Starting phenix.real_space_refine on Fri Mar 6 09:42:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vvz_21408/03_2026/6vvz_21408.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vvz_21408/03_2026/6vvz_21408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vvz_21408/03_2026/6vvz_21408.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vvz_21408/03_2026/6vvz_21408.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vvz_21408/03_2026/6vvz_21408.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vvz_21408/03_2026/6vvz_21408.map" } resolution = 3.72 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= 0.004 sd= 0.089 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 127 5.49 5 Mg 1 5.21 5 S 99 5.16 5 C 18328 2.51 5 N 5327 2.21 5 O 5976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29860 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1716 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 210} Chain: "B" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1759 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 220} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 8577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 8577 Classifications: {'peptide': 1111} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1048} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "D" Number of atoms: 9873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1266, 9873 Classifications: {'peptide': 1266} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 59, 'TRANS': 1205} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 76} Chain: "F" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2503 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 310} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 4, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "J" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 875 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1241 Classifications: {'peptide': 159} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 153} Chain: "P" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1270 Classifications: {'DNA': 62} Link IDs: {'rna3p': 61} Chain breaks: 1 Chain: "O" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1336 Classifications: {'DNA': 65} Link IDs: {'rna3p': 64} Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 58 Unusual residues: {'SRN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19116 SG CYS D 891 112.320 87.855 105.454 1.00176.22 S ATOM 19683 SG CYS D 968 108.714 88.823 104.330 1.00159.66 S ATOM 19725 SG CYS D 975 108.987 86.684 107.379 1.00164.31 S ATOM 19743 SG CYS D 978 110.917 90.554 107.426 1.00167.96 S ATOM 12558 SG CYS D 60 56.811 64.408 74.360 1.00192.32 S ATOM 12576 SG CYS D 62 54.864 64.732 71.352 1.00187.10 S ATOM 12711 SG CYS D 78 58.795 66.927 71.695 1.00186.73 S Time building chain proxies: 5.69, per 1000 atoms: 0.19 Number of scatterers: 29860 At special positions: 0 Unit cell: (139.1, 167.7, 193.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 99 16.00 P 127 15.00 Mg 1 11.99 O 5976 8.00 N 5327 7.00 C 18328 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 968 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 975 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 978 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 78 " Number of angles added : 6 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6464 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 47 sheets defined 42.6% alpha, 14.1% beta 55 base pairs and 101 stacking pairs defined. Time for finding SS restraints: 3.69 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 removed outlier: 3.693A pdb=" N SER A 44 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 203 through 224 removed outlier: 4.072A pdb=" N LEU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 45 removed outlier: 3.690A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 203 through 224 removed outlier: 4.013A pdb=" N LEU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 3.892A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 77 removed outlier: 3.981A pdb=" N ARG C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 233 through 241 removed outlier: 4.239A pdb=" N LEU C 237 " --> pdb=" O PRO C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 250 Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 288 through 301 removed outlier: 3.612A pdb=" N THR C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU C 297 " --> pdb=" O GLN C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 380 through 407 removed outlier: 4.070A pdb=" N VAL C 399 " --> pdb=" O ARG C 395 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 444 through 452 Processing helix chain 'C' and resid 532 through 538 Processing helix chain 'C' and resid 590 through 594 Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 613 removed outlier: 4.184A pdb=" N ARG C 613 " --> pdb=" O ALA C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 638 Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 779 through 783 removed outlier: 4.285A pdb=" N ASP C 783 " --> pdb=" O VAL C 780 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 826 Processing helix chain 'C' and resid 922 through 926 Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 953 through 957 Processing helix chain 'C' and resid 981 through 991 removed outlier: 4.010A pdb=" N CYS C 991 " --> pdb=" O GLY C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1036 through 1040 Processing helix chain 'C' and resid 1069 through 1079 Processing helix chain 'C' and resid 1081 through 1090 removed outlier: 3.609A pdb=" N LEU C1085 " --> pdb=" O ALA C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1095 through 1108 removed outlier: 3.901A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS C1101 " --> pdb=" O VAL C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1131 removed outlier: 3.505A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 removed outlier: 3.533A pdb=" N SER D 24 " --> pdb=" O ILE D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 90 Processing helix chain 'D' and resid 104 through 107 Processing helix chain 'D' and resid 112 through 118 Processing helix chain 'D' and resid 121 through 129 Processing helix chain 'D' and resid 140 through 186 removed outlier: 4.929A pdb=" N ASN D 146 " --> pdb=" O GLU D 142 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N THR D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 228 Processing helix chain 'D' and resid 238 through 247 removed outlier: 3.633A pdb=" N ASP D 246 " --> pdb=" O ARG D 242 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG D 247 " --> pdb=" O GLU D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 252 removed outlier: 3.790A pdb=" N TYR D 251 " --> pdb=" O TYR D 248 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE D 252 " --> pdb=" O GLY D 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 248 through 252' Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 269 through 284 removed outlier: 3.913A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 305 removed outlier: 3.977A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 340 through 361 Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 393 through 397 removed outlier: 3.660A pdb=" N ARG D 397 " --> pdb=" O PRO D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 411 through 419 Processing helix chain 'D' and resid 445 through 452 removed outlier: 3.949A pdb=" N GLU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 482 through 492 Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 578 through 590 Processing helix chain 'D' and resid 614 through 624 Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 668 through 675 Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 727 removed outlier: 3.874A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 762 Processing helix chain 'D' and resid 766 through 793 Processing helix chain 'D' and resid 797 through 806 removed outlier: 3.835A pdb=" N VAL D 803 " --> pdb=" O ILE D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 818 removed outlier: 3.999A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 882 removed outlier: 4.157A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 917 removed outlier: 3.845A pdb=" N ILE D 916 " --> pdb=" O ASP D 913 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU D 917 " --> pdb=" O PRO D 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 913 through 917' Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 964 through 968 removed outlier: 3.796A pdb=" N CYS D 968 " --> pdb=" O VAL D 965 " (cutoff:3.500A) Processing helix chain 'D' and resid 994 through 1005 Processing helix chain 'D' and resid 1006 through 1009 Processing helix chain 'D' and resid 1027 through 1036 Processing helix chain 'D' and resid 1117 through 1145 removed outlier: 3.690A pdb=" N VAL D1121 " --> pdb=" O ASP D1117 " (cutoff:3.500A) Proline residue: D1127 - end of helix removed outlier: 3.614A pdb=" N VAL D1130 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR D1142 " --> pdb=" O VAL D1138 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1162 removed outlier: 3.875A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE D1157 " --> pdb=" O HIS D1153 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1195 removed outlier: 3.502A pdb=" N ASN D1190 " --> pdb=" O PHE D1186 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG D1191 " --> pdb=" O GLU D1187 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG D1192 " --> pdb=" O ALA D1188 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA D1195 " --> pdb=" O ARG D1191 " (cutoff:3.500A) Processing helix chain 'D' and resid 1209 through 1216 removed outlier: 3.675A pdb=" N LEU D1215 " --> pdb=" O THR D1211 " (cutoff:3.500A) Processing helix chain 'D' and resid 1219 through 1225 removed outlier: 4.040A pdb=" N SER D1225 " --> pdb=" O LEU D1221 " (cutoff:3.500A) Processing helix chain 'D' and resid 1228 through 1240 removed outlier: 4.490A pdb=" N ASP D1235 " --> pdb=" O ARG D1231 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA D1236 " --> pdb=" O VAL D1232 " (cutoff:3.500A) Processing helix chain 'D' and resid 1247 through 1254 removed outlier: 3.746A pdb=" N ASN D1251 " --> pdb=" O GLY D1247 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE D1253 " --> pdb=" O LYS D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1264 through 1269 removed outlier: 3.884A pdb=" N ASN D1269 " --> pdb=" O ASN D1265 " (cutoff:3.500A) Processing helix chain 'D' and resid 1275 through 1280 Processing helix chain 'E' and resid 33 through 37 removed outlier: 3.902A pdb=" N THR E 36 " --> pdb=" O LEU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 49 through 71 Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'F' and resid 210 through 220 Processing helix chain 'F' and resid 226 through 236 Processing helix chain 'F' and resid 242 through 266 Processing helix chain 'F' and resid 274 through 308 removed outlier: 3.622A pdb=" N ASP F 289 " --> pdb=" O CYS F 285 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ARG F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 334 Processing helix chain 'F' and resid 342 through 362 removed outlier: 3.913A pdb=" N TYR F 346 " --> pdb=" O LYS F 342 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TRP F 349 " --> pdb=" O THR F 345 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TRP F 350 " --> pdb=" O TYR F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 391 Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 