Conformation dependent library (CDL) restraints added in 956.4 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: 0.81 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: 4.23 Time building geometry restraints manager: 2.62 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 - 17.54: 11012 17.54 - 35.08: 1091 35.08 - 52.62: 180 52.62 - 70.16: 33 70.16 - 87.69: 20 Dihedral angle restraints: 12336 sinusoidal: 5019 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 12333 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.730 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:7.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 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 : 14.198 87.694 7570 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/Z covalent geometry : bond 0.00361 / 0.16 (20854) covalent geometry : angle 0.57880 / 0.28 (28253) SS BOND : bond 0.00236 / 0.11 ( 10) SS BOND : angle 2.04617 / 1.09 ( 20) hydrogen bonds : bond 0.25600 / 17.13 ( 961) hydrogen bonds : angle 7.85158 / 5.53 ( 2799) link_BETA1-4 : bond 0.00844 / 0.40 ( 9) link_BETA1-4 : angle 3.38168 / 2.25 ( 27) link_NAG-ASN : bond 0.01174 / 0.57 ( 7) link_NAG-ASN : angle 6.90832 / 4.78 ( 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 : 0.787 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: 0.7252 (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: 0.5355 time to fit residues: 197.0044 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 : 0.783 ------------------------------------------------------------------------------- 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... 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 = 0.196975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.128703 restraints weight = 25363.987| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.41 r_work: 0.3096 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20880 Z= 0.140 Angle : 0.630 17.122 28321 Z= 0.311 Chirality : 0.045 0.533 3234 Planarity : 0.004 0.080 3554 Dihedral : 5.071 53.370 2762 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.17 % Favored : 95.75 % Rotamer: Outliers : 1.76 % Allowed : 10.41 % Favored : 87.83 % 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: -0.43 (0.17), residues: 2472 helix: 0.51 (0.15), residues: 1224 sheet: -0.44 (0.30), residues: 284 loop : -1.19 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 157 TYR 0.011 0.001 TYR D 409 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/Z covalent geometry : bond 0.00288 / 0.14 (20854) covalent geometry : angle 0.60526 / 0.31 (28253) SS BOND : bond 0.00283 / 0.13 ( 10) SS BOND : angle 1.69002 / 0.90 ( 20) hydrogen bonds : bond 0.05406 / 3.49 ( 961) hydrogen bonds : angle 5.01806 / 3.50 ( 2799) link_BETA1-4 : bond 0.00946 / 0.44 ( 9) link_BETA1-4 : angle 2.45489 / 1.57 ( 27) link_NAG-ASN : bond 0.01100 / 0.54 ( 7) link_NAG-ASN : angle 5.71649 / 3.96 ( 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 : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 107 ARG cc_start: 0.0995 (mtt-85) cc_final: 0.0514 (mtm110) REVERT: C 177 MET cc_start: -0.0236 (pp-130) cc_final: -0.0517 (ppp) REVERT: C 344 ASP cc_start: 0.4496 (t0) cc_final: 0.4273 (t0) REVERT: A 165 GLU cc_start: 0.8163 (tp30) cc_final: 0.7871 (pt0) REVERT: A 209 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7806 (mm) REVERT: A 266 LYS cc_start: 0.7264 (pptt) cc_final: 0.7046 (pttt) REVERT: A 334 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.8021 (ppt170) REVERT: A 1012 ILE cc_start: 0.8334 (mt) cc_final: 0.8131 (mt) REVERT: A 1208 GLU cc_start: 0.6784 (pp20) cc_final: 0.6569 (pp20) REVERT: A 1210 MET cc_start: 0.5585 (tpt) cc_final: 0.4324 (tmt) REVERT: A 1269 TRP cc_start: 0.7614 (OUTLIER) cc_final: 0.5509 (m-90) REVERT: A 1370 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7265 (mt0) REVERT: D 794 VAL cc_start: 0.8856 (t) cc_final: 0.8647 (p) REVERT: D 803 GLN cc_start: 0.7666 (mp-120) cc_final: 0.7312 (mm-40) REVERT: D 806 LEU cc_start: 0.8847 (tp) cc_final: 0.8425 (tm) REVERT: D 883 MET cc_start: 0.8394 (tpt) cc_final: 0.8062 (tpt) REVERT: D 985 ASN cc_start: 0.7544 (OUTLIER) cc_final: 0.7020 (m-40) outliers start: 39 outliers final: 13 residues processed: 287 average time/residue: 0.5114 time to fit residues: 169.5535 Evaluate side-chains 251 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 233 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 334 ARG 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: 0.9980 chunk 152 optimal weight: 9.9990 chunk 170 optimal weight: 3.9990 chunk 85 optimal weight: 0.0670 chunk 91 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 149 optimal weight: 40.0000 chunk 62 optimal weight: 20.0000 chunk 84 optimal weight: 0.9980 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4185 r_free = 0.4185 target = 0.197284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.127759 restraints weight = 25520.634| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.34 r_work: 0.3093 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20880 Z= 0.118 Angle : 0.578 16.105 28321 Z= 0.281 Chirality : 0.044 0.483 3234 Planarity : 0.004 0.064 3554 Dihedral : 4.922 52.667 2759 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.33 % Favored : 95.59 % Rotamer: Outliers : 2.49 % Allowed : 13.08 % 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: -0.14 (0.17), residues: 2472 helix: 0.80 (0.15), residues: 1238 sheet: -0.32 (0.31), residues: 283 loop : -1.15 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 984 TYR 0.009 0.001 TYR D 409 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/Z covalent geometry : bond 0.00249 / 0.12 (20854) covalent geometry : angle 0.55283 / 0.28 (28253) SS BOND : bond 0.00274 / 0.12 ( 10) SS BOND : angle 1.48343 / 0.79 ( 20) hydrogen bonds : bond 0.04516 / 2.93 ( 961) hydrogen bonds : angle 4.65643 / 3.24 ( 2799) link_BETA1-4 : bond 0.00894 / 0.40 ( 9) link_BETA1-4 : angle 2.32163 / 1.57 ( 27) link_NAG-ASN : bond 0.01091 / 0.53 ( 7) link_NAG-ASN : angle 5.44854 / 3.74 ( 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 319 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 264 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 107 ARG cc_start: 0.1100 (mtt-85) cc_final: 0.0592 (mtp-110) REVERT: C 304 ILE cc_start: 0.5281 (mm) cc_final: 0.5039 (tt) REVERT: A 134 LEU cc_start: 0.8569 (mt) cc_final: 0.8321 (mt) REVERT: A 165 GLU cc_start: 0.8220 (tp30) cc_final: 0.7874 (pt0) REVERT: A 209 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7770 (mm) REVERT: A 258 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.6646 (tp40) REVERT: A 266 LYS cc_start: 0.7232 (pptt) cc_final: 0.6992 (pttt) REVERT: A 291 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8098 (mp0) REVERT: A 293 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.6158 (p90) REVERT: A 373 MET cc_start: 0.8777 (mmt) cc_final: 0.8141 (mmp) REVERT: A 402 LEU cc_start: 0.8457 (tp) cc_final: 0.8165 (mm) REVERT: A 562 LEU cc_start: 0.8047 (mm) cc_final: 0.7784 (mm) REVERT: A 1012 ILE cc_start: 0.8346 (mt) cc_final: 0.8128 (mt) REVERT: A 1018 ILE cc_start: 0.8274 (mm) cc_final: 0.7833 (mp) REVERT: A 1053 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8057 (mt-10) REVERT: A 1208 GLU cc_start: 0.6787 (pp20) cc_final: 0.6578 (pp20) REVERT: A 1269 TRP cc_start: 0.7545 (OUTLIER) cc_final: 0.5361 (m-90) REVERT: A 1534 MET cc_start: 0.5555 (mpp) cc_final: 0.4131 (pmt) REVERT: A 1536 MET cc_start: 0.3345 (OUTLIER) cc_final: 0.3035 (mpp) REVERT: D 678 GLU cc_start: 0.8105 (pt0) cc_final: 0.6544 (mm-30) REVERT: D 803 GLN cc_start: 0.7669 (mp-120) cc_final: 0.7295 (mm-40) REVERT: D 883 MET cc_start: 0.8361 (tpt) cc_final: 0.8058 (tpt) REVERT: D 985 ASN cc_start: 0.7532 (OUTLIER) cc_final: 0.6863 (m-40) REVERT: D 1017 MET cc_start: 0.7895 (ttm) cc_final: 0.7599 (ttm) outliers start: 55 outliers final: 17 residues processed: 300 average time/residue: 0.4816 time to fit residues: 167.4619 Evaluate side-chains 267 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 242 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 258 GLN 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 1008 VAL 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 1454 LEU Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1536 MET Chi-restraints excluded: chain D residue 63 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 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: 10.0000 chunk 246 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 224 optimal weight: 7.9990 chunk 199 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 chunk 133 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4158 r_free = 0.4158 target = 0.194590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3322 r_free = 0.3322 target = 0.123413 restraints weight = 25421.762| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.59 r_work: 0.3060 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20880 Z= 0.169 Angle : 0.634 16.067 28321 Z= 0.306 Chirality : 0.046 0.521 3234 Planarity : 0.004 0.058 3554 Dihedral : 5.055 56.005 2755 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.65 % Favored : 95.27 % Rotamer: Outliers : 3.03 % Allowed : 15.38 % Favored : 81.58 % 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: 0.79 (0.15), residues: 1226 sheet: -0.39 (0.31), residues: 283 loop : -1.24 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 499 TYR 0.016 0.001 TYR D1068 PHE 0.030 0.001 PHE A1212 TRP 0.011 0.001 TRP D 113 HIS 0.004 0.001 HIS D 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (20854) covalent geometry : angle 0.60985 / 0.30 (28253) SS BOND : bond 0.00318 / 0.14 ( 10) SS BOND : angle 1.80902 / 0.96 ( 20) hydrogen bonds : bond 0.04417 / 2.90 ( 961) hydrogen bonds : angle 4.60986 / 3.20 ( 2799) link_BETA1-4 : bond 0.00865 / 0.39 ( 9) link_BETA1-4 : angle 2.45673 / 1.75 ( 27) link_NAG-ASN : bond 0.00880 / 0.43 ( 7) link_NAG-ASN : angle 5.53101 / 3.78 ( 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 318 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 251 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 255 GLU cc_start: 0.3398 (OUTLIER) cc_final: 0.2576 (tt0) REVERT: C 304 ILE cc_start: 0.4983 (mm) cc_final: 0.4742 (tt) REVERT: C 343 GLU cc_start: 0.6519 (mm-30) cc_final: 0.5851 (pt0) REVERT: A 165 GLU cc_start: 0.8143 (tp30) cc_final: 0.7835 (pt0) REVERT: A 209 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7740 (mm) REVERT: A 291 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8060 (mp0) REVERT: A 293 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.6326 (p90) REVERT: A 312 GLU cc_start: 0.6954 (pm20) cc_final: 0.6713 (pt0) REVERT: A 373 MET cc_start: 0.8871 (mmt) cc_final: 0.8235 (mmt) REVERT: A 402 LEU cc_start: 0.8495 (tp) cc_final: 0.8171 (mm) REVERT: A 562 LEU cc_start: 0.8132 (mm) cc_final: 0.7928 (mm) REVERT: A 984 ARG cc_start: 0.8381 (ttp80) cc_final: 0.8153 (ttp-110) REVERT: A 1012 ILE cc_start: 0.8414 (mt) cc_final: 0.8190 (mt) REVERT: A 1018 ILE cc_start: 0.8263 (mm) cc_final: 0.7819 (mp) REVERT: A 1199 TRP cc_start: 0.6561 (OUTLIER) cc_final: 0.5448 (t60) REVERT: A 1208 GLU cc_start: 0.6817 (pp20) cc_final: 0.6579 (pp20) REVERT: A 1269 TRP cc_start: 0.7637 (OUTLIER) cc_final: 0.5317 (m-90) REVERT: A 1534 MET cc_start: 0.5560 (mpp) cc_final: 0.4120 (pmt) REVERT: A 1536 MET cc_start: 0.3378 (mpp) cc_final: 0.3049 (mpp) REVERT: D 803 GLN cc_start: 0.7685 (mp-120) cc_final: 0.7229 (mm-40) REVERT: D 883 MET cc_start: 0.8326 (tpt) cc_final: 0.8060 (tpt) REVERT: D 985 ASN cc_start: 0.7522 (OUTLIER) cc_final: 0.6985 (m-40) REVERT: D 1017 MET cc_start: 0.7843 (ttm) cc_final: 0.7553 (ttm) outliers start: 67 outliers final: 28 residues processed: 296 average time/residue: 0.5395 time to fit residues: 185.5099 Evaluate side-chains 265 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 230 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 644 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 1053 GLU Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1199 TRP Chi-restraints excluded: chain A residue 1250 VAL 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 1454 LEU Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 536 ILE 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 798 VAL 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 1064 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 238 optimal weight: 0.6980 chunk 172 optimal weight: 0.9980 chunk 40 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 216 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 136 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 996 ASN D 108 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 972 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.196490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.126375 restraints weight = 25292.004| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.85 r_work: 0.3133 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20880 Z= 0.117 Angle : 0.581 14.581 28321 Z= 0.281 Chirality : 0.044 0.494 3234 Planarity : 0.004 0.055 3554 Dihedral : 4.877 54.435 2755 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.77 % Favored : 95.15 % Rotamer: Outliers : 2.17 % Allowed : 17.15 % Favored : 80.68 % 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: -0.02 (0.17), residues: 2472 helix: 0.99 (0.15), residues: 1229 sheet: -0.39 (0.31), residues: 284 loop : -1.18 (0.20), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1029 TYR 0.009 0.001 TYR D 512 PHE 0.031 0.001 PHE A1147 TRP 0.010 0.001 TRP A1103 HIS 0.002 0.000 HIS C 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (20854) covalent geometry : angle 0.55864 / 0.28 (28253) SS BOND : bond 0.00369 / 0.17 ( 10) SS BOND : angle 1.92119 / 1.00 ( 20) hydrogen bonds : bond 0.03854 / 2.53 ( 961) hydrogen bonds : angle 4.41914 / 3.05 ( 2799) link_BETA1-4 : bond 0.00890 / 0.40 ( 9) link_BETA1-4 : angle 2.32266 / 1.63 ( 27) link_NAG-ASN : bond 0.00952 / 0.47 ( 7) link_NAG-ASN : angle 4.95417 / 3.40 ( 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 293 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 245 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 107 ARG cc_start: 0.1115 (mtt-85) cc_final: 0.0594 (mtp-110) REVERT: C 177 MET cc_start: -0.0541 (pp-130) cc_final: -0.0866 (ppp) REVERT: C 255 GLU cc_start: 0.3288 (OUTLIER) cc_final: 0.2544 (tt0) REVERT: C 304 ILE cc_start: 0.5023 (mm) cc_final: 0.4789 (tt) REVERT: C 343 GLU cc_start: 0.6507 (mm-30) cc_final: 0.5834 (pt0) REVERT: A 165 GLU cc_start: 0.8031 (tp30) cc_final: 0.7754 (pt0) REVERT: A 293 PHE cc_start: 0.8888 (OUTLIER) cc_final: 0.6432 (p90) REVERT: A 312 GLU cc_start: 0.6995 (pm20) cc_final: 0.6698 (pt0) REVERT: A 373 MET cc_start: 0.8821 (mmt) cc_final: 0.8257 (mmt) REVERT: A 402 LEU cc_start: 0.8416 (tp) cc_final: 0.8159 (mm) REVERT: A 562 LEU cc_start: 0.8140 (mm) cc_final: 0.7919 (mm) REVERT: A 984 ARG cc_start: 0.8294 (ttp80) cc_final: 0.8079 (ttp-110) REVERT: A 1012 ILE cc_start: 0.8299 (mt) cc_final: 0.8092 (mt) REVERT: A 1018 ILE cc_start: 0.8336 (mm) cc_final: 0.7904 (mp) REVERT: A 1053 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8138 (mt-10) REVERT: A 1269 TRP cc_start: 0.7566 (OUTLIER) cc_final: 0.5217 (m-90) REVERT: A 1324 MET cc_start: 0.7944 (mmt) cc_final: 0.7577 (tpp) REVERT: A 1534 MET cc_start: 0.5552 (mpp) cc_final: 0.4200 (pmm) REVERT: A 1536 MET cc_start: 0.3241 (mpp) cc_final: 0.2882 (mpp) REVERT: D 157 ARG cc_start: 0.8823 (mtp85) cc_final: 0.8568 (mtp85) REVERT: D 268 THR cc_start: 0.9130 (OUTLIER) cc_final: 0.8850 (t) REVERT: D 279 MET cc_start: 0.9186 (ttm) cc_final: 0.8917 (ttp) REVERT: D 420 ARG cc_start: 0.8228 (mmm160) cc_final: 0.8020 (mmt180) REVERT: D 604 ASN cc_start: 0.8100 (m-40) cc_final: 0.7807 (m-40) REVERT: D 803 GLN cc_start: 0.7745 (mp-120) cc_final: 0.7337 (mm-40) REVERT: D 883 MET cc_start: 0.8309 (tpt) cc_final: 0.8004 (tpt) REVERT: D 985 ASN cc_start: 0.7644 (OUTLIER) cc_final: 0.7106 (m-40) REVERT: D 1017 MET cc_start: 0.7923 (ttm) cc_final: 0.7563 (ttm) outliers start: 48 outliers final: 18 residues processed: 281 average time/residue: 0.5629 time to fit residues: 183.0450 Evaluate side-chains 259 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 235 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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 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 1053 GLU Chi-restraints excluded: chain A residue 1256 VAL 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 1454 LEU Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 297 ASN 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 196 optimal weight: 0.8980 chunk 199 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 chunk 228 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 194 optimal weight: 0.5980 chunk 247 optimal weight: 0.0570 chunk 22 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.197191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.126307 restraints weight = 25314.300| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.64 r_work: 0.3101 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2098 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= 0.109 Angle : 0.565 13.756 28321 Z= 0.274 Chirality : 0.044 0.482 3234 Planarity : 0.004 0.053 3554 Dihedral : 4.748 52.131 2755 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.61 % Favored : 95.31 % Rotamer: Outliers : 1.99 % Allowed : 18.42 % Favored : 79.59 % 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: 0.09 (0.17), residues: 2472 helix: 1.11 (0.15), residues: 1234 sheet: -0.40 (0.31), residues: 286 loop : -1.16 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1029 TYR 0.008 0.001 TYR D 512 PHE 0.035 0.001 PHE A1147 TRP 0.011 0.001 TRP A1199 HIS 0.002 0.000 HIS C 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (20854) covalent geometry : angle 0.54598 / 0.27 (28253) SS BOND : bond 0.00245 / 0.11 ( 10) SS BOND : angle 1.34091 / 0.72 ( 20) hydrogen bonds : bond 0.03574 / 2.34 ( 961) hydrogen bonds : angle 4.31391 / 2.97 ( 2799) link_BETA1-4 : bond 0.00867 / 0.39 ( 9) link_BETA1-4 : angle 2.25540 / 1.58 ( 27) link_NAG-ASN : bond 0.00901 / 0.44 ( 7) link_NAG-ASN : angle 4.59377 / 3.17 ( 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 294 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 250 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 177 MET cc_start: -0.0564 (pp-130) cc_final: -0.0880 (ppp) REVERT: C 255 GLU cc_start: 0.3416 (OUTLIER) cc_final: 0.2626 (tt0) REVERT: C 343 GLU cc_start: 0.6568 (mm-30) cc_final: 0.5874 (pt0) REVERT: A 165 GLU cc_start: 0.8063 (tp30) cc_final: 0.7743 (pt0) REVERT: A 291 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8128 (tp30) REVERT: A 293 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.6400 (p90) REVERT: A 373 MET cc_start: 0.8831 (mmt) cc_final: 0.8277 (mmt) REVERT: A 402 LEU cc_start: 0.8404 (tp) cc_final: 0.8163 (mm) REVERT: A 1012 ILE cc_start: 0.8290 (mt) cc_final: 0.8077 (mt) REVERT: A 1018 ILE cc_start: 0.8276 (mm) cc_final: 0.7848 (mp) REVERT: A 1053 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8129 (mt-10) REVERT: A 1210 MET cc_start: 0.5539 (tpt) cc_final: 0.4099 (tmt) REVERT: A 1269 TRP cc_start: 0.7572 (OUTLIER) cc_final: 0.5222 (m-90) REVERT: A 1324 MET cc_start: 0.7945 (mmt) cc_final: 0.7596 (tpp) REVERT: A 1534 MET cc_start: 0.5605 (mpp) cc_final: 0.4345 (pmm) REVERT: D 268 THR cc_start: 0.9104 (OUTLIER) cc_final: 0.8812 (t) REVERT: D 279 MET cc_start: 0.9171 (ttm) cc_final: 0.8952 (tpp) REVERT: D 604 ASN cc_start: 0.8211 (m-40) cc_final: 0.7918 (m-40) REVERT: D 678 GLU cc_start: 0.8097 (pt0) cc_final: 0.6514 (mm-30) REVERT: D 803 GLN cc_start: 0.7683 (mp-120) cc_final: 0.7255 (mm-40) REVERT: D 883 MET cc_start: 0.8313 (tpt) cc_final: 0.8042 (tpt) REVERT: D 985 ASN cc_start: 0.7464 (OUTLIER) cc_final: 0.6899 (m-40) REVERT: D 1017 MET cc_start: 0.7910 (ttm) cc_final: 0.7549 (ttm) outliers start: 44 outliers final: 23 residues processed: 280 average time/residue: 0.5430 time to fit residues: 175.9286 Evaluate side-chains 261 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 231 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 268 VAL 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 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 D residue 63 LYS Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 268 THR 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 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 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: 5.9990 chunk 15 optimal weight: 20.0000 chunk 219 optimal weight: 0.0670 chunk 171 optimal weight: 1.9990 chunk 236 optimal weight: 0.9980 chunk 173 optimal weight: 0.7980 chunk 186 optimal weight: 3.9990 chunk 189 optimal weight: 0.6980 chunk 227 optimal weight: 0.8980 chunk 230 optimal weight: 0.7980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 108 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 972 GLN D1042 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.196858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.126386 restraints weight = 25349.030| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.20 r_work: 0.3152 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20880 Z= 0.107 Angle : 0.558 13.048 28321 Z= 0.271 Chirality : 0.043 0.478 3234 Planarity : 0.004 0.051 3554 Dihedral : 4.662 50.094 2755 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.45 % Favored : 95.47 % Rotamer: Outliers : 2.26 % Allowed : 18.37 % Favored : 79.37 % 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: 0.14 (0.17), residues: 2472 helix: 1.17 (0.15), residues: 1234 sheet: -0.41 (0.31), residues: 286 loop : -1.15 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1029 TYR 0.007 0.001 TYR D1068 PHE 0.027 0.001 PHE D 686 TRP 0.010 0.001 TRP D 205 HIS 0.001 0.000 HIS C 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (20854) covalent geometry : angle 0.53965 / 0.27 (28253) SS BOND : bond 0.00240 / 0.11 ( 10) SS BOND : angle 1.11229 / 0.59 ( 20) hydrogen bonds : bond 0.03463 / 2.27 ( 961) hydrogen bonds : angle 4.24855 / 2.92 ( 2799) link_BETA1-4 : bond 0.00853 / 0.38 ( 9) link_BETA1-4 : angle 2.22915 / 1.55 ( 27) link_NAG-ASN : bond 0.00812 / 0.40 ( 7) link_NAG-ASN : angle 4.58141 / 3.22 ( 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 295 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 245 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 115 ILE cc_start: 0.1604 (tt) cc_final: 0.1324 (tp) REVERT: C 177 MET cc_start: -0.0533 (pp-130) cc_final: -0.0814 (ppp) REVERT: C 255 GLU cc_start: 0.3432 (OUTLIER) cc_final: 0.2668 (tt0) REVERT: C 343 GLU cc_start: 0.6387 (mm-30) cc_final: 0.5704 (pt0) REVERT: A 165 GLU cc_start: 0.7961 (tp30) cc_final: 0.7652 (pt0) REVERT: A 261 LEU cc_start: 0.8484 (tp) cc_final: 0.8233 (tm) REVERT: A 293 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.6310 (p90) REVERT: A 373 MET cc_start: 0.8866 (mmt) cc_final: 0.8272 (mmt) REVERT: A 402 LEU cc_start: 0.8367 (tp) cc_final: 0.8115 (mm) REVERT: A 562 LEU cc_start: 0.7875 (mm) cc_final: 0.7594 (mm) REVERT: A 999 LYS cc_start: 0.7515 (ttmt) cc_final: 0.6720 (mptt) REVERT: A 1012 ILE cc_start: 0.8211 (mt) cc_final: 0.7999 (mt) REVERT: A 1018 ILE cc_start: 0.8182 (mm) cc_final: 0.7760 (mp) REVERT: A 1053 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8067 (mt-10) REVERT: A 1210 MET cc_start: 0.5275 (tpt) cc_final: 0.3897 (tmt) REVERT: A 1269 TRP cc_start: 0.7593 (OUTLIER) cc_final: 0.5248 (m-90) REVERT: A 1324 MET cc_start: 0.7963 (mmt) cc_final: 0.7596 (tpp) REVERT: A 1534 MET cc_start: 0.5570 (mpp) cc_final: 0.4346 (pmm) REVERT: D 268 THR cc_start: 0.9115 (OUTLIER) cc_final: 0.8812 (t) REVERT: D 604 ASN cc_start: 0.8196 (m-40) cc_final: 0.7888 (m-40) REVERT: D 678 GLU cc_start: 0.7997 (pt0) cc_final: 0.6393 (mm-30) REVERT: D 803 GLN cc_start: 0.7620 (mp-120) cc_final: 0.7178 (mm-40) REVERT: D 883 MET cc_start: 0.8221 (tpt) cc_final: 0.7938 (tpt) REVERT: D 985 ASN cc_start: 0.7584 (OUTLIER) cc_final: 0.7031 (m-40) REVERT: D 1017 MET cc_start: 0.7915 (ttm) cc_final: 0.7579 (ttm) outliers start: 50 outliers final: 26 residues processed: 281 average time/residue: 0.5057 time to fit residues: 166.3488 Evaluate side-chains 263 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 231 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 268 VAL 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 1008 VAL Chi-restraints excluded: chain A residue 1053 GLU Chi-restraints excluded: chain A residue 1269 TRP Chi-restraints excluded: chain A residue 1275 LEU 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 D residue 63 LYS Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 268 THR 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 806 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 47 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 176 optimal weight: 0.8980 chunk 164 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 chunk 197 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 745 ASN A 996 ASN D 885 HIS D 972 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.195557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.125598 restraints weight = 25315.017| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.24 r_work: 0.3137 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20880 Z= 0.127 Angle : 0.587 12.912 28321 Z= 0.282 Chirality : 0.044 0.490 3234 Planarity : 0.004 0.051 3554 Dihedral : 4.731 49.627 2755 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.33 % Favored : 95.59 % Rotamer: Outliers : 1.99 % Allowed : 19.10 % Favored : 78.91 % 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: 0.13 (0.17), residues: 2472 helix: 1.18 (0.15), residues: 1225 sheet: -0.40 (0.31), residues: 286 loop : -1.16 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1029 TYR 0.011 0.001 TYR D1068 PHE 0.035 0.001 PHE A1147 TRP 0.011 0.001 TRP A1199 HIS 0.004 0.000 HIS D 885 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (20854) covalent geometry : angle 0.56877 / 0.28 (28253) SS BOND : bond 0.00271 / 0.12 ( 10) SS BOND : angle 1.23251 / 0.65 ( 20) hydrogen bonds : bond 0.03586 / 2.36 ( 961) hydrogen bonds : angle 4.26558 / 2.93 ( 2799) link_BETA1-4 : bond 0.00861 / 0.38 ( 9) link_BETA1-4 : angle 2.26983 / 1.60 ( 27) link_NAG-ASN : bond 0.00781 / 0.38 ( 7) link_NAG-ASN : angle 4.58610 / 3.20 ( 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 281 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 237 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 115 ILE cc_start: 0.1740 (tt) cc_final: 0.1468 (tp) REVERT: C 177 MET cc_start: -0.0520 (pp-130) cc_final: -0.0797 (ppp) REVERT: C 255 GLU cc_start: 0.3520 (OUTLIER) cc_final: 0.2704 (tt0) REVERT: C 304 ILE cc_start: 0.4911 (OUTLIER) cc_final: 0.4634 (tt) REVERT: C 343 GLU cc_start: 0.6333 (mm-30) cc_final: 0.5511 (pt0) REVERT: A 165 GLU cc_start: 0.7842 (tp30) cc_final: 0.7625 (pt0) REVERT: A 293 PHE cc_start: 0.8845 (OUTLIER) cc_final: 0.6255 (p90) REVERT: A 373 MET cc_start: 0.8874 (mmt) cc_final: 0.8260 (mmt) REVERT: A 402 LEU cc_start: 0.8350 (tp) cc_final: 0.8100 (mm) REVERT: A 999 LYS cc_start: 0.7554 (ttmt) cc_final: 0.7318 (ttmm) REVERT: A 1012 ILE cc_start: 0.8238 (mt) cc_final: 0.8031 (mt) REVERT: A 1018 ILE cc_start: 0.8191 (mm) cc_final: 0.7754 (mp) REVERT: A 1053 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8065 (mt-10) REVERT: A 1199 TRP cc_start: 0.6191 (OUTLIER) cc_final: 0.4907 (t60) REVERT: A 1210 MET cc_start: 0.5330 (tpt) cc_final: 0.3916 (tmt) REVERT: A 1269 TRP cc_start: 0.7606 (OUTLIER) cc_final: 0.5284 (m-90) REVERT: A 1324 MET cc_start: 0.7971 (mmt) cc_final: 0.7606 (tpp) REVERT: A 1534 MET cc_start: 0.5576 (mpp) cc_final: 0.4346 (pmm) REVERT: D 604 ASN cc_start: 0.8180 (m-40) cc_final: 0.7880 (m-40) REVERT: D 678 GLU cc_start: 0.7995 (pt0) cc_final: 0.6390 (mm-30) REVERT: D 803 GLN cc_start: 0.7628 (mp-120) cc_final: 0.7176 (mm-40) REVERT: D 883 MET cc_start: 0.8185 (tpt) cc_final: 0.7901 (tpt) REVERT: D 985 ASN cc_start: 0.7603 (OUTLIER) cc_final: 0.7050 (m-40) REVERT: D 1017 MET cc_start: 0.7922 (ttm) cc_final: 0.7683 (ttm) outliers start: 44 outliers final: 28 residues processed: 269 average time/residue: 0.5274 time to fit residues: 165.2437 Evaluate side-chains 265 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 230 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 129 ASP 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 63 LYS Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 268 THR 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 798 VAL Chi-restraints excluded: chain D residue 851 VAL Chi-restraints excluded: chain D residue 985 ASN Chi-restraints excluded: chain D residue 1009 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.8912 > 50: distance: 84 - 85: 4.998 distance: 85 - 86: 8.281 distance: 85 - 88: 31.042 distance: 86 - 87: 39.289 distance: 86 - 90: 26.520 distance: 88 - 89: 14.419 distance: 90 - 91: 27.158 distance: 91 - 92: 22.177 distance: 91 - 94: 24.046 distance: 92 - 93: 23.997 distance: 92 - 99: 47.405 distance: 94 - 95: 19.026 distance: 95 - 96: 13.770 distance: 96 - 97: 4.203 distance: 96 - 98: 32.534 distance: 99 - 100: 48.376 distance: 100 - 101: 33.875 distance: 100 - 103: 40.165 distance: 101 - 102: 19.938 distance: 101 - 108: 46.564 distance: 103 - 104: 36.850 distance: 104 - 105: 52.741 distance: 105 - 106: 5.504 distance: 105 - 107: 39.069 distance: 108 - 109: 44.952 distance: 108 - 114: 41.732 distance: 110 - 111: 39.379 distance: 110 - 115: 9.462 distance: 112 - 113: 26.263 distance: 113 - 114: 42.135 distance: 115 - 116: 40.671 distance: 116 - 117: 62.279 distance: 116 - 119: 28.105 distance: 117 - 118: 40.320 distance: 117 - 122: 3.108 distance: 119 - 120: 39.252 distance: 123 - 124: 59.570 distance: 123 - 126: 22.439 distance: 124 - 125: 16.223 distance: 124 - 129: 58.250 distance: 126 - 127: 3.091 distance: 126 - 128: 24.040 distance: 130 - 131: 13.467 distance: 130 - 133: 40.146 distance: 131 - 132: 34.297 distance: 131 - 137: 24.840 distance: 134 - 135: 47.680 distance: 134 - 136: 41.677 distance: 137 - 138: 33.029 distance: 138 - 139: 32.748 distance: 138 - 141: 44.906 distance: 139 - 140: 6.108 distance: 139 - 145: 14.177 distance: 140 - 172: 29.398 distance: 141 - 142: 17.037 distance: 142 - 144: 40.044 distance: 149 - 150: 3.097 distance: 150 - 151: 19.912 distance: 150 - 152: 37.163 distance: 151 - 153: 21.339 distance: 152 - 154: 31.622 distance: 153 - 155: 32.612 distance: 154 - 155: 7.800 distance: 157 - 158: 3.942 distance: 158 - 159: 38.919 distance: 158 - 164: 33.920 distance: 160 - 161: 38.933 distance: 161 - 162: 8.200 distance: 161 - 163: 15.680