406 through 418 Processing helix chain 'F' and resid 448 through 466 Processing helix chain 'F' and resid 468 through 480 Processing helix chain 'F' and resid 488 through 497 Processing helix chain 'F' and resid 499 through 515 Processing helix chain 'F' and resid 516 through 525 removed outlier: 6.446A pdb=" N VAL F 522 " --> pdb=" O SER F 518 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LEU F 523 " --> pdb=" O ARG F 519 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 87 Processing helix chain 'J' and resid 90 through 110 Processing helix chain 'M' and resid 52 through 57 Processing helix chain 'M' and resid 63 through 74 Processing helix chain 'M' and resid 84 through 99 Processing helix chain 'M' and resid 100 through 118 removed outlier: 3.840A pdb=" N GLU M 117 " --> pdb=" O ARG M 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 143 Processing helix chain 'M' and resid 146 through 156 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 9 Processing sheet with id=AA2, first strand: chain 'A' and resid 8 through 9 removed outlier: 6.182A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 100 removed outlier: 8.047A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 93 through 100 removed outlier: 3.540A pdb=" N SER A 166 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 85 through 86 removed outlier: 3.571A pdb=" N SER A 86 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 117 " --> pdb=" O SER A 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.536A pdb=" N SER B 10 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL B 22 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 93 through 100 removed outlier: 3.671A pdb=" N SER B 53 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLU B 141 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL B 51 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY B 143 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ALA B 49 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB2, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.419A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 96 through 97 removed outlier: 3.930A pdb=" N GLU C 138 " --> pdb=" O SER C 106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 110 through 112 removed outlier: 6.323A pdb=" N LEU C 133 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB6, first strand: chain 'C' and resid 376 through 379 Processing sheet with id=AB7, first strand: chain 'C' and resid 184 through 191 removed outlier: 3.945A pdb=" N LEU C 212 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 215 through 216 Processing sheet with id=AB9, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AC1, first strand: chain 'C' and resid 505 through 506 removed outlier: 6.511A pdb=" N ILE C 512 " --> pdb=" O LEU C 531 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU C 531 " --> pdb=" O ILE C 512 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N THR C 514 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL C 529 " --> pdb=" O THR C 514 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N TYR C 516 " --> pdb=" O GLU C 527 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU C 527 " --> pdb=" O TYR C 516 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LYS C 518 " --> pdb=" O SER C 525 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 505 through 506 removed outlier: 3.703A pdb=" N VAL C 541 " --> pdb=" O ARG C 562 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 642 through 644 removed outlier: 6.968A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 648 through 652 removed outlier: 6.787A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC6, first strand: chain 'C' and resid 717 through 722 removed outlier: 8.590A pdb=" N ILE C 915 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU C 720 " --> pdb=" O ILE C 915 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 751 through 760 removed outlier: 3.635A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY C 845 " --> pdb=" O VAL C 796 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC9, first strand: chain 'C' and resid 801 through 803 removed outlier: 7.009A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 906 through 907 Processing sheet with id=AD2, first strand: chain 'C' and resid 944 through 945 Processing sheet with id=AD3, first strand: chain 'C' and resid 1007 through 1008 Processing sheet with id=AD4, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 6.301A pdb=" N CYS D 441 " --> pdb=" O MET D 515 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL D 517 " --> pdb=" O CYS D 441 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N LEU D 443 " --> pdb=" O VAL D 517 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN D 523 " --> pdb=" O GLY D 442 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1066 through 1067 removed outlier: 3.820A pdb=" N GLN C1066 " --> pdb=" O VAL D 422 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AD7, first strand: chain 'D' and resid 93 through 102 removed outlier: 7.274A pdb=" N ASP D 315 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 11.878A pdb=" N ALA D 99 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N VAL D 313 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 234 through 235 Processing sheet with id=AD9, first strand: chain 'F' and resid 421 through 422 removed outlier: 3.915A pdb=" N GLN D 329 " --> pdb=" O SER J 9 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N GLU F 440 " --> pdb=" O GLY J 8 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AE2, first strand: chain 'D' and resid 886 through 888 Processing sheet with id=AE3, first strand: chain 'D' and resid 898 through 899 Processing sheet with id=AE4, first strand: chain 'D' and resid 929 through 930 removed outlier: 3.501A pdb=" N VAL D 938 " --> pdb=" O ALA D 929 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1075 through 1081 removed outlier: 5.815A pdb=" N VAL D1076 " --> pdb=" O ILE D1066 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE D1066 " --> pdb=" O VAL D1076 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ASP D1078 " --> pdb=" O ILE D1064 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ILE D1064 " --> pdb=" O ASP D1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1085 through 1086 removed outlier: 4.717A pdb=" N ARG D1085 " --> pdb=" O GLU D1113 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1179 through 1182 Processing sheet with id=AE8, first strand: chain 'D' and resid 1271 through 1274 removed outlier: 3.531A pdb=" N ALA D1271 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR E 107 " --> pdb=" O ALA D1271 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 39 through 42 Processing sheet with id=AF1, first strand: chain 'M' and resid 45 through 49 removed outlier: 5.539A pdb=" N TYR M 34 " --> pdb=" O ILE M 22 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE M 22 " --> pdb=" O TYR M 34 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL M 36 " --> pdb=" O GLU M 20 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 26 through 27 1236 hydrogen bonds defined for protein. 3486 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 142 hydrogen bonds 284 hydrogen bond angles 0 basepair planarities 55 basepair parallelities 101 stacking parallelities Total time for adding SS restraints: 7.33 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4947 1.31 - 1.43: 7936 1.43 - 1.56: 17298 1.56 - 1.68: 269 1.68 - 1.81: 178 Bond restraints: 30628 Sorted by residual: bond pdb=" C9 SRN C1201 " pdb=" O3 SRN C1201 " ideal model delta sigma weight residual 1.429 1.807 -0.378 2.00e-02 2.50e+03 3.56e+02 bond pdb=" C8 SRN C1201 " pdb=" O3 SRN C1201 " ideal model delta sigma weight residual 1.434 1.789 -0.355 2.00e-02 2.50e+03 3.15e+02 bond pdb=" C28 SRN C1201 " pdb=" C29 SRN C1201 " ideal model delta sigma weight residual 1.330 1.607 -0.277 2.00e-02 2.50e+03 1.92e+02 bond pdb=" C13 SRN C1201 " pdb=" C14 SRN C1201 " ideal model delta sigma weight residual 1.328 1.599 -0.271 2.00e-02 2.50e+03 1.84e+02 bond pdb=" C2 SRN C1201 " pdb=" C3 SRN C1201 " ideal model delta sigma weight residual 1.341 1.586 -0.245 2.00e-02 2.50e+03 1.51e+02 ... (remaining 30623 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.38: 41842 4.38 - 8.75: 175 8.75 - 13.13: 14 13.13 - 17.51: 2 17.51 - 21.88: 1 Bond angle restraints: 42034 Sorted by residual: angle pdb=" C8 SRN C1201 " pdb=" O3 SRN C1201 " pdb=" C9 SRN C1201 " ideal model delta sigma weight residual 108.56 86.68 21.88 3.00e+00 1.11e-01 5.32e+01 angle pdb=" N VAL F 448 " pdb=" CA VAL F 448 " pdb=" C VAL F 448 " ideal model delta sigma weight residual 112.96 105.98 6.98 1.00e+00 1.00e+00 4.87e+01 angle pdb=" CA ARG C 584 " pdb=" CB ARG C 584 " pdb=" CG ARG C 584 " ideal model delta sigma weight residual 114.10 125.13 -11.03 2.00e+00 2.50e-01 3.04e+01 angle pdb=" C LYS C 229 " pdb=" N ARG C 230 " pdb=" CA ARG C 230 " ideal model delta sigma weight residual 121.54 130.97 -9.43 1.91e+00 2.74e-01 2.44e+01 angle pdb=" C GLU D1059 " pdb=" N ARG D1060 " pdb=" CA ARG D1060 " ideal model delta sigma weight residual 121.54 130.65 -9.11 1.91e+00 2.74e-01 2.27e+01 ... (remaining 42029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 17197 35.46 - 70.91: 1189 70.91 - 106.37: 28 106.37 - 141.82: 3 141.82 - 177.28: 4 Dihedral angle restraints: 18421 sinusoidal: 8373 harmonic: 10048 Sorted by residual: dihedral pdb=" CA ALA D 501 " pdb=" C ALA D 501 " pdb=" N PRO D 502 " pdb=" CA PRO D 502 " ideal model delta harmonic sigma weight residual -180.00 -118.86 -61.14 0 5.00e+00 4.00e-02 1.50e+02 dihedral pdb=" CA ARG C 282 " pdb=" C ARG C 282 " pdb=" N PRO C 283 " pdb=" CA PRO C 283 " ideal model delta harmonic sigma weight residual -180.00 -124.00 -56.00 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA ARG D 578 " pdb=" C ARG D 578 " pdb=" N LEU D 579 " pdb=" CA LEU D 579 " ideal model delta harmonic sigma weight residual -180.00 -144.67 -35.33 0 5.00e+00 4.00e-02 4.99e+01 ... (remaining 18418 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3860 0.065 - 0.130: 852 0.130 - 0.195: 68 0.195 - 0.260: 9 0.260 - 0.325: 7 Chirality restraints: 4796 Sorted by residual: chirality pdb=" C35 SRN C1201 " pdb=" C34 SRN C1201 " pdb=" C8 SRN C1201 " pdb=" O8 SRN C1201 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" C12 SRN C1201 " pdb=" C10 SRN C1201 " pdb=" C13 SRN C1201 " pdb=" O8 SRN C1201 " both_signs ideal model delta sigma weight residual False 2.40 2.71 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CG LEU C 274 " pdb=" CB LEU C 274 " pdb=" CD1 LEU C 274 " pdb=" CD2 LEU C 274 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 4793 not shown) Planarity restraints: 5076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 501 " 0.068 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO D 502 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO D 502 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO D 502 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 282 " -0.055 5.00e-02 4.00e+02 8.47e-02 1.15e+01 pdb=" N PRO C 283 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO C 283 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 283 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 413 " 0.051 5.00e-02 4.00e+02 7.74e-02 9.59e+00 pdb=" N PRO C 414 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO C 414 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 414 " 0.043 5.00e-02 4.00e+02 ... (remaining 5073 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 1559 2.70 - 3.25: 28465 3.25 - 3.80: 55544 3.80 - 4.35: 62912 4.35 - 4.90: 101696 Nonbonded interactions: 250176 Sorted by model distance: nonbonded pdb=" OD1 ASP D 537 " pdb="MG MG D2002 " model vdw 2.145 2.170 nonbonded pdb=" OD2 ASP D 539 " pdb="MG MG D2002 " model vdw 2.168 2.170 nonbonded pdb=" N CYS D 62 " pdb="ZN ZN D2001 " model vdw 2.201 2.310 nonbonded pdb=" OD1 ASP D 535 " pdb="MG MG D2002 " model vdw 2.214 2.170 nonbonded pdb=" OD2 ASP D 537 " pdb="MG MG D2002 " model vdw 2.234 2.170 ... (remaining 250171 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 'A' and (resid 2 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 or (resid 186 \ and (name N or name CA or name C or name O or name CB )) or resid 187 through 2 \ 23 or (resid 224 and (name N or name CA or name C or name O or name CB )) or res \ id 225 through 226)) selection = (chain 'B' and resid 2 through 226) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.100 Set scattering table: 0.050 Process input model: 32.830 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 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 : 0.010 0.378 30635 Z= 0.479 Angle : 0.947 21.885 42040 Z= 0.512 Chirality : 0.053 0.325 4796 Planarity : 0.007 0.104 5076 Dihedral : 20.484 177.280 11957 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.14 % Favored : 92.80 % Rotamer: Outliers : 6.36 % Allowed : 25.99 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.06 % Twisted Proline : 1.14 % Twisted General : 0.06 % 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: -3.51 (0.12), residues: 3488 helix: -1.93 (0.11), residues: 1350 sheet: -2.96 (0.21), residues: 397 loop : -2.47 (0.13), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 206 TYR 0.019 0.002 TYR B 96 PHE 0.021 0.002 PHE D 811 TRP 0.017 0.003 TRP D 723 HIS 0.008 0.002 HIS D 525 Details of bonding type rmsd covalent geometry : bond 0.00989 (30628) covalent geometry : angle 0.94013 (42034) hydrogen bonds : bond 0.17060 ( 1366) hydrogen bonds : angle 7.14035 ( 3770) metal coordination : bond 0.14078 ( 7) metal coordination : angle 9.52310 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 257 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.9061 (tt0) cc_final: 0.8693 (tp30) REVERT: B 141 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8060 (tt0) REVERT: B 191 LYS cc_start: 0.9322 (ttpt) cc_final: 0.8874 (ptmm) REVERT: C 126 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8433 (t0) REVERT: C 250 GLU cc_start: 0.6393 (OUTLIER) cc_final: 0.5873 (pt0) REVERT: C 393 MET cc_start: 0.9670 (mmt) cc_final: 0.9306 (mmm) REVERT: C 396 MET cc_start: 0.9325 (pp-130) cc_final: 0.8663 (pp-130) REVERT: C 404 MET cc_start: 0.9141 (tpp) cc_final: 0.8810 (ttt) REVERT: C 429 GLU cc_start: 0.9164 (tp30) cc_final: 0.8733 (tp30) REVERT: C 456 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8024 (tt) REVERT: C 570 TYR cc_start: 0.9208 (OUTLIER) cc_final: 0.8957 (m-80) REVERT: C 584 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7515 (pmm-80) REVERT: C 593 MET cc_start: 0.8750 (mtp) cc_final: 0.8362 (mmm) REVERT: C 607 MET cc_start: 0.9034 (mtt) cc_final: 0.8578 (mtm) REVERT: C 611 MET cc_start: 0.9374 (tpp) cc_final: 0.8928 (mmp) REVERT: C 661 MET cc_start: 0.8292 (tpt) cc_final: 0.7934 (tpt) REVERT: C 757 ILE cc_start: 0.9654 (OUTLIER) cc_final: 0.9425 (tt) REVERT: C 885 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8560 (mt) REVERT: C 1094 ASP cc_start: 0.8820 (m-30) cc_final: 0.7319 (t0) REVERT: C 1104 GLU cc_start: 0.9509 (tt0) cc_final: 0.9199 (tm-30) REVERT: D 37 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8185 (mtm110) REVERT: D 244 LEU cc_start: 0.9769 (tt) cc_final: 0.9488 (mt) REVERT: D 342 ASP cc_start: 0.9396 (OUTLIER) cc_final: 0.8887 (p0) REVERT: D 373 MET cc_start: 0.8983 (mtp) cc_final: 0.8402 (mtp) REVERT: D 402 LEU cc_start: 0.9544 (OUTLIER) cc_final: 0.9332 (tt) REVERT: D 404 ASP cc_start: 0.8436 (m-30) cc_final: 0.8184 (m-30) REVERT: D 498 LEU cc_start: 0.9628 (OUTLIER) cc_final: 0.9302 (mp) REVERT: D 504 LEU cc_start: 0.9163 (mp) cc_final: 0.8500 (tp) REVERT: D 509 ILE cc_start: 0.9371 (mt) cc_final: 0.9101 (tp) REVERT: D 533 ASN cc_start: 0.9422 (t0) cc_final: 0.9124 (t0) REVERT: D 556 ARG cc_start: 0.9213 (OUTLIER) cc_final: 0.8568 (ttt-90) REVERT: D 576 MET cc_start: 0.9167 (ttp) cc_final: 0.8506 (ppp) REVERT: D 581 MET cc_start: 0.9538 (mtm) cc_final: 0.9162 (mtm) REVERT: D 582 VAL cc_start: 0.9715 (OUTLIER) cc_final: 0.9430 (m) REVERT: D 600 GLN cc_start: 0.9390 (OUTLIER) cc_final: 0.9056 (pm20) REVERT: D 676 LEU cc_start: 0.9644 (OUTLIER) cc_final: 0.9403 (mp) REVERT: D 862 ASP cc_start: 0.9099 (t70) cc_final: 0.8808 (t0) REVERT: D 865 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9167 (pp) REVERT: E 50 LYS cc_start: 0.9321 (ptpt) cc_final: 0.8942 (mtmm) REVERT: E 66 ASP cc_start: 0.9300 (m-30) cc_final: 0.9075 (p0) REVERT: E 70 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7544 (tt0) REVERT: F 325 ASN cc_start: 0.9144 (m-40) cc_final: 0.8765 (m110) REVERT: F 332 VAL cc_start: 0.9712 (OUTLIER) cc_final: 0.9510 (m) REVERT: F 377 ASN cc_start: 0.9462 (m-40) cc_final: 0.9168 (m-40) REVERT: F 438 PHE cc_start: 0.9102 (m-80) cc_final: 0.8695 (m-80) REVERT: F 459 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.8788 (tt0) REVERT: F 511 MET cc_start: 0.9569 (mmm) cc_final: 0.9106 (mmm) REVERT: F 514 LEU cc_start: 0.9764 (OUTLIER) cc_final: 0.9467 (mt) REVERT: J 60 MET cc_start: 0.8232 (ptp) cc_final: 0.7886 (ptp) REVERT: J 69 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7832 (tm) REVERT: M 55 TYR cc_start: 0.8988 (m-10) cc_final: 0.8736 (m-10) REVERT: M 65 GLU cc_start: 0.9317 (OUTLIER) cc_final: 0.8966 (pm20) REVERT: M 72 GLN cc_start: 0.9513 (tt0) cc_final: 0.9149 (tm-30) REVERT: M 115 ASP cc_start: 0.8830 (OUTLIER) cc_final: 0.8522 (t70) outliers start: 185 outliers final: 40 residues processed: 429 average time/residue: 0.1869 time to fit residues: 129.3506 Evaluate side-chains 230 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 166 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain C residue 777 SER Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 885 LEU Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 556 ARG Chi-restraints excluded: chain D residue 567 SER Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 600 GLN Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 730 THR Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1211 THR Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 459 GLN Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 514 LEU Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 83 ASP Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 65 GLU Chi-restraints excluded: chain M residue 115 ASP Chi-restraints excluded: chain M residue 121 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 4.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS A 119 HIS A 124 HIS C 81 ASN C 141 ASN C 298 ASN C 419 ASN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 612 GLN C 775 ASN C 920 HIS C 941 HIS C1034 HIS C1035 HIS ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 5 ASN D 35 ASN D 239 ASN D 307 ASN D 341 ASN D 368 ASN D 416 ASN D 505 HIS D 544 HIS D 639 GLN ** D 767 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 852 ASN D1001 GLN D1145 GLN D1190 ASN F 234 GLN F 353 GLN F 388 GLN F 425 GLN ** J 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 14 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.052080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.036175 restraints weight = 191172.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.037365 restraints weight = 95105.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.038159 restraints weight = 61198.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.038663 restraints weight = 46198.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.038960 restraints weight = 38760.859| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30635 Z= 0.144 Angle : 0.631 12.608 42040 Z= 0.332 Chirality : 0.042 0.161 4796 Planarity : 0.005 0.086 5076 Dihedral : 19.259 176.647 5426 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.09 % Allowed : 26.30 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.06 % Twisted Proline : 1.14 % Twisted General : 0.03 % 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: -1.99 (0.13), residues: 3488 helix: -0.18 (0.13), residues: 1387 sheet: -2.45 (0.23), residues: 395 loop : -2.01 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 101 TYR 0.022 0.001 TYR B 176 PHE 0.012 0.001 PHE C 430 TRP 0.011 0.001 TRP D 723 HIS 0.005 0.001 HIS C1042 Details of bonding type rmsd covalent geometry : bond 0.00309 (30628) covalent geometry : angle 0.62856 (42034) hydrogen bonds : bond 0.04304 ( 1366) hydrogen bonds : angle 5.26561 ( 3770) metal coordination : bond 0.00659 ( 7) metal coordination : angle 4.78429 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 209 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.9010 (tt0) cc_final: 0.8379 (tp30) REVERT: A 173 LYS cc_start: 0.9241 (ttmt) cc_final: 0.8559 (tttm) REVERT: B 1 MET cc_start: 0.8807 (mmm) cc_final: 0.8517 (mtp) REVERT: C 393 MET cc_start: 0.9664 (mmt) cc_final: 0.9379 (mmm) REVERT: C 396 MET cc_start: 0.9342 (pp-130) cc_final: 0.8691 (pp-130) REVERT: C 429 GLU cc_start: 0.9299 (tp30) cc_final: 0.8790 (tp30) REVERT: C 436 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9202 (mm) REVERT: C 607 MET cc_start: 0.8931 (mtt) cc_final: 0.8661 (mtp) REVERT: C 611 MET cc_start: 0.9310 (mpp) cc_final: 0.8886 (mmp) REVERT: C 661 MET cc_start: 0.8342 (tpt) cc_final: 0.7922 (tpt) REVERT: C 753 GLU cc_start: 0.7940 (tp30) cc_final: 0.7687 (tm-30) REVERT: C 885 LEU cc_start: 0.8989 (mp) cc_final: 0.8781 (mt) REVERT: C 1028 MET cc_start: 0.9144 (OUTLIER) cc_final: 0.8721 (tpp) REVERT: C 1051 MET cc_start: 0.9083 (tpt) cc_final: 0.8451 (tpp) REVERT: C 1087 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8496 (mt-10) REVERT: C 1088 LEU cc_start: 0.9588 (mt) cc_final: 0.9363 (mt) REVERT: C 1104 GLU cc_start: 0.9497 (tt0) cc_final: 0.9141 (tm-30) REVERT: D 92 MET cc_start: 0.8453 (mtp) cc_final: 0.7979 (mmm) REVERT: D 312 MET cc_start: 0.9190 (mtp) cc_final: 0.8750 (mtm) REVERT: D 329 GLN cc_start: 0.9615 (OUTLIER) cc_final: 0.9335 (pp30) REVERT: D 373 MET cc_start: 0.9005 (mtp) cc_final: 0.8285 (mpp) REVERT: D 404 ASP cc_start: 0.8638 (m-30) cc_final: 0.8384 (m-30) REVERT: D 504 LEU cc_start: 0.9147 (mp) cc_final: 0.8419 (tp) REVERT: D 520 LYS cc_start: 0.8741 (pttt) cc_final: 0.8331 (pttt) REVERT: D 533 ASN cc_start: 0.9381 (t0) cc_final: 0.9099 (t0) REVERT: D 581 MET cc_start: 0.9370 (mtm) cc_final: 0.8963 (mtm) REVERT: D 640 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8781 (mt) REVERT: D 667 THR cc_start: 0.9422 (OUTLIER) cc_final: 0.9189 (t) REVERT: D 862 ASP cc_start: 0.9001 (t70) cc_final: 0.8690 (t0) REVERT: D 865 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9074 (pp) REVERT: D 1250 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8255 (pm20) REVERT: E 35 ILE cc_start: 0.9744 (tp) cc_final: 0.9479 (mm) REVERT: E 66 ASP cc_start: 0.9299 (m-30) cc_final: 0.9009 (m-30) REVERT: E 70 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7040 (tm-30) REVERT: F 278 ARG cc_start: 0.9390 (OUTLIER) cc_final: 0.8841 (ttp-110) REVERT: F 302 LEU cc_start: 0.9865 (tp) cc_final: 0.9485 (mt) REVERT: F 315 MET cc_start: 0.7195 (mmm) cc_final: 0.6947 (mmm) REVERT: F 317 PHE cc_start: 0.8956 (t80) cc_final: 0.8624 (t80) REVERT: F 323 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8542 (mm-30) REVERT: F 325 ASN cc_start: 0.9335 (m-40) cc_final: 0.9073 (m110) REVERT: F 403 MET cc_start: 0.8995 (mmt) cc_final: 0.8769 (mmm) REVERT: F 437 ASP cc_start: 0.9293 (t0) cc_final: 0.9045 (t0) REVERT: F 438 PHE cc_start: 0.9049 (m-80) cc_final: 0.8728 (m-80) REVERT: F 511 MET cc_start: 0.9556 (mmm) cc_final: 0.9082 (mmp) REVERT: F 514 LEU cc_start: 0.9696 (OUTLIER) cc_final: 0.9471 (mt) REVERT: J 64 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8815 (tt) REVERT: M 25 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8672 (ttp80) REVERT: M 55 TYR cc_start: 0.8873 (m-10) cc_final: 0.8562 (m-10) REVERT: M 72 GLN cc_start: 0.9371 (tt0) cc_final: 0.9000 (tm-30) REVERT: M 115 ASP cc_start: 0.8741 (OUTLIER) cc_final: 0.8459 (p0) outliers start: 119 outliers final: 33 residues processed: 319 average time/residue: 0.1917 time to fit residues: 98.5154 Evaluate side-chains 221 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 174 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1028 MET Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1073 CYS Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 1060 ARG Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1250 GLU Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain F residue 278 ARG Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 514 LEU Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain M residue 25 ARG Chi-restraints excluded: chain M residue 85 TRP Chi-restraints excluded: chain M residue 115 ASP Chi-restraints excluded: chain M residue 128 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 176 optimal weight: 0.9990 chunk 332 optimal weight: 3.9990 chunk 182 optimal weight: 5.9990 chunk 119 optimal weight: 0.0050 chunk 305 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 186 optimal weight: 10.0000 chunk 222 optimal weight: 7.9990 chunk 267 optimal weight: 1.9990 chunk 341 optimal weight: 7.9990 chunk 344 optimal weight: 10.0000 overall best weight: 2.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 HIS ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 767 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1109 GLN E 100 HIS ** F 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.051526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.035705 restraints weight = 193456.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.036877 restraints weight = 95738.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.037660 restraints weight = 61601.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.038118 restraints weight = 46539.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.038464 restraints weight = 39319.396| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 30635 Z= 0.175 Angle : 0.623 12.518 42040 Z= 0.325 Chirality : 0.041 0.200 4796 Planarity : 0.005 0.082 5076 Dihedral : 19.030 176.469 5347 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 4.23 % Allowed : 26.30 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.06 % Twisted Proline : 1.14 % Twisted General : 0.03 % 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: -1.27 (0.14), residues: 3488 helix: 0.59 (0.14), residues: 1379 sheet: -2.20 (0.23), residues: 420 loop : -1.69 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 77 TYR 0.024 0.001 TYR B 32 PHE 0.017 0.001 PHE F 479 TRP 0.015 0.002 TRP M 112 HIS 0.004 0.001 HIS C1042 Details of bonding type rmsd covalent geometry : bond 0.00378 (30628) covalent geometry : angle 0.62100 (42034) hydrogen bonds : bond 0.04214 ( 1366) hydrogen bonds : angle 4.98020 ( 3770) metal coordination : bond 0.01517 ( 7) metal coordination : angle 3.88094 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 176 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.9042 (tt0) cc_final: 0.8507 (tp30) REVERT: A 173 LYS cc_start: 0.9217 (ttmt) cc_final: 0.8787 (ttpt) REVERT: B 1 MET cc_start: 0.8864 (mmm) cc_final: 0.8575 (mtm) REVERT: B 123 MET cc_start: 0.9016 (ppp) cc_final: 0.8295 (ptm) REVERT: B 176 TYR cc_start: 0.9110 (p90) cc_final: 0.8906 (p90) REVERT: C 103 MET cc_start: 0.9196 (ptt) cc_final: 0.8884 (ppp) REVERT: C 258 MET cc_start: 0.6166 (ppp) cc_final: 0.5887 (ppp) REVERT: C 393 MET cc_start: 0.9660 (mmt) cc_final: 0.9379 (mmm) REVERT: C 396 MET cc_start: 0.9323 (pp-130) cc_final: 0.8710 (pp-130) REVERT: C 429 GLU cc_start: 0.9282 (tp30) cc_final: 0.8773 (tp30) REVERT: C 586 MET cc_start: 0.9448 (ppp) cc_final: 0.8515 (ppp) REVERT: C 607 MET cc_start: 0.8880 (mtt) cc_final: 0.8601 (mtp) REVERT: C 611 MET cc_start: 0.9294 (mpp) cc_final: 0.8895 (mmp) REVERT: C 661 MET cc_start: 0.8036 (tpt) cc_final: 0.7533 (tpt) REVERT: C 754 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8517 (tm-30) REVERT: C 1028 MET cc_start: 0.9179 (ttm) cc_final: 0.8785 (tpp) REVERT: C 1051 MET cc_start: 0.8973 (tpt) cc_final: 0.8496 (tpp) REVERT: C 1087 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8560 (mt-10) REVERT: C 1088 LEU cc_start: 0.9579 (mt) cc_final: 0.9344 (mt) REVERT: C 1104 GLU cc_start: 0.9500 (tt0) cc_final: 0.9168 (tm-30) REVERT: D 238 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7449 (tm-30) REVERT: D 329 GLN cc_start: 0.9593 (OUTLIER) cc_final: 0.9341 (pp30) REVERT: D 342 ASP cc_start: 0.9379 (m-30) cc_final: 0.8790 (p0) REVERT: D 373 MET cc_start: 0.8954 (mtp) cc_final: 0.8311 (mtp) REVERT: D 404 ASP cc_start: 0.8602 (m-30) cc_final: 0.8342 (m-30) REVERT: D 504 LEU cc_start: 0.9166 (mp) cc_final: 0.8455 (tp) REVERT: D 520 LYS cc_start: 0.8812 (pttt) cc_final: 0.8425 (pttt) REVERT: D 524 LEU cc_start: 0.9240 (tp) cc_final: 0.9005 (tt) REVERT: D 533 ASN cc_start: 0.9367 (t0) cc_final: 0.9093 (t0) REVERT: D 581 MET cc_start: 0.9385 (mtm) cc_final: 0.8973 (mtm) REVERT: D 667 THR cc_start: 0.9403 (OUTLIER) cc_final: 0.9124 (t) REVERT: D 820 MET cc_start: 0.8232 (tpp) cc_final: 0.7991 (tpp) REVERT: D 862 ASP cc_start: 0.8992 (t70) cc_final: 0.8712 (t0) REVERT: D 865 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9059 (pp) REVERT: D 879 ASP cc_start: 0.8650 (OUTLIER) cc_final: 0.7771 (t0) REVERT: D 983 MET cc_start: 0.8377 (mmm) cc_final: 0.7998 (tpp) REVERT: D 1250 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8126 (pm20) REVERT: E 35 ILE cc_start: 0.9728 (tp) cc_final: 0.9504 (mm) REVERT: E 66 ASP cc_start: 0.9294 (m-30) cc_final: 0.8978 (m-30) REVERT: F 278 ARG cc_start: 0.9318 (OUTLIER) cc_final: 0.8750 (ttp-110) REVERT: F 317 PHE cc_start: 0.8965 (t80) cc_final: 0.8582 (t80) REVERT: F 325 ASN cc_start: 0.9501 (m-40) cc_final: 0.9138 (m110) REVERT: F 438 PHE cc_start: 0.9061 (m-80) cc_final: 0.8818 (m-80) REVERT: F 511 MET cc_start: 0.9549 (mmm) cc_final: 0.9053 (mmp) REVERT: J 64 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8779 (tt) REVERT: M 55 TYR cc_start: 0.8838 (m-10) cc_final: 0.8520 (m-10) REVERT: M 72 GLN cc_start: 0.9391 (tt0) cc_final: 0.9066 (tm-30) REVERT: M 115 ASP cc_start: 0.8877 (OUTLIER) cc_final: 0.8513 (p0) outliers start: 123 outliers final: 62 residues processed: 285 average time/residue: 0.1949 time to fit residues: 89.5204 Evaluate side-chains 235 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 162 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1073 CYS Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1093 SER Chi-restraints excluded: chain C residue 1097 VAL Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 663 MET Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 879 ASP Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 1060 ARG Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1133 HIS Chi-restraints excluded: chain D residue 1165 VAL Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1250 GLU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain F residue 278 ARG Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 85 TRP Chi-restraints excluded: chain M residue 115 ASP Chi-restraints excluded: chain M residue 128 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 244 optimal weight: 0.9980 chunk 283 optimal weight: 0.0010 chunk 232 optimal weight: 8.9990 chunk 251 optimal weight: 9.9990 chunk 141 optimal weight: 8.9990 chunk 332 optimal weight: 0.7980 chunk 260 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 298 optimal weight: 10.0000 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 930 GLN ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN D 852 ASN D1084 GLN E 69 ASN F 388 GLN J 28 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.052557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.036792 restraints weight = 189743.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.037991 restraints weight = 93614.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.038787 restraints weight = 60021.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.039302 restraints weight = 45242.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.039630 restraints weight = 37829.673| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2937 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30635 Z= 0.124 Angle : 0.582 10.344 42040 Z= 0.302 Chirality : 0.041 0.214 4796 Planarity : 0.004 0.072 5076 Dihedral : 18.723 175.176 5337 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.71 % Allowed : 26.68 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.06 % Twisted Proline : 1.14 % 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: -0.82 (0.14), residues: 3488 helix: 0.97 (0.14), residues: 1388 sheet: -1.72 (0.24), residues: 409 loop : -1.54 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 500 TYR 0.022 0.001 TYR M 89 PHE 0.015 0.001 PHE D1226 TRP 0.014 0.001 TRP M 112 HIS 0.004 0.001 HIS C1042 Details of bonding type rmsd covalent geometry : bond 0.00270 (30628) covalent geometry : angle 0.58061 (42034) hydrogen bonds : bond 0.03681 ( 1366) hydrogen bonds : angle 4.71760 ( 3770) metal coordination : bond 0.00301 ( 7) metal coordination : angle 2.79963 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 188 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.9002 (tt0) cc_final: 0.8440 (tp30) REVERT: C 127 MET cc_start: 0.8683 (ptp) cc_final: 0.7965 (pmm) REVERT: C 258 MET cc_start: 0.6190 (ppp) cc_final: 0.5933 (ppp) REVERT: C 393 MET cc_start: 0.9673 (mmt) cc_final: 0.9391 (mmm) REVERT: C 396 MET cc_start: 0.9343 (pp-130) cc_final: 0.8727 (pp-130) REVERT: C 429 GLU cc_start: 0.9253 (tp30) cc_final: 0.8796 (tp30) REVERT: C 586 MET cc_start: 0.9420 (ppp) cc_final: 0.8291 (ppp) REVERT: C 593 MET cc_start: 0.9084 (mmm) cc_final: 0.8833 (mmp) REVERT: C 607 MET cc_start: 0.8842 (mtt) cc_final: 0.8390 (mtp) REVERT: C 611 MET cc_start: 0.9217 (mpp) cc_final: 0.8791 (mmp) REVERT: C 661 MET cc_start: 0.8115 (tpt) cc_final: 0.7754 (tpt) REVERT: C 753 GLU cc_start: 0.8210 (tp30) cc_final: 0.7970 (tp30) REVERT: C 1028 MET cc_start: 0.9001 (ttm) cc_final: 0.8640 (tpp) REVERT: C 1051 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8437 (tpp) REVERT: C 1074 TRP cc_start: 0.9046 (m-10) cc_final: 0.7790 (m-90) REVERT: C 1088 LEU cc_start: 0.9618 (mt) cc_final: 0.9354 (mt) REVERT: C 1104 GLU cc_start: 0.9493 (tt0) cc_final: 0.9160 (tm-30) REVERT: D 238 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7474 (tm-30) REVERT: D 256 MET cc_start: 0.7803 (ttm) cc_final: 0.7329 (ttm) REVERT: D 312 MET cc_start: 0.9193 (mtp) cc_final: 0.8717 (mtm) REVERT: D 342 ASP cc_start: 0.9363 (m-30) cc_final: 0.8768 (p0) REVERT: D 373 MET cc_start: 0.9060 (mtp) cc_final: 0.8567 (mtp) REVERT: D 404 ASP cc_start: 0.8631 (m-30) cc_final: 0.8419 (m-30) REVERT: D 504 LEU cc_start: 0.9123 (mp) cc_final: 0.8435 (tp) REVERT: D 520 LYS cc_start: 0.8861 (pttt) cc_final: 0.8376 (pttt) REVERT: D 533 ASN cc_start: 0.9303 (t0) cc_final: 0.9021 (t0) REVERT: D 581 MET cc_start: 0.9398 (mtm) cc_final: 0.9018 (mtm) REVERT: D 640 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8792 (mt) REVERT: D 820 MET cc_start: 0.8006 (tpp) cc_final: 0.7771 (tpp) REVERT: D 849 TYR cc_start: 0.8355 (t80) cc_final: 0.8112 (t80) REVERT: D 865 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9024 (pp) REVERT: D 879 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8227 (t70) REVERT: D 943 ASP cc_start: 0.8856 (OUTLIER) cc_final: 0.8384 (t70) REVERT: D 983 MET cc_start: 0.8476 (mmm) cc_final: 0.8105 (tpp) REVERT: D 1250 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8173 (pm20) REVERT: E 35 ILE cc_start: 0.9716 (tp) cc_final: 0.9504 (mm) REVERT: E 66 ASP cc_start: 0.9272 (m-30) cc_final: 0.9018 (t0) REVERT: F 302 LEU cc_start: 0.9818 (tp) cc_final: 0.9412 (mt) REVERT: F 317 PHE cc_start: 0.8889 (t80) cc_final: 0.8449 (t80) REVERT: F 325 ASN cc_start: 0.9446 (m-40) cc_final: 0.8940 (m110) REVERT: F 437 ASP cc_start: 0.9243 (t0) cc_final: 0.8992 (t0) REVERT: F 438 PHE cc_start: 0.9068 (m-80) cc_final: 0.8823 (m-80) REVERT: F 511 MET cc_start: 0.9546 (mmm) cc_final: 0.8991 (mmp) REVERT: J 64 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8762 (tt) REVERT: M 55 TYR cc_start: 0.8820 (m-10) cc_final: 0.8556 (m-10) REVERT: M 115 ASP cc_start: 0.8947 (OUTLIER) cc_final: 0.8499 (p0) REVERT: M 133 GLN cc_start: 0.9420 (tp-100) cc_final: 0.9152 (tm-30) outliers start: 108 outliers final: 56 residues processed: 286 average time/residue: 0.1907 time to fit residues: 88.8633 Evaluate side-chains 228 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 163 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain C residue 1091 ILE Chi-restraints excluded: chain C residue 1093 SER Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 663 MET Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 879 ASP Chi-restraints excluded: chain D residue 943 ASP Chi-restraints excluded: chain D residue 1060 ARG Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1133 HIS Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1250 GLU Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain F residue 278 ARG Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 85 TRP Chi-restraints excluded: chain M residue 115 ASP Chi-restraints excluded: chain M residue 128 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 342 optimal weight: 9.9990 chunk 6 optimal weight: 0.8980 chunk 316 optimal weight: 10.0000 chunk 169 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 310 optimal weight: 2.9990 chunk 338 optimal weight: 0.0070 chunk 62 optimal weight: 9.9990 chunk 275 optimal weight: 9.9990 chunk 312 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 overall best weight: 2.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 ASN ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 72 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.051452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.035608 restraints weight = 193627.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.036769 restraints weight = 96184.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.037544 restraints weight = 62065.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.038037 restraints weight = 46955.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.038314 restraints weight = 39449.204| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 30635 Z= 0.183 Angle : 0.612 9.646 42040 Z= 0.317 Chirality : 0.041 0.170 4796 Planarity : 0.004 0.069 5076 Dihedral : 18.680 175.839 5337 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.16 % Allowed : 26.71 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.06 % Twisted Proline : 1.14 % 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: -0.65 (0.14), residues: 3488 helix: 1.13 (0.14), residues: 1381 sheet: -1.66 (0.25), residues: 406 loop : -1.45 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 500 TYR 0.027 0.001 TYR B 176 PHE 0.014 0.001 PHE C 300 TRP 0.029 0.002 TRP C 211 HIS 0.004 0.001 HIS C 200 Details of bonding type rmsd covalent geometry : bond 0.00398 (30628) covalent geometry : angle 0.61102 (42034) hydrogen bonds : bond 0.03943 ( 1366) hydrogen bonds : angle 4.75738 ( 3770) metal coordination : bond 0.00596 ( 7) metal coordination : angle 3.06350 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 158 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.9005 (tt0) cc_final: 0.8455 (tp30) REVERT: B 1 MET cc_start: 0.8514 (mtm) cc_final: 0.8050 (mtm) REVERT: B 141 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8159 (tt0) REVERT: C 103 MET cc_start: 0.9220 (pmm) cc_final: 0.8602 (pmm) REVERT: C 127 MET cc_start: 0.8716 (ptp) cc_final: 0.8000 (pmm) REVERT: C 211 TRP cc_start: 0.8641 (m-10) cc_final: 0.8291 (m100) REVERT: C 393 MET cc_start: 0.9650 (mmt) cc_final: 0.9339 (mmm) REVERT: C 396 MET cc_start: 0.9322 (pp-130) cc_final: 0.8656 (pp-130) REVERT: C 429 GLU cc_start: 0.9280 (tp30) cc_final: 0.8794 (tp30) REVERT: C 440 MET cc_start: 0.8349 (tpp) cc_final: 0.7969 (ttt) REVERT: C 586 MET cc_start: 0.9457 (ppp) cc_final: 0.8196 (ppp) REVERT: C 593 MET cc_start: 0.9234 (mmm) cc_final: 0.8736 (mmm) REVERT: C 607 MET cc_start: 0.8829 (mtt) cc_final: 0.8564 (mtp) REVERT: C 611 MET cc_start: 0.9218 (mpp) cc_final: 0.8830 (mmp) REVERT: C 661 MET cc_start: 0.7880 (tpt) cc_final: 0.7501 (tpt) REVERT: C 753 GLU cc_start: 0.8269 (tp30) cc_final: 0.8026 (tp30) REVERT: C 754 GLU cc_start: 0.9086 (OUTLIER) cc_final: 0.8311 (tm-30) REVERT: C 926 MET cc_start: 0.8806 (tpp) cc_final: 0.7489 (tpp) REVERT: C 1028 MET cc_start: 0.9101 (ttm) cc_final: 0.8732 (tpp) REVERT: C 1051 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8409 (tpp) REVERT: C 1104 GLU cc_start: 0.9502 (tt0) cc_final: 0.9192 (tm-30) REVERT: D 92 MET cc_start: 0.9095 (mtp) cc_final: 0.8124 (mmm) REVERT: D 155 MET cc_start: 0.5731 (tpt) cc_final: 0.5491 (tpt) REVERT: D 213 GLN cc_start: 0.9219 (tp-100) cc_final: 0.9001 (tp-100) REVERT: D 238 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7350 (tm-30) REVERT: D 312 MET cc_start: 0.9230 (mtp) cc_final: 0.8795 (mtm) REVERT: D 373 MET cc_start: 0.8978 (mtp) cc_final: 0.8494 (mtp) REVERT: D 404 ASP cc_start: 0.8591 (m-30) cc_final: 0.8322 (m-30) REVERT: D 515 MET cc_start: 0.8211 (mtm) cc_final: 0.7837 (mtm) REVERT: D 520 LYS cc_start: 0.8867 (pttt) cc_final: 0.8354 (pttt) REVERT: D 533 ASN cc_start: 0.9327 (t0) cc_final: 0.9057 (t0) REVERT: D 576 MET cc_start: 0.8710 (mtp) cc_final: 0.8437 (mtp) REVERT: D 581 MET cc_start: 0.9395 (mtm) cc_final: 0.8985 (mtm) REVERT: D 640 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8821 (mt) REVERT: D 667 THR cc_start: 0.9452 (OUTLIER) cc_final: 0.9244 (t) REVERT: D 820 MET cc_start: 0.8193 (tpp) cc_final: 0.7890 (tpp) REVERT: D 865 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9046 (pp) REVERT: D 879 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.8076 (t0) REVERT: D 943 ASP cc_start: 0.8896 (OUTLIER) cc_final: 0.8419 (t70) REVERT: D 983 MET cc_start: 0.8516 (mmm) cc_final: 0.8153 (tpp) REVERT: D 1250 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8006 (pm20) REVERT: E 35 ILE cc_start: 0.9713 (tp) cc_final: 0.9495 (mm) REVERT: E 66 ASP cc_start: 0.9281 (m-30) cc_final: 0.8991 (m-30) REVERT: F 278 ARG cc_start: 0.9309 (OUTLIER) cc_final: 0.8735 (ttp-110) REVERT: F 281 MET cc_start: 0.9186 (ttt) cc_final: 0.8864 (ptm) REVERT: F 282 MET cc_start: 0.9202 (mmm) cc_final: 0.8937 (mmm) REVERT: F 302 LEU cc_start: 0.9832 (tp) cc_final: 0.9397 (mt) REVERT: F 325 ASN cc_start: 0.9501 (m-40) cc_final: 0.9026 (m110) REVERT: F 403 MET cc_start: 0.8939 (mmt) cc_final: 0.8716 (mmp) REVERT: F 437 ASP cc_start: 0.9261 (t0) cc_final: 0.9023 (t0) REVERT: F 438 PHE cc_start: 0.9069 (m-80) cc_final: 0.8805 (m-80) REVERT: F 511 MET cc_start: 0.9547 (mmm) cc_final: 0.9022 (mmp) REVERT: J 6 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8495 (pp) REVERT: J 64 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8822 (tt) REVERT: M 55 TYR cc_start: 0.8839 (m-10) cc_final: 0.8566 (m-10) REVERT: M 115 ASP cc_start: 0.8969 (OUTLIER) cc_final: 0.8493 (p0) outliers start: 121 outliers final: 81 residues processed: 268 average time/residue: 0.1886 time to fit residues: 82.2022 Evaluate side-chains 249 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 154 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 841 HIS Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1093 SER Chi-restraints excluded: chain C residue 1097 VAL Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 474 ARG Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 663 MET Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 879 ASP Chi-restraints excluded: chain D residue 943 ASP Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1133 HIS Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1210 ILE Chi-restraints excluded: chain D residue 1250 GLU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 278 ARG Chi-restraints excluded: chain F residue 323 GLU Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain J residue 106 ARG Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 72 GLN Chi-restraints excluded: chain M residue 85 TRP Chi-restraints excluded: chain M residue 115 ASP Chi-restraints excluded: chain M residue 128 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 155 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 265 optimal weight: 8.9990 chunk 204 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 293 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 288 optimal weight: 9.9990 chunk 168 optimal weight: 6.9990 chunk 290 optimal weight: 30.0000 chunk 321 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN D 852 ASN ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.051198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.035402 restraints weight = 193329.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.036558 restraints weight = 96360.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.037311 restraints weight = 62181.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.037812 restraints weight = 47125.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.038122 restraints weight = 39592.188| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2884 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 30635 Z= 0.198 Angle : 0.626 10.605 42040 Z= 0.321 Chirality : 0.041 0.222 4796 Planarity : 0.004 0.067 5076 Dihedral : 18.656 175.899 5337 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.71 % Allowed : 26.40 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.06 % Twisted Proline : 1.14 % 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: -0.50 (0.14), residues: 3488 helix: 1.23 (0.14), residues: 1383 sheet: -1.60 (0.25), residues: 395 loop : -1.34 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 500 TYR 0.018 0.001 TYR B 176 PHE 0.015 0.001 PHE C 300 TRP 0.015 0.001 TRP M 112 HIS 0.004 0.001 HIS C 200 Details of bonding type rmsd covalent geometry : bond 0.00427 (30628) covalent geometry : angle 0.62522 (42034) hydrogen bonds : bond 0.03966 ( 1366) hydrogen bonds : angle 4.76897 ( 3770) metal coordination : bond 0.00659 ( 7) metal coordination : angle 3.11974 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 156 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8992 (tt0) cc_final: 0.8462 (tp30) REVERT: B 1 MET cc_start: 0.8627 (mtm) cc_final: 0.8232 (mtm) REVERT: B 141 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8110 (tt0) REVERT: C 103 MET cc_start: 0.9254 (pmm) cc_final: 0.8531 (pmm) REVERT: C 127 MET cc_start: 0.8739 (ptp) cc_final: 0.8495 (ptp) REVERT: C 211 TRP cc_start: 0.8601 (m-10) cc_final: 0.8331 (m100) REVERT: C 393 MET cc_start: 0.9642 (mmt) cc_final: 0.9330 (mmm) REVERT: C 396 MET cc_start: 0.9313 (pp-130) cc_final: 0.8622 (pp-130) REVERT: C 429 GLU cc_start: 0.9265 (tp30) cc_final: 0.8780 (tp30) REVERT: C 440 MET cc_start: 0.8494 (tpp) cc_final: 0.7701 (ttt) REVERT: C 586 MET cc_start: 0.9469 (ppp) cc_final: 0.8225 (ppp) REVERT: C 593 MET cc_start: 0.9159 (mmm) cc_final: 0.8665 (mmm) REVERT: C 607 MET cc_start: 0.8874 (mtt) cc_final: 0.8565 (mtp) REVERT: C 611 MET cc_start: 0.9211 (mpp) cc_final: 0.8856 (mmp) REVERT: C 661 MET cc_start: 0.7878 (tpt) cc_final: 0.7469 (tpt) REVERT: C 753 GLU cc_start: 0.8293 (tp30) cc_final: 0.8048 (tp30) REVERT: C 754 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8289 (tm-30) REVERT: C 926 MET cc_start: 0.8883 (tpp) cc_final: 0.7923 (tpp) REVERT: C 1028 MET cc_start: 0.9112 (ttm) cc_final: 0.8863 (tpp) REVERT: C 1051 MET cc_start: 0.8904 (tpt) cc_final: 0.8410 (tpp) REVERT: C 1071 MET cc_start: 0.9534 (mmm) cc_final: 0.9050 (mmm) REVERT: C 1074 TRP cc_start: 0.9231 (m-10) cc_final: 0.8111 (m-90) REVERT: C 1087 GLU cc_start: 0.9022 (OUTLIER) cc_final: 0.8623 (mt-10) REVERT: C 1104 GLU cc_start: 0.9494 (tt0) cc_final: 0.9194 (tm-30) REVERT: D 213 GLN cc_start: 0.9213 (tp-100) cc_final: 0.8978 (tp-100) REVERT: D 238 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7324 (tm-30) REVERT: D 312 MET cc_start: 0.9098 (mtp) cc_final: 0.8685 (mtm) REVERT: D 373 MET cc_start: 0.8968 (mtp) cc_final: 0.8493 (mtp) REVERT: D 404 ASP cc_start: 0.8620 (m-30) cc_final: 0.8415 (m-30) REVERT: D 462 ASP cc_start: 0.9364 (OUTLIER) cc_final: 0.8896 (m-30) REVERT: D 515 MET cc_start: 0.8278 (mtm) cc_final: 0.7763 (mtm) REVERT: D 520 LYS cc_start: 0.8834 (pttt) cc_final: 0.8282 (pttt) REVERT: D 533 ASN cc_start: 0.9324 (t0) cc_final: 0.9062 (t0) REVERT: D 576 MET cc_start: 0.8757 (mtp) cc_final: 0.8545 (mtp) REVERT: D 581 MET cc_start: 0.9396 (mtm) cc_final: 0.8996 (mtm) REVERT: D 640 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8840 (mt) REVERT: D 667 THR cc_start: 0.9470 (OUTLIER) cc_final: 0.9169 (t) REVERT: D 820 MET cc_start: 0.8231 (tpp) cc_final: 0.7985 (tpp) REVERT: D 865 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9045 (pp) REVERT: D 879 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7828 (t0) REVERT: D 943 ASP cc_start: 0.8911 (OUTLIER) cc_final: 0.8391 (t70) REVERT: D 983 MET cc_start: 0.8533 (mmm) cc_final: 0.8235 (tpp) REVERT: D 1250 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7985 (pm20) REVERT: E 35 ILE cc_start: 0.9724 (tp) cc_final: 0.9517 (mm) REVERT: E 66 ASP cc_start: 0.9270 (m-30) cc_final: 0.8980 (m-30) REVERT: F 325 ASN cc_start: 0.9513 (m-40) cc_final: 0.9035 (m110) REVERT: F 403 MET cc_start: 0.8942 (mmt) cc_final: 0.8703 (mmp) REVERT: F 438 PHE cc_start: 0.9083 (m-80) cc_final: 0.8861 (m-80) REVERT: F 509 LYS cc_start: 0.9433 (OUTLIER) cc_final: 0.9173 (tppt) REVERT: F 511 MET cc_start: 0.9566 (mmm) cc_final: 0.9039 (mmp) REVERT: J 6 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8556 (pp) REVERT: J 64 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8777 (tt) REVERT: J 69 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7791 (tm) REVERT: M 55 TYR cc_start: 0.8907 (m-10) cc_final: 0.8621 (m-10) REVERT: M 115 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.8373 (p0) REVERT: M 133 GLN cc_start: 0.9465 (tp-100) cc_final: 0.9206 (tm-30) outliers start: 137 outliers final: 92 residues processed: 283 average time/residue: 0.1968 time to fit residues: 90.5833 Evaluate side-chains 260 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 152 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1009 MET Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1093 SER Chi-restraints excluded: chain C residue 1097 VAL Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain D residue 474 ARG Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 656 TRP Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 732 SER Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 748 HIS Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 879 ASP Chi-restraints excluded: chain D residue 943 ASP Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 1055 LEU Chi-restraints excluded: chain D residue 1060 ARG Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1133 HIS Chi-restraints excluded: chain D residue 1165 VAL Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1210 ILE Chi-restraints excluded: chain D residue 1250 GLU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 278 ARG Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 323 GLU Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 509 LYS Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain J residue 106 ARG Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 85 TRP Chi-restraints excluded: chain M residue 115 ASP Chi-restraints excluded: chain M residue 128 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 47 optimal weight: 0.0970 chunk 212 optimal weight: 0.9990 chunk 184 optimal weight: 5.9990 chunk 205 optimal weight: 0.0770 chunk 351 optimal weight: 10.0000 chunk 209 optimal weight: 0.0570 chunk 319 optimal weight: 7.9990 chunk 321 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 293 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 overall best weight: 0.8458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 841 HIS ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 GLN ** D 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 72 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.052944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.037220 restraints weight = 190492.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.038404 restraints weight = 94084.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.039201 restraints weight = 60591.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.039712 restraints weight = 45590.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.040006 restraints weight = 38198.994| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30635 Z= 0.116 Angle : 0.589 14.495 42040 Z= 0.298 Chirality : 0.041 0.205 4796 Planarity : 0.004 0.068 5076 Dihedral : 18.508 177.136 5337 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.44 % Allowed : 27.54 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.06 % Twisted Proline : 1.14 % 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: -0.32 (0.14), residues: 3488 helix: 1.40 (0.14), residues: 1391 sheet: -1.45 (0.26), residues: 393 loop : -1.29 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1087 TYR 0.019 0.001 TYR B 176 PHE 0.014 0.001 PHE C 99 TRP 0.011 0.001 TRP D 656 HIS 0.004 0.001 HIS D 525 Details of bonding type rmsd covalent geometry : bond 0.00253 (30628) covalent geometry : angle 0.58904 (42034) hydrogen bonds : bond 0.03435 ( 1366) hydrogen bonds : angle 4.54873 ( 3770) metal coordination : bond 0.00166 ( 7) metal coordination : angle 2.01663 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 183 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8637 (mtm) cc_final: 0.8287 (mtm) REVERT: C 103 MET cc_start: 0.9152 (pmm) cc_final: 0.8631 (pmm) REVERT: C 127 MET cc_start: 0.8726 (ptp) cc_final: 0.8482 (ptp) REVERT: C 211 TRP cc_start: 0.8451 (m-10) cc_final: 0.8185 (m100) REVERT: C 357 VAL cc_start: 0.4834 (OUTLIER) cc_final: 0.4470 (t) REVERT: C 393 MET cc_start: 0.9642 (mmt) cc_final: 0.9187 (mmm) REVERT: C 396 MET cc_start: 0.9305 (pp-130) cc_final: 0.8410 (pp-130) REVERT: C 429 GLU cc_start: 0.9263 (tp30) cc_final: 0.8780 (tp30) REVERT: C 584 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7968 (ptp90) REVERT: C 586 MET cc_start: 0.9379 (ppp) cc_final: 0.7758 (ppp) REVERT: C 593 MET cc_start: 0.9241 (mmm) cc_final: 0.8607 (mmp) REVERT: C 607 MET cc_start: 0.8830 (mtt) cc_final: 0.8545 (mtp) REVERT: C 611 MET cc_start: 0.9125 (mpp) cc_final: 0.8804 (mmp) REVERT: C 702 ILE cc_start: 0.8946 (tt) cc_final: 0.8574 (mm) REVERT: C 713 MET cc_start: 0.8999 (tpp) cc_final: 0.8789 (tpp) REVERT: C 753 GLU cc_start: 0.8246 (tp30) cc_final: 0.7981 (tp30) REVERT: C 754 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.8389 (tm-30) REVERT: C 926 MET cc_start: 0.8899 (tpp) cc_final: 0.8055 (tpp) REVERT: C 1028 MET cc_start: 0.8967 (ttm) cc_final: 0.8647 (tpp) REVERT: C 1104 GLU cc_start: 0.9489 (tt0) cc_final: 0.9188 (tm-30) REVERT: D 30 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8592 (mmmm) REVERT: D 86 LYS cc_start: 0.9329 (tppt) cc_final: 0.9097 (tppt) REVERT: D 92 MET cc_start: 0.8974 (mtp) cc_final: 0.8073 (mmm) REVERT: D 213 GLN cc_start: 0.9155 (tp-100) cc_final: 0.8910 (tp-100) REVERT: D 238 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7237 (tm-30) REVERT: D 312 MET cc_start: 0.9146 (mtp) cc_final: 0.8745 (mtm) REVERT: D 342 ASP cc_start: 0.9346 (m-30) cc_final: 0.8802 (p0) REVERT: D 373 MET cc_start: 0.9012 (mtp) cc_final: 0.8490 (mtp) REVERT: D 404 ASP cc_start: 0.8655 (m-30) cc_final: 0.8434 (m-30) REVERT: D 515 MET cc_start: 0.8397 (mtm) cc_final: 0.7832 (mtm) REVERT: D 520 LYS cc_start: 0.8873 (pttt) cc_final: 0.8382 (pttt) REVERT: D 533 ASN cc_start: 0.9313 (t0) cc_final: 0.9028 (t0) REVERT: D 576 MET cc_start: 0.8650 (mtp) cc_final: 0.8440 (mtp) REVERT: D 581 MET cc_start: 0.9352 (mtm) cc_final: 0.9048 (mtm) REVERT: D 640 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8715 (mt) REVERT: D 849 TYR cc_start: 0.8288 (t80) cc_final: 0.8032 (t80) REVERT: D 865 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9006 (pp) REVERT: D 879 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7816 (t70) REVERT: D 943 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.8411 (t70) REVERT: D 983 MET cc_start: 0.8517 (mmm) cc_final: 0.8311 (tpp) REVERT: D 993 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7513 (mp0) REVERT: D 1250 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8318 (pm20) REVERT: E 66 ASP cc_start: 0.9220 (m-30) cc_final: 0.8916 (m-30) REVERT: E 68 TYR cc_start: 0.9345 (OUTLIER) cc_final: 0.8809 (m-10) REVERT: F 325 ASN cc_start: 0.9481 (m-40) cc_final: 0.9004 (m110) REVERT: F 403 MET cc_start: 0.8952 (mmt) cc_final: 0.8713 (mmp) REVERT: F 437 ASP cc_start: 0.9222 (t0) cc_final: 0.8989 (t0) REVERT: F 438 PHE cc_start: 0.9022 (m-80) cc_final: 0.8748 (m-80) REVERT: F 511 MET cc_start: 0.9515 (mmm) cc_final: 0.8996 (mmp) REVERT: J 64 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8581 (tt) REVERT: J 69 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7780 (tm) REVERT: M 115 ASP cc_start: 0.9044 (OUTLIER) cc_final: 0.8582 (p0) REVERT: M 133 GLN cc_start: 0.9437 (tp-100) cc_final: 0.9167 (tm-30) REVERT: M 144 SER cc_start: 0.9231 (m) cc_final: 0.8859 (p) outliers start: 100 outliers final: 63 residues processed: 274 average time/residue: 0.1837 time to fit residues: 80.6967 Evaluate side-chains 244 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 167 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 1009 MET Chi-restraints excluded: chain C residue 1093 SER Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 656 TRP Chi-restraints excluded: chain D residue 748 HIS Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 879 ASP Chi-restraints excluded: chain D residue 943 ASP Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 1060 ARG Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1133 HIS Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1210 ILE Chi-restraints excluded: chain D residue 1250 GLU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 278 ARG Chi-restraints excluded: chain F residue 323 GLU Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 72 GLN Chi-restraints excluded: chain M residue 85 TRP Chi-restraints excluded: chain M residue 115 ASP Chi-restraints excluded: chain M residue 128 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 171 optimal weight: 9.9990 chunk 261 optimal weight: 20.0000 chunk 99 optimal weight: 4.9990 chunk 216 optimal weight: 0.0980 chunk 165 optimal weight: 10.0000 chunk 132 optimal weight: 0.8980 chunk 104 optimal weight: 9.9990 chunk 191 optimal weight: 0.9990 chunk 131 optimal weight: 0.5980 chunk 220 optimal weight: 4.9990 chunk 233 optimal weight: 10.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 841 HIS ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1084 GLN ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.052429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.036665 restraints weight = 191288.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.037845 restraints weight = 94905.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.038619 restraints weight = 61041.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.039141 restraints weight = 46122.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.039416 restraints weight = 38579.927| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30635 Z= 0.131 Angle : 0.603 10.512 42040 Z= 0.305 Chirality : 0.041 0.243 4796 Planarity : 0.004 0.067 5076 Dihedral : 18.485 179.870 5335 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.51 % Allowed : 27.74 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.06 % Twisted Proline : 1.14 % 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: -0.20 (0.15), residues: 3488 helix: 1.48 (0.14), residues: 1390 sheet: -1.33 (0.25), residues: 404 loop : -1.21 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 209 TYR 0.018 0.001 TYR B 176 PHE 0.013 0.001 PHE C1019 TRP 0.011 0.001 TRP M 112 HIS 0.004 0.001 HIS C 200 Details of bonding type rmsd covalent geometry : bond 0.00289 (30628) covalent geometry : angle 0.60304 (42034) hydrogen bonds : bond 0.03515 ( 1366) hydrogen bonds : angle 4.53275 ( 3770) metal coordination : bond 0.00271 ( 7) metal coordination : angle 2.00064 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 171 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 211 TRP cc_start: 0.8462 (m-10) cc_final: 0.8176 (m100) REVERT: C 393 MET cc_start: 0.9644 (mmt) cc_final: 0.9324 (mmm) REVERT: C 396 MET cc_start: 0.9315 (pp-130) cc_final: 0.8600 (pp-130) REVERT: C 584 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8269 (ptp90) REVERT: C 586 MET cc_start: 0.9416 (ppp) cc_final: 0.7819 (ppp) REVERT: C 593 MET cc_start: 0.9134 (mmm) cc_final: 0.8619 (mmm) REVERT: C 607 MET cc_start: 0.8832 (mtt) cc_final: 0.8555 (mtp) REVERT: C 611 MET cc_start: 0.9095 (mpp) cc_final: 0.8761 (mmp) REVERT: C 702 ILE cc_start: 0.8953 (tt) cc_final: 0.8565 (mm) REVERT: C 753 GLU cc_start: 0.8244 (tp30) cc_final: 0.7979 (tp30) REVERT: C 754 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8372 (tm-30) REVERT: C 926 MET cc_start: 0.9122 (tpp) cc_final: 0.8219 (tpp) REVERT: C 1028 MET cc_start: 0.9021 (ttm) cc_final: 0.8455 (tpp) REVERT: C 1051 MET cc_start: 0.9116 (tpt) cc_final: 0.8355 (tpp) REVERT: C 1076 MET cc_start: 0.9172 (tpt) cc_final: 0.8576 (tpp) REVERT: C 1104 GLU cc_start: 0.9489 (tt0) cc_final: 0.9193 (tm-30) REVERT: D 86 LYS cc_start: 0.9348 (tppt) cc_final: 0.9135 (tppt) REVERT: D 92 MET cc_start: 0.8863 (mtp) cc_final: 0.7801 (mmm) REVERT: D 213 GLN cc_start: 0.9214 (tp-100) cc_final: 0.8958 (tp-100) REVERT: D 238 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7234 (tm-30) REVERT: D 312 MET cc_start: 0.9162 (mtp) cc_final: 0.8762 (mtm) REVERT: D 342 ASP cc_start: 0.9350 (m-30) cc_final: 0.8817 (p0) REVERT: D 373 MET cc_start: 0.9031 (mtp) cc_final: 0.8546 (mtp) REVERT: D 404 ASP cc_start: 0.8641 (m-30) cc_final: 0.8416 (m-30) REVERT: D 515 MET cc_start: 0.8378 (mtm) cc_final: 0.8147 (mtm) REVERT: D 520 LYS cc_start: 0.8837 (pttt) cc_final: 0.8329 (pttt) REVERT: D 533 ASN cc_start: 0.9298 (t0) cc_final: 0.9037 (t0) REVERT: D 576 MET cc_start: 0.8734 (mtp) cc_final: 0.8509 (mtp) REVERT: D 581 MET cc_start: 0.9346 (mtm) cc_final: 0.9032 (mtm) REVERT: D 640 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8784 (mt) REVERT: D 849 TYR cc_start: 0.8338 (t80) cc_final: 0.8082 (t80) REVERT: D 865 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9000 (pp) REVERT: D 879 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7767 (t0) REVERT: D 943 ASP cc_start: 0.8873 (OUTLIER) cc_final: 0.8446 (t70) REVERT: D 1161 MET cc_start: 0.9369 (tpp) cc_final: 0.9014 (tpp) REVERT: D 1250 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8286 (pm20) REVERT: E 66 ASP cc_start: 0.9220 (m-30) cc_final: 0.8926 (m-30) REVERT: F 302 LEU cc_start: 0.9816 (tp) cc_final: 0.9378 (mt) REVERT: F 325 ASN cc_start: 0.9540 (m-40) cc_final: 0.9048 (m110) REVERT: F 403 MET cc_start: 0.8903 (mmt) cc_final: 0.8657 (mmp) REVERT: F 437 ASP cc_start: 0.9228 (t0) cc_final: 0.9003 (t0) REVERT: F 438 PHE cc_start: 0.9023 (m-80) cc_final: 0.8754 (m-80) REVERT: F 509 LYS cc_start: 0.9418 (OUTLIER) cc_final: 0.9159 (tppt) REVERT: F 511 MET cc_start: 0.9546 (mmm) cc_final: 0.9013 (mmp) REVERT: J 6 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8370 (pp) REVERT: J 64 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8607 (tt) REVERT: J 69 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7857 (tm) REVERT: M 115 ASP cc_start: 0.8939 (OUTLIER) cc_final: 0.8397 (p0) REVERT: M 133 GLN cc_start: 0.9422 (tp-100) cc_final: 0.9149 (tm-30) REVERT: M 141 LEU cc_start: 0.9363 (mm) cc_final: 0.9015 (tp) REVERT: M 144 SER cc_start: 0.9262 (m) cc_final: 0.9026 (t) outliers start: 102 outliers final: 71 residues processed: 265 average time/residue: 0.1840 time to fit residues: 79.2257 Evaluate side-chains 246 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 162 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 1009 MET Chi-restraints excluded: chain C residue 1093 SER Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 656 TRP Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 732 SER Chi-restraints excluded: chain D residue 748 HIS Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 879 ASP Chi-restraints excluded: chain D residue 943 ASP Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 1060 ARG Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1133 HIS Chi-restraints excluded: chain D residue 1165 VAL Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1210 ILE Chi-restraints excluded: chain D residue 1248 LEU Chi-restraints excluded: chain D residue 1250 GLU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 278 ARG Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 509 LYS Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain J residue 106 ARG Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 85 TRP Chi-restraints excluded: chain M residue 115 ASP Chi-restraints excluded: chain M residue 128 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 286 optimal weight: 0.0060 chunk 266 optimal weight: 10.0000 chunk 152 optimal weight: 0.7980 chunk 235 optimal weight: 10.0000 chunk 271 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 300 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 229 optimal weight: 4.9990 chunk 256 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 overall best weight: 2.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 72 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.052659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.036917 restraints weight = 192822.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.038090 restraints weight = 95856.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.038873 restraints weight = 61790.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.039379 restraints weight = 46669.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.039695 restraints weight = 39146.100| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30635 Z= 0.149 Angle : 0.626 14.548 42040 Z= 0.314 Chirality : 0.041 0.255 4796 Planarity : 0.004 0.067 5076 Dihedral : 18.466 178.401 5335 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.47 % Allowed : 27.84 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.06 % Twisted Proline : 1.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.15), residues: 3488 helix: 1.48 (0.14), residues: 1400 sheet: -1.31 (0.26), residues: 404 loop : -1.18 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 474 TYR 0.018 0.001 TYR B 176 PHE 0.024 0.001 PHE C 99 TRP 0.012 0.001 TRP D 723 HIS 0.004 0.001 HIS C 200 Details of bonding type rmsd covalent geometry : bond 0.00327 (30628) covalent geometry : angle 0.62505 (42034) hydrogen bonds : bond 0.03570 ( 1366) hydrogen bonds : angle 4.54241 ( 3770) metal coordination : bond 0.00401 ( 7) metal coordination : angle 2.12317 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 164 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 127 MET cc_start: 0.8607 (ptp) cc_final: 0.7924 (pmm) REVERT: C 211 TRP cc_start: 0.8456 (m-10) cc_final: 0.8189 (m100) REVERT: C 393 MET cc_start: 0.9651 (mmt) cc_final: 0.9276 (mmm) REVERT: C 396 MET cc_start: 0.9282 (pp-130) cc_final: 0.8534 (pp-130) REVERT: C 584 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8261 (ptp90) REVERT: C 586 MET cc_start: 0.9416 (ppp) cc_final: 0.7844 (ppp) REVERT: C 593 MET cc_start: 0.9150 (mmm) cc_final: 0.8646 (mmt) REVERT: C 607 MET cc_start: 0.8831 (mtt) cc_final: 0.8568 (mtp) REVERT: C 611 MET cc_start: 0.9118 (mpp) cc_final: 0.8792 (mmp) REVERT: C 702 ILE cc_start: 0.8947 (tt) cc_final: 0.8556 (mm) REVERT: C 753 GLU cc_start: 0.8159 (tp30) cc_final: 0.7939 (tp30) REVERT: C 754 GLU cc_start: 0.9106 (OUTLIER) cc_final: 0.8390 (tm-30) REVERT: C 926 MET cc_start: 0.9131 (tpp) cc_final: 0.8267 (tpp) REVERT: C 1028 MET cc_start: 0.9046 (ttm) cc_final: 0.8640 (tpp) REVERT: C 1051 MET cc_start: 0.9099 (tpt) cc_final: 0.8307 (tpp) REVERT: C 1076 MET cc_start: 0.9236 (tpt) cc_final: 0.8612 (tpp) REVERT: C 1104 GLU cc_start: 0.9491 (tt0) cc_final: 0.9193 (tm-30) REVERT: D 30 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8608 (mmmm) REVERT: D 86 LYS cc_start: 0.9355 (tppt) cc_final: 0.9146 (tppt) REVERT: D 92 MET cc_start: 0.8894 (mtp) cc_final: 0.7849 (mmm) REVERT: D 213 GLN cc_start: 0.9262 (tp-100) cc_final: 0.8980 (tp-100) REVERT: D 238 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7246 (tm-30) REVERT: D 310 MET cc_start: 0.9235 (tpp) cc_final: 0.8973 (tpp) REVERT: D 312 MET cc_start: 0.8984 (mtp) cc_final: 0.8625 (mtm) REVERT: D 342 ASP cc_start: 0.9360 (m-30) cc_final: 0.8833 (p0) REVERT: D 373 MET cc_start: 0.9034 (mtp) cc_final: 0.8552 (mtp) REVERT: D 404 ASP cc_start: 0.8640 (m-30) cc_final: 0.8423 (m-30) REVERT: D 515 MET cc_start: 0.8383 (mtm) cc_final: 0.7707 (mtm) REVERT: D 520 LYS cc_start: 0.8847 (pttt) cc_final: 0.8327 (pttt) REVERT: D 533 ASN cc_start: 0.9306 (t0) cc_final: 0.9051 (t0) REVERT: D 576 MET cc_start: 0.8719 (mtp) cc_final: 0.8488 (mtp) REVERT: D 581 MET cc_start: 0.9366 (mtm) cc_final: 0.8980 (mtm) REVERT: D 640 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8796 (mt) REVERT: D 865 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9004 (pp) REVERT: D 879 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7796 (t0) REVERT: D 943 ASP cc_start: 0.8839 (OUTLIER) cc_final: 0.8406 (t70) REVERT: D 1250 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8128 (pm20) REVERT: E 66 ASP cc_start: 0.9221 (m-30) cc_final: 0.8928 (m-30) REVERT: F 325 ASN cc_start: 0.9569 (m-40) cc_final: 0.9109 (m110) REVERT: F 403 MET cc_start: 0.8923 (mmt) cc_final: 0.8673 (mmp) REVERT: F 437 ASP cc_start: 0.9259 (t0) cc_final: 0.9035 (t0) REVERT: F 438 PHE cc_start: 0.9020 (m-80) cc_final: 0.8751 (m-80) REVERT: F 509 LYS cc_start: 0.9414 (OUTLIER) cc_final: 0.9156 (tppt) REVERT: F 511 MET cc_start: 0.9557 (mmm) cc_final: 0.9025 (mmp) REVERT: J 6 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8449 (pp) REVERT: J 64 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8824 (tt) REVERT: J 69 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7882 (tm) REVERT: M 72 GLN cc_start: 0.9259 (OUTLIER) cc_final: 0.9011 (pp30) REVERT: M 115 ASP cc_start: 0.8822 (OUTLIER) cc_final: 0.8222 (p0) REVERT: M 141 LEU cc_start: 0.9366 (mm) cc_final: 0.9022 (tp) REVERT: M 144 SER cc_start: 0.9262 (m) cc_final: 0.9030 (t) outliers start: 101 outliers final: 78 residues processed: 258 average time/residue: 0.1904 time to fit residues: 79.7136 Evaluate side-chains 253 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 160 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 1009 MET Chi-restraints excluded: chain C residue 1093 SER Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 656 TRP Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 732 SER Chi-restraints excluded: chain D residue 748 HIS Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 879 ASP Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain D residue 943 ASP Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 1060 ARG Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1133 HIS Chi-restraints excluded: chain D residue 1165 VAL Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1210 ILE Chi-restraints excluded: chain D residue 1248 LEU Chi-restraints excluded: chain D residue 1250 GLU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 278 ARG Chi-restraints excluded: chain F residue 323 GLU Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 509 LYS Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain J residue 106 ARG Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 72 GLN Chi-restraints excluded: chain M residue 85 TRP Chi-restraints excluded: chain M residue 115 ASP Chi-restraints excluded: chain M residue 128 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 112 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 244 optimal weight: 0.9990 chunk 275 optimal weight: 10.0000 chunk 319 optimal weight: 0.9980 chunk 113 optimal weight: 10.0000 chunk 54 optimal weight: 0.4980 chunk 187 optimal weight: 0.0370 chunk 230 optimal weight: 0.4980 chunk 266 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 841 HIS ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 72 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.053782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.038016 restraints weight = 191061.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.039217 restraints weight = 94916.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.040025 restraints weight = 61155.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.040539 restraints weight = 46096.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.040868 restraints weight = 38623.443| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2964 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2964 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30635 Z= 0.115 Angle : 0.630 16.558 42040 Z= 0.312 Chirality : 0.041 0.263 4796 Planarity : 0.004 0.068 5076 Dihedral : 18.381 176.550 5335 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.89 % Allowed : 28.43 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.06 % Twisted Proline : 0.57 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.15), residues: 3488 helix: 1.57 (0.14), residues: 1386 sheet: -1.21 (0.26), residues: 387 loop : -1.15 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 474 TYR 0.018 0.001 TYR B 176 PHE 0.011 0.001 PHE D 6 TRP 0.011 0.001 TRP D 656 HIS 0.003 0.000 HIS D 525 Details of bonding type rmsd covalent geometry : bond 0.00251 (30628) covalent geometry : angle 0.62929 (42034) hydrogen bonds : bond 0.03321 ( 1366) hydrogen bonds : angle 4.46121 ( 3770) metal coordination : bond 0.00117 ( 7) metal coordination : angle 1.50009 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 174 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 SER cc_start: 0.7931 (m) cc_final: 0.7719 (m) REVERT: C 127 MET cc_start: 0.8575 (ptp) cc_final: 0.7880 (pmm) REVERT: C 393 MET cc_start: 0.9656 (mmt) cc_final: 0.9329 (mmm) REVERT: C 396 MET cc_start: 0.9324 (pp-130) cc_final: 0.8678 (pp-130) REVERT: C 586 MET cc_start: 0.9406 (ppp) cc_final: 0.7884 (ppp) REVERT: C 607 MET cc_start: 0.8839 (mtt) cc_final: 0.8552 (mtp) REVERT: C 611 MET cc_start: 0.9019 (mpp) cc_final: 0.8728 (mmp) REVERT: C 702 ILE cc_start: 0.9063 (tt) cc_final: 0.8701 (mm) REVERT: C 724 MET cc_start: 0.8391 (ppp) cc_final: 0.7815 (ppp) REVERT: C 753 GLU cc_start: 0.8103 (tp30) cc_final: 0.7870 (tp30) REVERT: C 754 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8345 (tm-30) REVERT: C 926 MET cc_start: 0.9111 (tpp) cc_final: 0.8278 (tpp) REVERT: C 1028 MET cc_start: 0.8960 (ttm) cc_final: 0.8621 (tpp) REVERT: C 1051 MET cc_start: 0.9051 (tpt) cc_final: 0.8186 (tpp) REVERT: C 1074 TRP cc_start: 0.9121 (m-10) cc_final: 0.8180 (m-90) REVERT: C 1076 MET cc_start: 0.9212 (tpt) cc_final: 0.8553 (tpp) REVERT: C 1104 GLU cc_start: 0.9487 (tt0) cc_final: 0.9194 (tm-30) REVERT: C 1136 GLU cc_start: 0.8296 (tp30) cc_final: 0.7910 (tm-30) REVERT: D 92 MET cc_start: 0.8739 (mtp) cc_final: 0.7808 (mmm) REVERT: D 126 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8363 (mp0) REVERT: D 213 GLN cc_start: 0.9224 (tp-100) cc_final: 0.8954 (tp-100) REVERT: D 238 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7254 (tm-30) REVERT: D 310 MET cc_start: 0.9211 (tpp) cc_final: 0.8835 (tpp) REVERT: D 312 MET cc_start: 0.9089 (mtp) cc_final: 0.8714 (mtm) REVERT: D 342 ASP cc_start: 0.9331 (m-30) cc_final: 0.8821 (p0) REVERT: D 373 MET cc_start: 0.9071 (mtp) cc_final: 0.8553 (mtp) REVERT: D 515 MET cc_start: 0.8395 (mtm) cc_final: 0.8144 (mtm) REVERT: D 520 LYS cc_start: 0.8852 (pttt) cc_final: 0.8319 (pttt) REVERT: D 533 ASN cc_start: 0.9225 (t0) cc_final: 0.9023 (t0) REVERT: D 576 MET cc_start: 0.8641 (mtp) cc_final: 0.8394 (mtp) REVERT: D 581 MET cc_start: 0.9307 (mtm) cc_final: 0.8992 (mtm) REVERT: D 849 TYR cc_start: 0.8266 (t80) cc_final: 0.8024 (t80) REVERT: D 865 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8965 (pp) REVERT: D 879 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7849 (t0) REVERT: D 943 ASP cc_start: 0.8936 (OUTLIER) cc_final: 0.8577 (t70) REVERT: D 1161 MET cc_start: 0.9367 (tpp) cc_final: 0.9115 (tpp) REVERT: D 1250 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8312 (pm20) REVERT: E 66 ASP cc_start: 0.9156 (m-30) cc_final: 0.8802 (m-30) REVERT: E 68 TYR cc_start: 0.9328 (OUTLIER) cc_final: 0.8838 (m-10) REVERT: F 315 MET cc_start: 0.8230 (mmm) cc_final: 0.7919 (mmt) REVERT: F 325 ASN cc_start: 0.9553 (m-40) cc_final: 0.9093 (m110) REVERT: F 343 PHE cc_start: 0.7918 (t80) cc_final: 0.7674 (t80) REVERT: F 403 MET cc_start: 0.8914 (mmt) cc_final: 0.8670 (mmp) REVERT: F 438 PHE cc_start: 0.8989 (m-80) cc_final: 0.8727 (m-80) REVERT: F 509 LYS cc_start: 0.9379 (OUTLIER) cc_final: 0.9126 (tppt) REVERT: F 511 MET cc_start: 0.9549 (mmm) cc_final: 0.8948 (mmp) REVERT: J 64 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8571 (tt) REVERT: J 69 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7847 (tm) REVERT: M 72 GLN cc_start: 0.9211 (OUTLIER) cc_final: 0.8917 (pp30) REVERT: M 115 ASP cc_start: 0.8987 (OUTLIER) cc_final: 0.8474 (p0) REVERT: M 133 GLN cc_start: 0.9381 (tp-100) cc_final: 0.9102 (tm-30) REVERT: M 141 LEU cc_start: 0.9342 (mm) cc_final: 0.9026 (tp) REVERT: M 144 SER cc_start: 0.9314 (m) cc_final: 0.9098 (t) outliers start: 84 outliers final: 63 residues processed: 250 average time/residue: 0.1903 time to fit residues: 77.3049 Evaluate side-chains 244 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 168 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 661 MET Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 1009 MET Chi-restraints excluded: chain C residue 1093 SER Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 656 TRP Chi-restraints excluded: chain D residue 748 HIS Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 879 ASP Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain D residue 943 ASP Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 1060 ARG Chi-restraints excluded: chain D residue 1133 HIS Chi-restraints excluded: chain D residue 1165 VAL Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1210 ILE Chi-restraints excluded: chain D residue 1248 LEU Chi-restraints excluded: chain D residue 1250 GLU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 278 ARG Chi-restraints excluded: chain F residue 509 LYS Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain J residue 106 ARG Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 72 GLN Chi-restraints excluded: chain M residue 85 TRP Chi-restraints excluded: chain M residue 115 ASP Chi-restraints excluded: chain M residue 128 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 314 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 264 optimal weight: 6.9990 chunk 194 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 218 optimal weight: 10.0000 chunk 271 optimal weight: 20.0000 chunk 297 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 chunk 130 optimal weight: 0.9980 chunk 277 optimal weight: 10.0000 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 ASN ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 72 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.051617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.035834 restraints weight = 195148.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.036984 restraints weight = 97624.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.037756 restraints weight = 63113.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.038255 restraints weight = 47689.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.038552 restraints weight = 40007.012| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 30635 Z= 0.200 Angle : 0.664 13.273 42040 Z= 0.335 Chirality : 0.041 0.253 4796 Planarity : 0.004 0.066 5076 Dihedral : 18.438 176.425 5329 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.03 % Allowed : 28.15 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.06 % Twisted Proline : 0.57 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.15), residues: 3488 helix: 1.56 (0.14), residues: 1393 sheet: -1.27 (0.26), residues: 392 loop : -1.13 (0.15), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 474 TYR 0.023 0.001 TYR B 32 PHE 0.024 0.001 PHE C 99 TRP 0.034 0.002 TRP C 211 HIS 0.004 0.001 HIS C 200 Details of bonding type rmsd covalent geometry : bond 0.00434 (30628) covalent geometry : angle 0.66340 (42034) hydrogen bonds : bond 0.03924 ( 1366) hydrogen bonds : angle 4.60882 ( 3770) metal coordination : bond 0.00691 ( 7) metal coordination : angle 2.64656 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6215.93 seconds wall clock time: 107 minutes 39.91 seconds (6459.91 seconds total)